David Pollock, PhD
Professor, Biochemistry & Molecular Genetics

Publications

  • 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 Jan;15(1):e0009020. PubMed PMID: 33406094
  • 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 K, Briggs J, van Gils M, 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 Feb 5. [Epub ahead of print] PubMed PMID: 33545711
  • Fukushima K, Pollock DD. Author Correction: Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution. Nat Commun. 2021 Sep 2;12(1):5313. PubMed PMID: 34475380
  • 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 Apr 20;118(16). PubMed PMID: 33879570
  • 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 Mar 25;11(1):6884. PubMed PMID: 33767307
  • 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 Apr;592(7853):277-282. PubMed PMID: 33545711
  • 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 Jan;15(1):e0009020. PubMed PMID: 33406094
  • Pollock DD. Society for Molecular Biology and Evolution, Council and Business Meetings, 2019, Manchester, United Kingdom. Mol Biol Evol. 2020 Jan 1;37(1):301-303. PubMed PMID: 31986214
  • 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. PubMed PMID: 32095164
  • 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 Sep 1;37(9):2706-2710. PubMed PMID: 32658964
  • Fukushima K, Pollock DD. Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution. Nat Commun. 2020 Sep 8;11(1):4459. PubMed PMID: 32900997
  • 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 Gils MJ, 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. PubMed PMID: 33398302
  • Pollock DD. Society for Molecular Biology and Evolution, Council and Business Meetings, 2018, Yokohama, Japan. Mol Biol Evol. 2019 Jan 1;36(1):204-206. PubMed PMID: 30657947
  • Pollock DD. Society for Molecular Biology and Evolution, Council and Business Meetings, 2018, Yokohama, Japan. Mol Biol Evol. 2019 Jan 1;36(1):204-206. PubMed PMID: 30657947
  • 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 Sep 14;430(18 Pt B):3234-3250. PubMed PMID: 29932944
  • 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 Jan 20;11(1):e0005292. PubMed PMID: 28107347
  • 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. PubMed PMID: 29062121
  • 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, Pálfalvi G, Pollard ST, Rozas J, Sánchez-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 6;1(3):59. PubMed PMID: 28812732
  • 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 Jan;11(1):e0005292. PubMed PMID: 28107347
  • 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 a-helical epitopes in hemagglutinin proteins from influenza a viruses. Biopolymers. 2016 Jan 21. [Epub ahead of print] PubMed PMID: 26799790
  • Goldstein RA, Pollock DD. The tangled bank of amino acids. Protein Sci. 2016 Jul;25(7):1354-62. PubMed PMID: 27028523
  • 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 a-helical epitopes in hemagglutinin proteins from influenza a viruses. Biopolymers. 2016 Jan 21. [Epub ahead of print] PubMed PMID: 26799790
  • Goldstein RA, Pollard ST, Shah SD, Pollock DD. Non-Adaptive Amino Acid Convergence Rates Decrease over Time. Mol Biol Evol. 2015 Mar 3. [Epub ahead of print] PubMed PMID: 25737491
  • 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 Feb 10;:physiolgenomics.00131.2014. [Epub ahead of print] PubMed PMID: 25670730
  • 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. PubMed PMID: 26244060
  • 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. PubMed PMID: 25737491
  • 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. PubMed PMID: 25670730
  • Pollock DD, Goldstein RA. Strong evidence for protein epistasis, weak evidence against it. Proc Natl Acad Sci U S A. 2014 Mar 20. [Epub ahead of print] PubMed PMID: 24706894
  • 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. PubMed PMID: 25671092
  • 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, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW Jr, 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, Gabaldón T, Paten B, Ray DA. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science. 2014 Dec 12;346(6215):1254449. PubMed PMID: 25504731
  • 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. PubMed PMID: 25121584
  • 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. PubMed PMID: 24706894
  • 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, 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. PubMed PMID: 24297902
  • 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, 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. PubMed PMID: 24297900
  • Castoe TA, Pollock DD. Chinese alligator genome illustrates molecular adaptations. Cell Res. 2013 Nov;23(11):1254-5. PubMed PMID: 24060849
  • 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 AJ, 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. [Epub ahead of print] PubMed PMID: 23537068
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Department: Biochemistry & Molecular Genetics
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