Table of Contents: August 2010

Synthetic dendrites of cortical pyramidal cells are indistinguishable from their real counterparts when constructed on the basis of the assumption that their morphology minimizes conduction times within the cell and the total amount of cytoplasm (see Cuntz et al., 10.1371/journal.pcbi.1000877).

Image Credit: Hermann Cuntz

Education Articles

An Introduction to Biomolecular Graphics

Cameron Mura, Colin M. McCrimmon, Jason Vertrees, Michael R. Sawaya

Research Articles

Frequency-Dependent Selection Predicts Patterns of Radiations and Biodiversity

Carlos J. Melián, David Alonso, Diego P. Vázquez, James Regetz, Stefano Allesina

Linking Changes in Epithelial Morphogenesis to Cancer Mutations Using Computational Modeling

Katarzyna A. Rejniak, Shizhen E. Wang, Nicole S. Bryce, Hang Chang, Bahram Parvin, Jerome Jourquin, Lourdes Estrada, Joe W. Gray, Carlos L. Arteaga, Alissa M. Weaver, Vito Quaranta, Alexander R. A. Anderson

Similar Impact of CD8+ T Cell Responses on Early Virus Dynamics during SIV Infections of Rhesus Macaques and Sooty Mangabeys

Roger D. Kouyos, Shari N. Gordon, Silvija I. Staprans, Guido Silvestri, Roland R. Regoes

Reverse Engineering of Oxygen Transport in the Lung: Adaptation to Changing Demands and Resources through Space-Filling Networks

Chen Hou, Stefan Gheorghiu, Virginia H. Huxley, Peter Pfeifer

Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors

Thomas C. Whisenant, David T. Ho, Ryan W. Benz, Jeffrey S. Rogers, Robyn M. Kaake, Elizabeth A. Gordon, Lan Huang, Pierre Baldi, Lee Bardwell

Nonlinear Gap Junctions Enable Long-Distance Propagation of Pulsating Calcium Waves in Astrocyte Networks

Mati Goldberg, Maurizio De Pittà, Vladislav Volman, Hugues Berry, Eshel Ben-Jacob

Gene Expression Variability within and between Human Populations and Implications toward Disease Susceptibility

Jingjing Li, Yu Liu, TaeHyung Kim, Renqiang Min, Zhaolei Zhang

Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles

Jonathan E. Kohn, Pavel V. Afonine, Jory Z. Ruscio, Paul D. Adams, Teresa Head-Gordon

A Mechanistic View of the Role of E3 in Sumoylation

Melda Tozluoğlu, Ezgi Karaca, Ruth Nussinov, Türkan Haliloğlu

Spike-Timing Theory of Working Memory

Botond Szatmáry, Eugene M. Izhikevich

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

Wayne Delport, Konrad Scheffler, Gordon Botha, Mike B. Gravenor, Spencer V. Muse, Sergei L. Kosakovsky Pond

Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model

M. Ahsanul Islam, Elizabeth A. Edwards, Radhakrishnan Mahadevan

MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations

Meromit Singer, Dario Boffelli, Joseph Dhahbi, Alexander Schönhuth, Gary P. Schroth, David I. K. Martin, Lior Pachter

Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data

Kakajan Komurov, Michael A. White, Prahlad T. Ram

Mathematical Description of Bacterial Traveling Pulses

Jonathan Saragosti, Vincent Calvez, Nikolaos Bournaveas, Axel Buguin, Pascal Silberzan, Benoît Perthame

Reinforcement Learning on Slow Features of High-Dimensional Input Streams

Robert Legenstein, Niko Wilbert, Laurenz Wiskott

Adaptive Contact Networks Change Effective Disease Infectiousness and Dynamics

Sven Van Segbroeck, Francisco C. Santos, Jorge M. Pacheco

Modeling Chemotaxis Reveals the Role of Reversed Phosphotransfer and a Bi-Functional Kinase-Phosphatase

Marcus J. Tindall, Steven L. Porter, Philip K. Maini, Judith P. Armitage

Dendritic Spikes Amplify the Synaptic Signal to Enhance Detection of Motion in a Simulation of the Direction-Selective Ganglion Cell

Michael J. Schachter, Nicholas Oesch, Robert G. Smith, W. Rowland Taylor

Computational Analysis of Phosphopeptide Binding to the Polo-Box Domain of the Mitotic Kinase PLK1 Using Molecular Dynamics Simulation

David J. Huggins, Grahame J. McKenzie, Daniel D. Robinson, Ana J. Narváez, Bryn Hardwick, Meredith Roberts-Thomson, Ashok R. Venkitaraman, Guy H. Grant, Mike C. Payne

Correlation of Influenza Virus Excess Mortality with Antigenic Variation: Application to Rapid Estimation of Influenza Mortality Burden

Aiping Wu, Yousong Peng, Xiangjun Du, Yuelong Shu, Taijiao Jiang

Computational Models of HIV-1 Resistance to Gene Therapy Elucidate Therapy Design Principles

Sharon Aviran, Priya S. Shah, David V. Schaffer, Adam P. Arkin

Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors

Jana Selent, Ferran Sanz, Manuel Pastor, Gianni De Fabritiis

A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny

Aziz Mithani, Gail M. Preston, Jotun Hein

Continuous Attractors with Morphed/Correlated Maps

Sandro Romani, Misha Tsodyks

Calcium Signals Driven by Single Channel Noise

Alexander Skupin, Helmut Kettenmann, Martin Falcke

Probability Matching as a Computational Strategy Used in Perception

David R. Wozny, Ulrik R. Beierholm, Ladan Shams

A Simple Self-Maintaining Metabolic System: Robustness, Autocatalysis, Bistability

Gabriel Piedrafita, Francisco Montero, Federico Morán, María Luz Cárdenas, Athel Cornish-Bowden

Connectivity, Cycles, and Persistence Thresholds in Metapopulation Networks

Yael Artzy-Randrup, Lewi Stone

One Rule to Grow Them All: A General Theory of Neuronal Branching and Its Practical Application

Hermann Cuntz, Friedrich Forstner, Alexander Borst, Michael Häusser