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Table of Contents

February 2011

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Navigating the genetic landscape.

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Small-scale genetic interactions have been used for decades to unravel biological pathways. In recent years, experimental techniques have been developed to map them at the genome level, providing large-scale genetic interaction networks. In particular, in budding yeast the genetic network mapped by Synthetic Genetic Array was revealed as both a powerful tool to identify functional modules in the cell and a tremendous resource ready for more exploration. This image shows a view of this genetic interaction network visualized with BioLayoutExpress3D. Patterns in the genetic network can help understand the organization of biological processes (see Michaut, et al. doi:10.1371/journal.pcbi.1001092).

Image Credit: Magali Michaut, University of Toronto

Message from ISCB

ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature

Richard H. Lathrop, Burkhard Rost, ISCB Membership, ISCB Executive Committee, ISCB Board of Directors, ISCB Public Affairs Committee

PLOS Computational Biology: published February 24, 2011 | https://doi.org/10.1371/journal.pcbi.1002014

Perspectives

Application of Biomarkers in Cancer Risk Management: Evaluation from Stochastic Clonal Evolutionary and Dynamic System Optimization Points of View

Xiaohong Li, Patricia L. Blount, Thomas L. Vaughan, Brian J. Reid

PLOS Computational Biology: published February 24, 2011 | https://doi.org/10.1371/journal.pcbi.1001087

Digital Atlasing and Standardization in the Mouse Brain

Michael Hawrylycz, Richard A. Baldock, Albert Burger, Tsutomu Hashikawa, G. Allan Johnson, Maryann Martone, Lydia Ng, Chris Lau, Stephen D. Larsen, Jonathan Nissanov, Luis Puelles, Seth Ruffins, Fons Verbeek, Ilya Zaslavsky, Jyl Boline

PLOS Computational Biology: published February 3, 2011 | https://doi.org/10.1371/journal.pcbi.1001065

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  1. Correction: Digital Atlasing and Standardization in the Mouse Brain

Research Articles

Power-Law Input-Output Transfer Functions Explain the Contrast-Response and Tuning Properties of Neurons in Visual Cortex

Erez Persi, David Hansel, Lionel Nowak, Pascal Barone, Carl van Vreeswijk

PLOS Computational Biology: published February 24, 2011 | https://doi.org/10.1371/journal.pcbi.1001078

Dynamically-Driven Inactivation of the Catalytic Machinery of the SARS 3C-Like Protease by the N214A Mutation on the Extra Domain

Jiahai Shi, Nanyu Han, Liangzhong Lim, Shixiong Lua, J. Sivaraman, Lushan Wang, Yuguang Mu, Jianxing Song

PLOS Computational Biology: published February 24, 2011 | https://doi.org/10.1371/journal.pcbi.1001084

Self-Organization of Muscle Cell Structure and Function

Anna Grosberg, Po-Ling Kuo, Chin-Lin Guo, Nicholas A. Geisse, Mark-Anthony Bray, William J. Adams, Sean P. Sheehy, Kevin Kit Parker

PLOS Computational Biology: published February 24, 2011 | https://doi.org/10.1371/journal.pcbi.1001088

Transition from Persistent to Anti-Persistent Correlations in Postural Sway Indicates Velocity-Based Control

Didier Delignières, Kjerstin Torre, Pierre-Louis Bernard

PLOS Computational Biology: published February 24, 2011 | https://doi.org/10.1371/journal.pcbi.1001089

Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations

Chikako Ragan, Michael Zuker, Mark A. Ragan

PLOS Computational Biology: published February 24, 2011 | https://doi.org/10.1371/journal.pcbi.1001090

Synaptic Plasticity and Connectivity Requirements to Produce Stimulus-Pair Specific Responses in Recurrent Networks of Spiking Neurons

Mark A. Bourjaily, Paul Miller

PLOS Computational Biology: published February 24, 2011 | https://doi.org/10.1371/journal.pcbi.1001091

Protein Complexes are Central in the Yeast Genetic Landscape

Magali Michaut, Anastasia Baryshnikova, Michael Costanzo, Chad L. Myers, Brenda J. Andrews, Charles Boone, Gary D. Bader

PLOS Computational Biology: published February 24, 2011 | https://doi.org/10.1371/journal.pcbi.1001092

First Principles Modeling of Nonlinear Incidence Rates in Seasonal Epidemics

José M. Ponciano, Marcos A. Capistrán

PLOS Computational Biology: published February 17, 2011 | https://doi.org/10.1371/journal.pcbi.1001079

Spike-Based Population Coding and Working Memory

Martin Boerlin, Sophie Denève

PLOS Computational Biology: published February 17, 2011 | https://doi.org/10.1371/journal.pcbi.1001080

Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics

Amber M. Smith, Frederick R. Adler, Julie L. McAuley, Ryan N. Gutenkunst, Ruy M. Ribeiro, Jonathan A. McCullers, Alan S. Perelson

