INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(78830, 2014, 'bio', 'Detecting differential peaks in ChIP-seq signals with ODIN', 'Allhoff, Manuel|Seré, Kristin|Chauvistré, Heike|Lin, Qiong|Zenke, Martin|Costa, Ivan G', 'IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil.|IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil.|IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil.|IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil.|IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil.|IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Germany, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Germany and Center of Informatics, Federal University of Pernambuco, Brazil IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany, Department of Cell Biology, Institute', 'Brazil|Brazil|Brazil|Brazil|Brazil|Brazil', 14, 'Animals|Chromatin Immunoprecipitation|Genomics|Histones|Markov Chains|Mice|Sequence Analysis, DNA|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/btu722', '25371479', 'Detection of changes in deoxyribonucleic acid (DNA)-protein interactions from ChIP-seq data is a crucial step in unraveling the regulatory networks behind biological processes. The simplest variation of this problem is the differential peak calling (DPC) problem. Here, one has to find genomic regions with ChIP-seq signal changes between two cellular conditions in the interaction of a protein with DNA. The great majority of peak calling methods can only analyze one ChIP-seq signal at a time and are unable to perform DPC. Recently, a few approaches based on the combination of these peak callers with statistical tests for detecting differential digital expression have been proposed. However, these methods fail to detect detailed changes of protein-DNA interactions.'),
(78831, 2015, 'bio', 'flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification', 'Malek, Mehrnoush|Taghiyar, Mohammad Jafar|Chong, Lauren|Finak, Greg|Gottardo, Raphael|Brinkman, Ryan R', 'Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.|Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.|Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.|Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.|Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.|Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.', 'Canada|Canada|Canada|Canada|Canada|Canada', 0, 'Algorithms|Biomarkers|Cell Physiological Phenomena|Cluster Analysis|Computational Biology|Databases, Factual|Flow Cytometry|Humans|Software', 'Journal Article', '10.1093/bioinformatics/btu677', '25378466', 'flowDensity facilitates reproducible, high-throughput analysis of flow cytometry data by automating a predefined manual gating approach. The algorithm is based on a sequential bivariate gating approach that generates a set of predefined cell populations. It chooses the best cut-off for individual markers using characteristics of the density distribution. The Supplementary Material is linked to the online version of the manuscript.'),
(78832, 2015, 'bio', 'TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm', 'Pey, Jon|Villar, Juan A|Tobalina, Luis|Rezola, Alberto|García, José Manuel|Beasley, John E|Planes, Francisco J', 'CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK.|CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK.|CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK.|CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK.|CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK.|CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK.|CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK.', 'Spain|Spain|Spain|Spain|Spain|Spain|Spain', 7, 'Acetates|Algorithms|Amino Acids|Escherichia coli|Gene Expression Profiling|Genome, Bacterial|Metabolic Flux Analysis|Metabolic Networks and Pathways|Programming, Linear|Software', 'Journal Article', '10.1093/bioinformatics/btu733', '25380956', 'Elementary flux modes (EFMs) analysis constitutes a fundamental tool in systems biology. However, the efficient calculation of EFMs in genome-scale metabolic networks (GSMNs) is still a challenge. We present a novel algorithm that uses a linear programming-based tree search and efficiently enumerates a subset of EFMs in GSMNs.'),
(78833, 2015, 'bio', 'Joint amalgamation of most parsimonious reconciled gene trees', 'Scornavacca, Celine|Jacox, Edwin|Szxc3xb6llxc5x91si, Gergely J', 'ISEM, UM2-CNRS-IRD, Place Eugxc3xa8ne Bataillon 34095 Montpellier, France, Institut de Biologie Computationnelle (IBC), 95 rue de la Galxc3xa9ra, 34095 Montpellier, France and ELTE-MTA Lendxc3xbclet Biophysics Research Group 1117 Bp., Pxc3xa1zmxc3xa1ny P. stny. 1A., Budapest, Hungary ISEM, UM2-CNRS-IRD, Place Eugxc3xa8ne Bataillon 34095 Montpellier, France, Institut de Biologie Computationnelle (IBC), 95 rue de la Galxc3xa9ra, 34095 Montpellier, France and ELTE-MTA Lendxc3xbclet Biophysics Research Group 1117 Bp., Pxc3xa1zmxc3xa1ny P. stny. 1A., Budapest, Hungary.|ISEM, UM2-CNRS-IRD, Place Eugxc3xa8ne Bataillon 34095 Montpellier, France, Institut de Biologie Computationnelle (IBC), 95 rue de la Galxc3xa9ra, 34095 Montpellier, France and ELTE-MTA Lendxc3xbclet Biophysics Research Group 1117 Bp., Pxc3xa1zmxc3xa1ny P. stny. 1A., Budapest, Hungary.|ISEM, UM2-CNRS-IRD, Place Eugxc3xa8ne Bataillon 34095 Montpellier, France, Institut de Biologie Computationnelle (IBC), 95 rue de la Galxc3xa9ra, 34095 Montpellier, France and ELTE-MTA Lendxc3xbclet Biophysics Research Group 1117 Bp., Pxc3xa1zmxc3xa1ny P. stny. 1A., Budapest, Hungary.', 'France|France|France', 0, 'Algorithms|Computer Simulation|Cyanobacteria|Evolution, Molecular|Gene Duplication|Genome, Bacterial|Multigene Family|Phylogeny', 'Journal Article', '10.1093/bioinformatics/btu728', '25380957', 'Traditionally, gene phylogenies have been reconstructed solely on the basis of molecular sequences, this, however, often does not provide enough information to distinguish between statistically equivalent relationships. To address this problem, several recent methods have incorporated information on the species phylogeny in gene tree reconstruction, leading to dramatic improvements in accuracy. Although probabilistic methods are able to estimate all model parameters but are computationally expensive, parsimony methods-generally computationally more efficient-require a prior estimate of parameters and of the statistical support.'),
(78834, 2015, 'bio', 'Development of a robust classifier for quality control of reverse-phase protein arrays', 'Ju, Zhenlin|Liu, Wenbin|Roebuck, Paul L|Siwak, Doris R|Zhang, Nianxiang|Lu, Yiling|Davies, Michael A|Akbani, Rehan|Weinstein, John N|Mills, Gordon B|Coombes, Kevin R', 'Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.|Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.|Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.|Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.|Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.|Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.|Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.|Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.|Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.|Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.|Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.', 'United States|United States|United States|United States|United States|United States|United States|United States|United States|United States|United States', 19, 'Algorithms|Protein Array Analysis|Proteomics|Quality Control|Software', 'Journal Article', '10.1093/bioinformatics/btu736', '25380958', 'High-throughput reverse-phase protein array (RPPA) technology allows for the parallel measurement of protein expression levels in approximately 1000 samples. However, the many steps required in the complex protocol (sample lysate preparation, slide printing, hybridization, washing and amplified detection) may create substantial variability in data quality. We are not aware of any other quality control algorithm that is tuned to the special characteristics of RPPAs.'),
(78835, 2015, 'bio', 'PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments', 'Bläßle, Alexander|Müller, Patrick', 'Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany.|Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany.', 'Germany|Germany', 0, 'Algorithms|Automation|Computer Graphics|Fluorescence|Photochemical Processes|Software', 'Journal Article', '10.1093/bioinformatics/btu735', '25380959', 'We developed the graphical user interface PyFDAP for the fitting of linear and non-linear decay functions to data from fluorescence decay after photoconversion (FDAP) experiments. PyFDAP structures and analyses large FDAP datasets and features multiple fitting and plotting options.'),
(78836, 2015, 'bio', 'IntSide: a web server for the chemical and biological examination of drug side effects', 'Juan-Blanco, Teresa|Duran-Frigola, Miquel|Aloy, Patrick', 'Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona) and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.|Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona) and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.|Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona) and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona) and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.', 'Spain|Spain|Spain', 16, 'Animals|Computational Biology|Databases, Pharmaceutical|Drug-Related Side Effects and Adverse Reactions|Humans|Internet|Pharmaceutical Preparations|Software|Toxicity Tests|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/btu688', '25380960', 'Drug side effects are one of the main health threats worldwide, and an important obstacle in drug development. Understanding how adverse reactions occur requires knowledge on drug mechanisms at the molecular level. Despite recent advances, the need for tools and methods that facilitate side effect anticipation still remains. Here, we present IntSide, a web server that integrates chemical and biological information to elucidate the molecular mechanisms underlying drug side effects. IntSide currently catalogs 1175 side effects caused by 996 drugs, associated with drug features divided into eight categories, belonging to either biology or chemistry. On the biological side, IntSide reports drug targets and off-targets, pathways, molecular functions and biological processes. From a chemical viewpoint, it includes molecular fingerprints, scaffolds and chemical entities. Finally, we also integrate additional biological data, such as protein interactions and disease-related genes, to facilitate mechanistic interpretations.'),
(78837, 2015, 'bio', 'Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries', 'Gillet-Markowska, Alexandre|Richard, Hugues|Fischer, Gilles|Lafontaine, Ingrid', 'Sorbonne Universités, UPMC University Paris 06, UMR 7238, Biologie Computationnelle et Quantitative and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France Sorbonne Universités, UPMC University Paris 06, UMR 7238, Biologie Computationnelle et Quantitative and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France.|Sorbonne Universités, UPMC University Paris 06, UMR 7238, Biologie Computationnelle et Quantitative and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France Sorbonne Universités, UPMC University Paris 06, UMR 7238, Biologie Computationnelle et Quantitative and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France.|Sorbonne Universités, UPMC University Paris 06, UMR 7238, Biologie Computationnelle et Quantitative and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France Sorbonne Universités, UPMC University Paris 06, UMR 7238, Biologie Computationnelle et Quantitative and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France.|Sorbonne Universités, UPMC University Paris 06, UMR 7238, Biologie Computationnelle et Quantitative and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France Sorbonne Universités, UPMC University Paris 06, UMR 7238, Biologie Computationnelle et Quantitative and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France.', 'France|France|France|France', 0, 'Breast Neoplasms|Female|Gene Library|Genome, Human|Genomic Structural Variation|Humans|Interspersed Repetitive Sequences|Mutagenesis, Insertional|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/btu730', '25380961', 'The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, large insert-size sequencing libraries (Mate-Pair libraries) provide higher physical coverage of the genome and give access to repeat-containing regions. They can thus theoretically overcome previous limitations as they are becoming routinely accessible. Nevertheless, broad insert size distributions and high rates of chimerical sequences are usually associated to this type of libraries, which makes the accurate annotation of SV challenging.'),
(78838, 2015, 'bio', 'CytoCom: a Cytoscape app to visualize, query and analyse disease comorbidity networks', 'Moni, Mohammad Ali|Xu, Haoming|Liò, Pietro', 'Computer Laboratory, University of Cambridge, Cambridge, UK and Department of CSE, Pabna University of Science and Technology, Pabna, Bangladesh Computer Laboratory, University of Cambridge, Cambridge, UK and Department of CSE, Pabna University of Science and Technology, Pabna, Bangladesh.|Computer Laboratory, University of Cambridge, Cambridge, UK and Department of CSE, Pabna University of Science and Technology, Pabna, Bangladesh.|Computer Laboratory, University of Cambridge, Cambridge, UK and Department of CSE, Pabna University of Science and Technology, Pabna, Bangladesh.', 'Bangladesh|Bangladesh|Bangladesh', 21, 'Cluster Analysis|Comorbidity|Computational Biology|Databases, Factual|Disease|Gene Regulatory Networks|Humans|Software', 'Journal Article', '10.1093/bioinformatics/btu731', '25380962', 'CytoCom is an interactive plugin for Cytoscape that can be used to search, explore, analyse and visualize human disease comorbidity network. It represents disease-disease associations in terms of bipartite graphs and provides International Classification of Diseases, Ninth Revision (ICD9)-centric and disease name centric views of disease information. It allows users to find associations between diseases based on the two measures: Relative Risk (RR) and [Formula: see text]-correlation values. In the disease network, the size of each node is based on the prevalence of that disease. CytoCom is capable of clustering disease network based on the ICD9 disease category. It provides user-friendly access that facilitates exploration of human diseases, and finds additional associated diseases by double-clicking a node in the existing network. Additional comorbid diseases are then connected to the existing network. It is able to assist users for interpretation and exploration of the human diseases by a variety of built-in functions. Moreover, CytoCom permits multi-colouring of disease nodes according to standard disease classification for expedient visualization.'),
(78839, 2015, 'bio', 'Comment on protein-protein binding affinity prediction from amino acid sequence', 'Moal, Iain H|Fernández-Recio, Juan', 'Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, Barcelona, Spain.|Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, Barcelona, Spain.', 'Spain|Spain', 6, 'Multiprotein Complexes|Protein Interaction Mapping', 'Letter', '10.1093/bioinformatics/btu682', '25381451', '-'),
(78840, 2015, 'bio', 'GlycoRDF: an ontology to standardize glycomics data in RDF', 'Ranzinger, Rene|Aoki-Kinoshita, Kiyoko F|Campbell, Matthew P|Kawano, Shin|Lütteke, Thomas|Okuda, Shujiro|Shinmachi, Daisuke|Shikanai, Toshihide|Sawaki, Hiromichi|Toukach, Philip|Matsubara, Masaaki|Yamada, Issaku|Narimatsu, Hisashi', 'Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.|Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.|Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.|Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.|Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.|Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.|Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.|Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.|Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.|Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.|Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.|Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.|Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.', 'Australia|Australia|Australia|Australia|Australia|Australia|Australia|Australia|Australia|Australia|', 22, 'Computational Biology|Database Management Systems|Databases, Factual|Documentation|Gene Ontology|Glycomics|Humans|Information Storage and Retrieval|Polysaccharides|Software', 'Journal Article', '10.1093/bioinformatics/btu732', '25388145', 'Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information.'),
(78841, 2015, 'bio', 'MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis', 'Bradbury, James|Genta-Jouve, Grégory|Allwood, J William|Dunn, Warwick B|Goodacre, Royston|Knowles, Joshua D|He, Shan|Viant, Mark R', 'School of Computer Science and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, Manchester Institute of Biotechnology, School of Chemistry and School of Computer Science, The University of Manchester, Manchester M13 9JD, UK.|School of Computer Science and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, Manchester Institute of Biotechnology, School of Chemistry and School of Computer Science, The University of Manchester, Manchester M13 9JD, UK.|School of Computer Science and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, Manchester Institute of Biotechnology, School of Chemistry and School of Computer Science, The University of Manchester, Manchester M13 9JD, UK.|School of Computer Science and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, Manchester Institute of Biotechnology, School of Chemistry and School of Computer Science, The University of Manchester, Manchester M13 9JD, UK.|School of Computer Science and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, Manchester Institute of Biotechnology, School of Chemistry and School of Computer Science, The University of Manchester, Manchester M13 9JD, UK School of Computer Science and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, Manchester Institute of Biotechnology, School of Chemistry and School of Computer Science, The University of Manchester, Manchester M13 9JD, UK.|School of Computer Science and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, Manchester Institute of Biotechnology, School of Chemistry and School of Computer Science, The University of Manchester, Manchester M13 9JD, UK.|School of Computer Science and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, Manchester Institute of Biotechnology, School of Chemistry and School of Computer Science, The University of Manchester, Manchester M13 9JD, UK.|School of Computer Science and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, Manchester Institute of Biotechnology, School of Chemistry and School of Computer Science, The University of Manchester, Manchester M13 9JD, UK.', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom', 0, 'Automation|Chromatography, Liquid|Software|Steroids|Tandem Mass Spectrometry', 'Journal Article', '10.1093/bioinformatics/btu740', '25388146', 'Developing liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses of (bio)chemicals is both time consuming and challenging, largely because of the large number of LC and MS instrument parameters that need to be optimized. This bottleneck significantly impedes our ability to establish new (bio)analytical methods in fields such as pharmacology, metabolomics and pesticide research. We report the development of a multi-platform, user-friendly software tool MUSCLE (multi-platform unbiased optimization of spectrometry via closed-loop experimentation) for the robust and fully automated multi-objective optimization of targeted LC-MS/MS analysis. MUSCLE shortened the analysis times and increased the analytical sensitivities of targeted metabolite analysis, which was demonstrated on two different manufacturers LC-MS/MS instruments.'),
(78842, 2015, 'bio', 'What handedness and angles between helices has the studied three-helical protein domain?', 'Pereyaslavets, Leonid B|Glyakina, Anna V|Dovidchenko, Nikita V|Sokolovskiy, Igor V|Galzitskaya, Oxana V', 'Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.|Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.|Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.|Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.|Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.', '-|-|-|-|-', 0, 'Algorithms|Databases, Protein|Functional Laterality|Protein Structure, Secondary|Protein Structure, Tertiary|Proteins', 'Journal Article', '10.1093/bioinformatics/btu737', '25388147', 'We have created a new server FoldHandedness. Using this server it is possible: (i) to define the regions of helices from two issues (from the PDB file and using the last version of the DSSP program), (ii) to determine the handedness for any chosen three helices and (iii) to calculate the angle and sign between the chosen pairs of the helices for large proteins and complexes of proteins with DNA or RNA.'),
(78843, 2015, 'bio', 'Distinct profiling of antimicrobial peptide families', 'Khamis, Abdullah M|Essack, Magbubah|Gao, Xin|Bajic, Vladimir B', 'Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.|Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.|Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.|Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.', 'Saudi Arabia|Saudi Arabia|Saudi Arabia|Saudi Arabia', 14, 'Anti-Infective Agents|Antimicrobial Cationic Peptides|Cluster Analysis|Computational Biology|Databases, Factual', 'Journal Article', '10.1093/bioinformatics/btu738', '25388148', 'The increased prevalence of multi-drug resistant (MDR) pathogens heightens the need to design new antimicrobial agents. Antimicrobial peptides (AMPs) exhibit broad-spectrum potent activity against MDR pathogens and kills rapidly, thus giving rise to AMPs being recognized as a potential substitute for conventional antibiotics. Designing new AMPs using current in-silico approaches is, however, challenging due to the absence of suitable models, large number of design parameters, testing cycles, production time and cost. To date, AMPs have merely been categorized into families according to their primary sequences, structures and functions. The ability to computationally determine the properties that discriminate AMP families from each other could help in exploring the key characteristics of these families and facilitate the in-silico design of synthetic AMPs.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(78844, 2015, 'bio', 'MeRP: a high-throughput pipeline for Mendelian randomization analysis', 'Yin, Peter|Voight, Benjamin F', 'Department of Biology, College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19143, USA, Department of Pharmacology and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19143, USA.|Department of Biology, College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19143, USA, Department of Pharmacology and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19143, USA Department of Biology, College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19143, USA, Department of Pharmacology and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19143, USA.', 'United States|United States', 0, 'Biomarkers|Blood Pressure|Bone Density|Computational Biology|Diabetes Mellitus, Type 2|High-Throughput Screening Assays|Humans|Linkage Disequilibrium|Mendelian Randomization Analysis|Phenotype|Polymorphism, Single Nucleotide|Software', 'Journal Article', '10.1093/bioinformatics/btu742', '25388149', 'We present a Mendelian randomization (MR) pipeline (MeRP) to facilitate rapid, causal inference analysis through automating key steps in developing and analyzing genetic instruments obtained from publicly available data. Our tool uses the National Human Genome Research Institute catalog of associations to generate instrumental variable trait files and provides methods for filtering of potential confounding associations as well as linkage disequilibrium. MeRP generates estimated causal effect scores via a MR-score analysis using summary data for disease endpoints typically found in the public domain. We utilize our pipeline to develop genetic instruments for seven traits and evaluate potential causal relationships with two disease endpoints, observing two putatively causal associations between blood pressure and bone-mineral density with type 2 diabetes. Our tool emphasizes the importance of careful but systematic screening of large datasets for discovery and systematic follow-up.'),
