Neeraja M. Krishnan, Sameer Z. Raina, David D. Pollock
Substitution patterns among nucleotides are often assumed to be constant in phylogenetic analyses. Although variation in the average rate of substitution among sites is commonly accounted for,...
Todd A. Castoe*, Hyun-Min Kim, Wanjun Gu, Brice P. Noonan, Zhi J. Jiang, ...
Convergence can mislead phylogenetic inference by mimicking shared ancestry, but has been detected only rarely in molecular evolution. Here, we show that significant convergence occurred in snake and...
Jiang, Zhi J, Castoe, Todd A, Austin, Christopher C, Burbrink, Frank T, Herron, Matthew D, McGuire, Jimmy A, ...
Abstract Background The mitochondrial genomes of snakes are characterized by an overall evolutionary rate that appears to be one of the most accelerated among vertebrates. They also possess other...
Gentles, Andrew J., Wakefield, Matthew J., Kohany, Oleksiy, Gu, Wanjun, Batzer, Mark A., Pollock, David D., ...
The genome of the gray short-tailed opossum Monodelphis domestica is notable for its large size (∼3.6 Gb). We characterized nearly 500 families of interspersed repeats from the Monodelphis. They...
Regional Variation in the Density of Essential Genes in Mice (2007)
Kathryn E. Hentges, David D. Pollock, Bin Liu, Monica J. Justice
In most species, and particularly in vertebrates, the percentage of genes absolutely required for survival, the essential genes, has not been estimated. To obtain this estimation, we used the mouse...
Regional variation in the density of essential genes in mice (2007)
Kathryn Hentges, David D. Pollock, Bin Liu, Monica J Justice
In most species, and particularly in vertebrates, the percentage of genes absolutely required for survival, the essential genes, has not been estimated. To obtain this estimation, we used the mouse...
EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity (2006)
Nahum, Laila A, Reynolds, Matthew T, Wang, Zhengyuan O, Faith, Jeremiah J, Jonna, Rahul, Jiang, Zhi J, ...
Abstract Background Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and...
EGenBio : a data management system for evolutionary genomics and biodiversity (2006)
Nahum, Laila A., Reynolds, Matthew T., Wang, Zhengyuan O., Faith, Jeremiah J., Jonna, Rahul, Jiang, Zhi J., ...
From The Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society Baton Rouge, Louisiana. 2–4 March, 2006.
EGenBio : a data management system for evolutionary genomics and biodiversity (2006)
Nahum, Laila A., Reynolds, Matthew T., Wang, Zhengyuan O., Faith, Jeremiah J., Jonna, Rahul, Jiang, Zhi J., ...
From The Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society Baton Rouge, Louisiana. 2–4 March, 2006.
Assessing the Accuracy of Ancestral Protein Reconstruction Methods (2006)
Paul D. Williams, David D. Pollock, Benjamin P. Blackburne, Richard A. Goldstein
The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of...
Accessing the Accuracy of Ancestral Protein Reconstruction Methods (2006)
Paul D Williams, David D Pollock, Benjamine P Blackburne, Richard Goldstein
The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of...
Paul D. Williams, David D. Pollock, Richard A. Goldstein
It has been known for some time that many proteins are marginally stable. This has inspired several explanations. Having noted that the functionality of many enzymes is correlated with subunit...
Goldstein, Richard A., Pollock, David D.
The authors of a recent manuscript in “Nature” claim to have discovered “universal trends” of amino acid gain and loss in protein evolution. Here, we show that this universal trend can be...
Wheat, Christopher W., Watt, Ward B., Pollock, David D., Schulte, Patricia M.
Colias eurytheme butterflies display extensive allozyme polymorphism in the enzyme phosphoglucose isomerase (PGI). Earlier studies on biochemical and fitness effects of these genotypes found evidence...
Goldstein, Richard A., Pollock, David D.
The authors of a recent manuscript in Nature claim to have discovered ‘universal trends’ of amino acid gain and loss in protein evolution. Here, we show that this ‘universal trend’ can be...
Wheat, Christopher W., Watt, Ward B., Pollock, David D., Schulte, Patricia M.
Colias eurytheme butterflies display extensive allozyme polymorphism in the enzyme phosphoglucose isomerase (PGI). Earlier studies on biochemical and fitness effects of these genotypes found evidence...
Evolution of base-substitution gradients in primate mitochondrial genomes (2005)
Raina, Sameer Z., Faith, Jeremiah J., Disotell, Todd R., Seligmann, Hervé, Stewart, Caro-Beth, Pollock, David D.
Inferences of phylogenies and dates of divergence rely on accurate modeling of evolutionary processes; they may be confounded by variation in substitution rates among sites and changes in...
Wheat, Christopher W., Watt, Ward B., Pollock, David D., Schulte, Patricia M.
Colias eurytheme butterflies display extensive allozyme polymorphism in the enzyme phosphoglucose isomerase (PGI). Earlier studies on biochemical and fitness effects of these genotypes found evidence...
Krishnan, Neeraja M., Seligmann, Hervé, Stewart, Caro-Beth, Pollock, David D.
Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and...
Krishnan, Neeraja M., Seligmann, Hervé, Stewart, Caro-Beth, Pollock, David D.
Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and...
Krishnan, Neeraja M., Seligmann, Hervé, Stewart, Caro-Beth, Pollock, David D.
Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and...
Is Sparse Taxon Sampling a Problem for Phylogenetic Inference? (2003)
Hillis, David M., Pollock, David D., McGuire, Jimmy A., Zwickl, Derrick J.