PLOS Computational Biology: published February 17, 2011 | https://doi.org/10.1371/journal.pcbi.1001081

Loss of Genetic Redundancy in Reductive Genome Evolution

André G. Mendonça, Renato J. Alves, José B. Pereira-Leal

PLOS Computational Biology: published February 17, 2011 | https://doi.org/10.1371/journal.pcbi.1001082

Automatic Design of Digital Synthetic Gene Circuits

Mario A. Marchisio, Jörg Stelling

PLOS Computational Biology: published February 17, 2011 | https://doi.org/10.1371/journal.pcbi.1001083

A Dynamical Systems Model for Combinatorial Cancer Therapy Enhances Oncolytic Adenovirus Efficacy by MEK-Inhibition

Neda Bagheri, Marisa Shiina, Douglas A. Lauffenburger, W. Michael Korn

PLOS Computational Biology: published February 17, 2011 | https://doi.org/10.1371/journal.pcbi.1001085

Molecular Dynamics Simulations of Forced Unbending of Integrin αVβ3

Wei Chen, Jizhong Lou, Jen Hsin, Klaus Schulten, Stephen C. Harvey, Cheng Zhu

PLOS Computational Biology: published February 17, 2011 | https://doi.org/10.1371/journal.pcbi.1001086

De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference

Jens Keilwagen, Jan Grau, Ivan A. Paponov, Stefan Posch, Marc Strickert, Ivo Grosse

PLOS Computational Biology: published February 10, 2011 | https://doi.org/10.1371/journal.pcbi.1001070

Related Articles

  1. Correction: De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference

A Computational Clonal Analysis of the Developing Mouse Limb Bud

Luciano Marcon, Carlos G. Arqués, Miguel S. Torres, James Sharpe

PLOS Computational Biology: published February 10, 2011 | https://doi.org/10.1371/journal.pcbi.1001071

Mitigation Strategies for Pandemic Influenza A: Balancing Conflicting Policy Objectives

T. Déirdre Hollingsworth, Don Klinkenberg, Hans Heesterbeek, Roy M. Anderson

PLOS Computational Biology: published February 10, 2011 | https://doi.org/10.1371/journal.pcbi.1001076

A Hybrid Model of Mammalian Cell Cycle Regulation

Rajat Singhania, R. Michael Sramkoski, James W. Jacobberger, John J. Tyson

PLOS Computational Biology: published February 10, 2011 | https://doi.org/10.1371/journal.pcbi.1001077

Stochastic Theory of Early Viral Infection: Continuous versus Burst Production of Virions

John E. Pearson, Paul Krapivsky, Alan S. Perelson

PLOS Computational Biology: published February 3, 2011 | https://doi.org/10.1371/journal.pcbi.1001058

Structural Properties of the Caenorhabditis elegans Neuronal Network

Lav R. Varshney, Beth L. Chen, Eric Paniagua, David H. Hall, Dmitri B. Chklovskii

PLOS Computational Biology: published February 3, 2011 | https://doi.org/10.1371/journal.pcbi.1001066

Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation

David M. Holloway, Francisco J. P. Lopes, Luciano da Fontoura Costa, Bruno A. N. Travençolo, Nina Golyandina, Konstantin Usevich, Alexander V. Spirov

PLOS Computational Biology: published February 3, 2011 | https://doi.org/10.1371/journal.pcbi.1001069

Related Articles

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Ribavirin-Induced Anemia in Hepatitis C Virus Patients Undergoing Combination Therapy

Sheeja M. Krishnan, Narendra M. Dixit

PLOS Computational Biology: published February 3, 2011 | https://doi.org/10.1371/journal.pcbi.1001072

Pharmacodynamic Modeling of Anti-Cancer Activity of Tetraiodothyroacetic Acid in a Perfused Cell Culture System

Hung-Yun Lin, Cornelia B. Landersdorfer, David London, Ran Meng, Chang-Uk Lim, Cassie Lin, Sharon Lin, Heng-Yuan Tang, David Brown, Brian Van Scoy, Robert Kulawy, Lurdes Queimado, George L. Drusano, Arnold Louie, Faith B. Davis, Shaker A. Mousa, Paul J. Davis

PLOS Computational Biology: published February 3, 2011 | https://doi.org/10.1371/journal.pcbi.1001073

Accurate Quantification of Functional Analogy among Close Homologs

Maria D. Chikina, Olga G. Troyanskaya

PLOS Computational Biology: published February 3, 2011 | https://doi.org/10.1371/journal.pcbi.1001074

A Mathematical Framework for Protein Structure Comparison

Wei Liu, Anuj Srivastava, Jinfeng Zhang

PLOS Computational Biology: published February 3, 2011 | https://doi.org/10.1371/journal.pcbi.1001075

The Free Energy Landscape of Small Molecule Unbinding

Danzhi Huang, Amedeo Caflisch

PLOS Computational Biology: published February 3, 2011 | https://doi.org/10.1371/journal.pcbi.1002002