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David Pollock

TitleProfessor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-BioChem&Molecular Genetics
Phone303/724-3234

    Collapse Research 
    Collapse research activities and funding
    R01GM097251     (POLLOCK, DAVID D)Apr 13, 2012 - Jan 31, 2017
    NIH
    Genome-wide mutation models to decipher function
    Role: Principal Investigator
    R01GM083127     (POLLOCK, DAVID D)Mar 1, 2009 - Feb 28, 2021
    NIH
    Modeling evolution of functional context in proteins
    Role: Principal Investigator
    R33GM065612     (POLLOCK, DAVID D)Aug 1, 2002 - May 31, 2008
    NIH
    Protein sequence, structure, and computational analysis
    Role: Principal Investigator
    R21GM065612     (POLLOCK, DAVID D)Aug 1, 2002 - Jul 31, 2004
    NIH
    Protein sequence, structure, and computational analysis
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Fukushima K, Pollock DD. Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence. Nat Ecol Evol. 2023 01; 7(1):155-170. PMID: 36604553.
      View in: PubMed
    2. Gumz ML, Shimbo D, Abdalla M, Balijepalli RC, Benedict C, Chen Y, Earnest DJ, Gamble KL, Garrison SR, Gong MC, Hogenesch JB, Hong Y, Ivy JR, Joe B, Laposky AD, Liang M, MacLaughlin EJ, Martino TA, Pollock DM, Redline S, Rogers A, Dan Rudic R, Schernhammer ES, Stergiou GS, St-Onge MP, Wang X, Wright J, Oh YS. Toward Precision Medicine: Circadian Rhythm of Blood Pressure and Chronotherapy for Hypertension - 2021 NHLBI Workshop Report. Hypertension. 2023 03; 80(3):503-522. PMID: 36448463.
      View in: PubMed
    3. Wade KJ, Tisa S, Barrington C, Henriksen JC, Crooks KR, Gignoux CR, Almand AT, Steel JJ, Sitko JC, Rohrer JW, Wickert DP, Almand EA, Pollock DD, Rissland OS. Phylodynamics of a regional SARS-CoV-2 rapid spreading event in Colorado in late 2020. PLoS One. 2022; 17(10):e0274050. PMID: 36194597.
      View in: PubMed
    4. Lund AJ, Wade KJ, Nikolakis ZL, Ivey KN, Perry BW, Pike HNC, Paull SH, Liu Y, Castoe TA, Pollock DD, Carlton EJ. Integrating genomic and epidemiologic data to accelerate progress toward schistosomiasis elimination. Elife. 2022 08 30; 11. PMID: 36040013.
      View in: PubMed
    5. Kemp SA, Collier DA, Datir RP, Ferreira IATM, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, Roberts DJ, Chandra A, Temperton N, Sharrocks K, Blane E, Modis Y, Leigh KE, Briggs JAG, van Gils MJ, Smith KGC, Bradley JR, Smith C, Doffinger R, Ceron-Gutierrez L, Barcenas-Morales G, Pollock DD, Goldstein RA, Smielewska A, Skittrall JP, Gouliouris T, Goodfellow IG, Gkrania-Klotsas E, Illingworth CJR, McCoy LE, Gupta RK. Author Correction: SARS-CoV-2 evolution during treatment of chronic infection. Nature. 2022 Aug; 608(7922):E23. PMID: 35864233.
      View in: PubMed
    6. Nikolakis ZL, Carlton EJ, Pollock DD, Castoe TA. A genomic can of worms for schistosome host-specificity. Trends Parasitol. 2022 07; 38(7):496-497. PMID: 35504822.
      View in: PubMed
    7. Fukushima K, Pollock DD. Author Correction: Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution. Nat Commun. 2021 Sep 02; 12(1):5313. PMID: 34475380.
      View in: PubMed
    8. Eccleston RC, Pollock DD, Goldstein RA. Selection for cooperativity causes epistasis predominately between native contacts and enables epistasis-based structure reconstruction. Proc Natl Acad Sci U S A. 2021 04 20; 118(16). PMID: 33879570.
