Table of Contents

November 2008

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).

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


Analyzing ChIP-chip Data Using Bioconductor

Joern Toedling, Wolfgang Huber


Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

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

Research Articles

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

Hierarchical Models in the Brain

Karl Friston

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A Hierarchy of Time-Scales and the Brain

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

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

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

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

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

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Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data

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