(78845, 2015, 'bio', 'Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods', 'Drxc3xb6ge, J|Gregor, I|McHardy, A C', 'Department for Algorithmic Bioinformatics, Heinrich Heine University, Universitxc3xa4tsstraxc3x9fe 1, 40225 Dxc3xbcsseldorf, Germany, Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbrxc3xbccken, Germany and Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraxc3x9fe 7, 38124 Braunschweig, Germany Department for Algorithmic Bioinformatics, Heinrich Heine University, Universitxc3xa4tsstraxc3x9fe 1, 40225 Dxc3xbcsseldorf, Germany, Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbrxc3xbccken, Germany and Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraxc3x9fe 7, 38124 Braunschweig, Germany.|Department for Algorithmic Bioinformatics, Heinrich Heine University, Universitxc3xa4tsstraxc3x9fe 1, 40225 Dxc3xbcsseldorf, Germany, Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbrxc3xbccken, Germany and Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraxc3x9fe 7, 38124 Braunschweig, Germany Department for Algorithmic Bioinformatics, Heinrich Heine University, Universitxc3xa4tsstraxc3x9fe 1, 40225 Dxc3xbcsseldorf, Germany, Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbrxc3xbccken, Germany and Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraxc3x9fe 7, 38124 Braunschweig, Germany.|Department for Algorithmic Bioinformatics, Heinrich Heine University, Universitxc3xa4tsstraxc3x9fe 1, 40225 Dxc3xbcsseldorf, Germany, Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbrxc3xbccken, Germany and Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraxc3x9fe 7, 38124 Braunschweig, Germany Department for Algorithmic Bioinformatics, Heinrich Heine University, Universitxc3xa4tsstraxc3x9fe 1, 40225 Dxc3xbcsseldorf, Germany, Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbrxc3xbccken, Germany and Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraxc3x9fe 7, 38124 Braunschweig, Germany Department for Algorithmic Bioinformatics, Heinrich Heine University, Universitxc3xa4tsstraxc3x9fe 1, 40225 Dxc3xbcsseldorf, Germany, Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbrxc3xbccken, Germany and Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraxc3x9fe 7, 38124 Braunschweig, Germany.', 'Germany|Germany|Germany', 0, 'Algorithms|Bacteria|Genomics|Metagenome|Phylogeny|Software', 'Journal Article', '10.1093/bioinformatics/btu745', '25388150', 'Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows identifying the sequenced community members and reconstructing taxonomic bins with sequence data for the individual taxa. For the massive datasets generated by next-generation sequencing technologies, this cannot be performed with de-novo phylogenetic inference methods. We describe an algorithm and the accompanying software, taxator-tk, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(78846, 2015, 'bio', 'EVpedia: a community web portal for extracellular vesicles research', 'Kim, Dae-Kyum|Lee, Jaewook|Kim, Sae Rom|Choi, Dong-Sic|Yoon, Yae Jin|Kim, Ji Hyun|Go, Gyeongyun|Nhung, Dinh|Hong, Kahye|Jang, Su Chul|Kim, Si-Hyun|Park, Kyong-Su|Kim, Oh Youn|Park, Hyun Taek|Seo, Ji Hye|Aikawa, Elena|Baj-Krzyworzeka, Monika|van Balkom, Bas W M|Belting, Mattias|Blanc, Lionel|Bond, Vincent|Bongiovanni, Antonella|Borrxc3xa0s, Francesc E|Buxc3xa9e, Luc|Buzxc3xa1s, Edit I|Cheng, Lesley|Clayton, Aled|Cocucci, Emanuele|Dela Cruz, Charles S|Desiderio, Dominic M|Di Vizio, Dolores|Ekstrxc3xb6m, Karin|Falcon-Perez, Juan M|Gardiner, Chris|Giebel, Bernd|Greening, David W|Gross, Julia Christina|Gupta, Dwijendra|Hendrix, An|Hill, Andrew F|Hill, Michelle M|Nolte-	 Hoen, Esther|Hwang, Do Won|Inal, Jameel|Jagannadham, Medicharla V|Jayachandran, Muthuvel|Jee, Young-Koo|Jxc3xb8rgensen, Malene|Kim, Kwang Pyo|Kim, Yoon-Keun|Kislinger, Thomas|Lxc3xa4sser, Cecilia|Lee, Dong Soo|Lee, Hakmo|van Leeuwen, Johannes|Lener, Thomas|Liu, Ming-Lin|Lxc3xb6tvall, Jan|Marcilla, Antonio|Mathivanan, Suresh|Mxc3xb6ller, Andreas|Morhayim, Jess|Mullier, Franxc3xa7ois|Nazarenko, Irina|Nieuwland, Rienk|Nunes, Diana N|Pang, Ken|Park, Jaesung|Patel, Tushar|Pocsfalvi, Gabriella|Del Portillo, Hernando|Putz, Ulrich|Ramirez, Marcel I|Rodrigues, Marcio L|Roh, Tae-Young|Royo, Felix|Sahoo, Susmita|Schiffelers, Raymond|Sharma, Shivani|Siljander, Pia|Simpson, Richard J|Soekmadji, Carolina|Stahl, Philip|Stensballe, Allan|Stxc4x99piexc5x84, Ewa|Tahara, Hidetoshi|Trummer, Arne|Valadi, Hadi|Vella, Laura J|Wai, Sun Nyunt|Witwer, Kenneth|Yxc3xa1xc3xb1ez-Mxc3xb3, Marxc3xada|Youn, Hyewon|Zeidler, Reinhard|Gho, Yong Song', 'Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Childrens Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M|Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston C', 'Australia|Australia|Australia|Australia|Australia|Australia|Australia|Australia|Australia|Australia|', 0, 'Biomedical Research|Computational Biology|Database Management Systems|Databases, Factual|Exosomes|Extracellular Space|Humans|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/btu741', '25388151', 'Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(78847, 2015, 'bio', 'GASS: identifying enzyme active sites with genetic algorithms', 'Izidoro, Sandro C|de Melo-Minardi, Raquel C|Pappa, Gisele L', 'Advanced Campus at Itabira, Universidade Federal de Itajubá, Itajubá, MG 35903-087, Brazil and Department of Computer Science and Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.|Advanced Campus at Itabira, Universidade Federal de Itajubá, Itajubá, MG 35903-087, Brazil and Department of Computer Science and Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil Advanced Campus at Itabira, Universidade Federal de Itajubá, Itajubá, MG 35903-087, Brazil and Department of Computer Science and Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.|Advanced Campus at Itabira, Universidade Federal de Itajubá, Itajubá, MG 35903-087, Brazil and Department of Computer Science and Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil Advanced Campus at Itabira, Universidade Federal de Itajubá, Itajubá, MG 35903-087, Brazil and Department of Computer Science and Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.', 'Brazil|Brazil|Brazil', 14, 'Algorithms|Binding Sites|Catalytic Domain|Computer Simulation|Databases, Protein|Humans|Protein Structure, Tertiary|Proteins', 'Journal Article', '10.1093/bioinformatics/btu746', '25388152', 'Currently, 25% of proteins annotated in Pfam have their function unknown. One way of predicting proteins function is by looking at their active site, which has two main parts: the catalytic site and the substrate binding site. The active site is more conserved than the other residues of the protein and can be a rich source of information for protein function prediction. This article presents a new heuristic method, named genetic active site search (GASS), which searches for given active site 3D templates in unknown proteins. The method can perform non-exact amino acid matches (conservative mutations), is able to find amino acids in different chains and does not impose any restrictions on the active site size.'),
(78848, 2015, 'bio', 'Optimization method for obtaining nearest-neighbour DNA entropies and enthalpies directly from melting temperatures', 'Weber, Gerald', 'Departamento de Física, Universidade Federal Minas Gerais, Belo Horizonte-MG, Brazil.', 'Brazil', 11, 'Cluster Analysis|DNA|Datasets as Topic|Entropy|Nucleic Acid Denaturation|Programming Languages|Software|Temperature', 'Journal Article', '10.1093/bioinformatics/btu751', '25391397', 'Free energy nearest-neighbour (NN) thermodynamics is widely used in DNA biochemistry, ranging from the calculation of melting temperatures to the prediction of secondary structures. Methods to calculate NN parameters require the knowledge of total sequence entropies and enthalpies, which are not always available.'),
(78849, 2015, 'bio', 'Rclick: a web server for comparison of RNA 3D structures', 'Nguyen, Minh N|Verma, Chandra', 'Biomolecular Modeling and Design Division, Singapore 138671 Singapore, Department of Biological Sciences, National University of Singapore, Singapore and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.|Biomolecular Modeling and Design Division, Singapore 138671 Singapore, Department of Biological Sciences, National University of Singapore, Singapore and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore Biomolecular Modeling and Design Division, Singapore 138671 Singapore, Department of Biological Sciences, National University of Singapore, Singapore and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore Biomolecular Modeling and Design Division, Singapore 138671 Singapore, Department of Biological Sciences, National University of Singapore, Singapore and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.', 'Singapore|Singapore', 15, 'Amino Acid Sequence|Base Sequence|Molecular Sequence Data|Nucleic Acid Conformation|Protein Conformation|RNA|RNA-Binding Proteins|Sequence Alignment|Sequence Homology, Amino Acid|Software', 'Journal Article', '10.1093/bioinformatics/btu752', '25391398', 'RNA molecules play important roles in key biological processes in the cell and are becoming attractive for developing therapeutic applications. Since the function of RNA depends on its structure and dynamics, comparing and classifying the RNA 3D structures is of crucial importance to molecular biology. In this study, we have developed Rclick, a web server that is capable of superimposing RNA 3D structures by using clique matching and 3D least-squares fitting. Our server Rclick has been benchmarked and compared with other popular servers and methods for RNA structural alignments. In most cases, Rclick alignments were better in terms of structure overlap. Our server also recognizes conformational changes between structures. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server for comparison of RNA, RNA-protein complexes and RNA-ligand structures.'),
(78850, 2015, 'bio', 'DISOPRED3: precise disordered region predictions with annotated protein-binding activity', 'Jones, David T|Cozzetto, Domenico', 'Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK.|Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK.', 'United Kingdom|United Kingdom', 283, 'Binding Sites|Computational Biology|Databases, Factual|Intrinsically Disordered Proteins|Molecular Sequence Annotation|Neural Networks (Computer)|Protein Binding|Protein Interaction Domains and Motifs|Software', 'Journal Article', '10.1093/bioinformatics/btu744', '25391399', 'A sizeable fraction of eukaryotic proteins contain intrinsically disordered regions (IDRs), which act in unfolded states or by undergoing transitions between structured and unstructured conformations. Over time, sequence-based classifiers of IDRs have become fairly accurate and currently a major challenge is linking IDRs to their biological roles from the molecular to the systems level.'),
(78851, 2015, 'bio', 'Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data', 'Li, Wenyuan|Gong, Ke|Li, Qingjiao|Alber, Frank|Zhou, Xianghong Jasmine', 'Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.|Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.|Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.|Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.|Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.', 'United States|United States|United States|United States|United States', 36, 'Algorithms|Chromatin|Chromosome Mapping|Chromosomes, Human|Genome, Human|Genomic Library|Humans|Models, Statistical|Software', 'Journal Article', '10.1093/bioinformatics/btu747', '25391400', 'Genome-wide proximity ligation assays, e.g. Hi-C and its variant TCC, have recently become important tools to study spatial genome organization. Removing biases from chromatin contact matrices generated by such techniques is a critical preprocessing step of subsequent analyses. The continuing decline of sequencing costs has led to an ever-improving resolution of the Hi-C data, resulting in very large matrices of chromatin contacts. Such large-size matrices, however, pose a great challenge on the memory usage and speed of its normalization. Therefore, there is an urgent need for fast and memory-efficient methods for normalization of Hi-C data. We developed Hi-Corrector, an easy-to-use, open source implementation of the Hi-C data normalization algorithm. Its salient features are (i) scalability-the software is capable of normalizing Hi-C data of any size in reasonable times, (ii) memory efficiency-the sequential version can run on any single computer with very limited memory, no matter how little, (iii) fast speed-the parallel version can run very fast on multiple computing nodes with limited local memory.'),
(78852, 2015, 'bio', 'SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP', 'van Rens, Karen E|Mäkinen, Veli|Tomescu, Alexandru I', 'Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and HAN University of Applied Sciences, Nijmegen, The Netherlands Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and HAN University of Applied Sciences, Nijmegen, The Netherlands.|Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and HAN University of Applied Sciences, Nijmegen, The Netherlands.|Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and HAN University of Applied Sciences, Nijmegen, The Netherlands.', 'Finland|Finland|Finland', 8, 'Computational Biology|Computer Simulation|High-Throughput Nucleotide Sequencing|Humans|Neoplasms|Phylogeny|Polymorphism, Single Nucleotide|Programming, Linear|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/btu755', '25398608', 'Recent studies sequenced tumor samples from the same progenitor at different development stages and showed that by taking into account the phylogeny of this development, single-nucleotide variant (SNV) calling can be improved. Accurate SNV calls can better reveal early-stage tumors, identify mechanisms of cancer progression or help in drug targeting.'),
(78853, 2015, 'bio', 'UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches', 'Suzek, Baris E|Wang, Yuqi|Huang, Hongzhan|McGarvey, Peter B|Wu, Cathy H|UniProt Consortium', 'Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muxc4x9fla Sxc4xb1tkxc4xb1 Koxc3xa7man University, Muxc4x9fla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muxc4x9fla Sxc4xb1tkxc4xb1 Koxc3xa7man University, Muxc4x9fla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.|Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muxc4x9fla Sxc4xb1tkxc4xb1 Koxc3xa7man University, Muxc4x9fla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.|Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muxc4x9fla Sxc4xb1tkxc4xb1 Koxc3xa7man University, Muxc4x9fla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.|Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muxc4x9fla Sxc4xb1tkxc4xb1 Koxc3xa7man University, Muxc4x9fla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.|Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muxc4x9fla Sxc4xb1tkxc4xb1 Koxc3xa7man University, Muxc4x9fla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muxc4x9fla Sxc4xb1tkxc4xb1 Koxc3xa7man University, Muxc4x9fla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.|Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muxc4x9fla Sxc4xb1tkxc4xb1 Koxc3xa7man University, Muxc4x9fla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muxc4x9fla Sxc4xb1tkxc4xb1 Koxc3xa7man University, Muxc4x9fla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.', 'Switzerland|Switzerland|Switzerland|Switzerland|Switzerland|Switzerland', 286, 'AlkB Homolog 5, RNA Demethylase|Cluster Analysis|Computational Biology|Databases, Protein|Dioxygenases|Gene Ontology|Humans|Information Storage and Retrieval|Membrane Proteins|Molecular Sequence Annotation|Proteins|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/btu739', '25398609', 'UniRef databases provide full-scale clustering of UniProtKB sequences and are utilized for a broad range of applications, particularly similarity-based functional annotation. Non-redundancy and intra-cluster homogeneity in UniRef were recently improved by adding a sequence length overlap threshold. Our hypothesis is that these improvements would enhance the speed and sensitivity of similarity searches and improve the consistency of annotation within clusters.'),
(78854, 2014, 'bio', 'SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips', 'Marcus, Shoshana|Lee, Hayan|Schatz, Michael C', 'Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA and Department of Computer Science, Stony Brook University, Stony Brook, NY 11794, USA.|Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA and Department of Computer Science, Stony Brook University, Stony Brook, NY 11794, USA Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA and Department of Computer Science, Stony Brook University, Stony Brook, NY 11794, USA.|Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA and Department of Computer Science, Stony Brook University, Stony Brook, NY 11794, USA Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA and Department of Computer Science, Stony Brook University, Stony Brook, NY 11794, USA.', 'United States|United States|United States', 47, 'Algorithms|Bacillus anthracis|Escherichia coli|Genome, Bacterial|Genomics|Sequence Analysis, DNA', 'Journal Article', '10.1093/bioinformatics/btu756', '25398610', 'Genomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach that analyzes multiple individuals together. A compressed de Bruijn graph is a sophisticated data structure for representing the genomes of entire populations. It robustly encodes shared segments, simple single-nucleotide polymorphisms and complex structural variations far beyond what can be represented in a collection of linear sequences alone.'),
(78855, 2015, 'bio', 'M3D: a kernel-based test for spatially correlated changes in methylation profiles', 'Mayo, Tom R|Schweikert, Gabriele|Sanguinetti, Guido', 'IANC, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB and Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.|IANC, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB and Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK IANC, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB and Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.|IANC, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB and Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.', 'United Kingdom|United Kingdom|United Kingdom', 14, 'Animals|Computer Simulation|DNA Methylation|Embryonic Stem Cells|Epigenomics|Humans|Mice|Models, Statistical|Software', 'Journal Article', '10.1093/bioinformatics/btu749', '25398611', 'DNA methylation is an intensely studied epigenetic mark implicated in many biological processes of direct clinical relevance. Although sequencing-based technologies are increasingly allowing high-resolution measurements of DNA methylation, statistical modelling of such data is still challenging. In particular, statistical identification of differentially methylated regions across different conditions poses unresolved challenges in accounting for spatial correlations within the statistical testing procedure.'),
(78856, 2015, 'bio', 'M-path: a compass for navigating potential metabolic pathways', 'Araki, Michihiro|Cox, Robert Sidney|Makiguchi, Hiroki|Ogawa, Teppei|Taniguchi, Takeshi|Miyaoku, Kohei|Nakatsui, Masahiko|Hara, Kiyotaka Y|Kondo, Akihiko', 'Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.|Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.|Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.|Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.|Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.|Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.|Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.|Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.|Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.', 'Japan|Japan|Japan|Japan|Japan|Japan|Japan|Japan|Japan', 18, 'Algorithms|Amino Acids|Databases, Factual|Metabolic Networks and Pathways|Software', 'Journal Article', '10.1093/bioinformatics/btu750', '25398612', 'Construction of synthetic metabolic pathways promises sustainable production of diverse chemicals and materials. To design synthetic metabolic pathways of high value, computational methods are needed to expand present knowledge by mining comprehensive chemical and enzymatic information databases. Several computational methods have been already reported for the metabolic pathway design, but until now computation complexity has limited the diversity of chemical and enzymatic data used.'),
(78857, 2015, 'bio', 'ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing', 'Jayasundara, Duleepa|Saeed, I|Maheswararajah, Suhinthan|Chang, B C|Tang, S-L|Halgamuge, Saman K', 'Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Portland House Research and Advisors Ltd., Melbourne, VIC 3000, Australia, Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan and Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.|Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Portland House Research and Advisors Ltd., Melbourne, VIC 3000, Australia, Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan and Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.|Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Portland House Research and Advisors Ltd., Melbourne, VIC 3000, Australia, Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan and Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.|Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Portland House Research and Advisors Ltd., Melbourne, VIC 3000, Australia, Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan and Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.|Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Portland House Research and Advisors Ltd., Melbourne, VIC 3000, Australia, Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan and Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.|Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Portland House Research and Advisors Ltd., Melbourne, VIC 3000, Australia, Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan and Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.', 'Australia|Australia|Australia|Australia|Australia|Australia', 16, 'Algorithms|Foot-and-Mouth Disease Virus|HIV-1|Haplotypes|High-Throughput Nucleotide Sequencing|Humans', 'Journal Article', '10.1093/bioinformatics/btu754', '25398613', 'The combined effect of a high replication rate and the low fidelity of the viral polymerase in most RNA viruses and some DNA viruses results in the formation of a viral quasispecies. Uncovering information about quasispecies populations significantly benefits the study of disease progression, antiviral drug design, vaccine design and viral pathogenesis. We present a new analysis pipeline called ViQuaS for viral quasispecies spectrum reconstruction using short next-generation sequencing reads. ViQuaS is based on a novel reference-assisted de novo assembly algorithm for constructing local haplotypes. A significantly extended version of an existing global strain reconstruction algorithm is also used.'),
