David D Pollock

Summary

Affiliation: University of Colorado Denver
Country: USA

Publications

  1. pmc Repetitive elements may comprise over two-thirds of the human genome
    A P Jason De Koning
    Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA
    PLoS Genet 7:e1002384. 2011
  2. pmc Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
    PLoS ONE 7:e30953. 2012
  3. pmc Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, USA
    Genome Biol Evol 3:641-53. 2011
  4. pmc Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions
    David D Pollock
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
    PLoS ONE 6:e26105. 2011
  5. pmc Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes
    John A St John
    Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
    Genome Biol 13:415. 2012
  6. pmc Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 12801 17th Ave, Aurora, CO 80045, USA
    Genome Biol 12:406. 2011
  7. pmc Phylogenetics, likelihood, evolution and complexity
    A P Jason De Koning
    Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
    Bioinformatics 28:2989-90. 2012
  8. pmc The Burmese python genome reveals the molecular basis for extreme adaptation in snakes
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
    Proc Natl Acad Sci U S A 110:20645-50. 2013
  9. pmc Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
    Andrew J Gentles
    Department of Radiology, School of Medicine, Stanford University, Stanford, California 94305, USA
    Genome Res 17:992-1004. 2007
  10. doi request reprint Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Mol Ecol Resour 12:1105-13. 2012

Research Grants

Collaborators

Detail Information

Publications23

  1. pmc Repetitive elements may comprise over two-thirds of the human genome
    A P Jason De Koning
    Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA
    PLoS Genet 7:e1002384. 2011
    ..These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed...
  2. pmc Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
    PLoS ONE 7:e30953. 2012
    ..Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable...
  3. pmc Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, USA
    Genome Biol Evol 3:641-53. 2011
    ....
  4. pmc Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions
    David D Pollock
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
    PLoS ONE 6:e26105. 2011
    ..This approach, which we call Simultaneous Ultra high-throughput Ligand Dissociation EXperiment (SULDEX), is theoretically capable of rapid and accurate elucidation of an entire TF-binding repertoire...
  5. pmc Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes
    John A St John
    Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
    Genome Biol 13:415. 2012
    ..The status of these projects and our planned analyses are described...
  6. pmc Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 12801 17th Ave, Aurora, CO 80045, USA
    Genome Biol 12:406. 2011
    ..Here, we describe how this will be done, what analyses this work will include, and provide a timeline...
  7. pmc Phylogenetics, likelihood, evolution and complexity
    A P Jason De Koning
    Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
    Bioinformatics 28:2989-90. 2012
    ..Future versions will support detection of co-evolutionary interactions between sites, probabilistic tests of convergent evolution and rigorous testing of evolutionary hypotheses in a Bayesian framework...
  8. pmc The Burmese python genome reveals the molecular basis for extreme adaptation in snakes
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
    Proc Natl Acad Sci U S A 110:20645-50. 2013
    ..Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome. ..
  9. pmc Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
    Andrew J Gentles
    Department of Radiology, School of Medicine, Stanford University, Stanford, California 94305, USA
    Genome Res 17:992-1004. 2007
    ..Many of these conserved repeats are also present in human, and are highly over-represented in predicted cis-regulatory modules. Seventy-six of the 83 families are present in chicken in addition to mammals...
  10. doi request reprint Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Mol Ecol Resour 12:1105-13. 2012
    ....
  11. pmc Evidence for an ancient adaptive episode of convergent molecular evolution
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Proc Natl Acad Sci U S A 106:8986-91. 2009
    ....
  12. pmc Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories
    A P Jason De Koning
    Department of Biochemistry and Molecular Genetics, and Consortium for Comparative Genomics, University of Colorado Denver School of Medicine, USA
    Mol Biol Evol 27:249-65. 2010
    ..Partial sampling of substitutions thus dramatically improves the utility of likelihood approaches for analyzing complex evolutionary processes on large data sets...
  13. pmc SP transcription factor paralogs and DNA-binding sites coevolve and adaptively converge in mammals and birds
    Ken Daigoro Yokoyama
    Department of Biochemistry and Molecular Genetics, University of Colorado, Denver School of Medicine, USA
    Genome Biol Evol 4:1102-17. 2012
    ..Thus, multiple lines of evidence indicate that selection has driven convergent evolution of transcription factors along with their binding sites and coregulatory proteins...
  14. pmc Identification of repeat structure in large genomes using repeat probability clouds
    Wanjun Gu
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Anal Biochem 380:77-83. 2008
    ..This method should be extremely useful as a tool for use in de novo identification of repeat structure in large newly sequenced genomes...
  15. doi request reprint Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence
    Todd A Castoe
    Consortium for Comparative Genomics, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA Department of Biology, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX 76019, USA
    Mol Ecol Resour 10:341-7. 2010
    ..The random sequencing-based approach to identify microsatellites was rapid, cost-effective and identified thousands of useful microsatellite loci in a previously unstudied species...
  16. pmc A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus)
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045 USA
    BMC Res Notes 4:310. 2011
    ..abstract:..
  17. pmc Adaptive evolution and functional redesign of core metabolic proteins in snakes
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
    PLoS ONE 3:e2201. 2008
    ..Adaptive evolutionary episodes in core metabolic proteins are uncommon, and are even more rarely linked to major macroevolutionary shifts...
  18. ncbi request reprint SINEs, evolution and genome structure in the opossum
    Wanjun Gu
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Gene 396:46-58. 2007
    ..Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state...
  19. pmc Amino acid coevolution induces an evolutionary Stokes shift
    David D Pollock
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Proc Natl Acad Sci U S A 109:E1352-9. 2012
    ..The observation of an evolutionary Stokes shift has profound implications for the study of protein evolution and the modeling of evolutionary processes...
  20. pmc Report from the first snake genomics and integrative biology meeting
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
    Stand Genomic Sci 7:150-2. 2012
    ..Goals of the meeting included coordination of genomic data collection and fostering collaborative interactions among researchers using snakes as model systems...
  21. pmc Gene-specific RNA polymerase II phosphorylation and the CTD code
    Hyunmin Kim
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
    Nat Struct Mol Biol 17:1279-86. 2010
    ..Nrd1 and Pcf11 frequently colocalize, suggesting functional overlap. Unexpectedly, Pcf11 is enriched at centromeres and Pol III-transcribed genes...
  22. pmc Intrinsic amino acid side-chain hydrophilicity/hydrophobicity coefficients determined by reversed-phase high-performance liquid chromatography of model peptides: comparison with other hydrophilicity/hydrophobicity scales
    Colin T Mant
    Department of Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
    Biopolymers 92:573-95. 2009
    ..We have shown that the intrinsic scale determined here is in full agreement with the structural characteristics of amino acid side-chains...
  23. pmc Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing
    J Kirk Harris
    Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    Appl Environ Microbiol 76:3863-8. 2010
    ..Further, population studies to examine genetic variation, which require even lower levels of sequencing, should be possible where thousands of individual bar-coded amplicons are examined in parallel...

Research Grants2

  1. Modeling evolution of functional context in proteins
    David D Pollock; Fiscal Year: 2010
    ....
  2. Modeling evolution of functional context in proteins
    David D Pollock; Fiscal Year: 2010
    ....