Table of Contents

May 2011

In the top right image the simulated methylation patterns in a nonhierarchical (classical) malignancy, indicated with different colors, radiate outward from the center. In the bottom left image, in contrast, the patterns occurring in a hierarchical (CSC-driven) tumor spread as patch-like colonies, increasing the overall intratumor heterogeneity and greatly affecting the evolutionary properties of the cancer cell population. (See Sottoriva et al., doi: 10.1371/journal.pcbi.1001132)

Image Credit: Andrea Sottoriva, Cambridge University, United Kingdom


Ten Simple Rules for Providing a Scientific Web Resource

Sebastian J. Schultheiss


Research Articles

How Modeling Can Reconcile Apparently Discrepant Experimental Results: The Case of Pacemaking in Dopaminergic Neurons

Guillaume Drion, Laurent Massotte, Rodolphe Sepulchre, Vincent Seutin

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

Daniel-Adriano Silva, Gregory R. Bowman, Alejandro Sosa-Peinado, Xuhui Huang

Speed/Accuracy Trade-Off between the Habitual and the Goal-Directed Processes

Mehdi Keramati, Amir Dezfouli, Payam Piray

An Acidic Loop and Cognate Phosphorylation Sites Define a Molecular Switch That Modulates Ubiquitin Charging Activity in Cdc34-Like Enzymes

Elena Papaleo, Valeria Ranzani, Farida Tripodi, Alessandro Vitriolo, Claudia Cirulli, Piercarlo Fantucci, Lilia Alberghina, Marco Vanoni, Luca De Gioia, Paola Coccetti

Simulation of the Undiseased Human Cardiac Ventricular Action Potential: Model Formulation and Experimental Validation

Thomas O'Hara, László Virág, András Varró, Yoram Rudy

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

Andrew McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark G. F. Sun, Malachi Griffith, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk, Marina Pacheco, Marco A. Marra, Martin Hirst, Torsten O. Nielsen, S. Cenk Sahinalp, David Huntsman, Sohrab P. Shah

Topological Cluster Analysis Reveals the Systemic Organization of the Caenorhabditis elegans Connectome

Yunkyu Sohn, Myung-Kyu Choi, Yong-Yeol Ahn, Junho Lee, Jaeseung Jeong

Spatial Learning and Action Planning in a Prefrontal Cortical Network Model

Louis-Emmanuel Martinet, Denis Sheynikhovich, Karim Benchenane, Angelo Arleo

Integrative Analysis of Transgenic Alfalfa (Medicago sativa L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis

Yun Lee, Fang Chen, Lina Gallego-Giraldo, Richard A. Dixon, Eberhard O. Voit

A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35

Jessica Nasica-Labouze, Massimiliano Meli, Philippe Derreumaux, Giorgio Colombo, Normand Mousseau

Attracting Dynamics of Frontal Cortex Ensembles during Memory-Guided Decision-Making

Emili Balaguer-Ballester, Christopher C. Lapish, Jeremy K. Seamans, Daniel Durstewitz

How Structure Determines Correlations in Neuronal Networks

Volker Pernice, Benjamin Staude, Stefano Cardanobile, Stefan Rotter

An Imperfect Dopaminergic Error Signal Can Drive Temporal-Difference Learning

Wiebke Potjans, Markus Diesmann, Abigail Morrison

Epistasis in a Model of Molecular Signal Transduction

Alain Pumir, Boris Shraiman

Transcriptional Regulation: Effects of Promoter Proximal Pausing on Speed, Synchrony and Reliability

Alistair N. Boettiger, Peter L. Ralph, Steven N. Evans

Emergence of Switch-Like Behavior in a Large Family of Simple Biochemical Networks

Dan Siegal-Gaskins, Maria Katherine Mejia-Guerra, Gregory D. Smith, Erich Grotewold

Quantitative Epistasis Analysis and Pathway Inference from Genetic Interaction Data

Hilary Phenix, Katy Morin, Cory Batenchuk, Jacob Parker, Vida Abedi, Liu Yang, Lioudmila Tepliakova, Theodore J. Perkins, Mads Kærn

Theoretical Model for Cellular Shapes Driven by Protrusive and Adhesive Forces

Doron Kabaso, Roie Shlomovitz, Kathrin Schloen, Theresia Stradal, Nir S. Gov

Simulating the Mammalian Blastocyst - Molecular and Mechanical Interactions Pattern the Embryo

Pawel Krupinski, Vijay Chickarmane, Carsten Peterson

Feedback Control Architecture and the Bacterial Chemotaxis Network

Abdullah Hamadeh, Mark A. J. Roberts, Elias August, Patrick E. McSharry, Philip K. Maini, Judith P. Armitage, Antonis Papachristodoulou

Detecting Network Communities: An Application to Phylogenetic Analysis

Roberto F. S. Andrade, Ivan C. Rocha-Neto, Leonardo B. L. Santos, Charles N. de Santana, Marcelo V. C. Diniz, Thierry Petit Lobão, Aristóteles Goés-Neto, Suani T. R. Pinho, Charbel N. El-Hani

Modeling Evolutionary Dynamics of Epigenetic Mutations in Hierarchically Organized Tumors

Andrea Sottoriva, Louis Vermeulen, Simon Tavaré

Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations

Jonathan Perreault, Zasha Weinberg, Adam Roth, Olivia Popescu, Pascal Chartrand, Gerardo Ferbeyre, Ronald R. Breaker

How Molecular Motors Are Arranged on a Cargo Is Important for Vesicular Transport

Robert P. Erickson, Zhiyuan Jia, Steven P. Gross, Clare C. Yu

Gene Expression in the Rodent Brain is Associated with Its Regional Connectivity

Lior Wolf, Chen Goldberg, Nathan Manor, Roded Sharan, Eytan Ruppin

Temporal Encoding in a Nervous System

Zane N. Aldworth, Alexander G. Dimitrov, Graham I. Cummins, Tomáš Gedeon, John P. Miller

Combinations of Protein-Chemical Complex Structures Reveal New Targets for Established Drugs

Olga V. Kalinina, Oliver Wichmann, Gordana Apic, Robert B. Russell

Distributions of Transposable Elements Reveal Hazardous Zones in Mammalian Introns

Ying Zhang, Mark T. Romanish, Dixie L. Mager