Table of Contents

July 2007

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).


Introduction to Computational Proteomics

Jacques Colinge, Keiryn L Bennett


Quantitative Analysis of Cell Nucleus Organisation

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

Research Articles

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

Sarcomere Lattice Geometry Influences Cooperative Myosin Binding in Muscle

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

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

Protein–Protein Interaction Hotspots Carved into Sequences

Yanay Ofran, Burkhard Rost

Evolution of Function in the “Two Dinucleotide Binding Domains” Flavoproteins

Sunil Ojha, Elaine C Meng, Patricia C Babbitt

Efficiency, Selectivity, and Robustness of Nucleocytoplasmic Transport

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

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

Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network

Reut Shalgi, Daniel Lieber, Moshe Oren, Yitzhak Pilpel

Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes

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

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

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