School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China, School of Information Science & Engineering, Central South University, Changsha 410083, China, Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan and Center for Computational System Biology, Fudan University, Shanghai 200433, China.