March 2008

A typical frequency-modulated pulse-emitting bat (Myotis myotis) in a world of complex echoes (see Yovel et al., e1000032).

Image Credit: Image by Yossi Yovel and Dietmar Nill.

Editorial

Open Access: Taking Full Advantage of the Content

Philip E. Bourne, J. Lynn Fink, Mark Gerstein

PLOS Computational Biology: published March 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000037

Perspective

Computational Biology in Costa Rica: The Role of a Small Country in the Global Context of Bioinformatics

Edgardo Moreno, Bruno Lomonte, José-María Gutiérrez

PLOS Computational Biology: published March 14, 2008 | https://doi.org/10.1371/journal.pcbi.1000040

Research Articles

Robustness of Learning That Is Based on Covariance-Driven Synaptic Plasticity

Yonatan Loewenstein

PLOS Computational Biology: published March 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000007

Entropy Measures Quantify Global Splicing Disorders in Cancer

William Ritchie, Samuel Granjeaud, Denis Puthier, Daniel Gautheret

PLOS Computational Biology: published March 14, 2008 | https://doi.org/10.1371/journal.pcbi.1000011

Representing Where along with What Information in a Model of a Cortical Patch

Yasser Roudi, Alessandro Treves

PLOS Computational Biology: published March 21, 2008 | https://doi.org/10.1371/journal.pcbi.1000012

Intrinsically Disordered Proteins Display No Preference for Chaperone Binding In Vivo

Hedi Hegyi, Peter Tompa

PLOS Computational Biology: published March 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000017

Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses

Feng-Jie Sun, Gustavo Caetano-Anollés

PLOS Computational Biology: published March 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000018

Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation

Bin Kang, Yuan-Yuan Li, Xiao Chang, Lei Liu, Yi-Xue Li

PLOS Computational Biology: published March 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000019

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, Ilya Shmulevich

PLOS Computational Biology: published March 21, 2008 | https://doi.org/10.1371/journal.pcbi.1000021

Structure of Spontaneous UP and DOWN Transitions Self-Organizing in a Cortical Network Model

Siu Kang, Katsunori Kitano, Tomoki Fukai

PLOS Computational Biology: published March 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000022

A Continuum Model for Metabolic Gas Exchange in Pear Fruit

Q. Tri Ho, Pieter Verboven, Bert E. Verlinden, Jeroen Lammertyn, Stefan Vandewalle, Bart M. Nicolaï

PLOS Computational Biology: published March 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000023

Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution

Ilya Nemenman, Geoffrey D. Lewen, William Bialek, Rob R. de Ruyter van Steveninck

PLOS Computational Biology: published March 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000025

The Evolution of Robust Development and Homeostasis in Artificial Organisms

David Basanta, Mark Miodownik, Buzz Baum

PLOS Computational Biology: published March 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000030

Plant Classification from Bat-Like Echolocation Signals

Yossi Yovel, Matthias Otto Franz, Peter Stilz, Hans-Ulrich Schnitzler

PLOS Computational Biology: published March 21, 2008 | https://doi.org/10.1371/journal.pcbi.1000032

Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595

Lars V. Schäfer, Gerrit Groenhof, Martial Boggio-Pasqua, Michael A. Robb, Helmut Grubmüller

PLOS Computational Biology: published March 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000034

Electrotonic Signals along Intracellular Membranes May Interconnect Dendritic Spines and Nucleus

Isaac Shemer, Björn Brinne, Jesper Tegnér, Sten Grillner

PLOS Computational Biology: published March 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000036

Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions

Thomas Manke, Helge G. Roider, Martin Vingron

PLOS Computational Biology: published March 21, 2008 | https://doi.org/10.1371/journal.pcbi.1000039

A Hidden Feedback in Signaling Cascades Is Revealed

Alejandra C. Ventura, Jacques-A. Sepulchre, Sofía D. Merajver

PLOS Computational Biology: published March 21, 2008 | https://doi.org/10.1371/journal.pcbi.1000041

Shaping Embodied Neural Networks for Adaptive Goal-directed Behavior

Zenas C. Chao, Douglas J. Bakkum, Steve M. Potter

PLOS Computational Biology: published March 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000042

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, Ferdinando Di Cunto

PLOS Computational Biology: published March 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000043

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, Ziv Bar-Joseph

PLOS Computational Biology: published March 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000044

The Dynamics of Human Body Weight Change

Carson C. Chow, Kevin D. Hall

PLOS Computational Biology: published March 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000045

Neurobiological Models of Two-Choice Decision Making Can Be Reduced to a One-Dimensional Nonlinear Diffusion Equation

Alex Roxin, Anders Ledberg

PLOS Computational Biology: published March 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000046

Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms

Sichun Yang, Benoît Roux

PLOS Computational Biology: published March 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000047

Cover

Typical FM bat in a virtual world of stochastic echoes