Niko Beerenwinkel, Colin N Dewey, Kevin M Woods
inference of recombination with an application
Parametric inference of recombination in HIV genomes (2008)
Niko Beerenwinkel, Colin N. Dewey, Kevin M. Woods
Recombination is an important event in the evolution of HIV. It affects the global spread of the pandemic as well as evolutionary escape from host immune response and from drug therapy within single...
Begun, David J, Holloway, Alisha K, Stevens, Kristian, Hillier, Ladeana W, Poh, Yu-Ping, Hahn, Matthew W, ...
The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between...
David J. Begun, Alisha K. Holloway, Kristian Stevens, LaDeana W. Hillier, Yu-Ping Poh, Matthew W. Hahn, ...
The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between...
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures (2007)
Lin, Michael F, Kheradpour, Pouya, Pedersen, Jakob S, Parts, Leopold, Carlson, Joseph W, ...
Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12...
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
Dewey, Colin N, Rogozin, Igor B, Koonin, Eugene V
Abstract Background The signals that determine the specificity and efficiency of splicing are multiple and complex, and are not fully understood. Among other factors, the relative contributions of...
Parametric Alignment of Drosophila Genomes (2006)
Colin N. Dewey, Peter M. Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter
The classic algorithms of Needleman–Wunsch and Smith–Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). To process large genomes that have undergone...
Evolution at the nucleotide level: the problem of multiple whole-genome alignment (2006)
Dewey, Colin N., Pachter, Lior
With the genome sequences of numerous species at hand, we have the opportunity to discover how evolution has acted at each and every nucleotide in our genome. To this end, we must identify sets of...
Parametric inference of recombination in HIV genomes (2005)
Beerenwinkel, Niko, Dewey, Colin N., Woods, Kevin M.
Recombination is an important event in the evolution of HIV. It affects the global spread of the pandemic as well as evolutionary escape from host immune response and from drug therapy within single...
Parametric Alignment of Drosophila Genomes
Dewey, Colin N, Huggins, Peter M, Woods, Kevin, Sturmfels, Bernd, Pachter, Lior
The classic algorithms of Needleman–Wunsch and Smith–Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). To process large genomes that have undergone...
Parametric Alignment of Drosophila Genomes
Dewey, Colin N, Huggins, Peter M, Woods, Kevin, Sturmfels, Bernd, Pachter, Lior
The classic algorithms of Needleman–Wunsch and Smith–Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). To process large genomes that have undergone...
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
Begun, David J, Holloway, Alisha K, Stevens, Kristian, Hillier, LaDeana W, Poh, Yu-Ping, Hahn, Matthew W, ...
The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between...
Fine-Scale Phylogenetic Discordance across the House Mouse Genome
White, Michael A., Ané, Cécile, Dewey, Colin N., Larget, Bret R., Payseur, Bret A.
Population genetic theory predicts discordance in the true phylogeny of different genomic regions when studying recently diverged species. Despite this expectation, genome-wide discordance in young...