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).

Editorials

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

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000650

A Review of 2009 for PLoS Computational Biology

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

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000687

Education

How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens

Florian Markowetz

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000655

Perspective

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

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000673

Review

A Primer on Metagenomics

John C. Wooley, Adam Godzik, Iddo Friedberg

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000667

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

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000684

Computational Complementation: A Modelling Approach to Study Signalling Mechanisms during Legume Autoregulation of Nodulation

Liqi Han, Jim Hanan, Peter M. Gresshoff

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000685

Spatial Simulations of Myxobacterial Development

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

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000686

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

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000688

Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease

Neema L. Salimi, Bosco Ho, David A. Agard

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000689

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species

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

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000690

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

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

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000691

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

PLOS Computational Biology: published February 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000692

Amplification of Asynchronous Inhibition-Mediated Synchronization by Feedback in Recurrent Networks

Sashi Marella, Bard Ermentrout

PLOS Computational Biology: published February 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000679

Self versus Environment Motion in Postural Control

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

PLOS Computational Biology: published February 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000680

Identifying the Rules of Engagement Enabling Leukocyte Rolling, Activation, and Adhesion

Jonathan Tang, C. Anthony Hunt

PLOS Computational Biology: published February 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000681

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

PLOS Computational Biology: published February 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000682

A Bayesian Approach to Quantifying the Effects of Mass Poultry Vaccination upon the Spatial and Temporal Dynamics of H5N1 in Northern Vietnam

Patrick G. T. Walker, Simon Cauchemez, Raphaëlle Métras, Do Huu Dung, Dirk Pfeiffer, Azra C. Ghani

PLOS Computational Biology: published February 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000683

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

Takashi Nakano, Tomokazu Doi, Junichiro Yoshimoto, Kenji Doya

PLOS Computational Biology: published February 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000670

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

PLOS Computational Biology: published February 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000671

Conditions for the Evolution of Gene Clusters in Bacterial Genomes

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

PLOS Computational Biology: published February 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000672

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

Ester Vilaprinyo, Rui Alves, Albert Sorribas

PLOS Computational Biology: published February 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000674

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

PLOS Computational Biology: published February 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000675

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

PLOS Computational Biology: published February 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000662

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

PLOS Computational Biology: published February 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000663

A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes

Wanjun Gu, Tong Zhou, Claus O. Wilke

PLOS Computational Biology: published February 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000664

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

PLOS Computational Biology: published February 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000665

Explicit Kinetic Heterogeneity: Mathematical Models for Interpretation of Deuterium Labeling of Heterogeneous Cell Populations

Vitaly V. Ganusov, José A. M. Borghans, Rob J. De Boer

PLOS Computational Biology: published February 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000666

The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures

Fred P. Davis, Andrej Sali

PLOS Computational Biology: published February 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000668

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

PLOS Computational Biology: published February 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000669

Cover

Computational complementation.

Editorials

Education

Perspective

Review

Research Articles

Related Articles