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Table of Contents: February 2011

COVER

Navigating the genetic landscape.

Image Credit: Magali Michaut, University of Toronto
Issue Image

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).

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Perspectives

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

Research Articles

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

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

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

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

Loss of Genetic Redundancy in Reductive Genome Evolution

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

Automatic Design of Digital Synthetic Gene Circuits

Mario A. Marchisio, Jörg Stelling

Molecular Dynamics Simulations of Forced Unbending of Integrin αVβ3

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

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

A Computational Clonal Analysis of the Developing Mouse Limb Bud

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

Mitigation Strategies for Pandemic Influenza A: Balancing Conflicting Policy Objectives

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

A Hybrid Model of Mammalian Cell Cycle Regulation

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

Structural Properties of the Caenorhabditis elegans Neuronal Network

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

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

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

A Mathematical Framework for Protein Structure Comparison

Wei Liu, Anuj Srivastava, Jinfeng Zhang