(78858, 2015, 'bio', 'Local statistics allow quantification of cell-to-cell variability from high-throughput microscope images', 'Handfield, Louis-François|Strome, Bob|Chong, Yolanda T|Moses, Alan M', 'Department of Computer Science, Department of Cell & Systems Biology and Department of Molecular Genetics, University of Toronto, Ontario M5S 3B2, Canada.|Department of Computer Science, Department of Cell & Systems Biology and Department of Molecular Genetics, University of Toronto, Ontario M5S 3B2, Canada.|Department of Computer Science, Department of Cell & Systems Biology and Department of Molecular Genetics, University of Toronto, Ontario M5S 3B2, Canada.|Department of Computer Science, Department of Cell & Systems Biology and Department of Molecular Genetics, University of Toronto, Ontario M5S 3B2, Canada Department of Computer Science, Department of Cell & Systems Biology and Department of Molecular Genetics, University of Toronto, Ontario M5S 3B2, Canada.', 'Canada|Canada|Canada|Canada', 9, 'Cell Lineage|Diagnostic Imaging|High-Throughput Screening Assays|Microscopy, Fluorescence|Models, Statistical|Proteomics|Saccharomyces cerevisiae|Saccharomyces cerevisiae Proteins', 'Journal Article', '10.1093/bioinformatics/btu759', '25398614', 'Quantifying variability in protein expression is a major goal of systems biology and cell-to-cell variability in subcellular localization pattern has not been systematically quantified.'),
(78859, 2015, 'bio', 'mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens', 'Petrenko, Pavel|Doxey, Andrew C', 'Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.|Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.', 'Canada|Canada', 7, 'Amino Acid Sequence|Bacteria|Bacterial Infections|Bacterial Proteins|Host-Pathogen Interactions|Humans|Molecular Mimicry|Molecular Sequence Data|Proteome|Sequence Homology, Amino Acid|Software|Virulence Factors', 'Journal Article', '10.1093/bioinformatics/btu681', '25399027', 'mimicMe is a web server for prediction and analysis of host-like proteins (mimics) encoded by microbial pathogens. Users select a host species and any set of pathogen and control proteomes (bacterial, fungal, protozoan or viral) and mimicMe reports host-like proteins that are unique to or enriched among pathogens. Additional server features include visualization of structural similarities between pathogen and host proteins as well as function-enrichment analysis.'),
(78860, 2015, 'bio', 'SYSBIONS: nested sampling for systems biology', 'Johnson, Rob|Kirk, Paul|Stumpf, Michael P H', 'Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.|Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.|Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.', 'United Kingdom|United Kingdom|United Kingdom', 0, 'Algorithms|Bayes Theorem|Models, Biological|Probability|Software|Systems Biology', 'Journal Article', '10.1093/bioinformatics/btu675', '25399028', 'Model selection is a fundamental part of the scientific process in systems biology. Given a set of competing hypotheses, we routinely wish to choose the one that best explains the observed data. In the Bayesian framework, models are compared via Bayes factors (the ratio of evidences), where a models evidence is the support given to the model by the data. A parallel interest is inferring the distribution of the parameters that define a model. Nested sampling is a method for the computation of a models evidence and the generation of samples from the posterior parameter distribution.'),
(78861, 2015, 'bio', 'E-MEM: efficient computation of maximal exact matches for very large genomes', 'Khiste, Nilesh|Ilie, Lucian', 'Department of Computer Science, University of Western Ontario, London, Ontario, N6A 5B7, Canada.|Department of Computer Science, University of Western Ontario, London, Ontario, N6A 5B7, Canada.', 'Canada|Canada', 13, 'Algorithms|Animals|Databases, Factual|Genome|Humans|Mice|Programming Languages|Sequence Alignment|Sequence Analysis, DNA|Software|Species Specificity|Systems Biology|Triticum', 'Comparative Study', '10.1093/bioinformatics/btu687', '25399029', 'Alignment of similar whole genomes is often performed using anchors given by the maximal exact matches (MEMs) between their sequences. In spite of significant amount of research on this problem, the computation of MEMs for large genomes remains a challenging problem. The leading current algorithms employ full text indexes, the sparse suffix array giving the best results. Still, their memory requirements are high, the parallelization is not very efficient, and they cannot handle very large genomes.'),
(78862, 2015, 'bio', 'WemIQ: an accurate and robust isoform quantification method for RNA-seq data', 'Zhang, Jing|Kuo, C-C Jay|Chen, Liang', 'Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089, USA and Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.|Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089, USA and Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.|Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089, USA and Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.', 'United States|United States|United States', 0, 'Algorithms|Exons|Gene Expression Profiling|Humans|Models, Theoretical|Protein Isoforms|RNA|Sequence Analysis, RNA|Software', 'Journal Article', '10.1093/bioinformatics/btu757', '25406327', 'The deconvolution of isoform expression from RNA-seq remains challenging because of non-uniform read sampling and subtle differences among isoforms.'),
(78863, 2015, 'bio', 'Graphical model for joint segmentation and tracking of multiple dividing cells', 'Schiegg, Martin|Hanslovsky, Philipp|Haubold, Carsten|Koethe, Ullrich|Hufnagel, Lars|Hamprecht, Fred A', 'University of Heidelberg, IWR/HCI, 69115 Heidelberg, Germany and European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.|University of Heidelberg, IWR/HCI, 69115 Heidelberg, Germany and European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.|University of Heidelberg, IWR/HCI, 69115 Heidelberg, Germany and European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.|University of Heidelberg, IWR/HCI, 69115 Heidelberg, Germany and European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.|University of Heidelberg, IWR/HCI, 69115 Heidelberg, Germany and European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.|University of Heidelberg, IWR/HCI, 69115 Heidelberg, Germany and European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.', 'Germany|Germany|Germany|Germany|Germany|Germany', 0, 'Algorithms|Animals|Cell Division|Cell Nucleus|Drosophila|Embryo, Nonmammalian|Imaging, Three-Dimensional|Models, Statistical', 'Journal Article', '10.1093/bioinformatics/btu764', '25406328', 'To gain fundamental insight into the development of embryos, biologists seek to understand the fate of each and every embryonic cell. For the generation of cell tracks in embryogenesis, so-called tracking-by-assignment methods are flexible approaches. However, as every two-stage approach, they suffer from irrevocable errors propagated from the first stage to the second stage, here from segmentation to tracking. It is therefore desirable to model segmentation and tracking in a joint holistic assignment framework allowing the two stages to maximally benefit from each other.'),
(78864, 2015, 'bio', 'EPGA: de novo assembly using the distributions of reads and insert size', 'Luo, Junwei|Wang, Jianxin|Zhang, Zhen|Wu, Fang-Xiang|Li, Min|Pan, Yi', 'School of Information Science and Engineering, Central South University, ChangSha 410083, China, College of Computer Science and Technology, Henan Polytechnic University, JiaoZuo, 454000, China, Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan S7N 5A9, Canada and Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA School of Information Science and Engineering, Central South University, ChangSha 410083, China, College of Computer Science and Technology, Henan Polytechnic University, JiaoZuo, 454000, China, Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan S7N 5A9, Canada and Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA.|School of Information Science and Engineering, Central South University, ChangSha 410083, China, College of Computer Science and Technology, Henan Polytechnic University, JiaoZuo, 454000, China, Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan S7N 5A9, Canada and Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA.|School of Information Science and Engineering, Central South University, ChangSha 410083, China, College of Computer Science and Technology, Henan Polytechnic University, JiaoZuo, 454000, China, Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan S7N 5A9, Canada and Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA.|School of Information Science and Engineering, Central South University, ChangSha 410083, China, College of Computer Science and Technology, Henan Polytechnic University, JiaoZuo, 454000, China, Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan S7N 5A9, Canada and Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA.|School of Information Science and Engineering, Central South University, ChangSha 410083, China, College of Computer Science and Technology, Henan Polytechnic University, JiaoZuo, 454000, China, Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan S7N 5A9, Canada and Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA.|School of Information Science and Engineering, Central South University, ChangSha 410083, China, College of Computer Science and Technology, Henan Polytechnic University, JiaoZuo, 454000, China, Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan S7N 5A9, Canada and Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA.', 'Canada|Canada|Canada|Canada|Canada|Canada', 14, 'Algorithms|Bacteria|Genome, Bacterial|Repetitive Sequences, Nucleic Acid|Sequence Analysis, DNA', 'Journal Article', '10.1093/bioinformatics/btu762', '25406329', 'In genome assembly, the primary issue is how to determine upstream and downstream sequence regions of sequence seeds for constructing long contigs or scaffolds. When extending one sequence seed, repetitive regions in the genome always cause multiple feasible extension candidates which increase the difficulty of genome assembly. The universally accepted solution is choosing one based on read overlaps and paired-end (mate-pair) reads. However, this solution faces difficulties with regard to some complex repetitive regions. In addition, sequencing errors may produce false repetitive regions and uneven sequencing depth leads some sequence regions to have too few or too many reads. All the aforementioned problems prohibit existing assemblers from getting satisfactory assembly results.'),
(78865, 2015, 'bio', 'XenoSite server: a web-available site of metabolism prediction tool', 'Matlock, Matthew K|Hughes, Tyler B|Swamidass, S Joshua', 'Division of Biology and Biological Sciences and Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63130, USA.|Division of Biology and Biological Sciences and Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63130, USA.|Division of Biology and Biological Sciences and Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63130, USA.', 'United States|United States|United States', 31, 'Antipsychotic Agents|Computational Biology|Cytochrome P-450 Enzyme System|Dibenzothiepins|Humans|Internet|Metabolic Networks and Pathways|Molecular Docking Simulation|Neural Networks (Computer)|Probability|Small Molecule Libraries|Xenobiotics', 'Journal Article', '10.1093/bioinformatics/btu761', '25411327', 'Cytochrome P450 enzymes (P450s) are metabolic enzymes that process the majority of FDA-approved, small-molecule drugs. Understanding how these enzymes modify molecule structure is key to the development of safe, effective drugs. XenoSite server is an online implementation of the XenoSite, a recently published computational model for P450 metabolism. XenoSite predicts which atomic sites of a molecule--sites of metabolism (SOMs)--are modified by P450s. XenoSite server accepts input in common chemical file formats including SDF and SMILES and provides tools for visualizing the likelihood that each atomic site is a site of metabolism for a variety of important P450s, as well as a flat file download of SOM predictions.'),
(78866, 2015, 'bio', 'jNMFMA: a joint non-negative matrix factorization meta-analysis of transcriptomics data', 'Wang, Hong-Qiang|Zheng, Chun-Hou|Zhao, Xing-Ming', 'Machine Intelligence and Computational Biology Lab, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, China, College of Electrical Engineering and Automation, Anhui University, Hefei 230031, China and Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China.|Machine Intelligence and Computational Biology Lab, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, China, College of Electrical Engineering and Automation, Anhui University, Hefei 230031, China and Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China.|Machine Intelligence and Computational Biology Lab, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, China, College of Electrical Engineering and Automation, Anhui University, Hefei 230031, China and Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China.', 'China|China|China', 0, 'Algorithms|Computer Simulation|DNA Methylation|Gene Expression Profiling|Gene Expression Regulation, Neoplastic|Gene Regulatory Networks|Humans|Lung Neoplasms|Meta-Analysis as Topic|Oligonucleotide Array Sequence Analysis', 'Journal Article', '10.1093/bioinformatics/btu679', '25411328', 'Tremendous amount of omics data being accumulated poses a pressing challenge of meta-analyzing the heterogeneous data for mining new biological knowledge. Most existing methods deal with each gene independently, thus often resulting in high false positive rates in detecting differentially expressed genes (DEG). To our knowledge, no or little effort has been devoted to methods that consider dependence structures underlying transcriptomics data for DEG identification in meta-analysis context.'),
(78867, 2015, 'bio', 'Unsupervised discovery of information structure in biomedical documents', 'Kiela, Douwe|Guo, Yufan|Stenius, Ulla|Korhonen, Anna', 'Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK and Institute of Environmental Medicine, Karolinska Institutet, Stockholm SE-171 77, Sweden.|Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK and Institute of Environmental Medicine, Karolinska Institutet, Stockholm SE-171 77, Sweden.|Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK and Institute of Environmental Medicine, Karolinska Institutet, Stockholm SE-171 77, Sweden.|Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK and Institute of Environmental Medicine, Karolinska Institutet, Stockholm SE-171 77, Sweden.', 'Sweden|Sweden|Sweden|Sweden', 0, 'Algorithms|Biomedical Research|Computational Biology|Data Mining|Humans|Periodicals as Topic|PubMed|Software', 'Journal Article', '10.1093/bioinformatics/btu758', '25411329', 'Information structure (IS) analysis is a text mining technique, which classifies text in biomedical articles into categories that capture different types of information, such as objectives, methods, results and conclusions of research. It is a highly useful technique that can support a range of Biomedical Text Mining tasks and can help readers of biomedical literature find information of interest faster, accelerating the highly time-consuming process of literature review. Several approaches to IS analysis have been presented in the past, with promising results in real-world biomedical tasks. However, all existing approaches, even weakly supervised ones, require several hundreds of hand-annotated training sentences specific to the domain in question. Because biomedicine is subject to considerable domain variation, such annotations are expensive to obtain. This makes the application of IS analysis across biomedical domains difficult. In this article, we investigate an unsupervised approach to IS analysis and evaluate the performance of several unsupervised methods on a large corpus of biomedical abstracts collected from PubMed.'),
(78868, 2015, 'bio', 'HyDRA: gene prioritization via hybrid distance-score rank aggregation', 'Kim, Minji|Farnoud, Farzad|Milenkovic, Olgica', 'Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.|Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.|Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.', 'United States|United States|United States', 0, 'Algorithms|Artificial Intelligence|Databases, Genetic|Disease|Genes|Genetic Predisposition to Disease|Genomics|Humans|Software', 'Journal Article', '10.1093/bioinformatics/btu766', '25411330', 'Gene prioritization refers to a family of computational techniques for inferring disease genes through a set of training genes and carefully chosen similarity criteria. Test genes are scored based on their average similarity to the training set, and the rankings of genes under various similarity criteria are aggregated via statistical methods. The contributions of our work are threefold: (i) first, based on the realization that there is no unique way to define an optimal aggregate for rankings, we investigate the predictive quality of a number of new aggregation methods and known fusion techniques from machine learning and social choice theory. Within this context, we quantify the influence of the number of training genes and similarity criteria on the diagnostic quality of the aggregate and perform in-depth cross-validation studies, (ii) second, we propose a new approach to genomic data aggregation, termed HyDRA (Hybrid Distance-score Rank Aggregation), which combines the advantages of score-based and combinatorial aggregation techniques. We also propose incorporating a new top-versus-bottom (TvB) weighting feature into the hybrid schemes. The TvB feature ensures that aggregates are more reliable at the top of the list, rather than at the bottom, since only top candidates are tested experimentally, (iii) third, we propose an iterative procedure for gene discovery that operates via successful augmentation of the set of training genes by genes discovered in previous rounds, checked for consistency.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(78869, 2015, 'bio', 'CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites', 'Naito, Yuki|Hino, Kimihiro|Bono, Hidemasa|Ui-Tei, Kumiko', 'Database Center for Life Science (DBCLS), National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan and Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan Database Center for Life Science (DBCLS), National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan and Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.|Database Center for Life Science (DBCLS), National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan and Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan Database Center for Life Science (DBCLS), National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan and Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.|Database Center for Life Science (DBCLS), National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan and Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan Database Center for Life Science (DBCLS), National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan and Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.|Database Center for Life Science (DBCLS), National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan and Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.', 'Japan|Japan|Japan|Japan', 0, 'Animals|Base Sequence|CRISPR-Cas Systems|DNA|Drug Design|Endonucleases|Gene Expression Regulation|Genome|Genomics|Humans|Mice|Molecular Sequence Data|RNA Editing|RNA, Guide|Rats|Software', 'Journal Article', '10.1093/bioinformatics/btu743', '25414360', 'CRISPRdirect is a simple and functional web server for selecting rational CRISPR/Cas targets from an input sequence. The CRISPR/Cas system is a promising technique for genome engineering which allows target-specific cleavage of genomic DNA guided by Cas9 nuclease in complex with a guide RNA (gRNA), that complementarily binds to a xe2x88xbc 20 nt targeted sequence. The target sequence requirements are twofold. First, the 5-NGG protospacer adjacent motif (PAM) sequence must be located adjacent to the target sequence. Second, the target sequence should be specific within the entire genome in order to avoid off-target editing. CRISPRdirect enables users to easily select rational target sequences with minimized off-target sites by performing exhaustive searches against genomic sequences. The server currently incorporates the genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast.'),
(78870, 2015, 'bio', 'Evolutionary non-linear modelling for selecting vaccines against antigenically variable viruses', 'Rahman, Tameera|Mahapatra, Mana|Laing, Emma|Jin, Yaochu', 'Department of Computing, University of Surrey, Guildford GU2 7XH, UK, The Pirbright Institute, Pirbright GU24 0NF, UK and Department of Microbial and Cellular Sciences, University of Surrey, Guildford GU2 7XH, UK.|Department of Computing, University of Surrey, Guildford GU2 7XH, UK, The Pirbright Institute, Pirbright GU24 0NF, UK and Department of Microbial and Cellular Sciences, University of Surrey, Guildford GU2 7XH, UK.|Department of Computing, University of Surrey, Guildford GU2 7XH, UK, The Pirbright Institute, Pirbright GU24 0NF, UK and Department of Microbial and Cellular Sciences, University of Surrey, Guildford GU2 7XH, UK.|Department of Computing, University of Surrey, Guildford GU2 7XH, UK, The Pirbright Institute, Pirbright GU24 0NF, UK and Department of Microbial and Cellular Sciences, University of Surrey, Guildford GU2 7XH, UK.', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom', 2, 'Algorithms|Animals|Antibodies, Neutralizing|Antigenic Variation|Antigens, Viral|Biological Evolution|Capsid Proteins|Computational Biology|Computer Simulation|Foot-and-Mouth Disease|Foot-and-Mouth Disease Virus|Influenza Vaccines|Nonlinear Dynamics', 'Journal Article', '10.1093/bioinformatics/btu768', '25414361', 'In vitro and in vivo selection of vaccines is time consuming, expensive and the selected vaccines may not be able to provide protection against broad-spectrum viruses because of emerging antigenically novel disease strains. A powerful computational model that incorporates these protein/DNA or RNA level fluctuations can effectively predict antigenically variant strains, and can minimize the amount of resources spent on exclusive serological testing of vaccines and make wide spectrum vaccines possible for many diseases. However, in silico vaccine prediction remains a grand challenge. To address the challenge, we investigate the use of linear and non-linear regression models to predict the antigenic similarity in foot-and-mouth disease virus strains and in influenza strains, where the structure and parameters of the non-linear model are optimized using an evolutionary algorithm (EA). In addition, we examine two different scoring methods for weighting the type of amino acid substitutions in the linear and non-linear models. We also test our models with some unseen data.'),
