David D. Pollock, Ph.D. - Publications

Affiliations: 
University of Colorado, Boulder, Boulder, CO, United States 
Area:
Theoretical and experimental evolution
Website:
http://evolutionarygenomics.com

65 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Shortt JA, Card DC, Schield DR, Liu Y, Zhong B, Castoe TA, Carlton EJ, Pollock DD. Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia. Plos Neglected Tropical Diseases. 11: e0005292. PMID 28107347 DOI: 10.1371/journal.pntd.0005292  0.96
2016 Jiang Z, Gera L, Mant CT, Hirsch B, Yan Z, Qian Z, Holmes KV, Shortt JA, Pollock DD, Hodges RS. Platform technology to generate broadly cross-reactive antibodies to α-helical epitopes in hemagglutinin proteins from influenza a viruses. Biopolymers. PMID 26799790 DOI: 10.1002/bip.22808  0.52
2015 Castoe TA, Poole AW, de Koning AP, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, Pollock DD. Correction: Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake. Plos One. 10: e0136465. PMID 26291821 DOI: 10.1371/journal.pone.0136465  0.96
2015 Goldstein RA, Pollard ST, Shah SD, Pollock DD. Nonadaptive Amino Acid Convergence Rates Decrease over Time. Molecular Biology and Evolution. 32: 1373-81. PMID 25737491 DOI: 10.1093/molbev/msv041  0.92
2015 Andrew AL, Card DC, Ruggiero RP, Schield DR, Adams RH, Pollock DD, Secor SM, Castoe TA. Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding. Physiological Genomics. 47: 147-57. PMID 25670730 DOI: 10.1152/physiolgenomics.00131.2014  0.92
2015 Hoen DR, Hickey G, Bourque G, Casacuberta J, Cordaux R, Feschotte C, Fiston-Lavier AS, Hua-Van A, Hubley R, Kapusta A, Lerat E, Maumus F, Pollock DD, Quesneville H, Smit A, et al. A call for benchmarking transposable element annotation methods Mobile Dna. 6. DOI: 10.1186/s13100-015-0044-6  0.92
2014 Li C, Zhang Y, Li J, Kong L, Hu H, Pan H, Xu L, Deng Y, Li Q, Jin L, Yu H, Chen Y, Liu B, Yang L, Liu S, ... ... Pollock DD, et al. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. Gigascience. 3: 27. PMID 25671092 DOI: 10.1186/2047-217X-3-27  0.92
2014 Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, ... ... Pollock DD, et al. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science (New York, N.Y.). 346: 1254449. PMID 25504731 DOI: 10.1126/science.1254449  0.92
2014 Wacholder AC, Cox C, Meyer TJ, Ruggiero RP, Vemulapalli V, Damert A, Carbone L, Pollock DD. Inference of transposable element ancestry. Plos Genetics. 10: e1004482. PMID 25121584 DOI: 10.1371/journal.pgen.1004482  0.92
2014 Pollock DD, Goldstein RA. Strong evidence for protein epistasis, weak evidence against it. Proceedings of the National Academy of Sciences of the United States of America. 111: E1450. PMID 24706894 DOI: 10.1073/pnas.1401112111  0.92
2014 Castoe TA, De Koning APJ, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, ... ... Pollock DD, et al. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes (Proceedings of the National Academy of Sciences of the United States of America (2013) 110, 51, (20645-20650) DOI: 10.1073/pnas. 1314475110) Proceedings of the National Academy of Sciences of the United States of America. 111: 3194. DOI: 10.1073/pnas.1324133111  0.92
2013 Castoe TA, de Koning AP, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, ... ... Pollock DD, et al. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences of the United States of America. 110: 20645-50. PMID 24297902 DOI: 10.1073/pnas.1314475110  0.92
2013 Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, Wüster W, Woods AE, Logan JM, Harrison RA, Castoe TA, ... ... Pollock DD, et al. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceedings of the National Academy of Sciences of the United States of America. 110: 20651-6. PMID 24297900 DOI: 10.1073/pnas.1314702110  0.92
