Research Topics
| David D PollockSummaryAffiliation: University of Colorado Denver Country: USA Publications
Research Grants
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Detail Information
Publications
Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactionsDavid 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...- Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotesJohn 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... - Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakesTodd 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... - Repetitive elements may comprise over two-thirds of the human genomeA 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... - Evidence for an ancient adaptive episode of convergent molecular evolutionTodd 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.... 
Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related speciesTodd 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....- Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snakeTodd 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... - Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencingTodd A Castoe
Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, USA
Genome Biol Evol 3:641-53. 2011.... - Rapid likelihood analysis on large phylogenies using partial sampling of substitution historiesA 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... - 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:.. - Phylogenetics, likelihood, evolution and complexityA 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... - Amino acid coevolution induces an evolutionary Stokes shiftDavid 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... - Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequenceTodd 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... - Identification of repeat structure in large genomes using repeat probability cloudsWanjun 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... - Adaptive evolution and functional redesign of core metabolic proteins in snakesTodd 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... - Gene-specific RNA polymerase II phosphorylation and the CTD codeHyunmin 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... - Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencingJ 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... - Intrinsic amino acid side-chain hydrophilicity/hydrophobicity coefficients determined by reversed-phase high-performance liquid chromatography of model peptides: comparison with other hydrophilicity/hydrophobicity scalesColin 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... 
SINEs, evolution and genome structure in the opossumWanjun 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...
Research Grants
- Modeling evolution of functional context in proteinsDavid D Pollock; Fiscal Year: 2010....
- Modeling evolution of functional context in proteinsDavid D Pollock; Fiscal Year: 2010....