(78871, 2015, 'bio', 'Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning', 'Xu, Ying-Ying|Yang, Fan|Zhang, Yang|Shen, Hong-Bin', 'Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.|Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.|Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.|Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.', 'China|China|China|China', 0, 'Algorithms|Biomarkers, Tumor|Cellular Structures|Computational Biology|Databases, Protein|Humans|Neoplasm Proteins|Neoplasms|Software|Subcellular Fractions', 'Journal Article', '10.1093/bioinformatics/btu772', '25414362', 'There is a long-term interest in the challenging task of finding translocated and mislocated cancer biomarker proteins. Bioimages of subcellular protein distribution are new data sources which have attracted much attention in recent years because of their intuitive and detailed descriptions of protein distribution. However, automated methods in large-scale biomarker screening suffer significantly from the lack of subcellular location annotations for bioimages from cancer tissues. The transfer prediction idea of applying models trained on normal tissue proteins to predict the subcellular locations of cancerous ones is arbitrary because the protein distribution patterns may differ in normal and cancerous states.'),
(78872, 2015, 'bio', 'Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens', 'Tsukui, Takahiro|Nagano, Nozomi|Umemura, Myco|Kumagai, Toshitaka|Terai, Goro|Machida, Masayuki|Asai, Kiyoshi', 'Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, Fermlab Inc., Tokyo 135-0021, Japan, INTEC Inc., Tokyo 136-8637, Japan, and Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan.|Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, Fermlab Inc., Tokyo 135-0021, Japan, INTEC Inc., Tokyo 136-8637, Japan, and Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, Fermlab Inc., Tokyo 135-0021, Japan, INTEC Inc., Tokyo 136-8637, Japan, and Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan.|Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, Fermlab Inc., Tokyo 135-0021, Japan, INTEC Inc., Tokyo 136-8637, Japan, and Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan.|Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, Fermlab Inc., Tokyo 135-0021, Japan, INTEC Inc., Tokyo 136-8637, Japan, and Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan.|Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, Fermlab Inc., Tokyo 135-0021, Japan, INTEC Inc., Tokyo 136-8637, Japan, and Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan.|Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, Fermlab Inc., Tokyo 135-0021, Japan, INTEC Inc., Tokyo 136-8637, Japan, and Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan.|Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, Fermlab Inc., Tokyo 135-0021, Japan, INTEC Inc., Tokyo 136-8637, Japan, and Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, Fermlab Inc., Tokyo 135-0021, Japan, INTEC Inc., Tokyo 136-8637, Japan, and Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan.', 'Japan|Japan|Japan|Japan|Japan|Japan|Japan', 0, 'Amino Acid Sequence|Biosynthetic Pathways|Fungal Proteins|Genes, Fungal|Genome, Fungal|Molecular Sequence Data|Multigene Family|Peptides, Cyclic|Ribosomes|Sequence Analysis, DNA|Sequence Homology, Amino Acid|Ustilago', 'Journal Article', '10.1093/bioinformatics/btu753', '25414363', 'Ustiloxins A and B are toxic cyclic tetrapeptides, Tyr-Val/Ala-Ile-Gly (Y-V/A-I-G), that were originally identified from Ustilaginoidea virens, a pathogenic fungus affecting rice plants. Contrary to our report that ustiloxin B is ribosomally synthesized in Aspergillus flavus, a recent report suggested that ustiloxins are synthesized by a non-ribosomal peptide synthetase in U.virens. Thus, we analyzed the U.virens genome, to identify the responsible gene cluster.'),
(78873, 2015, 'bio', 'The Victor C++ library for protein representation and advanced manipulation', 'Hirsh, Layla|Piovesan, Damiano|Giollo, Manuel|Ferrari, Carlo|Tosatto, Silvio C E', 'Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, Department of Engineering, Pontificia Universidad Católica del Perú, San Miguel, 32 Lima, Perú and Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, Department of Engineering, Pontificia Universidad Católica del Perú, San Miguel, 32 Lima, Perú and Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy.|Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, Department of Engineering, Pontificia Universidad Católica del Perú, San Miguel, 32 Lima, Perú and Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy.|Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, Department of Engineering, Pontificia Universidad Católica del Perú, San Miguel, 32 Lima, Perú and Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, Department of Engineering, Pontificia Universidad Católica del Perú, San Miguel, 32 Lima, Perú and Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy.|Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, Department of Engineering, Pontificia Universidad Católica del Perú, San Miguel, 32 Lima, Perú and Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy.|Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, Department of Engineering, Pontificia Universidad Católica del Perú, San Miguel, 32 Lima, Perú and Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy.', 'Italy|Italy|Italy|Italy|Italy', 2, 'Computational Biology|Databases, Protein|Humans|Libraries, Digital|Proteins|Sequence Alignment|Software|Structural Homology, Protein', 'Journal Article', '10.1093/bioinformatics/btu773', '25414364', 'Protein sequence and structure representation and manipulation require dedicated software libraries to support methods of increasing complexity. Here, we describe the VIrtual Constrution TOol for pRoteins (Victor) C++ library, an open source platform dedicated to enabling inexperienced users to develop advanced tools and gathering contributions from the community. The provided application examples cover statistical energy potentials, profile-profile sequence alignments and ab initio loop modeling. Victor was used over the last 15 years in several publications and optimized for efficiency. It is provided as a GitHub repository with source files and unit tests, plus extensive online documentation, including a Wiki with help files and tutorials, examples and Doxygen documentation.'),
(78874, 2015, 'bio', 'SAMNetWeb: identifying condition-specific networks linking signaling and transcription', 'Gosline, Sara J C|Oh, Coyin|Fraenkel, Ernest', 'Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.', 'United States|United States|United States', 0, 'Algorithms|Biomarkers, Tumor|Breast Neoplasms|Data Interpretation, Statistical|Female|Gene Expression Profiling|Gene Regulatory Networks|Genomics|Humans|Internet|Lung Neoplasms|Proteomics|RNA, Messenger|Signal Transduction|Software|Systems Biology|Tumor Cells, Cultured', 'Journal Article', '10.1093/bioinformatics/btu748', '25414365', 'High-throughput datasets such as genetic screens, mRNA expression assays and global phospho-proteomic experiments are often difficult to interpret due to inherent noise in each experimental system. Computational tools have improved interpretation of these datasets by enabling the identification of biological processes and pathways that are most likely to explain the measured results. These tools are primarily designed to analyse data from a single experiment (e.g. drug treatment versus control), creating a need for computational algorithms that can handle heterogeneous datasets across multiple experimental conditions at once.'),
(78875, 2015, 'bio', 'Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data', 'Kyoda, Koji|Tohsato, Yukako|Ho, Kenneth H L|Onami, Shuichi', 'Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan and.|Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan and.|Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan and.|Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan and National Bioscience Database Center, Japan Science and Technology Agency, Tokyo 102-0081, Japan.', 'Japan|Japan|Japan|Japan', 5, 'Computational Biology|Computer Graphics|Computer Simulation|Databases, Factual|Humans|Models, Biological|Programming Languages|Signal Transduction|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/btu767', '25414366', 'Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats.'),
(78876, 2015, 'bio', 'Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data', 'Liu, Zhenqiu|Sun, Fengzhu|Braun, Jonathan|McGovern, Dermot P B|Piantadosi, Steven', 'Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA, Molecular and Computational Biology Program, Department of Biological Sciences, USC, Los Angeles, CA 90089, USA, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA and F. Widjaja Foundation - Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.|Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA, Molecular and Computational Biology Program, Department of Biological Sciences, USC, Los Angeles, CA 90089, USA, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA and F. Widjaja Foundation - Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.|Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA, Molecular and Computational Biology Program, Department of Biological Sciences, USC, Los Angeles, CA 90089, USA, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA and F. Widjaja Foundation - Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.|Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA, Molecular and Computational Biology Program, Department of Biological Sciences, USC, Los Angeles, CA 90089, USA, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA and F. Widjaja Foundation - Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.|Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA, Molecular and Computational Biology Program, Department of Biological Sciences, USC, Los Angeles, CA 90089, USA, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA and F. Widjaja Foundation - Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.', 'United States|United States|United States|United States|United States', 0, 'Algorithms|Bacteria|Computational Biology|Gene Regulatory Networks|Humans|Metagenomics|Phenotype|Regression Analysis|Software', 'Journal Article', '10.1093/bioinformatics/btu778', '25416747', 'Identifying disease associated taxa and constructing networks for bacteria interactions are two important tasks usually studied separately. In reality, differentiation of disease associated taxa and correlation among taxa may affect each other. One genus can be differentiated because it is highly correlated with another highly differentiated one. In addition, network structures may vary under different clinical conditions. Permutation tests are commonly used to detect differences between networks in distinct phenotypes, and they are time-consuming.'),
(78877, 2015, 'bio', 'Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development', 'Chen, Haifen|Guo, Jing|Mishra, Shital K|Robson, Paul|Niranjan, Mahesan|Zheng, Jie', 'School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore, Genome Institute of Singapore, Biopolis, Singapore 138672, Singapore and School of Electronics and Computer Science, University of Southampton, Highfield, Southampton SO17 1BJ, UK.|School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore, Genome Institute of Singapore, Biopolis, Singapore 138672, Singapore and School of Electronics and Computer Science, University of Southampton, Highfield, Southampton SO17 1BJ, UK.|School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore, Genome Institute of Singapore, Biopolis, Singapore 138672, Singapore and School of Electronics and Computer Science, University of Southampton, Highfield, Southampton SO17 1BJ, UK.|School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore, Genome Institute of Singapore, Biopolis, Singapore 138672, Singapore and School of Electronics and Computer Science, University of Southampton, Highfield, Southampton SO17 1BJ, UK.|School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore, Genome Institute of Singapore, Biopolis, Singapore 138672, Singapore and School of Electronics and Computer Science, University of Southampton, Highfield, Southampton SO17 1BJ, UK.|School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore, Genome Institute of Singapore, Biopolis, Singapore 138672, Singapore and School of Electronics and Computer Science, University of Southampton, Highfield, Southampton SO17 1BJ, UK School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore, Genome Institute of Singapore, Biopolis, Singapore 138672, Singapore and School of Electronics and Computer Science, University of Southampton, Highfield, Southampton SO17 1BJ, UK.', 'Singapore|Singapore|Singapore|Singapore|Singapore|Singapore', 26, 'Algorithms|Animals|Cell Differentiation|Cell Lineage|Embryo, Mammalian|Gene Expression Regulation|Gene Regulatory Networks|Mice|Models, Theoretical|Single-Cell Analysis', 'Journal Article', '10.1093/bioinformatics/btu777', '25416748', 'Transcriptional regulatory networks controlling cell fate decisions in mammalian embryonic development remain elusive despite a long time of research. The recent emergence of single-cell RNA profiling technology raises hope for new discovery. Although experimental works have obtained intriguing insights into the mouse early development, a holistic and systematic view is still missing. Mathematical models of cell fates tend to be concept-based, not designed to learn from real data. To elucidate the regulatory mechanisms behind cell fate decisions, it is highly desirable to synthesize the data-driven and knowledge-driven modeling approaches.'),
(78878, 2015, 'bio', 'NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei', 'Poulet, Axel|Arganda-Carreras, Ignacio|Legland, David|Probst, Aline V|Andrey, Philippe|Tatout, Christophe', 'UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.|UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.|UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.|UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.|UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.|UMR CNRS 6293 INSERM U 1103, GRED, Clermont Université, Aubière, France, UMR INRA-AgroParisTech 1318 ERL CNRS 3559, IJPB, Versailles, France, UMR INRA-AgroParisTech 782, Food Process Engineering and Microbiology, Thiverval-Grignon, France and Sorbonne Universités, UPMC Univ Paris 06 UFR 927, Paris, France.', 'France|France|France|France|France|France', 21, 'Algorithms|Cell Nucleus|Humans|Image Processing, Computer-Assisted|Imaging, Three-Dimensional|Interphase', 'Journal Article', '10.1093/bioinformatics/btu774', '25416749', 'NucleusJ is a simple and user-friendly ImageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D. Starting from image stacks, the nuclear boundary is delimited by combining the Otsu segmentation method with optimization of nuclear sphericity. Chromatin domains are segmented by partitioning the nucleus using a 3D watershed algorithm and by thresholding a contrast measure over the resulting regions. As output, NucleusJ quantifies 15 parameters including shape and size of nuclei as well as intra-nuclear objects and their position within the nucleus. A step-by-step documentation is available for self-training, together with data sets of nuclei with different nuclear organization.'),
(78879, 2015, 'bio', 'Molecular principles of human virus protein-protein interactions', 'Halehalli, Rachita Ramachandra|Nagarajaram, Hampapathalu Adimurthy', 'Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001, India and Graduate School, Manipal University, Manipal, 576104, Karnataka, India Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001, India and Graduate School, Manipal University, Manipal, 576104, Karnataka, India.|Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001, India and Graduate School, Manipal University, Manipal, 576104, Karnataka, India.', 'India|India', 15, 'Binding Sites|Computational Biology|Databases, Protein|Evolution, Molecular|Gene Regulatory Networks|Host-Pathogen Interactions|Humans|Protein Binding|Protein Interaction Domains and Motifs|Protein Interaction Maps|Protein Structure, Tertiary|Proteins|Virus Diseases|Viruses', 'Journal Article', '10.1093/bioinformatics/btu763', '25417202', 'Viruses, from the human protein-protein interaction network perspective, target hubs, bottlenecks and interconnected nodes enriched in certain biological pathways. However, not much is known about the general characteristic features of the human proteins interacting with viral proteins (referred to as hVIPs) as well as the motifs and domains utilized by human-virus protein-protein interactions (referred to as Hu-Vir PPIs).'),
(78880, 2015, 'bio', 'Efficient searching and annotation of metabolic networks using chemical similarity', 'Pertusi, Dante A|Stine, Andrew E|Broadbelt, Linda J|Tyo, Keith E J', 'Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.|Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.|Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.|Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.', 'United States|United States|United States|United States', 28, 'Algorithms|Computational Biology|Databases, Chemical|Hemiterpenes|Metabolic Networks and Pathways|Metabolomics|Molecular Sequence Annotation|Organophosphorus Compounds|Pharmaceutical Preparations|Software', 'Journal Article', '10.1093/bioinformatics/btu760', '25417203', 'The urgent need for efficient and sustainable biological production of fuels and high-value chemicals has elicited a wave of in silico techniques for identifying promising novel pathways to these compounds in large putative metabolic networks. To date, these approaches have primarily used general graph search algorithms, which are prohibitively slow as putative metabolic networks may exceed 1 million compounds. To alleviate this limitation, we report two methods--SimIndex (SI) and SimZyme--which use chemical similarity of 2D chemical fingerprints to efficiently navigate large metabolic networks and propose enzymatic connections between the constituent nodes. We also report a Byers-Waterman type pathway search algorithm for further paring down pertinent networks.'),
(78881, 2015, 'bio', 'Genomation: a toolkit to summarize, annotate and visualize genomic intervals', 'Akalin, Altuna|Franke, Vedran|Vlahovixc4x8dek, Kristian|Mason, Christopher E|Schxc3xbcbeler, Dirk', 'Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland, Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia, Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA, Faculty of Science, University of Basel, 4051 Basel, Switzerland and Department of Informatics, University of Oslo, NO-0316 Oslo, Norway.|Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland, Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia, Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA, Faculty of Science, University of Basel, 4051 Basel, Switzerland and Department of Informatics, University of Oslo, NO-0316 Oslo, Norway.|Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland, Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia, Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA, Faculty of Science, University of Basel, 4051 Basel, Switzerland and Department of Informatics, University of Oslo, NO-0316 Oslo, Norway Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland, Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia, Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA, Faculty of Science, University of Basel, 4051 Basel, Switzerland and Department of Informatics, University of Oslo, NO-0316 Oslo, Norway.|Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland, Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia, Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA, Faculty of Science, University of Basel, 4051 Basel, Switzerland and Department of Informatics, University of Oslo, NO-0316 Oslo, Norway.|Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland, Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia, Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA, Faculty of Science, University of Basel, 4051 Basel, Switzerland and Department of Informatics, University of Oslo, NO-0316 Oslo, Norway Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland, Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia, Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA, Faculty of Science, University of Basel, 4051 Basel, Switzerland and Department of Informatics, University of Oslo, NO-0316 Oslo, Norway.', 'Switzerland|Switzerland|Switzerland|Switzerland|Switzerland', 70, 'Computational Biology|Computer Graphics|Databases, Genetic|Exons|Genome, Human|Genomics|High-Throughput Nucleotide Sequencing|Humans|Introns|Molecular Sequence Annotation|Software', 'Journal Article', '10.1093/bioinformatics/btu775', '25417204', 'Biological insights can be obtained through computational integration of genomics data sets consisting of diverse types of information. The integration is often hampered by a large variety of existing file formats, often containing similar information, and the necessity to use complicated tools to achieve the desired results. We have built an R package, genomation, to expedite the extraction of biological information from high throughput data. The package works with a variety of genomic interval file types and enables easy summarization and annotation of high throughput data sets with given genomic annotations.'),
(78882, 2015, 'bio', 'QuasR: quantification and annotation of short reads in R', 'Gaidatzis, Dimos|Lerch, Anita|Hahne, Florian|Stadler, Michael B', 'Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland.|Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland.|Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland.|Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland.', 'Switzerland|Switzerland|Switzerland|Switzerland', 103, 'Algorithms|Computational Biology|Contig Mapping|Genomics|High-Throughput Nucleotide Sequencing|Humans|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/btu781', '25417205', 'QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. paired-end, stranded, spliced and allele-specific), and is integrated in Bioconductor so that its output can be directly processed for statistical analysis and visualization.'),
(78883, 2015, 'bio', 'DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent', 'Jones, Graham|Aydin, Zeynep|Oxelman, Bengt', 'Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE 405 30 Göteborg, Sweden and Department of Biology, Faculty of Sciences, University of Dicle, 21280 Diyarbakir, Turkey.|Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE 405 30 Göteborg, Sweden and Department of Biology, Faculty of Sciences, University of Dicle, 21280 Diyarbakir, Turkey Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE 405 30 Göteborg, Sweden and Department of Biology, Faculty of Sciences, University of Dicle, 21280 Diyarbakir, Turkey.|Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE 405 30 Göteborg, Sweden and Department of Biology, Faculty of Sciences, University of Dicle, 21280 Diyarbakir, Turkey.', 'Sweden|Sweden|Sweden', 98, 'Algorithms|Animals|Bayes Theorem|Computational Biology|Computer Simulation|Genetic Speciation|Gophers|Markov Chains|Monte Carlo Method|Phylogeny|Silene', 'Journal Article', '10.1093/bioinformatics/btu770', '25422051', 'The multispecies coalescent model provides a formal framework for the assignment of individual organisms to species, where the species are modeled as the branches of the sp tree. None of the available approaches so far have simultaneously co-estimated all the relevant parameters in the model, without restricting the parameter space by requiring a guide tree and/or prior assignment of individuals to clusters or species.'),
