Table of Contents: March 2010

The cytoplasm of the gram-negative bacterium Escherichia coli is very densely packed with macromolecules, and this highly crowded environment is expected to have a significant impact on the diffusive and thermodynamic properties of its constituents. Continuing progress in the field of structural biology now allows molecular simulations of the cytoplasm to be performed with structurally detailed models, providing a new, computational view of macromolecular behavior in vivo (see McGuffee, Elcock, doi:10.1371/journal.pcbi.1000694).

Image Credit: Adrian H Elcock (University of Iowa)

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Getting Started in Gene Orthology and Functional Analysis

Gang Fang, Nitin Bhardwaj, Rebecca Robilotto, Mark B. Gerstein

Research Articles

Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance

Bernie J. Daigle Jr, Alicia Deng, Tracey McLaughlin, Samuel W. Cushman, Margaret C. Cam, Gerald Reaven, Philip S. Tsao, Russ B. Altman

Specialization Can Drive the Evolution of Modularity

Carlos Espinosa-Soto, Andreas Wagner

Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV

Max von Kleist, Stephan Menz, Wilhelm Huisinga

The Impact of Contact Tracing in Clustered Populations

Thomas House, Matt J. Keeling

Investigating Homology between Proteins using Energetic Profiles

James O. Wrabl, Vincent J. Hilser

A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions

Chuan-Yun Li, Yong Zhang, Zhanbo Wang, Yan Zhang, Chunmei Cao, Ping-Wu Zhang, Shu-Juan Lu, Xiao-Mo Li, Quan Yu, Xiaofeng Zheng, Quan Du, George R. Uhl, Qing-Rong Liu, Liping Wei

Tumor Growth Rate Determines the Timing of Optimal Chronomodulated Treatment Schedules

Samuel Bernard, Branka Čajavec Bernard, Francis Lévi, Hanspeter Herzel

Estimating the Stoichiometry of HIV Neutralization

Carsten Magnus, Roland R. Regoes

Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation

Carey D. Nadell, Kevin R. Foster, João B. Xavier

Predicted Auxiliary Navigation Mechanism of Peritrichously Flagellated Chemotactic Bacteria

Nikita Vladimirov, Dirk Lebiedz, Victor Sourjik

Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function

Daniel E. Almonacid, Emmanuel R. Yera, John B. O. Mitchell, Patricia C. Babbitt

Non-Linear Neuronal Responses as an Emergent Property of Afferent Networks: A Case Study of the Locust Lobula Giant Movement Detector

Sergi Bermúdez i Badia, Ulysses Bernardet, Paul F. M. J. Verschure

Effects of Transcriptional Pausing on Gene Expression Dynamics

Tiina Rajala, Antti Häkkinen, Shannon Healy, Olli Yli-Harja, Andre S. Ribeiro

Detailed Simulations of Cell Biology with Smoldyn 2.1

Steven S. Andrews, Nathan J. Addy, Roger Brent, Adam P. Arkin

Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells

Jun Cai, Dan Xie, Zhewen Fan, Hiram Chipperfield, John Marden, Wing H. Wong, Sheng Zhong

Comparing Families of Dynamic Causal Models

Will D. Penny, Klaas E. Stephan, Jean Daunizeau, Maria J. Rosa, Karl J. Friston, Thomas M. Schofield, Alex P. Leff

Neocortical Axon Arbors Trade-off Material and Conduction Delay Conservation

Julian M. L. Budd, Krisztina Kovács, Alex S. Ferecskó, Péter Buzás, Ulf T. Eysel, Zoltán F. Kisvárday

Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods

Christelle Reynès, Hélène Host, Anne-Claude Camproux, Guillaume Laconde, Florence Leroux, Anne Mazars, Benoit Deprez, Robin Fahraeus, Bruno O. Villoutreix, Olivier Sperandio

Parameter Estimation and Model Selection in Computational Biology

Gabriele Lillacci, Mustafa Khammash

Within- and Cross-Modal Distance Information Disambiguate Visual Size-Change Perception

Peter W. Battaglia, Massimiliano Di Luca, Marc O. Ernst, Paul R. Schrater, Tonja Machulla, Daniel Kersten

Systematic Planning of Genome-Scale Experiments in Poorly Studied Species

Yuanfang Guan, Maitreya Dunham, Amy Caudy, Olga Troyanskaya

Estimating the Stochastic Bifurcation Structure of Cellular Networks

Carl Song, Hilary Phenix, Vida Abedi, Matthew Scott, Brian P. Ingalls, Mads Kærn, Theodore J. Perkins

Related Articles

  1. Correction: Estimating the Stochastic Bifurcation Structure of Cellular Networks

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement

Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot, Andrei Zinovyev