| | Perspective Genome-Scale Computational Biology and Bioinformatics in Australia Mark A. Ragan, Tim Littlejohn, and Bruce Ross PMCID: PMC2440818 Editorial Mean-Fields and Neural Masses Karl Friston PMCID: PMC2435274 Message from ISCB Getting Started in Computational Immunology Steven H. Kleinstein PMCID: PMC2518523 Review The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical
Fields Gustavo Deco, Viktor K. Jirsa, Peter A. Robinson, Michael Breakspear, and Karl Friston PMCID: PMC2519166 Research Articles Geometric Interpretation of Gene Coexpression Network Analysis Steve Horvath and Jun Dong PMCID: PMC2446438 Efficient Algorithms for Probing the RNA Mutation Landscape Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, and Peter Clote PMCID: PMC2475669 Regulatory Control and the Costs and Benefits of Biochemical Noise Sorin Tănase-Nicola and Pieter Rein ten Wolde PMCID: PMC2518519 Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements M. Cecchini, A. Houdusse, and M. Karplus PMCID: PMC2497441 Modeling the Violation of Reward Maximization and Invariance in Reinforcement Schedules Giancarlo La Camera and Barry J. Richmond PMCID: PMC2453237 Stroke Rehabilitation Reaches a Threshold Cheol E. Han, Michael A. Arbib, and Nicolas Schweighofer PMCID: PMC2527783 Predicting Human Nucleosome Occupancy from Primary Sequence Shobhit Gupta, Jonathan Dennis, Robert E. Thurman, Robert Kingston, John A. Stamatoyannopoulos, and William Stafford Noble PMCID: PMC2515632 Innate Visual Learning through Spontaneous Activity Patterns Mark V. Albert, Adam Schnabel, and David J. Field PMCID: PMC2446436 Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers Jihua Hao, Adrian W. R. Serohijos, Gail Newton, Gina Tassone, Zuncai Wang, Dennis C. Sgroi, Nikolay V. Dokholyan, and James P. Basilion PMCID: PMC2453235 A Model of Stimulus-Specific Neural Assemblies in the Insect Antennal Lobe Dominique Martinez and Noelia Montejo PMCID: PMC2536510 Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality Elena Zotenko, Julian Mestre, Dianne P. O'Leary, and Teresa M. Przytycka PMCID: PMC2467474 Embedding mRNA Stability in Correlation Analysis of Time-Series Gene Expression Data Lorenzo Farina, Alberto De Santis, Samanta Salvucci, Giorgio Morelli, and Ida Ruberti PMCID: PMC2453326 Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies Ranyee A. Chiang, Andrej Sali, and Patricia C. Babbitt PMCID: PMC2453236 Falling towards Forgetfulness: Synaptic Decay Prevents Spontaneous Recovery of Memory James V. Stone and Peter E. Jupp PMCID: PMC2516185 Retroviral Integration Process in the Human Genome: Is It Really Non-Random? A New Statistical Approach Alessandro Ambrosi, Claudia Cattoglio, and Clelia Di Serio PMCID: PMC2453317 Intramolecular Cohesion of Coils Mediated by Phenylalanine–Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin V. V. Krishnan, Edmond Y. Lau, Justin Yamada, Daniel P. Denning, Samir S. Patel, Michael E. Colvin, and Michael F. Rexach PMCID: PMC2475668 Classifying RNA-Binding Proteins Based on Electrostatic Properties Shula Shazman and Yael Mandel-Gutfreund PMCID: PMC2518515 A General Definition and Nomenclature for Alternative Splicing Events Michael Sammeth, Sylvain Foissac, and Roderic Guigó PMCID: PMC2467475 Coordinate Regulation of G Protein Signaling via Dynamic Interactions of Receptor and GAP Marc Turcotte, Wei Tang, and Elliott M. Ross PMCID: PMC2518520 Host Control of Malaria Infections: Constraints on Immune and Erythropoeitic Response Kinetics Philip G. McQueen and F. Ellis McKenzie PMCID: PMC2491590 Self Containment, a Property of Modular RNA Structures, Distinguishes microRNAs Miler T. Lee and Junhyong Kim PMCID: PMC2517099 A Novel Three-Phase Model of Brain Tissue Microstructure Jana L. Gevertz and Salvatore Torquato PMCID: PMC2495040 Structure and Dynamics of Interphase Chromosomes Angelo Rosa and Ralf Everaers PMCID: PMC2515109 A Feature-Based Approach to Modeling Protein–DNA Interactions Eilon Sharon, Shai Lubliner, and Eran Segal PMCID: PMC2516605 The Effect of a ΔK280 Mutation on the Unfolded State of a Microtubule-Binding Repeat in Tau Austin Huang and Collin M. Stultz PMCID: PMC2494868 PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling Rahul Siddharthan PMCID: PMC2518514 Nonlinear Muscles, Passive Viscoelasticity and Body Taper Conspire To Create Neuromechanical Phase Lags in Anguilliform Swimmers T. McMillen, T. Williams, and P. Holmes PMCID: PMC2518218 Modeling ChIP Sequencing In Silico with Applications Zhengdong D. Zhang, Joel Rozowsky, Michael Snyder, Joseph Chang, and Mark Gerstein PMCID: PMC2507756 Combining Structural Connectivity and Response Latencies to Model the Structure of the Visual System Michael Capalbo, Eric Postma, and Rainer Goebel PMCID: PMC2507758 Biophysical Parameters Modification Could Overcome Essential Hearing Gaps A. Kern, C. Heid, W.-H. Steeb, N. Stoop, and R. Stoop PMCID: PMC2516184 Inference of Protein Complex Activities from Chemical-Genetic Profile and Its Applications: Predicting Drug-Target Pathways Sangjo Han and Dongsup Kim PMCID: PMC2515108 Cooperative Transition between Open and Closed Conformations in Potassium Channels Turkan Haliloglu and Nir Ben-Tal PMCID: PMC2528004 Network Inference Algorithms Elucidate Nrf2 Regulation of Mouse Lung Oxidative Stress Ronald C. Taylor, George Acquaah-Mensah, Mudita Singhal, Deepti Malhotra, and Shyam Biswal PMCID: PMC2516606 Noise Reduction by Diffusional Dissipation in a Minimal Quorum Sensing Motif Yu Tanouchi, Dennis Tu, Jungsang Kim, and Lingchong You PMCID: PMC2507755 Correction Correction: Classifying RNA-Binding Proteins Based on Electrostatic Properties Shula Shazman and Yael Mandel-Gutfreund PMCID: PMC2651598 Corrects: Shula Shazman, et al. Classifying RNA-Binding Proteins Based on Electrostatic Properties. PLoS Comput Biol. 2008 August; 4(8): e1000146. |
