David D Pollock

David D Pollock

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David D Pollock

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Society for Molecular Biology and Evolution, Council and Business Meetings, 2018, Yokohama, Japan.

Authors:
David D Pollock

Mol Biol Evol 2019 01;36(1):204-206

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO.

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http://dx.doi.org/10.1093/molbev/msy240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6340456PMC
January 2019

Biliverdin Reductase B Dynamics Are Coupled to Coenzyme Binding.

J Mol Biol 2018 09 20;430(18 Pt B):3234-3250. Epub 2018 Jun 20.

Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2018.06.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431292PMC
September 2018

Sequence entropy of folding and the absolute rate of amino acid substitutions.

Nat Ecol Evol 2017 Dec 23;1(12):1923-1930. Epub 2017 Oct 23.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA.

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http://dx.doi.org/10.1038/s41559-017-0338-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5701738PMC
December 2017

Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia.

PLoS Negl Trop Dis 2017 01 20;11(1):e0005292. Epub 2017 Jan 20.

Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States of America.

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https://dx.plos.org/10.1371/journal.pntd.0005292
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http://dx.doi.org/10.1371/journal.pntd.0005292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5287463PMC
January 2017

The tangled bank of amino acids.

Protein Sci 2016 07 12;25(7):1354-62. Epub 2016 May 12.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, 80045.

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http://dx.doi.org/10.1002/pro.2930DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918418PMC
July 2016

Platform technology to generate broadly cross-reactive antibodies to α-helical epitopes in hemagglutinin proteins from influenza A viruses.

Biopolymers 2016 Mar;106(2):144-159

Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045.

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http://dx.doi.org/10.1002/bip.22808DOI Listing
March 2016

A call for benchmarking transposable element annotation methods.

Mob DNA 2015 4;6:13. Epub 2015 Aug 4.

School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; McGill Centre for Bioinformatics, McGill University, Montréal, Québec Canada.

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http://dx.doi.org/10.1186/s13100-015-0044-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524446PMC
August 2015

Nonadaptive Amino Acid Convergence Rates Decrease over Time.

Mol Biol Evol 2015 Jun 3;32(6):1373-81. Epub 2015 Mar 3.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora

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http://dx.doi.org/10.1093/molbev/msv041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4572784PMC
June 2015

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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http://jarvislab.net/wp-content/uploads/2012/02/Green-et-al-
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http://www.sciencemag.org/cgi/doi/10.1126/science.1254449
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http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014

Inference of transposable element ancestry.

PLoS Genet 2014 Aug 14;10(8):e1004482. Epub 2014 Aug 14.

Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133154PMC
August 2014

Strong evidence for protein epistasis, weak evidence against it.

Proc Natl Acad Sci U S A 2014 Apr 20;111(15):E1450. Epub 2014 Mar 20.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045.

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http://dx.doi.org/10.1073/pnas.1401112111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992644PMC
April 2014

Chinese alligator genome illustrates molecular adaptations.

Cell Res 2013 Nov 24;23(11):1254-5. Epub 2013 Sep 24.

Department of Biology, University of Texas Arlington, Arlington, TX 76010, USA.

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http://dx.doi.org/10.1038/cr.2013.134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817551PMC
November 2013

SP transcription factor paralogs and DNA-binding sites coevolve and adaptively converge in mammals and birds.

Genome Biol Evol 2012 ;4(11):1102-17

Department of Biochemistry and Molecular Genetics, University of Colorado, Denver School of Medicine, USA.

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https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/
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http://dx.doi.org/10.1093/gbe/evs085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514965PMC
April 2013

Phylogenetics, likelihood, evolution and complexity.

Bioinformatics 2012 Nov 12;28(22):2989-90. Epub 2012 Sep 12.

Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496332PMC
November 2012

Amino acid coevolution induces an evolutionary Stokes shift.

Proc Natl Acad Sci U S A 2012 May 30;109(21):E1352-9. Epub 2012 Apr 30.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1073/pnas.1120084109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361410PMC
May 2012

Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development.

Open Biol 2012 Apr;2(4):120054

Population Biology and Conservation Biology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 75236 Uppsala, Sweden.

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http://dx.doi.org/10.1098/rsob.120054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376728PMC
April 2012

Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions.

PLoS One 2011 1;6(11):e26105. Epub 2011 Nov 1.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0026105PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206046PMC
March 2012

Repetitive elements may comprise over two-thirds of the human genome.

