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Table of Contents: July 2007

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Dynamic, biped walking is a difficult motor coordination problem for robots. "RunBot," shown here, contains two joint motors and two hip motors and an upper-body component. These actuators are dynamically controlled by a neural network that can adapt via simulated synaptic plasticity to novel situations, such as a change in the terrain. This way, RunBot's walking pattern looks rather human-like (see Video S2 5.1 MPG), and the little machine successfully tackles difficult walking situations (see Manoonpong et al, e134).

Education

Introduction to Computational Proteomics

Jacques Colinge, Keiryn L Bennett

Review

Quantitative Analysis of Cell Nucleus Organisation

Carol Shiels, Niall M Adams, Suhail A Islam, David A Stephens, Paul S Freemont

Research Articles

Detecting Emerging Transmissibility of Avian Influenza Virus in Human Households

Michiel van Boven, Marion Koopmans, Mirna Du Ry van Beest Holle, Adam Meijer, Don Klinkenberg, Christl A Donnelly, Hans (J. A. P.) Heesterbeek

Chemotaxis Receptor Complexes: From Signaling to Assembly

Robert G Endres, Joseph J Falke, Ned S Wingreen

Natively Unstructured Loops Differ from Other Loops

Avner Schlessinger, Jinfeng Liu, Burkhard Rost

Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster

Anastasia A Samsonova, Mahesan Niranjan, Steven Russell, Alvis Brazma

Sarcomere Lattice Geometry Influences Cooperative Myosin Binding in Muscle

Bertrand C. W Tanner, Thomas L Daniel, Michael Regnier

Efficiency, Selectivity, and Robustness of Nucleocytoplasmic Transport

Anton Zilman, Stefano Di Talia, Brian T Chait, Michael P Rout, Marcelo O Magnasco

Optimal Timing and Duration of Induction Therapy for HIV-1 Infection

Marcel E Curlin, Shyamala Iyer, John E Mittler

Adaptive, Fast Walking in a Biped Robot under Neuronal Control and Learning

Poramate Manoonpong, Tao Geng, Tomas Kulvicius, Bernd Porr, Florentin Wörgötter

Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation

Joti Giordano, Yongchao Ge, Yevgeniy Gelfand, György Abrusán, Gary Benson, Peter E Warburton

A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds

Konstantin B Zeldovich, Peiqiu Chen, Boris E Shakhnovich, Eugene I Shakhnovich

Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution

Fereydoun Hormozdiari, Petra Berenbrink, Nataša Pržulj, S. Cenk Sahinalp

A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes

Zizhen Yao, Jeffrey Barrick, Zasha Weinberg, Shane Neph, Ronald Breaker, Martin Tompa, Walter L Ruzzo

Sensitivity Analysis of Intracellular Signaling Pathway Kinetics Predicts Targets for Stem Cell Fate Control

Alborz Mahdavi, Ryan E Davey, Patrick Bhola, Ting Yin, Peter W Zandstra

Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes

Patricia A Ryan, Brian W Kirk, Chad W Euler, Raymond Schuch, Vincent A Fischetti

Key Role of Local Regulation in Chemosensing Revealed by a New Molecular Interaction-Based Modeling Method

Martin Meier-Schellersheim, Xuehua Xu, Bastian Angermann, Eric J Kunkel, Tian Jin, Ronald N Germain

Corrections