(78884, 2015, 'bio', 'Mechanotransduction map: simulation model, molecular pathway, gene set', 'Dent, Jennifer E|Devescovi, Valentina|Li, Han|Di Lena, Pietro|Lu, Youtao|Liu, Yuanhua|Nardini, Christine', 'Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, Peoples Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, Peoples Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy.|Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, Peoples Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy.|Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, Peoples Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy.|Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, Peoples Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy.|Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, Peoples Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy.|Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, Peoples Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy.|Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, Peoples Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy.', 'China|China|China|China|China|China|China', 4, 'Algorithms|Autoimmunity|Computer Simulation|Genes|Humans|Mechanotransduction, Cellular|Metabolic Networks and Pathways|Models, Biological|Signal Transduction|Software', 'Journal Article', '10.1093/bioinformatics/btu776', '25429059', 'Mechanotransduction--the ability to output a biochemical signal from a mechanical input--is related to the initiation and progression of a broad spectrum of molecular events. Yet, the characterization of mechanotransduction lacks some of the most basic tools as, for instance, it can hardly be recognized by enrichment analysis tools, nor could we find any pathway representation. This greatly limits computational testing and hypothesis generation on mechanotransduction biological relevance and involvement in disease or physiological mechanisms.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(78885, 2015, 'bio', 'A bio-inspired computing model for ovarian carcinoma classification and oncogene detection', 'Tsai, Meng-Hsiun|Chen, Mu-Yen|Huang, Steve G|Hung, Yao-Ching|Wang, Hsin-Chieh', 'Department of Management Information System and Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City 402, Taiwan, Department of Information Management, National Taichung University of Science and Technology, Taichung City 404, Taiwan, Institute of Nanotechnology, National Chiao Tung University, Hsinchu City 300, Taiwan and Department of Obstetrics and Gynecology, China Medical University and Hospital, Taichung City 404, Taiwan Department of Management Information System and Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City 402, Taiwan, Department of Information Management, National Taichung University of Science and Technology, Taichung City 404, Taiwan, Institute of Nanotechnology, National Chiao Tung University, Hsinchu City 300, Taiwan and Department of Obstetrics and Gynecology, China Medical University and Hospital, Taichung City 404, Taiwan.|Department of Management Information System and Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City 402, Taiwan, Department of Information Management, National Taichung University of Science and Technology, Taichung City 404, Taiwan, Institute of Nanotechnology, National Chiao Tung University, Hsinchu City 300, Taiwan and Department of Obstetrics and Gynecology, China Medical University and Hospital, Taichung City 404, Taiwan.|Department of Management Information System and Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City 402, Taiwan, Department of Information Management, National Taichung University of Science and Technology, Taichung City 404, Taiwan, Institute of Nanotechnology, National Chiao Tung University, Hsinchu City 300, Taiwan and Department of Obstetrics and Gynecology, China Medical University and Hospital, Taichung City 404, Taiwan.|Department of Management Information System and Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City 402, Taiwan, Department of Information Management, National Taichung University of Science and Technology, Taichung City 404, Taiwan, Institute of Nanotechnology, National Chiao Tung University, Hsinchu City 300, Taiwan and Department of Obstetrics and Gynecology, China Medical University and Hospital, Taichung City 404, Taiwan.|Department of Management Information System and Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City 402, Taiwan, Department of Information Management, National Taichung University of Science and Technology, Taichung City 404, Taiwan, Institute of Nanotechnology, National Chiao Tung University, Hsinchu City 300, Taiwan and Department of Obstetrics and Gynecology, China Medical University and Hospital, Taichung City 404, Taiwan.', 'China|China|China|China|China', 4, 'Algorithms|Biomarkers, Tumor|Computer Simulation|Databases, Factual|Female|Gene Expression Profiling|Humans|Neoplasm Staging|Oncogenes|Ovarian Neoplasms|Support Vector Machine', 'Journal Article', '10.1093/bioinformatics/btu782', '25429060', 'Ovarian cancer is the fifth leading cause of cancer deaths in women in the western world for 2013. In ovarian cancer, benign tumors turn malignant, but the point of transition is difficult to predict and diagnose. The 5-year survival rate of all types of ovarian cancer is 44%, but this can be improved to 92% if the cancer is found and treated before it spreads beyond the ovary. However, only 15% of all ovarian cancers are found at this early stage. Therefore, the ability to automatically identify and diagnose ovarian cancer precisely and efficiently as the tissue changes from benign to invasive is important for clinical treatment and for increasing the cure rate. This study proposes a new ovarian carcinoma classification model using two algorithms: a novel discretization of food sources for an artificial bee colony (DfABC), and a support vector machine (SVM). For the first time in the literature, oncogene detection using this method is also investigated.'),
(78886, 2015, 'bio', 'Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells', 'Keane, Peter|Ceredig, Rhodri|Seoighe, Cathal', 'School of Mathematics, Statistics and Applied Mathematics and Regenerative Medicine Institute, National University of Ireland, Galway, Ireland.|School of Mathematics, Statistics and Applied Mathematics and Regenerative Medicine Institute, National University of Ireland, Galway, Ireland.|School of Mathematics, Statistics and Applied Mathematics and Regenerative Medicine Institute, National University of Ireland, Galway, Ireland.', 'Ireland|Ireland|Ireland', 11, 'Animals|Cell Differentiation|Epithelial Cells|Gene Expression Profiling|Gene Expression Regulation|High-Throughput Nucleotide Sequencing|Mice|Organ Specificity|Protein Isoforms|RNA Splicing|RNA, Messenger|T-Lymphocytes|Thymus Gland|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/btu785', '25429061', 'The expression of tissue-restricted antigens (TRAs) in the thymus is required to ensure efficient negative selection of potentially auto-reactive T lymphocytes and avoid autoimmune disease. This promiscuous expression is under the control of the autoimmune regulator (AIRE), a transcription factor expressed in medullary thymic epithelial cells (mTECs). Tissue-specific alternative splicing may also produce TRAs but the extent to which splice isoforms that are restricted to specific tissues are expressed in mTECs is yet to be investigated.'),
(78887, 2015, 'bio', 'LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data', 'Fermin, Damian|Avtonomov, Dmitry|Choi, Hyungwon|Nesvizhskii, Alexey I', 'Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.|Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.|Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.|Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.', 'Singapore|Singapore|Singapore|Singapore', 16, 'Acetylation|Algorithms|Humans|Lysine|Muscle Proteins|Muscle, Skeletal|Peptide Fragments|Phosphorylation|Protein Processing, Post-Translational|Sequence Analysis, Protein|Software|Tandem Mass Spectrometry', 'Journal Article', '10.1093/bioinformatics/btu788', '25429062', 'We present LuciPHOr2, a site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data. As an extension of the original LuciPHOr (version 1) for phosphorylation site localization, the new software provides a site-level localization score for generic PTMs and associated false discovery rate called the false localization rate. We describe several novel features such as operating system independence and reduced computation time through multiple threading. We also discuss optimal parameters for different types of data and illustrate the new tool on a human skeletal muscle dataset for lysine-acetylation.'),
(78888, 2015, 'bio', 'MGAS: a powerful tool for multivariate gene-based genome-wide association analysis', 'Van der Sluis, Sophie|Dolan, Conor V|Li, Jiang|Song, Youqiang|Sham, Pak|Posthuma, Danielle|Li, Miao-Xin', 'Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands.|Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands.|Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands.|Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands Department of Complex Trait Genetics, |Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands Department of Complex Trait Genetics, |Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands.|Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands Department of Complex Trait Genetics, Section Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU Medical Center, Amsterdam, The Netherlands, Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands,Department of Biochemistry, State Key Laboratory for Cognitive and Brain Sciences, The Centre for Reproduction, Development and Growth, The Centre for Genomic Sciences and Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong and Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands Department of Complex Trait Genetics, ', 'Hong Kong|Hong Kong|Hong Kong|Hong Kong|Hong Kong|Hong Kong|Hong Kong', 25, 'Genome, Human|Genome-Wide Association Study|Humans|Metabolic Syndrome|Multivariate Analysis|Phenotype|Polymorphism, Single Nucleotide|Software', 'Journal Article', '10.1093/bioinformatics/btu783', '25431328', 'Standard genome-wide association studies, testing the association between one phenotype and a large number of single nucleotide polymorphisms (SNPs), are limited in two ways: (i) traits are often multivariate, and analysis of composite scores entails loss in statistical power and (ii) gene-based analyses may be preferred, e.g. to decrease the multiple testing problem.'),
(78889, 2015, 'bio', 'Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms', 'Park, Christopher Y|Krishnan, Arjun|Zhu, Qian|Wong, Aaron K|Lee, Young-Suk|Troyanskaya, Olga G', 'Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA.|Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA.|Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA.|Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA.|Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA.|Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA.', 'United States|United States|United States|United States|United States|United States', 15, 'Algorithms|Chromatin Immunoprecipitation|Computational Biology|Gene Regulatory Networks|Genomics|Humans|Organ Specificity|Phosphorylation|Protein Interaction Mapping|Protein-Serine-Threonine Kinases|RNA, Small Interfering|Signal Transduction|Software|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/btu786', '25431329', 'Leveraging the large compendium of genomic data to predict biomedical pathways and specific mechanisms of protein interactions genome-wide in metazoan organisms has been challenging. In contrast to unicellular organisms, biological and technical variation originating from diverse tissues and cell-lineages is often the largest source of variation in metazoan data compendia. Therefore, a new computational strategy accounting for the tissue heterogeneity in the functional genomic data is needed to accurately translate the vast amount of human genomic data into specific interaction-level hypotheses.'),
(78890, 2015, 'bio', 'SNiPA: an interactive, genetic variant-centered annotation browser', 'Arnold, Matthias|Raffler, Johannes|Pfeufer, Arne|Suhre, Karsten|Kastenmüller, Gabi', 'Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany and Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar.|Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany and Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar.|Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany and Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar.|Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany and Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany and Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar.|Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany and Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar.', 'Germany|Germany|Germany|Germany|Germany', 97, 'Databases, Genetic|Genetic Variation|Genome, Human|Genomics|Humans|Molecular Sequence Annotation|Software', 'Journal Article', '10.1093/bioinformatics/btu779', '25431330', 'Linking genes and functional information to genetic variants identified by association studies remains difficult. Resources containing extensive genomic annotations are available but often not fully utilized due to heterogeneous data formats. To enhance their accessibility, we integrated many annotation datasets into a user-friendly webserver.'),
(78891, 2015, 'bio', 'MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins', 'Jones, David T|Singh, Tanya|Kosciolek, Tomasz|Tetchner, Stuart', 'Bioinformatics Group, Department of Computer Science, University College London, London WC1E 6BT, UK.|Bioinformatics Group, Department of Computer Science, University College London, London WC1E 6BT, UK.|Bioinformatics Group, Department of Computer Science, University College London, London WC1E 6BT, UK.|Bioinformatics Group, Department of Computer Science, University College London, London WC1E 6BT, UK.', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom', 167, 'Algorithms|Computational Biology|Databases, Protein|Humans|Hydrogen Bonding|Protein Folding|Proteins|Sequence Alignment|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/btu791', '25431331', 'Recent developments of statistical techniques to infer direct evolutionary couplings between residue pairs have rendered covariation-based contact prediction a viable means for accurate 3D modelling of proteins, with no information other than the sequence required. To extend the usefulness of contact prediction, we have designed a new meta-predictor (MetaPSICOV) which combines three distinct approaches for inferring covariation signals from multiple sequence alignments, considers a broad range of other sequence-derived features and, uniquely, a range of metrics which describe both the local and global quality of the input multiple sequence alignment. Finally, we use a two-stage predictor, where the second stage filters the output of the first stage. This two-stage predictor is additionally evaluated on its ability to accurately predict the long range network of hydrogen bonds, including correctly assigning the donor and acceptor residues.'),
(78892, 2015, 'bio', 'A logical model of HIV-1 interactions with the T-cell activation signalling pathway', 'Oyeyemi, Oyebode J|Davies, Oluwafemi|Robertson, David L|Schwartz, Jean-Marc', 'Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.|Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.|Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.|Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom', 11, 'Computational Biology|Databases, Protein|HIV Infections|HIV-1|Host-Pathogen Interactions|Humans|Logistic Models|Lymphocyte Activation|Protein Interaction Mapping|Signal Transduction|T-Lymphocytes|Viral Proteins|Virus Replication', 'Journal Article', '10.1093/bioinformatics/btu787', '25431332', 'Human immunodeficiency virus type 1 (HIV-1) hijacks host cellular processes to replicate within its host. Through interactions with host proteins, it perturbs and interrupts signaling pathways that alter key cellular functions. Although networks of viral-host interactions have been relatively well characterized, the dynamics of the perturbation process is poorly understood. Dynamic models of infection have the potential to provide insights into the HIV-1 host interaction.'),
(78893, 2015, 'bio', 'Faster sequence homology searches by clustering subsequences', 'Suzuki, Shuji|Kakuta, Masanori|Ishida, Takashi|Akiyama, Yutaka', 'Graduate School of Information Science and Engineering, Tokyo Institute of Technology and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Tokyo 152-8550, Japan Graduate School of Information Science and Engineering, Tokyo Institute of Technology and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Tokyo 152-8550, Japan.|Graduate School of Information Science and Engineering, Tokyo Institute of Technology and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Tokyo 152-8550, Japan.|Graduate School of Information Science and Engineering, Tokyo Institute of Technology and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Tokyo 152-8550, Japan.|Graduate School of Information Science and Engineering, Tokyo Institute of Technology and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Tokyo 152-8550, Japan Graduate School of Information Science and Engineering, Tokyo Institute of Technology and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Tokyo 152-8550, Japan.', 'Japan|Japan|Japan|Japan', 25, 'Algorithms|Amino Acid Sequence|Animals|Cluster Analysis|Databases, Genetic|Humans|Metagenomics|Military Personnel|Molecular Sequence Data|Programming Languages|Sequence Analysis, DNA|Sequence Homology|Software|Soil', 'Journal Article', '10.1093/bioinformatics/btu780', '25432166', 'Sequence homology searches are used in various fields. New sequencing technologies produce huge amounts of sequence data, which continuously increase the size of sequence databases. As a result, homology searches require large amounts of computational time, especially for metagenomic analysis.'),
(78894, 2015, 'bio', 'PEASE: predicting B-cell epitopes utilizing antibody sequence', 'Sela-Culang, Inbal|Ashkenazi, Shaul|Peters, Bjoern|Ofran, Yanay', 'The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar-Ilan University, Ramat-Gan 52900, Israel and Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.|The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar-Ilan University, Ramat-Gan 52900, Israel and Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.|The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar-Ilan University, Ramat-Gan 52900, Israel and Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.|The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar-Ilan University, Ramat-Gan 52900, Israel and Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.', 'Israel|Israel|Israel|Israel', 19, 'Algorithms|Antibodies|Antigens|Artificial Intelligence|Complementarity Determining Regions|Epitope Mapping|Epitopes, B-Lymphocyte|Humans|Internet|Protein Conformation', 'Journal Article', '10.1093/bioinformatics/btu790', '25432167', 'Antibody epitope mapping is a key step in understanding antibody-antigen recognition and is of particular interest for drug development, diagnostics and vaccine design. Most computational methods for epitope prediction are based on properties of the antigen sequence and/or structure, not taking into account the antibody for which the epitope is predicted. Here, we introduce PEASE, a web server predicting antibody-specific epitopes, utilizing the sequence of the antibody. The predictions are provided both at the residue level and as patches on the antigen structure. The tradeoff between recall and precision can be tuned by the user, by changing the default parameters. The results are provided as text and HTML files as well as a graph, and can be viewed on the antigen 3D structure.'),
(78895, 2015, 'bio', 'LigDig: a web server for querying ligand-protein interactions', 'Fuller, Jonathan C|Martinez, Michael|Henrich, Stefan|Stank, Antonia|Richter, Stefan|Wade, Rebecca C', 'Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.|Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.|Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.|Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.|Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.|Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.', 'Germany|Germany|Germany|Germany|Germany|Germany', 9, 'Binding Sites|Databases, Factual|Fructosediphosphates|Humans|Internet|Ligands|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/btu784', '25433696', 'LigDig is a web server designed to answer questions that previously required several independent queries to diverse data sources. It also performs basic manipulations and analyses of the structures of protein-ligand complexes. The LigDig webserver is modular in design and consists of seven tools, which can be used separately, or via linking the output from one tool to the next, in order to answer more complex questions. Currently, the tools allow a user to: (i) perform a free-text compound search, (ii) search for suitable ligands, particularly inhibitors, of a protein and query their interaction network, (iii) search for the likely function of a ligand, (iv) perform a batch search for compound identifiers, (v) find structures of protein-ligand complexes, (vi) compare three-dimensional structures of ligand binding sites and (vii) prepare coordinate files of protein-ligand complexes for further calculations.'),
(78896, 2015, 'bio', 'Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge', 'Zur, Hadas|Tuller, Tamir', 'Department of Biomedical Engineering, The Engineering Faculty, Blavatnik School of Computer Science, Faculty of Exact Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel-Aviv 69978, Israel Department of Biomedical Engineering, The Engineering Faculty, Blavatnik School of Computer Science, Faculty of Exact Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel-Aviv 69978, Israel.|Department of Biomedical Engineering, The Engineering Faculty, Blavatnik School of Computer Science, Faculty of Exact Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel-Aviv 69978, Israel Department of Biomedical Engineering, The Engineering Faculty, Blavatnik School of Computer Science, Faculty of Exact Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel-Aviv 69978, Israel.', 'Israel|Israel', 12, 'Algorithms|Codon|Computational Biology|Escherichia coli|Escherichia coli Proteins|Gene Expression Regulation, Bacterial|Genome, Bacterial|Open Reading Frames|Protein Biosynthesis', 'Journal Article', '10.1093/bioinformatics/btu797', '25433697', 'Dozens of studies in recent years have demonstrated that codon usage encodes various aspects related to all stages of gene expression regulation. When relevant high-quality large-scale gene expression data are available, it is possible to statistically infer and model these signals, enabling analysing and engineering gene expression. However, when these data are not available, it is impossible to infer and validate such models.'),
