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The precise identification of the HIV-1 envelope glycoprotein (Env) responsible for productive clinical infection could be instrumental in elucidating the molecular basis of HIV-1 transmission and in designing effective vaccines. Here, we developed a mathematical model of random viral evolution and, together with phylogenetic tree construction, used it to(More)
Using a large set of orthologous human and mouse gene pairs, we have characterized genes that have been retained in duplicate in human over timescales comparable to the time of speciation of human and mouse. Orthologous gene pairs for which a paralogous gene has been present for much or all of the time since speciation show an increased rate of(More)
BACKGROUND Nonnegative Matrix Factorization (NMF) is an unsupervised learning technique that has been applied successfully in several fields, including signal processing, face recognition and text mining. Recent applications of NMF in bioinformatics have demonstrated its ability to extract meaningful information from high-dimensional data such as gene(More)
Multiple ancient genome duplications in Arabidopsis thaliana provide unique opportunities to assess factors that influence the fates of duplicated genes. We have found that genes retained in duplicate following one round of genome duplication are significantly more likely to be retained in duplicate again after a subsequent genome duplication. Genes(More)
MOTIVATION Accurate detection of positive Darwinian selection can provide important insights to researchers investigating the evolution of pathogens. However, many pathogens (particularly viruses) undergo frequent recombination and the phylogenetic methods commonly applied to detect positive selection have been shown to give misleading results when applied(More)
Probabilistic models of sequence evolution are in widespread use in phylogenetics and molecular sequence evolution. These models have become increasingly sophisticated and combined with statistical model comparison techniques have helped to shed light on how genes and proteins evolve. Models of codon evolution have been particularly useful, because, in(More)
The RV144 vaccine trial in Thailand demonstrated that an HIV vaccine could prevent infection in humans and highlights the importance of understanding protective immunity against HIV. We used a nonhuman primate model to define immune and genetic mechanisms of protection against mucosal infection by the simian immunodeficiency virus (SIV). A plasmid DNA(More)
The Saccharomyces cerevisiae genome sequence, augmented by new data on gene expression and function, continues to yield new findings about eukaryote genome evolution. Analysis of the duplicate gene pairs formed by whole-genome duplication indicates that selection for increased levels of gene expression was a significant factor determining which genes were(More)
Past analyses of the genome of the yeast Saccharomyces cerevisiae have revealed substantial regional variation in G+C content. Important questions remain, though, as to the origin, nature, significance, and generality of this variation. We conducted an extensive analysis of the yeast genome to try to answer these questions. Our results indicate that open(More)
One of the most important genetic factors known to affect the rate of disease progression in HIV-infected individuals is the genotype at the Class I Human Leukocyte Antigen (HLA) locus, which determines the HIV peptides targeted by cytotoxic T-lymphocytes (CTLs). Individuals with HLA-B*57 or B*5801 alleles, for example, target functionally important parts(More)