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).
Education
Analyzing ChIP-chip Data Using Bioconductor
PLOS Computational Biology: published November 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000227
Review
Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities
PLOS Computational Biology: published November 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000176
Research Articles
Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments
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A Model of Brain Circulation and Metabolism: NIRS Signal Changes during Physiological Challenges
PLOS Computational Biology: published November 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000212
Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks
PLOS Computational Biology: published November 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000213
Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes
PLOS Computational Biology: published November 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000214
Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
PLOS Computational Biology: published November 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000216
Inferring Pathway Activity toward Precise Disease Classification
PLOS Computational Biology: published November 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000217
Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins
PLOS Computational Biology: published November 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000218
Emergence of Functional Hierarchy in a Multiple Timescale Neural Network Model: A Humanoid Robot Experiment
PLOS Computational Biology: published November 7, 2008 | https://doi.org/10.1371/journal.pcbi.1000220
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A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates
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Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag
PLOS Computational Biology: published November 21, 2008 | https://doi.org/10.1371/journal.pcbi.1000225
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PLOS Computational Biology: published November 21, 2008 | https://doi.org/10.1371/journal.pcbi.1000226
Order-Based Representation in Random Networks of Cortical Neurons
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Behavioral Sequence Analysis Reveals a Novel Role for ß2* Nicotinic Receptors in Exploration
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Structural and Thermodynamic Approach to Peptide Immunogenicity
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Optimal Learning Rules for Discrete Synapses
PLOS Computational Biology: published November 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000230
Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence
PLOS Computational Biology: published November 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000232
PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution
PLOS Computational Biology: published November 28, 2008 | https://doi.org/10.1371/journal.pcbi.1000233
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Multistable Decision Switches for Flexible Control of Epigenetic Differentiation
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Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data
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