      View in: PubMed
    9. Shortt JA, Timm LE, Hales NR, Nikolakis ZL, Schield DR, Perry BW, Liu Y, Zhong B, Castoe TA, Carlton EJ, Pollock DD. Population genomic analyses of schistosome parasites highlight critical challenges facing endgame elimination efforts. Sci Rep. 2021 03 25; 11(1):6884. PMID: 33767307.
      View in: PubMed
    10. Becker BK, Johnston JG, Young CM, Torres Rodriguez AA, Jin C, Pollock DM. Endothelin B receptors impair baroreflex function and increase blood pressure variability during high salt diet. Auton Neurosci. 2021 05; 232:102796. PMID: 33798837.
      View in: PubMed
    11. Kemp SA, Collier DA, Datir RP, Ferreira IATM, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, Roberts DJ, Chandra A, Temperton N, Sharrocks K, Blane E, Modis Y, Leigh KE, Briggs JAG, van Gils MJ, Smith KGC, Bradley JR, Smith C, Doffinger R, Ceron-Gutierrez L, Barcenas-Morales G, Pollock DD, Goldstein RA, Smielewska A, Skittrall JP, Gouliouris T, Goodfellow IG, Gkrania-Klotsas E, Illingworth CJR, McCoy LE, Gupta RK. SARS-CoV-2 evolution during treatment of chronic infection. Nature. 2021 04; 592(7853):277-282. PMID: 33545711.
      View in: PubMed
    12. Nikolakis ZL, Hales NR, Perry BW, Schield DR, Timm LE, Liu Y, Zhong B, Kechris KJ, Carlton EJ, Pollock DD, Castoe TA. Patterns of relatedness and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum). PLoS Negl Trop Dis. 2021 01; 15(1):e0009020. PMID: 33406094.
      View in: PubMed
    13. Kemp SA, Collier DA, Datir R, Ferreira I, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, Roberts DJ, Chandra A, Temperton N, Sharrocks K, Blane E, Briggs J, van GM, Smith K, Bradley JR, Smith C, Doffinger R, Ceron-Gutierrez L, Barcenas-Morales G, Pollock DD, Goldstein RA, Smielewska A, Skittrall JP, Gouliouris T, Goodfellow IG, Gkrania-Klotsas E, Illingworth C, McCoy LE, Gupta RK. Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. medRxiv. 2020 Dec 29. PMID: 33398302.
      View in: PubMed
    14. Fukushima K, Pollock DD. Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution. Nat Commun. 2020 09 08; 11(1):4459. PMID: 32900997.
      View in: PubMed
    15. Pollock DD, Castoe TA, Perry BW, Lytras S, Wade KJ, Robertson DL, Holmes EC, Boni MF, Kosakovsky Pond SL, Parry R, Carlton EJ, Wood JLN, Pennings PS, Goldstein RA. Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2. Mol Biol Evol. 2020 09 01; 37(9):2706-2710. PMID: 32658964.
      View in: PubMed
    16. Sparkenbaugh EM, Kasztan M, Henderson MW, Ellsworth P, Davis PR, Wilson KJ, Reeves B, Key NS, Strickland S, McCrae K, Pollock DM, Pawlinski R. High molecular weight kininogen contributes to early mortality and kidney dysfunction in a mouse model of sickle cell disease. J Thromb Haemost. 2020 09; 18(9):2329-2340. PMID: 32573897.
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    17. Shortt JA, Ruggiero RP, Cox C, Wacholder AC, Pollock DD. Finding and extending ancient simple sequence repeat-derived regions in the human genome. Mob DNA. 2020; 11:11. PMID: 32095164.
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    18. Zhang D, Jin C, Obi IE, Rhoads MK, Soliman RH, Sedaka RS, Allan JM, Tao B, Speed JS, Pollock JS, Pollock DM. Loss of circadian gene Bmal1 in the collecting duct lowers blood pressure in male, but not female, mice. Am J Physiol Renal Physiol. 2020 03 01; 318(3):F710-F719. PMID: 31904281.
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    19. Pollock DD. Society for Molecular Biology and Evolution, Council and Business Meetings, 2019, Manchester, United Kingdom. Mol Biol Evol. 2020 Jan 01; 37(1):301-303. PMID: 31986214.
