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Table of Contents: November 2008

COVER

Phylogenetic dependency network for HIV adaptation.

Image Credit: Jonathan Carlson and David Heckerman (Microsoft Research).
Issue Image

A summary of the two types of HIV adaptations predicted by a new statistical model of HIV evolution is shown. The two types of adaptation are to (i) immune system molecules (e.g., B57) shown on the outside and (ii) other positions in HIV. The dense network implies that the same adaptations consistently arise in certain environments and may point to weak spots in the viral genome that will be important for vaccine and drug design (see Carlson et al., doi:10.1371/journal.pcbi.1000225).

Education

Analyzing ChIP-chip Data Using Bioconductor

Joern Toedling, Wolfgang Huber

Review

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

Marcel E. Dinger, Ken C. Pang, Tim R. Mercer, John S. Mattick

Research Articles

Optimal Learning Rules for Discrete Synapses

Adam B. Barrett, M. C. W. van Rossum

PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution

Jonathan M. Guberman, Allison Fay, Jonathan Dworkin, Ned S. Wingreen, Zemer Gitai

Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag

Jonathan M. Carlson, Zabrina L. Brumme, Christine M. Rousseau, Chanson J. Brumme, Philippa Matthews, Carl Kadie, James I. Mullins, Bruce D. Walker, P. Richard Harrigan, Philip J. R. Goulder, David Heckerman

Order-Based Representation in Random Networks of Cortical Neurons

Goded Shahaf, Danny Eytan, Asaf Gal, Einat Kermany, Vladimir Lyakhov, Christoph Zrenner, Shimon Marom

Behavioral Sequence Analysis Reveals a Novel Role for ß2* Nicotinic Receptors in Exploration

Nicolas Maubourguet, Annick Lesne, Jean-Pierre Changeux, Uwe Maskos, Philippe Faure

Structural and Thermodynamic Approach to Peptide Immunogenicity

Carlos J. Camacho, Yasuhiro Katsumata, Dana P. Ascherman

A Hierarchy of Time-Scales and the Brain

Stefan J. Kiebel, Jean Daunizeau, Karl J. Friston

A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates

Stefan Auer, Filip Meersman, Christopher M. Dobson, Michele Vendruscolo

Quantification of Local Morphodynamics and Local GTPase Activity by Edge Evolution Tracking

Yuki Tsukada, Kazuhiro Aoki, Takeshi Nakamura, Yuichi Sakumura, Michiyuki Matsuda, Shin Ishii

A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast

Anshul Kundaje, Xiantong Xin, Changgui Lan, Steve Lianoglou, Mei Zhou, Li Zhang, Christina Leslie

A Model of Brain Circulation and Metabolism: NIRS Signal Changes during Physiological Challenges

Murad Banaji, Alfred Mallet, Clare E. Elwell, Peter Nicholls, Chris E. Cooper

Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks

Sheila M. Reynolds, Lukas Käll, Michael E. Riffle, Jeff A. Bilmes, William Stafford Noble

Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes

Osnat Penn, Adi Stern, Nimrod D. Rubinstein, Julien Dutheil, Eran Bacharach, Nicolas Galtier, Tal Pupko

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

Yair Field, Noam Kaplan, Yvonne Fondufe-Mittendorf, Irene K. Moore, Eilon Sharon, Yaniv Lubling, Jonathan Widom, Eran Segal

Inferring Pathway Activity toward Precise Disease Classification

Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee

Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins

Mark Yandell, Barry Moore, Fidel Salas, Chris Mungall, Andrew MacBride, Charles White, Martin G. Reese