Table of Contents: February 2010

Autoregulation of nodulation (AON) is a long-distance, shoot-root signalling system for regulating nodule formation in legume plants. This visualisation, taken from a computational complementation experiment, demonstrates the possible allocation of an unidentified signal for inhibition of nodulation in soybean root. In this approach, an empirical model of a loss-of-function (non-AON) mutant is complemented with hypothetical AON mechanisms. If the resulting nodulation phenotype matches the wild-type plant, the hypotheses would be supported as reasonable. The first application of computational complementation predicted that soybean cotyledons participate in AON, which was subsequently confirmed by a real-plant experiment (see Han et al., doi:10.1371/journal.pcbi.1000685).

Image Credit: Liqi Han (University of Queensland).


Ten Simple Rules for Organizing a Virtual Conference—Anywhere

Nelson N. Gichora, Segun A. Fatumo, Mtakai V. Ngara, Noura Chelbat, Kavisha Ramdayal, Kenneth B. Opap, Geoffrey H. Siwo, Marion O. Adebiyi, Amina El Gonnouni, Denis Zofou, Amal A. M. Maurady, Ezekiel F. Adebiyi, Etienne P. de Villiers, Daniel K. Masiga, Jeffrey W. Bizzaro, Prashanth Suravajhala, Sheila C. Ommeh, Winston Hide

A Review of 2009 for PLoS Computational Biology

Rosemary Dickin, Cecy Marden, Catherine Nancarrow, Philip E. Bourne


Will Widgets and Semantic Tagging Change Computational Biology?

Philip E. Bourne, Bojan Beran, Chunxiao Bi, Wolfgang Bluhm, Roland Dunbrack, Andreas Prlić, Greg Quinn, Peter Rose, Raship Shah, Wendy Tao, Brian Weitzner, Ben Yukich


A Primer on Metagenomics

John C. Wooley, Adam Godzik, Iddo Friedberg

Research Articles

Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture

Ju Han, Hang Chang, Orsi Giricz, Genee Y. Lee, Frederick L. Baehner, Joe W. Gray, Mina J. Bissell, Paraic A. Kenny, Bahram Parvin

Spatial Simulations of Myxobacterial Development

Antony B. Holmes, Sara Kalvala, David E. Whitworth

Stochastic Model of Integrin-Mediated Signaling and Adhesion Dynamics at the Leading Edges of Migrating Cells

Murat Cirit, Matej Krajcovic, Colin K. Choi, Erik S. Welf, Alan F. Horwitz, Jason M. Haugh

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species

Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Uri Gophna, Roded Sharan, Eytan Ruppin

Temporal Sensitivity of Protein Kinase A Activation in Late-Phase Long Term Potentiation

MyungSook Kim, Ted Huang, Ted Abel, Kim T. Blackwell

Interpreting Metabolomic Profiles using Unbiased Pathway Models

Rahul C. Deo, Luke Hunter, Gregory D. Lewis, Guillaume Pare, Ramachandran S. Vasan, Daniel Chasman, Thomas J. Wang, Robert E. Gerszten, Frederick P. Roth

Self versus Environment Motion in Postural Control

Kalpana Dokka, Robert V. Kenyon, Emily A. Keshner, Konrad P. Kording

Numerical Modelling Of The V-J Combinations Of The T Cell Receptor TRA/TRD Locus

Florence Thuderoz, Maria-Ana Simonet, Olivier Hansen, Nicolas Pasqual, Aurélie Dariz, Thierry Pascal Baum, Vivien Hierle, Jacques Demongeot, Patrice Noël Marche, Evelyne Jouvin-Marche

A Kinetic Model of Dopamine- and Calcium-Dependent Striatal Synaptic Plasticity

Takashi Nakano, Tomokazu Doi, Junichiro Yoshimoto, Kenji Doya

Characterizing Dynamic Changes in the Human Blood Transcriptional Network

Jun Zhu, Yanqing Chen, Amy S. Leonardson, Kai Wang, John R. Lamb, Valur Emilsson, Eric E. Schadt

Conditions for the Evolution of Gene Clusters in Bacterial Genomes

Sara Ballouz, Andrew R. Francis, Ruiting Lan, Mark M. Tanaka

Minimization of Biosynthetic Costs in Adaptive Gene Expression Responses of Yeast to Environmental Changes

Ester Vilaprinyo, Rui Alves, Albert Sorribas

A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II

Shirley Pepke, Tamara Kinzer-Ursem, Stefan Mihalas, Mary B. Kennedy

Adaptable Functionality of Transcriptional Feedback in Bacterial Two-Component Systems

J. Christian J. Ray, Oleg A. Igoshin

Design of a Trichromatic Cone Array

Patrick Garrigan, Charles P. Ratliff, Jennifer M. Klein, Peter Sterling, David H. Brainard, Vijay Balasubramanian

Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization

Ivan Junier, Olivier Martin, François Képès

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets

Silpa Suthram, Joel T. Dudley, Annie P. Chiang, Rong Chen, Trevor J. Hastie, Atul J. Butte

In Silico Analysis of the Apolipoprotein E and the Amyloid β Peptide Interaction: Misfolding Induced by Frustration of the Salt Bridge Network

Jinghui Luo, Jean-Didier Maréchal, Sebastian Wärmländer, Astrid Gräslund, Alex Perálvarez-Marín

Predicted Functions of MdmX in Fine-Tuning the Response of p53 to DNA Damage

Sohyoung Kim, Mirit I. Aladjem, Geoffrey B. McFadden, Kurt W. Kohn

A Variant of TNFR2-Fc Fusion Protein Exhibits Improved Efficacy in Treating Experimental Rheumatoid Arthritis

Tong Yang, Zheng Wang, Fang Wu, Jingwei Tan, Yijun Shen, Erguang Li, Jingzhi Dai, Ronghai Shen, Gang Li, Jinsong Wu, Luochun Wang, Haibo Wang, Yanjun Liu