PLoS Genet 2011 Dec 1;7(12):e1002384. Epub 2011 Dec 1.

Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA.

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http://dx.doi.org/10.1371/journal.pgen.1002384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228813PMC
December 2011

A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus).

BMC Res Notes 2011 Aug 25;4:310. Epub 2011 Aug 25.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045 USA.

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http://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0
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http://dx.doi.org/10.1186/1756-0500-4-310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173347PMC
August 2011

Gene-specific RNA polymerase II phosphorylation and the CTD code.

Nat Struct Mol Biol 2010 Oct 12;17(10):1279-86. Epub 2010 Sep 12.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA.

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http://dx.doi.org/10.1038/nsmb.1913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048030PMC
October 2010

Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing.

Appl Environ Microbiol 2010 Jun 23;76(12):3863-8. Epub 2010 Apr 23.

Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.

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http://aem.asm.org/cgi/doi/10.1128/AEM.02585-09
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http://dx.doi.org/10.1128/AEM.02585-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2893486PMC
June 2010

The genome of a songbird.

Nature 2010 Apr;464(7289):757-62

The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature08819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187626PMC
April 2010

Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence.

Mol Ecol Resour 2010 Mar 30;10(2):341-7. Epub 2009 Jul 30.

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 & Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX 76019, USA.

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http://doi.wiley.com/10.1111/j.1755-0998.2009.02750.x
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http://dx.doi.org/10.1111/j.1755-0998.2009.02750.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172459PMC
March 2010

Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories.

Mol Biol Evol 2010 Feb 25;27(2):249-65. Epub 2009 Sep 25.

Department of Biochemistry and Molecular Genetics, and Consortium for Comparative Genomics, University of Colorado Denver School of Medicine, USA.

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http://dx.doi.org/10.1093/molbev/msp228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877550PMC
February 2010

Adaptive molecular convergence: Molecular evolution versus molecular phylogenetics.

Commun Integr Biol 2010 Jan;3(1):67-9

Department of Biochemistry and Molecular Genetics; University of Colorado School of Medicine; Aurora, CO USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881246PMC
http://dx.doi.org/10.4161/cib.3.1.10174DOI Listing
January 2010

Evidence for an ancient adaptive episode of convergent molecular evolution.

Proc Natl Acad Sci U S A 2009 Jun 28;106(22):8986-91. Epub 2009 Apr 28.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1073/pnas.0900233106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690048PMC
June 2009

Identification of repeat structure in large genomes using repeat probability clouds.

Anal Biochem 2008 Sep 20;380(1):77-83. Epub 2008 May 20.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1016/j.ab.2008.05.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533575PMC
September 2008

Adaptive evolution and functional redesign of core metabolic proteins in snakes.

PLoS One 2008 May 21;3(5):e2201. Epub 2008 May 21.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002201PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2376058PMC
May 2008

Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context.

J Mol Evol 2007 Nov;65(5):485-95

Department of Biological Sciences and Biological Computing and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1007/s00239-007-9018-8DOI Listing
November 2007

SINEs, evolution and genome structure in the opossum.

Gene 2007 Jul 19;396(1):46-58. Epub 2007 Mar 19.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1016/j.gene.2007.02.028DOI Listing
July 2007

Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica.

Genome Res 2007 Jul 10;17(7):992-1004. Epub 2007 May 10.

Department of Radiology, School of Medicine, Stanford University, Stanford, California 94305, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.6070707
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http://dx.doi.org/10.1101/gr.6070707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899126PMC
July 2007

Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region.

BMC Evol Biol 2007 Jul 26;7:123. Epub 2007 Jul 26.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA, USA.

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http://dx.doi.org/10.1186/1471-2148-7-123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950710PMC
July 2007

Regional variation in the density of essential genes in mice.

PLoS Genet 2007 May 21;3(5):e72. Epub 2007 Mar 21.

Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.0030072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1865562PMC
May 2007

Functionality and the evolution of marginal stability in proteins: inferences from lattice simulations.

Evol Bioinform Online 2007 Jan 16;2:91-101. Epub 2007 Jan 16.

Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674661PMC
January 2007

EGenBio: a data management system for evolutionary genomics and biodiversity.