(78897, 2015, 'bio', 'Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms', 'Ahmed, Zeeshan|Mayr, Michel|Zeeshan, Saman|Dandekar, Thomas|Mueller, Martin J|Fekete, Agnes', 'Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany.|Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany.|Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany.|Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany.|Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany.|Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany.', 'Germany|Germany|Germany|Germany|Germany|Germany', 18, 'Algorithms|Chromatography, Liquid|Databases, Factual|Humans|Lipids|Metabolomics|Software|Tandem Mass Spectrometry', 'Journal Article', '10.1093/bioinformatics/btu796', '25433698', 'A major challenge for mass spectrometric-based lipidomics, aiming at describing all lipid species in a biological sample, lies in the computational and bioinformatic processing of the large amount of data that arises after data acquisition. Lipid-Pro is a software tool that supports the identification of lipids by interpreting large datasets generated by liquid chromatography--tandem mass spectrometry (LC-MS/MS) using the advanced data-independent acquisition mode MS(E). In the MS(E) mode, the instrument fragments all molecular ions generated from a sample and records time-resolved molecular ion data as well as fragment ion data for every detectable molecular ion. Lipid-Pro matches the retention time-aligned mass-to-charge ratio data of molecular- and fragment ions with a lipid database and generates a report on all identified lipid species. For generation of the lipid database, Lipid-Pro provides a module for construction of lipid species and their fragments using a flexible building block approach. Hence, Lipid-Pro is an easy to use analysis tool to interpret complex MS(E) lipidomics data and also offers a module to generate a user-specific lipid database.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(78898, 2015, 'bio', 'Computer-assisted curation of a human regulatory core network from the biological literature', 'Thomas, Philippe|Durek, Pawel|Solt, Illxc3xa9s|Klinger, Bertram|Witzel, Franziska|Schulthess, Pascal|Mayer, Yvonne|Tikk, Domonkos|Blxc3xbcthgen, Nils|Leser, Ulf', 'Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany.|Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany.|Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany.|Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany.|Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany.|Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany.|Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany.|Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany.|Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany.|Humboldt-Universitxc3xa4t zu Berlin, Institute for Computer Science, Knowledge Management in Bioinformatics, 10099 Berlin, Germany, Institute of Pathology, Charitxc3xa9-Universitxc3xa4tsmedizin Berlin, Deutsches Rheuma Forschungszentrum, Charitxc3xa9platz 1, 10117 Berlin, Germany, Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary and Integrative Research Institute for the Life Sciences, Humboldt Universitxc3xa4t zu Berlin, Philippstr. 13 Haus 18, 10115 Berlin, Germany.', 'Germany|Germany|Germany|Germany|Germany|Germany|Germany|Germany|Germany|Germany', 4, 'Artificial Intelligence|Computer Simulation|Data Mining|Databases, Factual|Gene Expression Profiling|Gene Expression Regulation|Gene Regulatory Networks|Genome, Human|Humans|Information Storage and Retrieval|MEDLINE|Models, Biological|Neoplasms|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/btu795', '25433699', 'A highly interlinked network of transcription factors (TFs) orchestrates the context-dependent expression of human genes. ChIP-chip experiments that interrogate the binding of particular TFs to genomic regions are used to reconstruct gene regulatory networks at genome-scale, but are plagued by high false-positive rates. Meanwhile, a large body of knowledge on high-quality regulatory interactions remains largely unexplored, as it is available only in natural language descriptions scattered over millions of scientific publications. Such data are hard to extract and regulatory data currently contain together only 503 regulatory relations between human TFs.'),
(78899, 2015, 'bio', 'GenePainter v 20 resolves the taxonomic distribution of intron positions', 'Mühlhausen, Stefanie|Hellkamp, Marcel|Kollmar, Martin', 'Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.|Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.|Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.', 'Germany|Germany|Germany', 0, 'Chromosome Mapping|Computer Graphics|Exons|Humans|Introns|Microfilament Proteins|Phylogeny|Software', 'Journal Article', '10.1093/bioinformatics/btu798', '25434742', 'Conserved intron positions in eukaryotic genes can be used to reconstruct phylogenetic trees, to resolve ambiguous subfamily relationships in protein families and to infer the history of gene families. This version of GenePainter facilitates working with large datasets through options to select specific subsets for analysis and visualization, and through providing exhaustive statistics. GenePainters application in phylogenetic analyses is considerably extended by the newly implemented integration of the exon-intron pattern conservation with phylogenetic trees.'),
(78900, 2015, 'bio', 'An efficient TOF-SIMS image analysis with spatial correlation and alternating non-negativity-constrained least squares', 'Aram, Parham|Shen, Lingli|Pugh, John A|Vaidyanathan, Seetharaman|Kadirkamanathan, Visakan', 'Department of Automatic Control and Systems Engineering and Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK.|Department of Automatic Control and Systems Engineering and Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK.|Department of Automatic Control and Systems Engineering and Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK.|Department of Automatic Control and Systems Engineering and Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK.|Department of Automatic Control and Systems Engineering and Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK.', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom', 0, 'Algorithms|Computational Biology|Humans|Image Processing, Computer-Assisted|Least-Squares Analysis|Metabolomics|Spectrometry, Mass, Secondary Ion', 'Journal Article', '10.1093/bioinformatics/btu734', '25452330', 'Advances in analytical instrumentation towards acquiring high-resolution images of mass spectrometry constantly demand efficient approaches for data analysis. This is particularly true of time-of-flight secondary ion mass spectrometry imaging where recent advances enable acquisition of high-resolution data in multiple dimensions. In many applications, the distribution of different species from a sampled surface is spatially continuous in nature and a model that incorporates the spatial correlation across the surface would be preferable to estimations at discrete spatial locations. A key challenge here is the capability to analyse the high-resolution multidimensional data to extract relevant information reliably and efficiently.'),
(78901, 2015, 'bio', 'Adaptive settings for the nearest-neighbor particle tracking algorithm', 'Mazzaferri, Javier|Roy, Joannie|Lefrancois, Stephane|Costantino, Santiago', 'Centre de Recherche de lHôpital Maisonneuve-Rosemont, Montréal, Canada H1T 2M4, Département de Médecine, Université de Montréal, Montréal, Canada H3T 3J7 and Département dOphtalmologie et Institut de Génie Biomédical, Université de Montréal, Montréal, Canada H3T 1J4.|Centre de Recherche de lHôpital Maisonneuve-Rosemont, Montréal, Canada H1T 2M4, Département de Médecine, Université de Montréal, Montréal, Canada H3T 3J7 and Département dOphtalmologie et Institut de Génie Biomédical, Université de Montréal, Montréal, Canada H3T 1J4.|Centre de Recherche de lHôpital Maisonneuve-Rosemont, Montréal, Canada H1T 2M4, Département de Médecine, Université de Montréal, Montréal, Canada H3T 3J7 and Département dOphtalmologie et Institut de Génie Biomédical, Université de Montréal, Montréal, Canada H3T 1J4 Centre de Recherche de lHôpital Maisonneuve-Rosemont, Montréal, Canada H1T 2M4, Département de Médecine, Université de Montréal, Montréal, Canada H3T 3J7 and Département dOphtalmologie et Institut de Génie Biomédical, Université de Montréal, Montréal, Canada H3T 1J4.|Centre de Recherche de lHôpital Maisonneuve-Rosemont, Montréal, Canada H1T 2M4, Département de Médecine, Université de Montréal, Montréal, Canada H3T 3J7 and Département dOphtalmologie et Institut de Génie Biomédical, Université de Montréal, Montréal, Canada H3T 1J4 Centre de Recherche de lHôpital Maisonneuve-Rosemont, Montréal, Canada H1T 2M4, Département de Médecine, Université de Montréal, Montréal, Canada H3T 3J7 and Département dOphtalmologie et Institut de Génie Biomédical, Université de Montréal, Montréal, Canada H3T 1J4.', 'Canada|Canada|Canada|Canada', 6, 'Algorithms|Cell Movement|Cell Tracking|Cluster Analysis|Fluorescent Dyes|Humans|Neutrophils', 'Journal Article', '10.1093/bioinformatics/btu793', '25480371', 'The performance of the single particle tracking (SPT) nearest-neighbor algorithm is determined by parameters that need to be set according to the characteristics of the time series under study. Inhomogeneous systems, where these characteristics fluctuate spatially, are poorly tracked when parameters are set globally.'),
(78902, 2015, 'bio', 'Semiconductor sequencing: how many flows do you need?', 'Budczies, Jan|Bockmayr, Michael|Treue, Denise|Klauschen, Frederick|Denkert, Carsten', 'Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany.|Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany.|Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany.|Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany.|Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany.', 'Germany|Germany|Germany|Germany|Germany', 2, 'Algorithms|Genome, Human|Genomics|High-Throughput Nucleotide Sequencing|Humans|Neoplasms|Semiconductors|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/btu805', '25480372', 'Semiconductor sequencing directly translates chemically encoded information (A, C, G or T) into voltage signals that are detected by a semiconductor device. Changes of pH value and thereby of the electric potential in the reaction well are detected during strand synthesis from nucleotides provided in cyclic repeated flows for each type of nucleotide. To minimize time requirement and costs, it is necessary to know the number of flows that are required for complete coverage of the templates.'),
(78903, 2015, 'bio', 'Graphical algorithm for integration of genetic and biological data: proof of principle using psoriasis as a model', 'Tsoi, Lam C|Elder, James T|Abecasis, Goncalo R', 'Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA, Department of Dermatology, University of Michigan, Ann Arbor, MI, USA, and Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA.|Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA, Department of Dermatology, University of Michigan, Ann Arbor, MI, USA, and Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA, Department of Dermatology, University of Michigan, Ann Arbor, MI, USA, and Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA.|Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA, Department of Dermatology, University of Michigan, Ann Arbor, MI, USA, and Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA.', 'United States|United States|United States', 9, 'Algorithms|Computer Graphics|Computer Simulation|Databases, Factual|Gene Regulatory Networks|Humans|Meta-Analysis as Topic|Protein Interaction Maps|Psoriasis|Systems Biology', 'Journal Article', '10.1093/bioinformatics/btu799', '25480373', 'Pathway analysis to reveal biological mechanisms for results from genetic association studies have great potential to better understand complex traits with major human disease impact. However, current approaches have not been optimized to maximize statistical power to identify enriched functions/pathways, especially when the genetic data derives from studies using platforms (e.g. Immunochip and Metabochip) customized to have pre-selected markers from previously identified top-rank loci. We present here a novel approach, called Minimum distance-based Enrichment Analysis for Genetic Association (MEAGA), with the potential to address both of these important concerns.'),
(78904, 2015, 'bio', 'Retrieval of Enterobacteriaceae drug targets using singular value decomposition', 'Silvério-Machado, Rita|Couto, Bráulio R G M|Dos Santos, Marcos A', 'Institute of Biological Sciences and Department of Computer Science, Federal University of Minas Gerais, Belo Horizonte, MG 31270-901, Brazil and Centro Universitário de Belo Horizonte/UNI-BH, Belo Horizonte, MG 30455-610, Brazil.|Institute of Biological Sciences and Department of Computer Science, Federal University of Minas Gerais, Belo Horizonte, MG 31270-901, Brazil and Centro Universitário de Belo Horizonte/UNI-BH, Belo Horizonte, MG 30455-610, Brazil.|Institute of Biological Sciences and Department of Computer Science, Federal University of Minas Gerais, Belo Horizonte, MG 31270-901, Brazil and Centro Universitário de Belo Horizonte/UNI-BH, Belo Horizonte, MG 30455-610, Brazil.', 'Brazil|Brazil|Brazil', 4, 'Algorithms|Anti-Bacterial Agents|Bacterial Proteins|Drug Delivery Systems|Drug Resistance, Bacterial|Enterobacteriaceae|Escherichia coli|Humans', 'Journal Article', '10.1093/bioinformatics/btu792', '25480374', 'The identification of potential drug target proteins in bacteria is important in pharmaceutical research for the development of new antibiotics to combat bacterial agents that cause diseases.'),
(78905, 2015, 'bio', 'QuASAR: quantitative allele-specific analysis of reads', 'Harvey, Chris T|Moyerbrailean, Gregory A|Davis, Gordon O|Wen, Xiaoquan|Luca, Francesca|Pique-Regi, Roger', 'Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540xe2x80x89E Canfield, Scott Hall, Detroit, MI 48201, USA and Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.|Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540xe2x80x89E Canfield, Scott Hall, Detroit, MI 48201, USA and Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.|Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540xe2x80x89E Canfield, Scott Hall, Detroit, MI 48201, USA and Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.|Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540xe2x80x89E Canfield, Scott Hall, Detroit, MI 48201, USA and Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.|Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540xe2x80x89E Canfield, Scott Hall, Detroit, MI 48201, USA and Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.|Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540xe2x80x89E Canfield, Scott Hall, Detroit, MI 48201, USA and Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.', 'United States|United States|United States|United States|United States|United States', 36, 'Alleles|B-Lymphocytes|Cells, Cultured|Genome, Human|Genotype|High-Throughput Nucleotide Sequencing|Human Umbilical Vein Endothelial Cells|Humans|RNA|Sequence Analysis, RNA|Software', 'Journal Article', '10.1093/bioinformatics/btu802', '25480375', 'Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls.'),
(78906, 2015, 'bio', 'SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data', 'Wise, Aaron|Bar-Joseph, Ziv', 'Lane Center for Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA.|Lane Center for Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA Lane Center for Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA.', 'United States|United States', 8, 'Animals|Brain|Gene Expression Profiling|Gene Expression Regulation, Developmental|Gene Regulatory Networks|Humans|Influenza A virus|Influenza, Human|Mice|Models, Theoretical|Software|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/btu800', '25480376', 'Current methods for reconstructing dynamic regulatory networks are focused on modeling a single response network using model organisms or cell lines. Unlike these models or cell lines, humans differ in their background expression profiles due to age, genetics and life factors. In addition, there are often differences in start and end times for time series human data and in the rate of progress based on the specific individual. Thus, new methods are required to integrate time series data from multiple individuals when modeling and constructing disease response networks.'),
(78907, 2015, 'bio', 'HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements', 'Hwang, Yih-Chii|Lin, Chiao-Feng|Valladares, Otto|Malamon, John|Kuksa, Pavel P|Zheng, Qi|Gregory, Brian D|Wang, Li-San', 'Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.|Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.|Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.|Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.|Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.|Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.|Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.|Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.', '-|-|-|-|-|-|-|-', 27, 'DNA|Enhancer Elements, Genetic|Humans|Programming Languages|Promoter Regions, Genetic|Sequence Analysis, DNA', 'Journal Article', '10.1093/bioinformatics/btu801', '25480377', 'We implemented a high-throughput identification pipeline for promoter interacting enhancer element to streamline the workflow from mapping raw Hi-C reads, identifying DNA-DNA interacting fragments with high confidence and quality control, detecting histone modifications and DNase hypersensitive enrichments in putative enhancer elements, to ultimately extracting possible intra- and inter-chromosomal enhancer-target gene relationships.'),
(78908, 2015, 'bio', 'GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences', 'Sato, Tetsuya|Suyama, Mikita', 'Medical Institute of Bioregulation, Kyushu University and CREST, Japan Science and Technology Agency, 812-8582 Fukuoka, Japan Medical Institute of Bioregulation, Kyushu University and CREST, Japan Science and Technology Agency, 812-8582 Fukuoka, Japan.|Medical Institute of Bioregulation, Kyushu University and CREST, Japan Science and Technology Agency, 812-8582 Fukuoka, Japan Medical Institute of Bioregulation, Kyushu University and CREST, Japan Science and Technology Agency, 812-8582 Fukuoka, Japan.', 'Japan|Japan', 3, 'Animals|Base Sequence|Computational Biology|Consensus Sequence|Evolution, Molecular|Genome|Genomics|Humans|Internet|Molecular Sequence Data|Sequence Alignment|Sequence Analysis, DNA|Sequence Homology, Nucleic Acid|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/btu803', '25480378', 'Genome sequence alignments provide valuable information on many aspects of molecular biological processes. In this study, we developed a web server, GenomeCons, for manipulating multiple genome sequence alignments and their consensus sequences for high-throughput genome sequence analyses. This server facilitates the visual inspection of multiple genome sequence alignments for a set of genomic intervals at a time. This allows the user to examine how these sites are evolutionarily conserved over time for their functional importance. The server also reports consensus sequences for the input genomic intervals, which can be applied to downstream analyses such as the identification of common motifs in the regions determined by ChIP-seq experiments.'),
(78909, 2015, 'bio', 'Improved gene tree error correction in the presence of horizontal gene transfer', 'Bansal, Mukul S|Wu, Yi-Chieh|Alm, Eric J|Kellis, Manolis', 'Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA.|Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA.|Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA.|Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA.', 'United States|United States|United States|United States', 27, 'Algorithms|Computational Biology|Cyanobacteria|Evolution, Molecular|Gene Duplication|Gene Transfer, Horizontal|Multigene Family|Phylogeny', 'Journal Article', '10.1093/bioinformatics/btu806', '25481006', 'The accurate inference of gene trees is a necessary step in many evolutionary studies. Although the problem of accurate gene tree inference has received considerable attention, most existing methods are only applicable to gene families unaffected by horizontal gene transfer. As a result, the accurate inference of gene trees affected by horizontal gene transfer remains a largely unaddressed problem.'),
(78910, 2015, 'bio', 'Kablammo: an interactive, web-based BLAST results visualizer', 'Wintersinger, Jeff A|Wasmuth, James D', 'Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.|Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.', 'Canada|Canada', 17, 'Animals|Computer Graphics|Genes, Helminth|Genome, Helminth|Haemonchus|Internet|Programming Languages|Sequence Alignment|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/btu808', '25481007', 'Kablammo is a web-based application that produces interactive, vector-based visualizations of sequence alignments generated by BLAST. These visualizations can illustrate many features, including shared protein domains, chromosome structural modifications and genome misassembly.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(78911, 2015, 'bio', 'flowCL: ontology-based cell population labelling in flow cytometry', 'Courtot, Mélanie|Meskas, Justin|Diehl, Alexander D|Droumeva, Radina|Gottardo, Raphael|Jalali, Adrin|Taghiyar, Mohammad Jafar|Maecker, Holden T|McCoy, J Philip|Ruttenberg, Alan|Scheuermann, Richard H|Brinkman, Ryan R', 'Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.|Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.|Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.|Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.|Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.|Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.|Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.|Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.|Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA. Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.|Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.|Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA. Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.|Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.', 'Canada|Canada|Canada|Canada|Canada|Canada|Canada|Canada|Canada|Canada|Canada|Canada', 14, 'Algorithms|Cell Physiological Phenomena|Flow Cytometry|Gene Ontology|Humans|Immunophenotyping|Leukocyte Common Antigens|Receptors, CCR7|Software', 'Journal Article', '10.1093/bioinformatics/btu807', '25481008', 'Finding one or more cell populations of interest, such as those correlating to a specific disease, is critical when analysing flow cytometry data. However, labelling of cell populations is not well defined, making it difficult to integrate the output of algorithms to external knowledge sources.'),
