| | Perspective Computational Biology in Costa Rica: The Role of a Small Country in the Global Context of Bioinformatics Edgardo Moreno, Bruno Lomonte, and José-María Gutiérrez PMCID: PMC2265517 Editorial Open Access: Taking Full Advantage of the Content Philip E. Bourne, J. Lynn Fink, and Mark Gerstein PMCID: PMC2275780 Research Articles Robustness of Learning That Is Based on Covariance-Driven Synaptic Plasticity Yonatan Loewenstein PMCID: PMC2265526 Entropy Measures Quantify Global Splicing Disorders in Cancer William Ritchie, Samuel Granjeaud, Denis Puthier, and Daniel Gautheret PMCID: PMC2268240 Representing Where along with What Information in a Model of a Cortical Patch Yasser Roudi and Alessandro Treves PMCID: PMC2268242 Intrinsically Disordered Proteins Display No Preference for Chaperone Binding In Vivo Hedi Hegyi and Peter Tompa PMCID: PMC2265518 Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses Feng-Jie Sun and Gustavo Caetano-Anollés PMCID: PMC2265525 Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation Bin Kang, Yuan-Yuan Li, Xiao Chang, Lei Liu, and Yi-Xue Li PMCID: PMC2267494 Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics Stephen A. Ramsey, Sandy L. Klemm, Daniel E. Zak, Kathleen A. Kennedy, Vesteinn Thorsson, Bin Li, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Vladimir Litvak, Garnet Navarro, Jared C. Roach, Carrie M. Rosenberger, Alistair G. Rust, Natalya Yudkovsky, Alan Aderem, and Ilya Shmulevich PMCID: PMC2265556 Structure of Spontaneous UP and DOWN Transitions Self-Organizing in a Cortical Network Model Siu Kang, Katsunori Kitano, and Tomoki Fukai PMCID: PMC2265465 A Continuum Model for Metabolic Gas Exchange in Pear Fruit Q. Tri Ho, Pieter Verboven, Bert E. Verlinden, Jeroen Lammertyn, Stefan Vandewalle, and Bart M. Nicolaï PMCID: PMC2265468 Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution Ilya Nemenman, Geoffrey D. Lewen, William Bialek, and Rob R. de Ruyter van Steveninck PMCID: PMC2265477 The Evolution of Robust Development and Homeostasis in Artificial Organisms David Basanta, Mark Miodownik, and Buzz Baum PMCID: PMC2274883 Plant Classification from Bat-Like Echolocation Signals Yossi Yovel, Matthias Otto Franz, Peter Stilz, and Hans-Ulrich Schnitzler PMCID: PMC2267002 Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595 Lars V. Schäfer, Gerrit Groenhof, Martial Boggio-Pasqua, Michael A. Robb, and Helmut Grubmüller PMCID: PMC2274881 Electrotonic Signals along Intracellular Membranes May Interconnect Dendritic Spines and Nucleus Isaac Shemer, Björn Brinne, Jesper Tegnér, and Sten Grillner PMCID: PMC2266990 Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions Thomas Manke, Helge G. Roider, and Martin Vingron PMCID: PMC2266803 A Hidden Feedback in Signaling Cascades Is Revealed Alejandra C. Ventura, Jacques-A. Sepulchre, and Sofía D. Merajver PMCID: PMC2265423 Shaping Embodied Neural Networks for Adaptive Goal-directed Behavior Zenas C. Chao, Douglas J. Bakkum, and Steve M. Potter PMCID: PMC2265558 Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis Ugo Ala, Rosario Michael Piro, Elena Grassi, Christian Damasco, Lorenzo Silengo, Martin Oti, Paolo Provero, and Ferdinando Di Cunto PMCID: PMC2268251 A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli Jason Ernst, Qasim K. Beg, Krin A. Kay, Gábor Balázsi, Zoltán N. Oltvai, and Ziv Bar-Joseph PMCID: PMC2266799 The Dynamics of Human Body Weight Change Carson C. Chow and Kevin D. Hall PMCID: PMC2266991 Neurobiological Models of Two-Choice Decision Making Can Be Reduced to a One-Dimensional Nonlinear Diffusion Equation Alex Roxin and Anders Ledberg PMCID: PMC2268007 Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms Sichun Yang and Benoît Roux PMCID: PMC2268010 Corrections Correction: Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics Stephen A. Ramsey, Sandy L. Klemm, Daniel E. Zak, Kathleen A. Kennedy, Vesteinn Thorsson, Bin Li, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Vladimir Litvak, Garnet Navarro, Jared C. Roach, Carrie M. Rosenberger, Alistair G. Rust, Natalya Yudkovsky, Alan Aderem, and Ilya Shmulevich PMCID: PMC2638128 Corrects: Stephen A. Ramsey, et al. Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics. PLoS Comput Biol. 2008 March; 4(3): e1000021. Correction: Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducens Daniel Segura, Radhakrishnan Mahadevan, Katy Juárez, and Derek R Lovley PMCID: PMC2637084 Corrects: Daniel Segura, et al. Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducens. PLoS Comput Biol. 2008 February; 4(2): e36. Correction: Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al David C Nickle, Nebojsa Jojic, David Heckerman, Vladimir Jojic, Darko Kirovski, Morgane Rolland, Sergei Kosakovsky Pond, and James I Mullins PMCID: PMC2637083 Corrects: David C Nickle, et al. Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al. PLoS Comput Biol. 2008 January; 4(1): e25. |