BMC Bioinformatics 2006 Sep 6;7 Suppl 2:S7. Epub 2006 Sep 6.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1186/1471-2105-7-S2-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1683573PMC
September 2006

Observations of amino acid gain and loss during protein evolution are explained by statistical bias.

Mol Biol Evol 2006 Jul 11;23(7):1444-9. Epub 2006 May 11.

Division of Mathematical Biology, National Institute of Medical Research, Mill Hill, London, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msl010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943954PMC
July 2006

Assessing the accuracy of ancestral protein reconstruction methods.

PLoS Comput Biol 2006 Jun 23;2(6):e69. Epub 2006 Jun 23.

Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.

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http://dx.doi.org/10.1371/journal.pcbi.0020069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480538PMC
June 2006

From DNA to fitness differences: sequences and structures of adaptive variants of Colias phosphoglucose isomerase (PGI).

Mol Biol Evol 2006 Mar 16;23(3):499-512. Epub 2005 Nov 16.

Department of Biological Sciences, Stanford University, USA.

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http://dx.doi.org/10.1093/molbev/msj062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943955PMC
March 2006

SELECTIVE ADVANTAGE OF RECOMBINATION IN EVOLVING PROTEIN POPULATIONS: A LATTICE MODEL STUDY.

Int J Mod Phys C 2006 Jan;17(1):75-90

Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London MW7 1AA, UK.

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http://dx.doi.org/10.1142/S0129183106008959DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249953PMC
January 2006

Divergence, recombination and retention of functionality during protein evolution.

Hum Genomics 2005 Sep;2(3):158-67

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943960PMC
September 2005

Context dependence and coevolution among amino acid residues in proteins.

Methods Enzymol 2005 ;395:779-90

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

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http://dx.doi.org/10.1016/S0076-6879(05)95040-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943952PMC
August 2005

Evolution of base-substitution gradients in primate mitochondrial genomes.

Genome Res 2005 May;15(5):665-73

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.3128605
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http://dx.doi.org/10.1101/gr.3128605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088294PMC
May 2005

The beetle gut: a hyperdiverse source of novel yeasts.

Mycol Res 2005 Mar;109(Pt 3):261-5

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943959PMC
March 2005

Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference.

Mol Biol Evol 2004 Oct 30;21(10):1871-83. Epub 2004 Jun 30.

Biological Computation and Visualization Center, Department of Biological Sciences, Louisiana State University, USA.

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http://dx.doi.org/10.1093/molbev/msh198DOI Listing
October 2004

The ambush hypothesis: hidden stop codons prevent off-frame gene reading.

DNA Cell Biol 2004 Oct;23(10):701-5

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

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http://dx.doi.org/10.1089/dna.2004.23.701DOI Listing
October 2004

Detecting gradients of asymmetry in site-specific substitutions in mitochondrial genomes.

DNA Cell Biol 2004 Oct;23(10):707-14

Biological Computation and Visualization Center, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

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http://dx.doi.org/10.1089/dna.2004.23.707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943950PMC
October 2004

Analysis of among-site variation in substitution patterns.

Biol Proced Online 2004;6:180-188. Epub 2004 Sep 3.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University. Baton Rouge, LA 70803. USA.

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http://dx.doi.org/10.1251/bpo88DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC516205PMC
September 2004

Estimating the degree of saturation in mutant screens.

Genetics 2004 Sep;168(1):489-502

Department of Biological Sciences, Louisiana State University, Baton Rouge 70803, USA.

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http://dx.doi.org/10.1534/genetics.103.024430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448089PMC
September 2004

Genomic biodiversity, phylogenetics and coevolution in proteins.

Authors:
David D Pollock

Appl Bioinformatics 2002 ;1(2):81-92

Department of Biological Sciences and Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, 70803, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943949PMC
June 2004

Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes.

Genetics 2003 Oct;165(2):735-45

Department of Biological Sciences and Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462789PMC
October 2003

Is sparse taxon sampling a problem for phylogenetic inference?

Syst Biol 2003 Feb;52(1):124-6

Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas, 1 University Station C0930, Austin, Texas 78712-0253, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943953PMC
http://dx.doi.org/10.1080/10635150390132911DOI Listing
February 2003

Increased taxon sampling is advantageous for phylogenetic inference.

Syst Biol 2002 Aug;51(4):664-71

Department of Biological Sciences and Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

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http://dx.doi.org/10.1080/10635150290102357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943957PMC
August 2002