(78912, 2015, 'bio', 'ICMA: an integrated cardiac modeling and analysis platform', 'Hussan, Jagir R|Hunter, Peter J|Gladding, Patrick A|Greenberg, Neil|Christie, Richard|Wu, Alan|Sorby, Hugh|Thomas, James D', 'Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand, Waitemata District Health Board, North Shore Hospital, Auckland 0622, New Zealand, National Space Biomedical Research Institute, Houston, TX 77030-1402, USA, Cleveland Clinic Foundation, Cleveland, OH 44195, USA and Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.|Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand, Waitemata District Health Board, North Shore Hospital, Auckland 0622, New Zealand, National Space Biomedical Research Institute, Houston, TX 77030-1402, USA, Cleveland Clinic Foundation, Cleveland, OH 44195, USA and Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.|Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand, Waitemata District Health Board, North Shore Hospital, Auckland 0622, New Zealand, National Space Biomedical Research Institute, Houston, TX 77030-1402, USA, Cleveland Clinic Foundation, Cleveland, OH 44195, USA and Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.|Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand, Waitemata District Health Board, North Shore Hospital, Auckland 0622, New Zealand, National Space Biomedical Research Institute, Houston, TX 77030-1402, USA, Cleveland Clinic Foundation, Cleveland, OH 44195, USA and Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand, Waitemata District Health Board, North Shore Hospital, Auckland 0622, New Zealand, National Space Biomedical Research Institute, Houston, TX 77030-1402, USA, Cleveland Clinic Foundation, Cleveland, OH 44195, USA and Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.|Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand, Waitemata District Health Board, North Shore Hospital, Auckland 0622, New Zealand, National Space Biomedical Research Institute, Houston, TX 77030-1402, USA, Cleveland Clinic Foundation, Cleveland, OH 44195, USA and Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.|Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand, Waitemata District Health Board, North Shore Hospital, Auckland 0622, New Zealand, National Space Biomedical Research Institute, Houston, TX 77030-1402, USA, Cleveland Clinic Foundation, Cleveland, OH 44195, USA and Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.|Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand, Waitemata District Health Board, North Shore Hospital, Auckland 0622, New Zealand, National Space Biomedical Research Institute, Houston, TX 77030-1402, USA, Cleveland Clinic Foundation, Cleveland, OH 44195, USA and Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.|Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand, Waitemata District Health Board, North Shore Hospital, Auckland 0622, New Zealand, National Space Biomedical Research Institute, Houston, TX 77030-1402, USA, Cleveland Clinic Foundation, Cleveland, OH 44195, USA and Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand, Waitemata District Health Board, North Shore Hospital, Auckland 0622, New Zealand, National Space Biomedical Research Institute, Houston, TX 77030-1402, USA, Cleveland Clinic Foundation, Cleveland, OH 44195, USA and Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.', 'New Zealand|New Zealand|New Zealand|New Zealand|New Zealand|New Zealand|New Zealand|New Zealand', 0, 'Computational Biology|Databases, Factual|Diagnostic Imaging|Heart|Heart Ventricles|Humans|Models, Cardiovascular|Software', 'Journal Article', '10.1093/bioinformatics/btu809', '25481009', 'ICMA, a software framework to create 3D finite element models of the left ventricle from cardiac ultrasound or magnetic resonance imaging (MRI) data, has been made available as an open-source code. The framework is hardware vendor independent and uses speckle tracking (endocardial border detection) on ultrasound (MRI) imaging data in the form of DICOM. Standard American Heart Association segment-based strain analysis can be performed using a browser-based interface. The speckle tracking, border detection and model fitting methods are implemented in C++ using open-source tools. They are wrapped as web services and orchestrated via a JBOSS-based application server.'),
(78913, 2015, 'bio', 'SNPlice: variants that modulate Intron retention from RNA-sequencing data', 'Mudvari, Prakriti|Movassagh, Mercedeh|Kowsari, Kamran|Seyfi, Ali|Kokkinaki, Maria|Edwards, Nathan J|Golestaneh, Nady|Horvath, Anelia', 'McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.|McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.|McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.|McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.|McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.|McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.|McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.|McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.', 'United States|United States|United States|United States|United States|United States|United States|United States', 10, 'Algorithms|Cells, Cultured|Exons|High-Throughput Nucleotide Sequencing|Humans|Introns|Neoplasms|RNA|RNA Splicing|Retinal Pigment Epithelium|Sequence Analysis, RNA|Software', 'Journal Article', '10.1093/bioinformatics/btu804', '25481010', 'The growing recognition of the importance of splicing, together with rapidly accumulating RNA-sequencing data, demand robust high-throughput approaches, which efficiently analyze experimentally derived whole-transcriptome splice profiles.'),
(78914, 2015, 'bio', 'Identification of deleterious synonymous variants in human genomes', 'Buske, Orion J|Manickaraj, AshokKumar|Mital, Seema|Ray, Peter N|Brudno, Michael', 'McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.|McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.|McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.|McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.|McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA.', 'United States|United States|United States|United States|United States', 1, '-', 'Published Erratum', '10.1093/bioinformatics/btu765', '25488928', '-'),
(78915, 2015, 'bio', 'Achievements and challenges in structural bioinformatics and computational biophysics', 'Samish, Ilan|Bourne, Philip E|Najmanovich, Rafael J', 'Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada.|Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada.|Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada.', 'Canada|Canada|Canada', 15, 'Achievement|Biomedical Research|Biophysics|Computational Biology|Humans', 'Journal Article', '10.1093/bioinformatics/btu769', '25488929', 'The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects.'),
(78916, 2015, 'bio', 'Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements', 'Raimondi, Daniele|Orlando, Gabriele|Vranken, Wim F', 'Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, CP 263, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2 and Structural Biology Research Center, VIB, 1050 Brussels, Belgium Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, CP 263, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2 and Structural Biology Research Center, VIB, 1050 Brussels, Belgium Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, CP 263, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2 and Structural Biology Research Center, VIB, 1050 Brussels, Belgium.|Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, CP 263, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2 and Structural Biology Research Center, VIB, 1050 Brussels, Belgium Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, CP 263, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2 and Structural Biology Research Center, VIB, 1050 Brussels, Belgium Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, CP 263, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2 and Structural Biology Research Center, VIB, 1050 Brussels, Belgium.|Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, CP 263, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2 and Structural Biology Research Center, VIB, 1050 Brussels, Belgium Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, CP 263, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2 and Structural Biology Research Center, VIB, 1050 Brussels, Belgium Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, CP 263, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2 and Structural Biology Research Center, VIB, 1050 Brussels, Belgium.', 'Belgium|Belgium|Belgium', 8, 'Algorithms|Amino Acid Sequence|Cluster Analysis|Cysteine|Disulfides|Humans|Models, Statistical|Molecular Sequence Data|Mutation|Proteins|Sequence Homology|Software', 'Journal Article', '10.1093/bioinformatics/btu794', '25492406', 'Cysteine residues have particular structural and functional relevance in proteins because of their ability to form covalent disulfide bonds. Bioinformatics tools that can accurately predict cysteine bonding states are already available, whereas it remains challenging to infer the disulfide connectivity pattern of unknown protein sequences. Improving accuracy in this area is highly relevant for the structural and functional annotation of proteins.'),
(78917, 2015, 'bio', 'State of the art prediction of HIV-1 protease cleavage sites', 'Rögnvaldsson, Thorsteinn|You, Liwen|Garwicz, Daniel', 'CAISR, School of Information Science, Computer and Electrical Engineering, Halmstad University, Halmstad, Sweden and Division of Clinical Chemistry and Pharmacology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.|CAISR, School of Information Science, Computer and Electrical Engineering, Halmstad University, Halmstad, Sweden and Division of Clinical Chemistry and Pharmacology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.|CAISR, School of Information Science, Computer and Electrical Engineering, Halmstad University, Halmstad, Sweden and Division of Clinical Chemistry and Pharmacology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.', 'Sweden|Sweden|Sweden', 20, 'Algorithms|Artificial Intelligence|HIV Protease|Humans|Oligopeptides|Support Vector Machine', 'Journal Article', '10.1093/bioinformatics/btu810', '25504647', 'Understanding the substrate specificity of human immunodeficiency virus (HIV)-1 protease is important when designing effective HIV-1 protease inhibitors. Furthermore, characterizing and predicting the cleavage profile of HIV-1 protease is essential to generate and test hypotheses of how HIV-1 affects proteins of the human host. Currently available tools for predicting cleavage by HIV-1 protease can be improved.'),
(78918, 2015, 'bio', 'andi: fast and accurate estimation of evolutionary distances between closely related genomes', 'Haubold, Bernhard|Klötzl, Fabian|Pfaffelhuber, Peter', 'Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany, Institue for Neuro- and Bioinformatics, Lübeck University, 23562 Lübeck, Germany and Mathematical Stochastics, Mathematical Institute, Freiburg University, Germany.|Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany, Institue for Neuro- and Bioinformatics, Lübeck University, 23562 Lübeck, Germany and Mathematical Stochastics, Mathematical Institute, Freiburg University, Germany Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany, Institue for Neuro- and Bioinformatics, Lübeck University, 23562 Lübeck, Germany and Mathematical Stochastics, Mathematical Institute, Freiburg University, Germany.|Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany, Institue for Neuro- and Bioinformatics, Lübeck University, 23562 Lübeck, Germany and Mathematical Stochastics, Mathematical Institute, Freiburg University, Germany.', 'Germany|Germany|Germany', 38, 'Algorithms|Animals|Biological Evolution|Databases, Genetic|Genome|Genomics|Humans|Phylogeny|Sequence Alignment|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/btu815', '25504847', 'A standard approach to classifying sets of genomes is to calculate their pairwise distances. This is difficult for large samples. We have therefore developed an algorithm for rapidly computing the evolutionary distances between closely related genomes.'),
(78919, 2015, 'bio', 'repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects', 'Liu, Bin|Liu, Fule|Fang, Longyun|Wang, Xiaolong|Chou, Kuo-Chen', 'School of Computer Science and Technology and Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Gordon Life Science Institute, Belmont, MA 02478, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia School of Computer Science and Technology and Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Gordon Life Science Institute, Belmont, MA 02478, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia School of Computer Science and Technology and Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Gordon Life Science Institute, Belmont, MA 02478, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia.|School of Computer Science and Technology and Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Gordon Life Science Institute, Belmont, MA 02478, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia.|School of Computer Science and Technology and Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Gordon Life Science Institute, Belmont, MA 02478, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia.|School of Computer Science and Technology and Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Gordon Life Science Institute, Belmont, MA 02478, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia School of Computer Science and Technology and Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Gordon Life Science Institute, Belmont, MA 02478, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia.|School of Computer Science and Technology and Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Gordon Life Science Institute, Belmont, MA 02478, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia School of Computer Science and Technology and Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Gordon Life Science Institute, Belmont, MA 02478, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia.', 'China|China|China|China|China', 0, 'Computational Biology|DNA|Humans|Oligonucleotides|Sequence Analysis, DNA|Software|Support Vector Machine', 'Journal Article', '10.1093/bioinformatics/btu820', '25504848', 'In order to develop powerful computational predictors for identifying the biological features or attributes of DNAs, one of the most challenging problems is to find a suitable approach to effectively represent the DNA sequences. To facilitate the studies of DNAs and nucleotides, we developed a Python package called representations of DNAs (repDNA) for generating the widely used features reflecting the physicochemical properties and sequence-order effects of DNAs and nucleotides. There are three feature groups composed of 15 features. The first group calculates three nucleic acid composition features describing the local sequence information by means of kmers, the second group calculates six autocorrelation features describing the level of correlation between two oligonucleotides along a DNA sequence in terms of their specific physicochemical properties, the third group calculates six pseudo nucleotide composition features, which can be used to represent a DNA sequence with a discrete model or vector yet still keep considerable sequence-order information via the physicochemical properties of its constituent oligonucleotides. In addition, these features can be easily calculated based on both the built-in and user-defined properties via using repDNA.'),
(78920, 2015, 'bio', 'MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory', 'Marchetti, Luca|Manca, Vincenzo', 'Department of Computer Science, University of Verona, 37134 Verona, Italy, Center for BioMedical Computing, University of Verona, 37134 Verona, Italy and The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (TN), Italy Department of Computer Science, University of Verona, 37134 Verona, Italy, Center for BioMedical Computing, University of Verona, 37134 Verona, Italy and The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (TN), Italy Department of Computer Science, University of Verona, 37134 Verona, Italy, Center for BioMedical Computing, University of Verona, 37134 Verona, Italy and The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (TN), Italy Department of Computer Science, University of Verona, 37134 Verona, Italy, Center for BioMedical Computing, University of Verona, 37134 Verona, Italy and The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (TN), Italy.|Department of Computer Science, University of Verona, 37134 Verona, Italy, Center for BioMedical Computing, University of Verona, 37134 Verona, Italy and The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (TN), Italy Department of Computer Science, University of Verona, 37134 Verona, Italy, Center for BioMedical Computing, University of Verona, 37134 Verona, Italy and The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (TN), Italy.', 'Italy|Italy', 0, 'Algorithms|Humans|Metabolism|Models, Biological|Programming Languages|Software|Systems Biology', 'Journal Article', '10.1093/bioinformatics/btu814', '25504849', 'MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R.'),
(78921, 2015, 'bio', 'GSDS 20: an upgraded gene feature visualization server', 'Hu, Bo|Jin, Jinpu|Guo, An-Yuan|Zhang, He|Luo, Jingchu|Gao, Ge', 'State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, Peoples Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, Peoples Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Peoples Republic of China State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, Peoples Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, Peoples Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Peoples Republic of China.|State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, Peoples Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, Peoples Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Peoples Republic of China.|State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, Peoples Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, Peoples Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Peoples Republic of China.|State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, Peoples Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, Peoples Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Peoples Republic of China.|State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, Peoples Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, Peoples Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Peoples Republic of China.|State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, Peoples Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, Peoples Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Peoples Republic of China.', 'China|China|China|China|China|China', 0, 'Genes|Genomics|Humans|Internet|Molecular Sequence Annotation|Phylogeny|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/btu817', '25504850', ': Visualizing genes structure and annotated features helps biologists to investigate their function and evolution intuitively. The Gene Structure Display Server (GSDS) has been widely used by more than 60xe2x80x89000 users since its first publication in 2007. Here, we reported the upgraded GSDS 2.0 with a newly designed interface, supports for more types of annotation features and formats, as well as an integrated visual editor for editing the generated figure. Moreover, a user-specified phylogenetic tree can be added to facilitate further evolutionary analysis. The full source code is also available for downloading.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(78922, 2015, 'bio', 'Identifying cancer-related microRNAs based on gene expression data', 'Zhao, Xing-Ming|Liu, Ke-Qin|Zhu, Guanghui|He, Feng|Duval, Béatrice|Richer, Jean-Michel|Huang, De-Shuang|Jiang, Chang-Jun|Hao, Jin-Kao|Chen, Luonan', 'School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.|School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.|School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.|School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.|School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.|School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.|School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.|School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.|School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.|School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, LERIA, University of Angers, 49045 Angers Cedex 01, France, Department of Mathematics, Shanghai University, Shanghai 200444, China and Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.', 'China|China|China|China|China|China|China|China|China|China', 44, 'Biomarkers, Tumor|Computational Biology|Gene Expression Profiling|Gene Expression Regulation, Neoplastic|Gene Regulatory Networks|Humans|MicroRNAs|Neoplasms|RNA, Messenger', 'Journal Article', '10.1093/bioinformatics/btu811', '25505085', 'MicroRNAs (miRNAs) are short non-coding RNAs that play important roles in post-transcriptional regulations as well as other important biological processes. Recently, accumulating evidences indicate that miRNAs are extensively involved in cancer. However, it is a big challenge to identify which miRNAs are related to which cancer considering the complex processes involved in tumors, where one miRNA may target hundreds or even thousands of genes and one gene may regulate multiple miRNAs. Despite integrative analysis of matched gene and miRNA expression data can help identify cancer-associated miRNAs, such kind of data is not commonly available. On the other hand, there are huge amount of gene expression data that are publicly accessible. It will significantly improve the efficiency of characterizing miRNAs function in cancer if we can identify cancer miRNAs directly from gene expression data.'),
(78923, 2015, 'bio', 'Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier', 'Navarro-Gomez, Daniel|Leipzig, Jeremy|Shen, Lishuang|Lott, Marie|Stassen, Alphons P M|Wallace, Douglas C|Wiggs, Janey L|Falk, Marni J|van Oven, Mannis|Gai, Xiaowu', 'Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, Center for Biomedical Informaticsand Center for Mitochondrial and Epigenomic Medicine, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA, Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, Division of Human Genetics, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA and Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.|Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, Center for Biomedical Informaticsand Center for Mitochondrial and Epigenomic Medicine, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA, Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, Division of Human Genetics, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA and Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.|Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, Center for Biomedical Informaticsand Center for Mitochondrial and Epigenomic Medicine, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA, Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, Division of Human Genetics, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA and Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.|Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, Center for Biomedical Informaticsand Center for Mitochondrial and Epigenomic Medicine, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA, Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, Division of Human Genetics, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA and Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.|Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, Center for Biomedical Informaticsand Center for Mitochondrial and Epigenomic Medicine, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA, Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, Division of Human Genetics, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA and Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.|Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, Center for Biomedical Informaticsand Center for Mitochondrial and Epigenomic Medicine, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA, Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, Division of Human Genetics, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA and Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, Center for Biomedical Informaticsand Center for Mitochondrial and Epigenomic Medicine, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA, Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, Division of Human Genetics, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA and Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.|Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, Center for Biomedical Informaticsand Center for Mitochondrial and Epigenomic Medicine, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA, Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, Division of Human Genetics, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA and Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.|Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, Center for Biomedical Informaticsand Center for Mitochondrial and Epigenomic Medicine, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA, Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, Division of Human Genetics, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA and Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, Center for Biomedical Informaticsand Center for Mitochondrial and Epigenomic Medicine, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA, Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, Division of Human Genetics, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA and Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.|Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, Center for Biomedical Informaticsand Center for Mitochondrial and Epigenomic Medicine, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA, Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, Division of Human Genetics, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA and Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.|Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, Center for Biomedical Informaticsand Center for Mitochondrial and Epigenomic Medicine, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA, Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, Division of Human Genetics, The Childrens Hospital of Philadelphia, Philadelphia, PA, USA and Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.', 'Netherlands|Netherlands|Netherlands|Netherlands|Netherlands|Netherlands|Netherlands|Netherlands|Neth', 0, 'Algorithms|DNA, Mitochondrial|Genetic Variation|Haplotypes|High-Throughput Nucleotide Sequencing|Humans|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/btu825', '25505086', 'All current mitochondrial haplogroup classification tools require variants to be detected from an alignment with the reference sequence and to be properly named according to the canonical nomenclature standards for describing mitochondrial variants, before they can be compared with the haplogroup determining polymorphisms. With the emergence of high-throughput sequencing technologies and hence greater availability of mitochondrial genome sequences, there is a strong need for an automated haplogroup classification tool that is alignment-free and agnostic to reference sequence.'),