2013 Castoe TA, Pollock DD. Chinese alligator genome illustrates molecular adaptations. Cell Research. 23: 1254-5. PMID 24060849 DOI: 10.1038/cr.2013.134  0.92
2013 Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, ... ... Pollock DD, et al. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology. 14: R28. PMID 23537068 DOI: 10.1186/gb-2013-14-3-r28  0.92
2012 Castoe TA, Braun EL, Bronikowski AM, Cox CL, Rabosky AR, Jason de Koning AP, Dobry J, Fujita MK, Giorgianni MW, Hargreaves A, Henkel CV, Mackessy SP, O'Meally D, Rokyta DR, Secor SM, ... ... Pollock DD, et al. Report from the first snake genomics and integrative biology meeting. Standards in Genomic Sciences. 7: 150-2. PMID 23451292 DOI: 10.4056/sigs.3106480  0.92
2012 Yokoyama KD, Pollock DD. SP transcription factor paralogs and DNA-binding sites coevolve and adaptively converge in mammals and birds. Genome Biology and Evolution. 4: 1102-17. PMID 23019068 DOI: 10.1093/gbe/evs085  0.92
2012 de Koning AP, Gu W, Castoe TA, Pollock DD. Phylogenetics, likelihood, evolution and complexity. Bioinformatics (Oxford, England). 28: 2989-90. PMID 22976081 DOI: 10.1093/bioinformatics/bts555  0.92
2012 Castoe TA, Streicher JW, Meik JM, Ingrasci MJ, Poole AW, de Koning AP, Campbell JA, Parkinson CL, Smith EN, Pollock DD. Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species. Molecular Ecology Resources. 12: 1105-13. PMID 22938699 DOI: 10.1111/1755-0998.12000  0.92
2012 Wang B, Ekblom R, Castoe TA, Jones EP, Kozma R, Bongcam-Rudloff E, Pollock DD, Höglund J. Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development. Open Biology. 2: 120054. PMID 22724064 DOI: 10.1098/rsob.120054  0.92
2012 Pollock DD, Thiltgen G, Goldstein RA. Amino acid coevolution induces an evolutionary Stokes shift. Proceedings of the National Academy of Sciences of the United States of America. 109: E1352-9. PMID 22547823 DOI: 10.1073/pnas.1120084109  0.92
2012 Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, ... ... Pollock DD, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/pro.2071  0.92
2012 Castoe TA, Poole AW, de Koning AP, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, Pollock DD. Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. Plos One. 7: e30953. PMID 22348032 DOI: 10.1371/journal.pone.0030953  0.92
2012 Nakayama M, Castoe T, Sosinowski T, He X, Johnson K, Haskins K, Vignali DA, Gapin L, Pollock D, Eisenbarth GS. Germline TRAV5D-4 T-cell receptor sequence targets a primary insulin peptide of NOD mice. Diabetes. 61: 857-65. PMID 22315318 DOI: 10.2337/db11-1113  0.92
2012 St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, ... ... Pollock DD, et al. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology. 13: 415. PMID 22293439 DOI: 10.1186/gb-2012-13-1-415  0.92
2012 Sun C, Shepard DB, Chong RA, López Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biology and Evolution. 4: 168-83. PMID 22200636 DOI: 10.1093/gbe/evr139  0.92
2011 de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD. Repetitive elements may comprise over two-thirds of the human genome. Plos Genetics. 7: e1002384. PMID 22144907 DOI: 10.1371/journal.pgen.1002384  0.92
2011 Pollock DD, de Koning AP, Kim H, Castoe TA, Churchill ME, Kechris KJ. Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions. Plos One. 6: e26105. PMID 22069446 DOI: 10.1371/journal.pone.0026105  0.92
2011 Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S, Shedlock AM, Botka C, Castoe TA, ... ... Pollock DD, et al. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 477: 587-91. PMID 21881562 DOI: 10.1038/nature10390  0.92
2011 Castoe TA, Fox SE, Jason de Koning A, Poole AW, Daza JM, Smith EN, Mockler TC, Secor SM, Pollock DD. A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus). Bmc Research Notes. 4: 310. PMID 21867488 DOI: 10.1186/1756-0500-4-310  0.92
