Table of Contents: June 2009

Cell division is a key mechanism in morphogenesis, yet the relationship between local cell division and global tissue architecture (e.g., the distribution of cell shapes) remains poorly understood. In this study (Nagpal et al., doi:10.1371/journal.pcbi.1000412), the authors present a computational framework for studying the topological networks that are created by proliferative cell division (image). This framework reveals how different cell division mechanisms create strikingly different "signature" tissue statistics, which can be used to infer necessary division properties. The model also suggests that while nearly identical cell shape distributions have been observed in proliferating plant and fruitfly epithelia, they achieve this by distinct cell division mechanisms.

Image Credit: Ankit Patel, Radhika Nagpal (Harvard University).


The Need for Centralization of Computational Biology Resources

Fran Lewitter, Michael Rebhan, Brent Richter, David Sexton

Ten Simple Rules for Choosing between Industry and Academia

David B. Searls


Establishing a Successful Bioinformatics Core Facility Team

Fran Lewitter, Michael Rebhan

Managing and Analyzing Next-Generation Sequence Data

Brent G. Richter, David P. Sexton

Research Articles

Exploring the Free Energy Landscape: From Dynamics to Networks and Back

Diego Prada-Gracia, Jesús Gómez-Gardeñes, Pablo Echenique, Fernando Falo

Quantitative Analysis of Mechanisms That Govern Red Blood Cell Age Structure and Dynamics during Anaemia

Nicholas J. Savill, William Chadwick, Sarah E. Reece

Optimal Control Predicts Human Performance on Objects with Internal Degrees of Freedom

Arne J. Nagengast, Daniel A. Braun, Daniel M. Wolpert

A Probabilistic Model of RNA Conformational Space

Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V. Mardia, Jesper Ferkinghoff-Borg, Thomas Hamelryck

Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans

Maria D. Chikina, Curtis Huttenhower, Coleen T. Murphy, Olga G. Troyanskaya

Taking the Lag out of Jet Lag through Model-Based Schedule Design

Dennis A. Dean , II, Daniel B. Forger, Elizabeth B. Klerman

The Dynamics of T-Cell Receptor Repertoire Diversity Following Thymus Transplantation for DiGeorge Anomaly

Stanca M. Ciupe, Blythe H. Devlin, M. Louise Markert, Thomas B. Kepler

Active Dendrites Enhance Neuronal Dynamic Range

Leonardo L. Gollo, Osame Kinouchi, Mauro Copelli

Directed Mammalian Gene Regulatory Networks Using Expression and Comparative Genomic Hybridization Microarray Data from Radiation Hybrids

Sangtae Ahn, Richard T. Wang, Christopher C. Park, Andy Lin, Richard M. Leahy, Kenneth Lange, Desmond J. Smith

Modeling the Impact of Lesions in the Human Brain

Jeffrey Alstott, Michael Breakspear, Patric Hagmann, Leila Cammoun, Olaf Sporns

Spatio-Temporal Dynamics of Yeast Mitochondrial Biogenesis: Transcriptional and Post-Transcriptional mRNA Oscillatory Modules

Gaëlle Lelandais, Yann Saint-Georges, Colette Geneix, Liza Al-Shikhley, Geneviève Dujardin, Claude Jacq

Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation

Bas Teusink, Anne Wiersma, Leo Jacobs, Richard A. Notebaart, Eddy J. Smid

Modeling and Inferring Cleavage Patterns in Proliferating Epithelia

Ankit B. Patel, William T. Gibson, Matthew C. Gibson, Radhika Nagpal

Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate

Yu Xia, Eric A. Franzosa, Mark B. Gerstein

Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening

Nobuyoshi Nagamine, Takayuki Shirakawa, Yusuke Minato, Kentaro Torii, Hiroki Kobayashi, Masaya Imoto, Yasubumi Sakakibara

The Effect of Ongoing Exposure Dynamics in Dose Response Relationships

Josep M. Pujol, Joseph E. Eisenberg, Charles N. Haas, James S. Koopman

The Voice of Bats: How Greater Mouse-eared Bats Recognize Individuals Based on Their Echolocation Calls

Yossi Yovel, Mariana Laura Melcon, Matthias O. Franz, Annette Denzinger, Hans-Ulrich Schnitzler

SpaK/SpaR Two-component System Characterized by a Structure-driven Domain-fusion Method and in Vitro Phosphorylation Studies

Anu Chakicherla, Carol L. Ecale Zhou, Martha Ligon Dang, Virginia Rodriguez, J. Norman Hansen, Adam Zemla

Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System

Erwin P. Gianchandani, Andrew R. Joyce, Bernhard Ø. Palsson, Jason A. Papin

FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling

Michal Brylinski, Jeffrey Skolnick