Increased Taxon Sampling Is Advantageous for Phylogenetic Inference (2002)
Pollock, David D., Zwickl, Derrick J., McGuire, Jimmy A., Hillis, David M.
Evolution of functionality in lattice proteins (2001)
Paul D. Williams, David D. Pollock, Richard A. Goldstein
We study the evolution of protein functionality using a two-dimensional lattice model. The characteristics particular to evolution, such as population dynamics and early evolutionary trajectories,...
A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity (2000)
Pollock, David D., Eisen, Jonathan A., Doggett, Norman A., Cummings, Michael P.
Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic...
Pollock, David D., Bruno, William J.
Assessment of the evolutionary process is crucial for understanding the effect of protein structure and function on sequence evolution and for many other analyses in molecular evolution. Here, we...
Coevolving protein residues: maximum likelihood identification and relationship to structure (1999)
David D. Pollock, William R. Taylor, Nick Goldman
There has been a great deal of recent research on
The relationship of sleep-deprivation to cerebral hemisphericity and temporal orientation. (1984)
Thesis (M.S.)--Pennsylvania State University.
Analysis of among-site variation in substitution patterns
Krishnan, Neeraja M., Raina, Sameer Z., Pollock, David D.
Substitution patterns among nucleotides are often assumed to be constant in phylogenetic analyses. Although variation in the average rate of substitution among sites is commonly accounted for,...
Evolution of base-substitution gradients in primate mitochondrial genomes
Raina, Sameer Z., Faith, Jeremiah J., Disotell, Todd R., Seligmann, Hervé, Stewart, Caro-Beth, Pollock, David D.
Inferences of phylogenies and dates of divergence rely on accurate modeling of evolutionary processes; they may be confounded by variation in substitution rates among sites and changes in...
Assessing the Accuracy of Ancestral Protein Reconstruction Methods
Williams, Paul D, Pollock, David D, Blackburne, Benjamin P, Goldstein, Richard A
The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of...
Estimating the Degree of Saturation in Mutant Screens
Pollock, David D., Larkin, John C.
Large-scale screens for loss-of-function mutants have played a significant role in recent advances in developmental biology and other fields. In such mutant screens, it is desirable to estimate the...
Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes.
Faith, Jeremiah J, Pollock, David D
Protein-coding genes in mitochondrial genomes have varying degrees of asymmetric skew in base frequencies at the third codon position. The variation in skew among genes appears to be caused by...
EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity
Nahum, Laila A, Reynolds, Matthew T, Wang, Zhengyuan O, Faith, Jeremiah J, Jonna, Rahul, Jiang, Zhi J, ...
Analysis of among-site variation in substitution patterns
Krishnan, Neeraja M., Raina, Sameer Z., Pollock, David D.
Substitution patterns among nucleotides are often assumed to be constant in phylogenetic analyses. Although variation in the average rate of substitution among sites is commonly accounted for,...
Evolution of base-substitution gradients in primate mitochondrial genomes
Raina, Sameer Z., Faith, Jeremiah J., Disotell, Todd R., Seligmann, Hervé, Stewart, Caro-Beth, Pollock, David D.
Inferences of phylogenies and dates of divergence rely on accurate modeling of evolutionary processes; they may be confounded by variation in substitution rates among sites and changes in...
Estimating the Degree of Saturation in Mutant Screens
Pollock, David D., Larkin, John C.
Large-scale screens for loss-of-function mutants have played a significant role in recent advances in developmental biology and other fields. In such mutant screens, it is desirable to estimate the...
Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes.
Faith, Jeremiah J, Pollock, David D
Protein-coding genes in mitochondrial genomes have varying degrees of asymmetric skew in base frequencies at the third codon position. The variation in skew among genes appears to be caused by...
Assessing the Accuracy of Ancestral Protein Reconstruction Methods
Williams, Paul D, Pollock, David D, Blackburne, Benjamin P, Goldstein, Richard A
The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of...
EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity
Nahum, Laila A, Reynolds, Matthew T, Wang, Zhengyuan O, Faith, Jeremiah J, Jonna, Rahul, Jiang, Zhi J, ...
Regional Variation in the Density of Essential Genes in Mice
Hentges, Kathryn E, Pollock, David D, Liu, Bin, Justice, Monica J
In most species, and particularly in vertebrates, the percentage of genes absolutely required for survival, the essential genes, has not been estimated. To obtain this estimation, we used the mouse...
Jiang, Zhi J, Castoe, Todd A, Austin, Christopher C, Burbrink, Frank T, Herron, Matthew D, McGuire, Jimmy A, ...
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
Gentles, Andrew J., Wakefield, Matthew J., Kohany, Oleksiy, Gu, Wanjun, Batzer, Mark A., Pollock, David D., ...
The genome of the gray short-tailed opossum Monodelphis domestica is notable for its large size (∼3.6 Gb). We characterized nearly 500 families of interspersed repeats from the Monodelphis. They...
Adaptive Evolution and Functional Redesign of Core Metabolic Proteins in Snakes
Castoe, Todd A., Jiang, Zhi J., Gu, Wanjun, Wang, Zhengyuan O., Pollock, David D.
Williams, Paul D., Pollock, David D., Goldstein, Richard A.
It has been known for some time that many proteins are marginally stable. This has inspired several explanations. Having noted that the functionality of many enzymes is correlated with subunit...