2011 Castoe TA, de Koning JA, Hall KT, Yokoyama KD, Gu W, Smith EN, Feschotte C, Uetz P, Ray DA, Dobry J, Bogden R, Mackessy SP, Bronikowski AM, Warren WC, Secor SM, ... Pollock DD, et al. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biology. 12: 406. PMID 21801464 DOI: 10.1186/gb-2011-12-7-406  0.92
2011 Castoe TA, Bronikowski AM, Brodie ED, Edwards SV, Pfrender ME, Shapiro MD, Pollock DD, Warren WC. A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Standards in Genomic Sciences. 4: 257-70. PMID 21677863 DOI: 10.4056/sigs.1664145  0.92
2011 Castoe TA, Hall KT, Guibotsy Mboulas ML, Gu W, de Koning AP, Fox SE, Poole AW, Vemulapalli V, Daza JM, Mockler T, Smith EN, Feschotte C, Pollock DD. Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing. Genome Biology and Evolution. 3: 641-53. PMID 21572095 DOI: 10.1093/gbe/evr043  0.92
2010 Castoe TA, Poole AW, Gu W, Jason de Koning AP, Daza JM, Smith EN, Pollock DD. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Molecular Ecology Resources. 10: 341-7. PMID 21565030 DOI: 10.1111/j.1755-0998.2009.02750.x  0.92
2010 Kim H, Erickson B, Luo W, Seward D, Graber JH, Pollock DD, Megee PC, Bentley DL. Gene-specific RNA polymerase II phosphorylation and the CTD code. Nature Structural & Molecular Biology. 17: 1279-86. PMID 20835241 DOI: 10.1038/nsmb.1913  0.92
2010 Castoe TA, de Koning AP, Pollock DD. Adaptive molecular convergence: Molecular evolution versus molecular phylogenetics. Communicative & Integrative Biology. 3: 67-9. PMID 20539788  0.96
2010 Harris JK, Sahl JW, Castoe TA, Wagner BD, Pollock DD, Spear JR. Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing. Applied and Environmental Microbiology. 76: 3863-8. PMID 20418443 DOI: 10.1128/AEM.02585-09  0.92
2010 Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, ... ... Pollock DD, et al. The genome of a songbird. Nature. 464: 757-62. PMID 20360741 DOI: 10.1038/nature08819  0.92
2010 de Koning AP, Gu W, Pollock DD. Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. Molecular Biology and Evolution. 27: 249-65. PMID 19783593 DOI: 10.1093/molbev/msp228  0.92
2009 Castoe TA, Gu W, de Koning AP, Daza JM, Jiang ZJ, Parkinson CL, Pollock DD. Dynamic nucleotide mutation gradients and control region usage in squamate reptile mitochondrial genomes. Cytogenetic and Genome Research. 127: 112-27. PMID 20215734 DOI: 10.1159/000295342  0.92
2009 Mant CT, Kovacs JM, Kim HM, Pollock DD, Hodges RS. 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. Biopolymers. 92: 573-95. PMID 19795449 DOI: 10.1002/bip.21316  0.92
2009 Castoe TA, de Koning AP, Kim HM, Gu W, Noonan BP, Naylor G, Jiang ZJ, Parkinson CL, Pollock DD. Evidence for an ancient adaptive episode of convergent molecular evolution. Proceedings of the National Academy of Sciences of the United States of America. 106: 8986-91. PMID 19416880 DOI: 10.1073/pnas.0900233106  0.92
2008 Gu W, Castoe TA, Hedges DJ, Batzer MA, Pollock DD. Identification of repeat structure in large genomes using repeat probability clouds. Analytical Biochemistry. 380: 77-83. PMID 18541131 DOI: 10.1016/j.ab.2008.05.015  0.92
2008 Castoe TA, Jiang ZJ, Gu W, Wang ZO, Pollock DD. Adaptive evolution and functional redesign of core metabolic proteins in snakes. Plos One. 3: e2201. PMID 18493604 DOI: 10.1371/journal.pone.0002201  0.92
2008 Thai V, Renesto P, Fowler CA, Brown DJ, Davis T, Gu W, Pollock DD, Kern D, Raoult D, Eisenmesser EZ. Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus. Journal of Molecular Biology. 378: 71-86. PMID 18342330 DOI: 10.1016/j.jmb.2007.08.051  0.92
2007 Jiang ZJ, Castoe TA, Austin CC, Burbrink FT, Herron MD, McGuire JA, Parkinson CL, Pollock DD. Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region. Bmc Evolutionary Biology. 7: 123. PMID 17655768 DOI: 10.1186/1471-2148-7-123  0.92