(78924, 2015, 'bio', 'Sputnik: ad hoc distributed computation', 'Völkel, Gunnar|Lausser, Ludwig|Schmid, Florian|Kraus, Johann M|Kestler, Hans A', 'Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena.|Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena.|Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena.|Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena.|Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena.', 'Germany|Germany|Germany|Germany|Germany', 0, 'Algorithms|Biomarkers|Computer Graphics|Gene Expression Profiling|Humans|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/btu818', '25505087', 'In bioinformatic applications, computationally demanding algorithms are often parallelized to speed up computation. Nevertheless, setting up computational environments for distributed computation is often tedious. Aim of this project were the lightweight ad hoc set up and fault-tolerant computation requiring only a Java runtime, no administrator rights, while utilizing all CPU cores most effectively.'),
(78925, 2015, 'bio', 'HYCUD: a computational tool for prediction of effective rotational correlation time in flexible proteins', 'Rezaei-Ghaleh, Nasrollah|Klama, Frederik|Munari, Francesca|Zweckstetter, Markus', 'Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany.|Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany.|Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany.|Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany.', 'Germany|Germany|Germany|Germany', 6, 'Computational Biology|Protein Structure, Tertiary|Ribosomal Proteins|Rotation|Software', 'Journal Article', '10.1093/bioinformatics/btu824', '25505088', 'A large fraction of eukaryotic proteins contain unstructured tails or linkers. The presence of flexible regions allows these systems to experience a high level of mobility facilitating their biological function. The complex nature of protein rotation in such flexible modular systems precludes a straightforward application of hydrodynamic methods to calculate their rotational motional properties. We describe the workflow of HYdrodynamic CoUpling of Domains (HYCUD), a program for prediction of effective rotational correlation times in multidomain proteins. The usage of HYCUD is demonstrated by its application to the ribosomal protein L7/L12. Rotational correlation times predicted by HYCUD might be used to detect molecular switch events mediated by disorder-order transitions in interdomain linkers.'),
(78926, 2015, 'bio', 'Response to the comment on protein-protein binding affinity prediction from amino acid sequence', 'Yugandhar, K|Gromiha, M Michael', 'Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai-600036, Tamil Nadu, India.|Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai-600036, Tamil Nadu, India.', 'India|India', 4, 'Multiprotein Complexes|Protein Interaction Mapping', 'Letter', '10.1093/bioinformatics/btu821', '25505089', '-'),
(78927, 2015, 'bio', '3Dmoljs: molecular visualization with WebGL', 'Rego, Nicholas|Koes, David', 'Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA and Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA and Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA and Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.', 'United States|United States', 0, 'Capsid Proteins|Computer Graphics|Internet|Programming Languages|Protein Conformation|Software', 'Journal Article', '10.1093/bioinformatics/btu829', '25505090', '3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in websites.'),
(78928, 2015, 'bio', 'JEPEG: a summary statistics based tool for gene-level joint testing of functional variants', 'Lee, Donghyung|Williamson, Vernell S|Bigdeli, T Bernard|Riley, Brien P|Fanous, Ayman H|Vladimirov, Vladimir I|Bacanu, Silviu-Alin', 'Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA.|Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA.|Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA.|Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA.|Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA.|Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA.|Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA.', 'United States|United States|United States|United States|United States|United States|United States', 0, 'Anorexia Nervosa|Biomarkers|Cohort Studies|Gene Expression Profiling|Gene Expression Regulation|Genome-Wide Association Study|Genomics|Genotype|Humans|Meta-Analysis as Topic|Phenotype|Polymorphism, Single Nucleotide|Quantitative Trait Loci|Software', 'Journal Article', '10.1093/bioinformatics/btu816', '25505091', 'Gene expression is influenced by variants commonly known as expression quantitative trait loci (eQTL). On the basis of this fact, researchers proposed to use eQTL/functional information univariately for prioritizing single nucleotide polymorphisms (SNPs) signals from genome-wide association studies (GWAS). However, most genes are influenced by multiple eQTLs which, thus, jointly affect any downstream phenotype. Therefore, when compared with the univariate prioritization approach, a joint modeling of eQTL action on phenotypes has the potential to substantially increase signal detection power. Nonetheless, a joint eQTL analysis is impeded by (i) not measuring all eQTLs in a gene and/or (ii) lack of access to individual genotypes.'),
(78929, 2015, 'bio', 'NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy', 'Lee, Woonghee|Tonelli, Marco|Markley, John L', 'National Magnetics Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.|National Magnetics Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.|National Magnetics Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.', 'United States|United States|United States', 448, 'Databases, Protein|Humans|Nuclear Magnetic Resonance, Biomolecular|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/btu830', '25505092', 'SPARKY (Goddard and Kneller, SPARKY 3) remains the most popular software program for NMR data analysis, despite the fact that development of the package by its originators ceased in 2001. We have taken over the development of this package and describe NMRFAM-SPARKY, which implements new functions reflecting advances in the biomolecular NMR field. NMRFAM-SPARKY has been repackaged with current versions of Python and Tcl/Tk, which support new tools for NMR peak simulation and graphical assignment determination. These tools, along with chemical shift predictions from the PACSY database, greatly accelerate protein side chain assignments. NMRFAM-SPARKY supports automated data format interconversion for interfacing with a variety of web servers including, PECAN , PINE, TALOS-N, CS-Rosetta, SHIFTX2 and PONDEROSA-C/S.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(78930, 2015, 'bio', 'diXa: a data infrastructure for chemical safety assessment', 'Hendrickx, Diana M|Aerts, Hugo J W L|Caiment, Florian|Clark, Dominic|Ebbels, Timothy M D|Evelo, Chris T|Gmuender, Hans|Hebels, Dennie G A J|Herwig, Ralf|Hescheler, Jürgen|Jennen, Danyel G J|Jetten, Marlon J A|Kanterakis, Stathis|Keun, Hector C|Matser, Vera|Overington, John P|Pilicheva, Ekaterina|Sarkans, Ugis|Segura-Lepe, Marcelo P|Sotiriadou, Isaia|Wittenberger, Timo|Wittwehr, Clemens|Zanzi, Antonella|Kleinjans, Jos C S', 'Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.|Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy.', 'Switzerland|Switzerland|Switzerland|Switzerland|Switzerland|Switzerland|Switzerland|Switzerland|Swit', 0, 'Animals|Databases, Chemical|Gene Expression Profiling|Humans|Metabolomics|Proteomics|Rats|Toxicogenetics', 'Journal Article', '10.1093/bioinformatics/btu827', '25505093', 'The field of toxicogenomics (the application of -omics technologies to risk assessment of compound toxicities) has expanded in the last decade, partly driven by new legislation, aimed at reducing animal testing in chemical risk assessment but mainly as a result of a paradigm change in toxicology towards the use and integration of genome wide data. Many research groups worldwide have generated large amounts of such toxicogenomics data. However, there is no centralized repository for archiving and making these data and associated tools for their analysis easily available.'),
(78931, 2015, 'bio', 'Detection of circular permutations within protein structures using CE-CP', 'Bliven, Spencer E|Bourne, Philip E|Prlixc4x87, Andreas', 'Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.|Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.|Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.', 'United States|United States|United States', 4, 'Algorithms|Computational Biology|Databases, Protein|Dynamins|Humans|Programming Languages|Protein Structure, Tertiary|Sequence Analysis, Protein|Structural Homology, Protein', 'Journal Article', '10.1093/bioinformatics/btu823', '25505094', 'Circular permutation is an important type of protein rearrangement. Natural circular permutations have implications for protein function, stability and evolution. Artificial circular permutations have also been used for protein studies. However, such relationships are difficult to detect for many sequence and structure comparison algorithms and require special consideration.'),
(78932, 2015, 'bio', 'Epock: rapid analysis of protein pocket dynamics', 'Laurent, Benoist|Chavent, Matthieu|Cragnolini, Tristan|Dahl, Anna Caroline E|Pasquali, Samuela|Derreumaux, Philippe|Sansom, Mark S P|Baaden, Marc', 'Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.|Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.|Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.|Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.|Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.|Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.|Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.|Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.', 'France|France|France|France|France|France|France|France', 0, 'Binding Sites|HSP90 Heat-Shock Proteins|Ion Channels|Molecular Dynamics Simulation|Protein Binding|Protein Conformation|Software', 'Journal Article', '10.1093/bioinformatics/btu822', '25505095', 'The volume of an internal protein pocket is fundamental to ligand accessibility. Few programs that compute such volumes manage dynamic data from molecular dynamics (MD) simulations. Limited performance often prohibits analysis of large datasets. We present Epock, an efficient command-line tool that calculates pocket volumes from MD trajectories. A plugin for the VMD program provides a graphical user interface to facilitate input creation, run Epock and analyse the results.'),
(78933, 2015, 'bio', 'LocNES: a computational tool for locating classical NESs in CRM1 cargo proteins', 'Xu, Darui|Marquis, Kara|Pei, Jimin|Fu, Szu-Chin|Caxc4x9fatay, Tolga|Grishin, Nick V|Chook, Yuh Min', 'Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.|Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.|Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.|Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.|Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.|Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.|Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.', 'United States|United States|United States|United States|United States|United States|United States', 55, 'Amino Acid Sequence|Consensus Sequence|Humans|Karyopherins|Nuclear Export Signals|Position-Specific Scoring Matrices|Receptors, Cytoplasmic and Nuclear|Sequence Analysis, Protein|Software|Support Vector Machine', 'Journal Article', '10.1093/bioinformatics/btu826', '25515756', 'Classical nuclear export signals (NESs) are short cognate peptides that direct proteins out of the nucleus via the CRM1-mediated export pathway. CRM1 regulates the localization of hundreds of macromolecules involved in various cellular functions and diseases. Due to the diverse and complex nature of NESs, reliable prediction of the signal remains a challenge despite several attempts made in the last decade.'),
(78934, 2015, 'bio', 'VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications', 'Mu, John C|Mohiyuddin, Marghoob|Li, Jian|Bani Asadi, Narges|Gerstein, Mark B|Abyzov, Alexej|Wong, Wing H|Lam, Hugo Y K', 'Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, Department of Statistics, Stanford University, Stanford, CA 94035, USA and Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, Department of Statistics, Stanford University, Stanford, CA 94035, USA and Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA.|Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, Department of Statistics, Stanford University, Stanford, CA 94035, USA and Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA.|Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, Department of Statistics, Stanford University, Stanford, CA 94035, USA and Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA.|Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, Department of Statistics, Stanford University, Stanford, CA 94035, USA and Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA.|Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, Department of Statistics, Stanford University, Stanford, CA 94035, USA and Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA.|Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, Department of Statistics, Stanford University, Stanford, CA 94035, USA and Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA.|Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, Department of Statistics, Stanford University, Stanford, CA 94035, USA and Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, Department of Statistics, Stanford University, Stanford, CA 94035, USA and Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA.|Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, Department of Statistics, Stanford University, Stanford, CA 94035, USA and Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA.', 'United States|United States|United States|United States|United States|United States|United States|United States', 0, 'Computer Simulation|Genetic Variation|Genomics|High-Throughput Nucleotide Sequencing|Humans|Mutation|Neoplasms|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/btu828', '25524895', 'VarSim is a framework for assessing alignment and variant calling accuracy in high-throughput genome sequencing through simulation or real data. In contrast to simulating a random mutation spectrum, it synthesizes diploid genomes with germline and somatic mutations based on a realistic model. This model leverages information such as previously reported mutations to make the synthetic genomes biologically relevant. VarSim simulates and validates a wide range of variants, including single nucleotide variants, small indels and large structural variants. It is an automated, comprehensive compute framework supporting parallel computation and multiple read simulators. Furthermore, we developed a novel map data structure to validate read alignments, a strategy to compare variants binned in size ranges and a lightweight, interactive, graphical report to visualize validation results with detailed statistics. Thus far, it is the most comprehensive validation tool for secondary analysis in next generation sequencing.'),
(78935, 2015, 'bio', 'PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes', 'Yoon, Hyejin|Leitner, Thomas', 'Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.|Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.', 'United States|United States', 0, 'DNA Primers|Genome, Viral|Genomics|HIV-1|Sequence Alignment|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/btu832', '25524896', 'Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. Furthermore, simultaneous optimization of several DNA primer design criteria may improve overall experimental efficiency and downstream bioinformatic processing. To achieve these goals, we developed PrimerDesign-M. It includes several options for multiple-primer design, allowing researchers to efficiently design walking primers that cover long DNA targets, such as entire HIV-1 genomes, and that optimizes primers simultaneously informed by genetic diversity in multiple alignments and experimental design constraints given by the user. PrimerDesign-M can also design primers that include DNA barcodes and minimize primer dimerization. PrimerDesign-M finds optimal primers for highly variable DNA targets and facilitates design flexibility by suggesting alternative designs to adapt to experimental conditions.'),
(78936, 2015, 'bio', 'Empowering biologists with multi-omics data: colorectal cancer as a paradigm', 'Zhu, Jing|Shi, Zhiao|Wang, Jing|Zhang, Bing', 'Department of Biomedical Informatics, Advanced Computing Center for Research and Education, Department of Electrical Engineering and Computer Science and Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, USA.|Department of Biomedical Informatics, Advanced Computing Center for Research and Education, Department of Electrical Engineering and Computer Science and Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, USA Department of Biomedical Informatics, Advanced Computing Center for Research and Education, Department of Electrical Engineering and Computer Science and Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, USA.|Department of Biomedical Informatics, Advanced Computing Center for Research and Education, Department of Electrical Engineering and Computer Science and Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, USA.|Department of Biomedical Informatics, Advanced Computing Center for Research and Education, Department of Electrical Engineering and Computer Science and Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, USA Department of Biomedical Informatics, Advanced Computing Center for Research and Education, Department of Electrical Engineering and Computer Science and Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, USA.', 'United States|United States|United States|United States', 0, 'Colorectal Neoplasms|Epigenesis, Genetic|Gene Regulatory Networks|Gene Silencing|Genomics|Humans|Neoplasms|Proteomics|Software|Transcriptome', 'Journal Article', '10.1093/bioinformatics/btu834', '25527095', 'Recent completion of the global proteomic characterization of The Cancer Genome Atlas (TCGA) colorectal cancer (CRC) cohort resulted in the first tumor dataset with complete molecular measurements at DNA, RNA and protein levels. Using CRC as a paradigm, we describe the application of the NetGestalt framework to provide easy access and interpretation of multi-omics data.'),
(78937, 2015, 'bio', 'The Cyni framework for network inference in Cytoscape', 'Guitart-Pla, Oriol|Kustagi, Manjunath|Rügheimer, Frank|Califano, Andrea|Schwikowski, Benno', 'Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA.|Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA.|Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA.|Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA.|Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA.', 'France|France|France|France|France', 0, 'Algorithms|Gene Regulatory Networks|Software', 'Journal Article', '10.1093/bioinformatics/btu812', '25527096', 'Research on methods for the inference of networks from biological data is making significant advances, but the adoption of network inference in biomedical research practice is lagging behind. Here, we present Cyni, an open-source fill-in-the-algorithm framework that provides common network inference functionality and user interface elements. Cyni allows the rapid transformation of Java-based network inference prototypes into apps of the popular open-source Cytoscape network analysis and visualization ecosystem. Merely placing the resulting app in the Cytoscape App Store makes the method accessible to a worldwide community of biomedical researchers by mouse click. In a case study, we illustrate the transformation of an ARACNE implementation into a Cytoscape app.'),
(78938, 2015, 'bio', 'CDvist: a webserver for identification and visualization of conserved domains in protein sequences', 'Adebali, Ogun|Ortega, Davi R|Zhulin, Igor B', 'Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37861, USA and Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37861, USA and Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.|Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37861, USA and Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37861, USA and Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.|Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37861, USA and Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37861, USA and Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.', 'United States|United States|United States', 23, 'Algorithms|Amino Acid Sequence|Computer Graphics|Conserved Sequence|Databases, Protein|Internet|Protein Structure, Tertiary|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/btu836', '25527097', 'Identification of domains in protein sequences allows their assigning to biological functions. Several webservers exist for identification of protein domains using similarity searches against various databases of protein domain models. However, none of them provides comprehensive domain coverage while allowing bulk querying and their visualization schemes can be improved. To address these issues, we developed CDvist (a comprehensive domain visualization tool), which combines the best available search algorithms and databases into a user-friendly framework. First, a given protein sequence is matched to domain models using high-specificity tools and only then unmatched segments are subjected to more sensitive algorithms resulting in a best possible comprehensive coverage. Bulk querying and rich visualization and download options provide improved functionality to domain architecture analysis.');