      View in: PubMed
    20. Becker BK, Zhang D, Soliman R, Pollock DM. Autonomic nerves and circadian control of renal function. Auton Neurosci. 2019 03; 217:58-65. PMID: 30704976.
      View in: PubMed
    21. Pollock DD. Society for Molecular Biology and Evolution, Council and Business Meetings, 2018, Yokohama, Japan. Mol Biol Evol. 2019 01 01; 36(1):204-206. PMID: 30657947.
      View in: PubMed
    22. Paukovich N, Xue M, Elder JR, Redzic JS, Blue A, Pike H, Miller BG, Pitts TM, Pollock DD, Hansen K, D'Alessandro A, Eisenmesser EZ. Biliverdin Reductase B Dynamics Are Coupled to Coenzyme Binding. J Mol Biol. 2018 09 14; 430(18 Pt B):3234-3250. PMID: 29932944.
      View in: PubMed
    23. Goldstein RA, Pollock DD. Sequence entropy of folding and the absolute rate of amino acid substitutions. Nat Ecol Evol. 2017 Dec; 1(12):1923-1930. PMID: 29062121.
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    24. Fukushima K, Fang X, Alvarez-Ponce D, Cai H, Carretero-Paulet L, Chen C, Chang TH, Farr KM, Fujita T, Hiwatashi Y, Hoshi Y, Imai T, Kasahara M, Librado P, Mao L, Mori H, Nishiyama T, Nozawa M, P?lfalvi G, Pollard ST, Rozas J, S?nchez-Gracia A, Sankoff D, Shibata TF, Shigenobu S, Sumikawa N, Uzawa T, Xie M, Zheng C, Pollock DD, Albert VA, Li S, Hasebe M. Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory. Nat Ecol Evol. 2017 Feb 06; 1(3):59. PMID: 28812732.
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    25. 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 Negl Trop Dis. 2017 01; 11(1):e0005292. PMID: 28107347.
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    26. Goldstein RA, Pollock DD. The tangled bank of amino acids. Protein Sci. 2016 07; 25(7):1354-62. PMID: 27028523.
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    27. Davenport AP, Hyndman KA, Dhaun N, Southan C, Kohan DE, Pollock JS, Pollock DM, Webb DJ, Maguire JJ. Endothelin. Pharmacol Rev. 2016 Apr; 68(2):357-418. PMID: 26956245.
      View in: PubMed
    28. Jiang Z, Gera L, Mant CT, Hirsch B, Yan Z, Shortt JA, Pollock DD, Qian Z, Holmes KV, Hodges RS. Platform technology to generate broadly cross-reactive antibodies to a-helical epitopes in hemagglutinin proteins from influenza A viruses. Biopolymers. 2016 Mar; 106(2):144-159. PMID: 26799790.
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    29. Speed JS, Heimlich JB, Hyndman KA, Fox BM, Patel V, Yanagisawa M, Pollock JS, Titze JM, Pollock DM. Endothelin-1 as a master regulator of whole-body Na+ homeostasis. FASEB J. 2015 Dec; 29(12):4937-44. PMID: 26268928.
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    30. 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, Wheeler TJ, Bureau TE, Blanchette M. A call for benchmarking transposable element annotation methods. Mob DNA. 2015; 6:13. PMID: 26244060.
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    31. Goldstein RA, Pollard ST, Shah SD, Pollock DD. Nonadaptive Amino Acid Convergence Rates Decrease over Time. Mol Biol Evol. 2015 Jun; 32(6):1373-81. PMID: 25737491.
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    32. 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. Physiol Genomics. 2015 May; 47(5):147-57. PMID: 25670730.
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    33. 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, Zhang Y, Lang Y, Xia J, He W, Shi Q, Subramanian S, Millar CD, Meader S, Rands CM, Fujita MK, Greenwold MJ, Castoe TA, Pollock DD, Gu W, Nam K, Ellegren H, Ho SY, Burt DW, Ponting CP, Jarvis ED, Gilbert MT, Yang H, Wang J, Lambert DM, Wang J, Zhang G. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. Gigascience. 2014; 3(1):27. PMID: 25671092.
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    34. Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Guti?rrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabald?n T, Paten B, Ray DA. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science. 2014 Dec 12; 346(6215):1254449. PMID: 25504731.