2007 Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, ... ... Pollock DD, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 447: 167-77. PMID 17495919 DOI: 10.1038/nature05805  0.92
2007 Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, Jurka J. Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Research. 17: 992-1004. PMID 17495012 DOI: 10.1101/gr.6070707  0.92
2007 Hentges KE, Pollock DD, Liu B, Justice MJ. Regional variation in the density of essential genes in mice. Plos Genetics. 3: e72. PMID 17480122 DOI: 10.1371/journal.pgen.0030072  0.92
2007 Gu W, Ray DA, Walker JA, Barnes EW, Gentles AJ, Samollow PB, Jurka J, Batzer MA, Pollock DD. SINEs, evolution and genome structure in the opossum. Gene. 396: 46-58. PMID 17442506 DOI: 10.1016/j.gene.2007.02.028  0.92
2006 Williams PD, Pollock DD, Goldstein RA. SELECTIVE ADVANTAGE OF RECOMBINATION IN EVOLVING PROTEIN POPULATIONS: A LATTICE MODEL STUDY. International Journal of Modern Physics. C, Physics and Computers. 17: 75-90. PMID 25473139 DOI: 10.1142/S0129183106008959  0.92
2006 Nahum LA, Reynolds MT, Wang ZO, Faith JJ, Jonna R, Jiang ZJ, Meyer TJ, Pollock DD. EGenBio: a data management system for evolutionary genomics and biodiversity. Bmc Bioinformatics. 7: S7. PMID 17118150 DOI: 10.1186/1471-2105-7-S2-S7  0.92
2006 Williams PD, Pollock DD, Blackburne BP, Goldstein RA. Assessing the accuracy of ancestral protein reconstruction methods. Plos Computational Biology. 2: e69. PMID 16789817 DOI: 10.1371/journal.pcbi.0020069  0.92
2006 Goldstein RA, Pollock DD. Observations of amino acid gain and loss during protein evolution are explained by statistical bias. Molecular Biology and Evolution. 23: 1444-9. PMID 16698770 DOI: 10.1093/molbev/msl010  0.92
2006 Wheat CW, Watt WB, Pollock DD, Schulte PM. From DNA to fitness differences: sequences and structures of adaptive variants of Colias phosphoglucose isomerase (PGI). Molecular Biology and Evolution. 23: 499-512. PMID 16292000 DOI: 10.1093/molbev/msj062  0.92
2005 Xu YO, Hall RW, Goldstein RA, Pollock DD. Divergence, recombination and retention of functionality during protein evolution. Human Genomics. 2: 158-67. PMID 16197733  0.92
2005 Raina SZ, Faith JJ, Disotell TR, Seligmann H, Stewart CB, Pollock DD. Evolution of base-substitution gradients in primate mitochondrial genomes. Genome Research. 15: 665-73. PMID 15867428 DOI: 10.1101/gr.3128605  0.92
2004 Krishnan NM, Seligmann H, Stewart CB, De Koning AP, Pollock DD. Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference. Molecular Biology and Evolution. 21: 1871-83. PMID 15229290 DOI: 10.1093/molbev/msh198  0.92
2003 Faith JJ, Pollock DD. Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics. 165: 735-45. PMID 14573484  0.92
2003 Hillis DM, Pollock DD, McGuire JA, Zwickl DJ. Is sparse taxon sampling a problem for phylogenetic inference? Systematic Biology. 52: 124-6. PMID 12554446  0.92
2002 Pollock DD, Zwickl DJ, McGuire JA, Hillis DM. Increased taxon sampling is advantageous for phylogenetic inference. Systematic Biology. 51: 664-71. PMID 12228008 DOI: 10.1080/10635150290102357  0.92
2001 Williams PD, Pollock DD, Goldstein RA. Evolution of functionality in lattice proteins. Journal of Molecular Graphics & Modelling. 19: 150-6. PMID 11381526 DOI: 10.1016/S1093-3263(00)00125-X  0.92
2000 Pollock DD, Bruno WJ. Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition. Molecular Biology and Evolution. 17: 1854-8. PMID 11110901  0.92
1999 Pollock DD, Taylor WR, Goldman N. Coevolving protein residues: maximum likelihood identification and relationship to structure. Journal of Molecular Biology. 287: 187-98. PMID 10074416 DOI: 10.1006/jmbi.1998.2601  0.92
1997 Pollock DD, Taylor WR. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Engineering. 10: 647-57. PMID 9278277  0.92
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