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Table of Contents: October 2009

COVER

Cloud topology in the yeast protein interaction network.

Image Credit: Hiroaki Kitano and Takeshi Hase
Issue Image

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).

Message from ISCB

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

Computational Resources in Infectious Disease: Limitations and Challenges

Eva C. Berglund, Björn Nystedt, Siv G. E. Andersson

Discovering the Phylodynamics of RNA Viruses

Edward C. Holmes, Bryan T. Grenfell

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

Wesley C. Van Voorhis, Wim G. J. Hol, Peter J. Myler, Lance J. Stewart

Research Articles

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

Ibrahim Barıs, Aytug Tuncel, Natali Ozber, Ozlem Keskin, Ibrahim Halil Kavakli

Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots

Mateusz Sikora, Joanna I. Sułkowska, Marek Cieplak

Gene Circuit Analysis of the Terminal Gap Gene huckebein

Maksat Ashyraliyev, Ken Siggens, Hilde Janssens, Joke Blom, Michael Akam, Johannes Jaeger

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

Steps in the Bacterial Flagellar Motor

Thierry Mora, Howard Yu, Yoshiyuki Sowa, Ned S. Wingreen

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

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

Structure-Based Predictive Models for Allosteric Hot Spots

Omar N. A. Demerdash, Michael D. Daily, Julie C. Mitchell

The Modular Organization of Protein Interactions in Escherichia coli

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