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    35. Wacholder AC, Cox C, Meyer TJ, Ruggiero RP, Vemulapalli V, Damert A, Carbone L, Pollock DD. Inference of transposable element ancestry. PLoS Genet. 2014 Aug; 10(8):e1004482. PMID: 25121584.
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    36. Su S, Wang X, Kapuku GK, Treiber FA, Pollock DM, Harshfield GA, McCall WV, Pollock JS. Adverse childhood experiences are associated with detrimental hemodynamics and elevated circulating endothelin-1 in adolescents and young adults. Hypertension. 2014 Jul; 64(1):201-7. PMID: 24777980.
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    37. Pollock DD, Goldstein RA. Strong evidence for protein epistasis, weak evidence against it. Proc Natl Acad Sci U S A. 2014 Apr 15; 111(15):E1450. PMID: 24706894.
      View in: PubMed
    38. Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, W?ster W, Woods AE, Logan JM, Harrison RA, Castoe TA, de Koning AP, Pollock DD, Yandell M, Calderon D, Renjifo C, Currier RB, Salgado D, Pla D, Sanz L, Hyder AS, Ribeiro JM, Arntzen JW, van den Thillart GE, Boetzer M, Pirovano W, Dirks RP, Spaink HP, Duboule D, McGlinn E, Kini RM, Richardson MK. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proc Natl Acad Sci U S A. 2013 Dec 17; 110(51):20651-6. PMID: 24297900.
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    39. 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, Polanco D, Dobry J, Vandewege MW, Li Q, Schott RK, Kapusta A, Minx P, Feschotte C, Uetz P, Ray DA, Hoffmann FG, Bogden R, Smith EN, Chang BS, Vonk FJ, Casewell NR, Henkel CV, Richardson MK, Mackessy SP, Bronikowski AM, Bronikowsi AM, Yandell M, Warren WC, Secor SM, Pollock DD. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proc Natl Acad Sci U S A. 2013 Dec 17; 110(51):20645-50. PMID: 24297902.
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    40. Castoe TA, Pollock DD. Chinese alligator genome illustrates molecular adaptations. Cell Res. 2013 Nov; 23(11):1254-5. PMID: 24060849.
      View in: PubMed
    41. Hyndman KA, Boesen EI, Elmarakby AA, Brands MW, Huang P, Kohan DE, Pollock DM, Pollock JS. Renal collecting duct NOS1 maintains fluid-electrolyte homeostasis and blood pressure. Hypertension. 2013 07; 62(1):91-8. PMID: 23608660.
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    42. 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, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning AP, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol. 2013 Mar 28; 14(3):R28. PMID: 23537068.
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    43. 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, Streicher JW, Wray KP, Yokoyama KD, Pollock DD. Report from the first snake genomics and integrative biology meeting. Stand Genomic Sci. 2012 Oct 10; 7(1):150-2. PMID: 23451292.
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    44. de Koning AP, Gu W, Castoe TA, Pollock DD. Phylogenetics, likelihood, evolution and complexity. Bioinformatics. 2012 Nov 15; 28(22):2989-90. PMID: 22976081.
      View in: PubMed
    45. 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. Mol Ecol Resour. 2012 Nov; 12(6):1105-13. PMID: 22938699.
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    46. Pollock DD, Thiltgen G, Goldstein RA. Amino acid coevolution induces an evolutionary Stokes shift. Proc Natl Acad Sci U S A. 2012 May 22; 109(21):E1352-9. PMID: 22547823.
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    47. 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, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sj?lander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci. 2012 Jun; 21(6):769-85. PMID: 22528593.
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    48. Wang B, Ekblom R, Castoe TA, Jones EP, Kozma R, Bongcam-Rudloff E, Pollock DD, H?glund J. Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development. Open Biol. 2012 Apr; 2(4):120054. PMID: 22724064.
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    49. 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. 2012; 7(2):e30953. PMID: 22348032.
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    50. 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. 2012 Apr; 61(4):857-65. PMID: 22315318.
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    51. 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, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ, Glenn TC, Green RE, Ray DA. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol. 2012 Jan 31; 13(1):415. PMID: 22293439.
