February 2008

Moving sinusoidal electrosensory gratings elicit direction-selective responses in the brains of Eigenmannia virescens (see Carver et al., e32).

Image Credit: Photograph of Eigenmannia by Will Kirk. Composite image composed and edited by Eric Fortune and Eatai Roth.

Message from ISCB

Getting Started in Biological Pathway Construction and Analysis

Ganesh A Viswanathan, Jeremy Seto, Sonali Patil, German Nudelman, Stuart C Sealfon

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.0040016

Education

Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor

Michał J Okoniewski, Crispin J Miller

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.0040006

Review

Computational Methods for Protein Identification from Mass Spectrometry Data

Leo McHugh, Jonathan W Arthur

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.0040012

Research Articles

Serotonin, Inhibition, and Negative Mood

Peter Dayan, Quentin J. M Huys

PLOS Computational Biology: published February 1, 2008 | https://doi.org/10.1371/journal.pcbi.0040004

Filling-In and Suppression of Visual Perception from Context: A Bayesian Account of Perceptual Biases by Contextual Influences

Li Zhaoping, Li Jingling

PLOS Computational Biology: published February 15, 2008 | https://doi.org/10.1371/journal.pcbi.0040014

Predicting the Receptive Range of Olfactory Receptors

Rafi Haddad, Liran Carmel, Noam Sobel, David Harel

PLOS Computational Biology: published February 1, 2008 | https://doi.org/10.1371/journal.pcbi.0040018

Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures

Dennis Kostka, Rainer Spang

PLOS Computational Biology: published February 15, 2008 | https://doi.org/10.1371/journal.pcbi.0040022

Evolution of Complex Modular Biological Networks

Arend Hintze, Christoph Adami

PLOS Computational Biology: published February 8, 2008 | https://doi.org/10.1371/journal.pcbi.0040023

How Force Might Activate Talin's Vinculin Binding Sites: SMD Reveals a Structural Mechanism

Vesa P Hytönen, Viola Vogel

PLOS Computational Biology: published February 15, 2008 | https://doi.org/10.1371/journal.pcbi.0040024

Modeling Cancer Progression via Pathway Dependencies

Elena J Edelman, Justin Guinney, Jen-Tsan Chi, Phillip G Febbo, Sayan Mukherjee

PLOS Computational Biology: published February 15, 2008 | https://doi.org/10.1371/journal.pcbi.0040028

Selective Adaptation in Networks of Heterogeneous Populations: Model, Simulation, and Experiment

Avner Wallach, Danny Eytan, Shimon Marom, Ron Meir

PLOS Computational Biology: published February 15, 2008 | https://doi.org/10.1371/journal.pcbi.0040029

Stimulus Design for Model Selection and Validation in Cell Signaling

Joshua F Apgar, Jared E Toettcher, Drew Endy, Forest M White, Bruce Tidor

PLOS Computational Biology: published February 15, 2008 | https://doi.org/10.1371/journal.pcbi.0040030

The Peri-Saccadic Perception of Objects and Space

Fred H Hamker, Marc Zirnsak, Dirk Calow, Markus Lappe

PLOS Computational Biology: published February 15, 2008 | https://doi.org/10.1371/journal.pcbi.0040031

Synaptic Plasticity Can Produce and Enhance Direction Selectivity

Sean Carver, Eatai Roth, Noah J Cowan, Eric S Fortune

PLOS Computational Biology: published February 15, 2008 | https://doi.org/10.1371/journal.pcbi.0040032

Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducens

Daniel Segura, Radhakrishnan Mahadevan, Katy Juárez, Derek R Lovley

PLOS Computational Biology: published February 8, 2008 | https://doi.org/10.1371/journal.pcbi.0040036

Modeling an Evolutionary Conserved Circadian Cis-Element

Eric R Paquet, Guillaume Rey, Felix Naef

PLOS Computational Biology: published February 15, 2008 | https://doi.org/10.1371/journal.pcbi.0040038

Control of Cation Permeation through the Nicotinic Receptor Channel

Hai-Long Wang, Xiaolin Cheng, Palmer Taylor, J. Andrew McCammon, Steven M Sine

PLOS Computational Biology: published February 15, 2008 | https://doi.org/10.1371/journal.pcbi.0040041

Accurate Structural Correlations from Maximum Likelihood Superpositions

Douglas L Theobald, Deborah S Wuttke

PLOS Computational Biology: published February 15, 2008 | https://doi.org/10.1371/journal.pcbi.0040043

Genome Landscapes and Bacteriophage Codon Usage

Julius B. Lucks, David R. Nelson, Grzegorz R. Kudla, Joshua B. Plotkin

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000001

How Protein Stability and New Functions Trade Off

Nobuhiko Tokuriki, Francois Stricher, Luis Serrano, Dan S. Tawfik

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000002

Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis

Lihua Zou, Sira Sriswasdi, Brian Ross, Patrycja V. Missiuro, Jun Liu, Hui Ge

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000003

Stochastic Differential Equation Model for Cerebellar Granule Cell Excitability

Antti Saarinen, Marja-Leena Linne, Olli Yli-Harja

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000004

The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks

Derek Ruths, Melissa Muller, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000005

Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes

Ivan Coluzza, Alfonso De Simone, Franca Fraternali, Daan Frenkel

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000006

Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding

Adrian W. R. Serohijos, Tamás Hegedűs, John R. Riordan, Nikolay V. Dokholyan

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000008

Computer-Based Screening of Functional Conformers of Proteins

Héctor Marlosti Montiel Molina, César Millán-Pacheco, Nina Pastor, Gabriel del Rio

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000009

A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval

Naomi Habib, Tommy Kaplan, Hanah Margalit, Nir Friedman

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000010

Sensing and Integration of Erk and PI3K Signals by Myc

Tae Lee, Guang Yao, Joseph Nevins, Lingchong You

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000013

Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation

Navin Elango, Seong-Ho Kim, NISC Comparative Sequencing Program, Eric Vigoda, Soojin V. Yi

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000015

Statistical Resolution of Ambiguous HLA Typing Data

Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Philip Goulder, David Heckerman

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000016

Identification of Synaptic Targets of Drosophila Pumilio

Gengxin Chen, Wanhe Li, Qing-Shuo Zhang, Michael Regulski, Nishi Sinha, Jody Barditch, Tim Tully, Adrian R. Krainer, Michael Q. Zhang, Josh Dubnau

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000026

Mouse Cognition-Related Behavior in the Open-Field: Emergence of Places of Attraction

Anna Dvorkin, Yoav Benjamini, Ilan Golani

PLOS Computational Biology: published February 29, 2008 | https://doi.org/10.1371/journal.pcbi.1000027

Correspondence

On the Process of Becoming a Great Scientist

Morgan C Giddings

PLOS Computational Biology: published February 15, 2008 | https://doi.org/10.1371/journal.pcbi.0040033

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