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Table of Contents: October 2009

This figure represents the protein-protein interaction network topology of budding yeast. The outermost circle shows proteins with smaller numbers of interactions (gray dots) and proteins that interact with these are located on inner circles. Most large hubs are placed here (blue dots). Inner circles are dominated by medium size hubs (red dots) that are extensively connected to each other. This topology is mathematically similar to the router-level topology of the internet and represents networks according to highly optimized tolerance (see Hase et al., doi:10.1371/journal.pcbi.1000550).

Image Credit: Hiroaki Kitano and Takeshi Hase

Messages from ISCB

Getting Started in Gene Expression Microarray Analysis

Donna K. Slonim, Itai Yanai

Perspectives

Computational Biology in Colombia

Silvia Restrepo, Andrés Pinzón, Luis Miguel Rodríguez-R, Roberto Sierra, Alejandro Grajales, Adriana Bernal, Emiliano Barreto, Pedro Moreno, Maria Mercedes Zambrano, Marco Cristancho, Andrés González, Harold Castro

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The Role of Medical Structural Genomics in Discovering New Drugs for Infectious Diseases

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Research Articles

Investigation of the Interaction between the Large and Small Subunits of Potato ADP-Glucose Pyrophosphorylase

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Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots

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Gene Circuit Analysis of the Terminal Gap Gene huckebein

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Tipping the Balance: Robustness of Tip Cell Selection, Migration and Fusion in Angiogenesis

Katie Bentley, Giovanni Mariggi, Holger Gerhardt, Paul A. Bates

Structure of Protein Interaction Networks and Their Implications on Drug Design

Takeshi Hase, Hiroshi Tanaka, Yasuhiro Suzuki, So Nakagawa, Hiroaki Kitano

Specific Entrainment of Mitral Cells during Gamma Oscillation in the Rat Olfactory Bulb

François O. David, Etienne Hugues, Tristan Cenier, Nicolas Fourcaud-Trocmé, Nathalie Buonviso

Intrinsic Structural Disorder Confers Cellular Viability on Oncogenic Fusion Proteins

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Steps in the Bacterial Flagellar Motor

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An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations

Holly J. Atkinson, Patricia C. Babbitt

Invariant Distribution of Promoter Activities in Escherichia coli

Alon Zaslaver, Shai Kaplan, Anat Bren, Adrian Jinich, Avi Mayo, Erez Dekel, Uri Alon, Shalev Itzkovitz

‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators

Marc Hafner, Heinz Koeppl, Martin Hasler, Andreas Wagner

Antigenic Diversity, Transmission Mechanisms, and the Evolution of Pathogens

Alexander Lange, Neil M. Ferguson

Subbarrel Patterns in Somatosensory Cortical Barrels Can Emerge from Local Dynamic Instabilities

Bard Ermentrout, Daniel J. Simons, Peter W. Land

Grasping Objects with Environmentally Induced Position Uncertainty

Vassilios N. Christopoulos, Paul R. Schrater

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, Makoto Taiji

Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

Yizhi Cai, Matthew W. Lux, Laura Adam, Jean Peccoud

Structure-Based Predictive Models for Allosteric Hot Spots

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Towards a Mathematical Theory of Cortical Micro-circuits

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The Modular Organization of Protein Interactions in Escherichia coli

José M. Peregrín-Alvarez, Xuejian Xiong, Chong Su, John Parkinson