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    52. Yokoyama KD, Pollock DD. SP transcription factor paralogs and DNA-binding sites coevolve and adaptively converge in mammals and birds. Genome Biol Evol. 2012; 4(11):1102-17. PMID: 23019068.
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    53. Sun C, Shepard DB, Chong RA, L?pez Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biol Evol. 2012; 4(2):168-83. PMID: 22200636.
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    54. de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011 Dec; 7(12):e1002384. PMID: 22144907.
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    55. 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. 2011; 6(11):e26105. PMID: 22069446.
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    56. Alf?ldi 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, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D, Heger A, Heiman D, Janes DE, Johnson J, de Jong PJ, Koriabine MY, Lara M, Novick PA, Organ CL, Peach SE, Poe S, Pollock DD, de Queiroz K, Sanger T, Searle S, Smith JD, Smith Z, Swofford R, Turner-Maier J, Wade J, Young S, Zadissa A, Edwards SV, Glenn TC, Schneider CJ, Losos JB, Lander ES, Breen M, Ponting CP, Lindblad-Toh K. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 2011 Aug 31; 477(7366):587-91. PMID: 21881562.
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    57. 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 Res Notes. 2011 Aug 25; 4:310. PMID: 21867488.
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    58. 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. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biol. 2011 Jul 28; 12(7):406. PMID: 21801464.
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    59. 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 Biol Evol. 2011; 3:641-53. PMID: 21572095.
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    60. 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). Stand Genomic Sci. 2011 Apr 29; 4(2):257-70. PMID: 21677863.
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    61. 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. Nat Struct Mol Biol. 2010 Oct; 17(10):1279-86. PMID: 20835241.
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    62. 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. Appl Environ Microbiol. 2010 Jun; 76(12):3863-8. PMID: 20418443.
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    63. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, K?nstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backstr?m N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, V?lker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK. The genome of a songbird. Nature. 2010 Apr 01; 464(7289):757-62. PMID: 20360741.
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    64. 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. Cytogenet Genome Res. 2009; 127(2-4):112-27. PMID: 20215734.
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    65. Castoe TA, de Koning AP, Pollock DD. Adaptive molecular convergence: Molecular evolution versus molecular phylogenetics. Commun Integr Biol. 2010 Jan; 3(1):67-9. PMID: 20539788.
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    66. de Koning AP, Gu W, Pollock DD. Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. Mol Biol Evol. 2010 Feb; 27(2):249-65. PMID: 19783593.
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    67. 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. Mol Ecol Resour. 2010 Mar; 10(2):341-7. PMID: 21565030.
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    68. 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. Proc Natl Acad Sci U S A. 2009 Jun 02; 106(22):8986-91. PMID: 19416880.
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    69. 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. 2009; 92(6):573-95. PMID: 19795449.
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    70. Castoe TA, Jiang ZJ, Gu W, Wang ZO, Pollock DD. Adaptive evolution and functional redesign of core metabolic proteins in snakes. PLoS One. 2008 May 21; 3(5):e2201. PMID: 18493604.
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    71. Gu W, Castoe TA, Hedges DJ, Batzer MA, Pollock DD. Identification of repeat structure in large genomes using repeat probability clouds. Anal Biochem. 2008 Sep 01; 380(1):77-83. PMID: 18541131.
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    72. Wang ZO, Pollock DD. Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context. J Mol Evol. 2007 Nov; 65(5):485-95. PMID: 17955155.
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    73. 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. J Mol Biol. 2008 Apr 18; 378(1):71-86. PMID: 18342330.
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    74. 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 Evol Biol. 2007 Jul 26; 7:123. PMID: 17655768.
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    75. 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 Res. 2007 Jul; 17(7):992-1004. PMID: 17495012.
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    76. 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, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 2007 May 10; 447(7141):167-77. PMID: 17495919.
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    77. Hentges KE, Pollock DD, Liu B, Justice MJ. Regional variation in the density of essential genes in mice. PLoS Genet. 2007 May 04; 3(5):e72. PMID: 17480122.
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    78. 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. 2007 Jul 01; 396(1):46-58. PMID: 17442506.
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    79. Williams PD, Pollock DD, Goldstein RA. Functionality and the evolution of marginal stability in proteins: inferences from lattice simulations. Evol Bioinform Online. 2007 Jan 16; 2:91-101. PMID: 19455204.
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    80. 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. 2006 Sep 06; 7 Suppl 2:S7. PMID: 17118150.
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    81. Williams PD, Pollock DD, Blackburne BP, Goldstein RA. Assessing the accuracy of ancestral protein reconstruction methods. PLoS Comput Biol. 2006 Jun 23; 2(6):e69. PMID: 16789817.
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    82. Goldstein RA, Pollock DD. Observations of amino acid gain and loss during protein evolution are explained by statistical bias. Mol Biol Evol. 2006 Jul; 23(7):1444-9. PMID: 16698770.
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    83. Stocks JM, Brantly M, Pollock D, Barker A, Kueppers F, Strange C, Donohue JF, Sandhaus R. Multi-center study: the biochemical efficacy, safety and tolerability of a new alpha1-proteinase inhibitor, Zemaira. COPD. 2006 Mar; 3(1):17-23. PMID: 17175661.
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    84. Williams PD, Pollock DD, Goldstein RA. SELECTIVE ADVANTAGE OF RECOMBINATION IN EVOLVING PROTEIN POPULATIONS: A LATTICE MODEL STUDY. Int J Mod Phys C. 2006 Jan; 17(1):75-90. PMID: 25473139.
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    85. Wheat CW, Watt WB, Pollock DD, Schulte PM. From DNA to fitness differences: sequences and structures of adaptive variants of Colias phosphoglucose isomerase (PGI). Mol Biol Evol. 2006 Mar; 23(3):499-512. PMID: 16292000.
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    86. Xu YO, Hall RW, Goldstein RA, Pollock DD. Divergence, recombination and retention of functionality during protein evolution. Hum Genomics. 2005 Sep; 2(3):158-67. PMID: 16197733.
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    87. Raina SZ, Faith JJ, Disotell TR, Seligmann H, Stewart CB, Pollock DD. Evolution of base-substitution gradients in primate mitochondrial genomes. Genome Res. 2005 May; 15(5):665-73. PMID: 15867428.
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    88. Wang ZO, Pollock DD. Context dependence and coevolution among amino acid residues in proteins. Methods Enzymol. 2005; 395:779-90. PMID: 15865995.
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    89. Krishnan NM, Seligmann H, Raina SZ, Pollock DD. Detecting gradients of asymmetry in site-specific substitutions in mitochondrial genomes. DNA Cell Biol. 2004 Oct; 23(10):707-14. PMID: 15585129.
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    90. 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. Mol Biol Evol. 2004 Oct; 21(10):1871-83. PMID: 15229290.
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    91. Sasser JM, Sullivan JC, Elmarakby AA, Kemp BE, Pollock DM, Pollock JS. Reduced NOS3 phosphorylation mediates reduced NO/cGMP signaling in mesenteric arteries of deoxycorticosterone acetate-salt hypertensive rats. Hypertension. 2004 May; 43(5):1080-5. PMID: 14993198.
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    92. Faith JJ, Pollock DD. Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics. 2003 Oct; 165(2):735-45. PMID: 14573484.
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    93. Pollock DD. Genomic biodiversity, phylogenetics and coevolution in proteins. Appl Bioinformatics. 2002; 1(2):81-92. PMID: 15130847.
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    94. Pollock DD, Eisen JA, Doggett NA, Cummings MP. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Mol Biol Evol. 2000 Dec; 17(12):1776-88. PMID: 11110893.
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    95. Pollock DD, Bruno WJ. Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition. Mol Biol Evol. 2000 Dec; 17(12):1854-8. PMID: 11110901.
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    96. Quattro JM, Pollock DD, Powell M, Woods HA, Powers DA. Evolutionary relations among vertebrate muscle-type lactate dehydrogenases. Mol Mar Biol Biotechnol. 1995 Sep; 4(3):224-31. PMID: 7670598.
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    97. Pollock D, Bauer CE, Scolnik PA. Transcription of the Rhodobacter capsulatus nifHDK operon is modulated by the nitrogen source. Construction of plasmid expression vectors based on the nifHDK promoter. Gene. 1988 May 30; 65(2):269-75. PMID: 3410321.
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