David Pollock, PhD

C. Mant, J. M. Kovacs, H. Kim, and D. D. Pollock, and R.S. Hodges “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 (Peptide Science), 92(6):573-595 (2009).

T. A. Castoe*, A. P. J. de Koning*, and D. D. Pollock, ?Adaptive molecular convergences?Molecular evolution versus molecular phylogenetics.? Communicative and Integrative Biology, 3(1): 67-69, (2009).

T. A. Castoe*, A. P. J. de Koning*, H. Kim, W. Gu, B. P Noonan, G. Naylor, Z. J. Jiang, C. L. Parkinson, and D. D. Pollock, ?From the Cover: Evidence for an ancient adaptive episode of convergent molecular evolution.? Proceeding of the National Academy of Sciences 106(22):8986-91, (2009). a. T. A. Castoe*, A. P. J. de Koning*, H. Kim, W. Gu, B. P Noonan, Z. J. Jiang, C. L. Parkinson, and D. D. Pollock, ?An ancient adaptive episode of convergent molecular evolution confounds phylogenetic inference.? Available from Nature Precedings, (2008). b. See commentary by S.A. Edwards, ?Natural selection and phylogenetic analysis?, Proceeding of the National Academy of Sciences 106(22):8799-8800, (2009)

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

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

T. A. Castoe, A. W. Poole, W. Gu, A. P. J. de Koning, J. M. Daza, E. N. Smith, and D. D. Pollock, ?Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence.? Molecular Ecology Resources, in press [Published Online, 30 July] (2009).

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

10. T. A. Castoe, A. W. Poole, W. Gu, A. P. J. de Koning, J. M. Daza, E. N. Smith, and D. D. Pollock, “Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence.” Molecular Ecology Resources, Published Online, 30 July (2009), 10(2):341-347 (2010).

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

9. T. A. Castoe*, A. P. J. de Koning*, and D. D. Pollock, “Adaptive molecular convergences—Molecular evolution versus molecular phylogenetics.” Communicative and Integrative Biology, Jan;3(1):67-9, (2010).

8. A. P. J. de Koning, W. Gu, and D. D. Pollock, “Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories.” Molecular Biology and Evolution, Feb;27(2):249-65, (2010).

7. H. Kim, B. Erickson, W. Luo, D. Seward, J. H. Graber, D.D. Pollock, P. C. Megee, and D. L. Bentley. “Gene-specific RNA polymerase II phosphorylation and the CTD code”. Nature Struc. Mol. Biol., 17(10): 1279-86. Epub Sep 12 (2010).

6. J. K. Harris, J.W. Sahl, T.A. Castoe, D.D. Pollock, and J.R. Spear. “Comparison of normalization methods for construction of large multiplex amplicon pools for next-generation sequencing”. Applied and Environmental Microbiology, 76(12):3863-8. Epub Apr 23, (2010).

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

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

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

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

5. Warren, W.C.,…D. D. Pollock, …, and R.K. Wilson, “The genome of a songbird.” Nature, 464 (7269):757-62 (2010).

1. Castoe, T. A., K. Hall, M. L. Guibotsy Mboulas, W. Gu, A. P. J. de Koning, A. W. Poole, V. Vemulapalli, J. M. Daza, C. Feschotte, and D. D. Pollock. “Discovery of highly divergent repeat landscapes in snake genomes using high throughput sequencing”. Genome Biology and Evolution, x: xx-xx, in press pending acceptance of minor revisions. (2011).

16. T. A. Castoe, A. M. Bronikowski, E. Brodie III, S. V. Edwards, M. Pfrender, M. Shipiro, D. D. Pollock, and W. Warren. “A proposal to sequence the genome of a garter snake.” Standards in Genomic Sciences, 4:257-270, (2011).

15. T. A. Castoe, A. P. J. de Koning, K. Hall, K. D. Yokoyama, W. Gu, E. N. Smith, C. Feschotte, P. Uetz, D. A. Ray, J. Dobry, R. Bogden, S. P. Mackessey, A. M. Bronikowski , W. C. Warren, S. Secor, and D. D. Pollock. “Sequencing the genome of the Burmese python (Python molurus bivittatus) - a model for studying extreme adaptations in snakes.” Genome Biology, 12(7):406. (2011).

14. T. A. Castoe, K. Hall, M. L. Guibotsy Mboulas, W. Gu, A. P. J. de Koning, A. W. Poole, V. Vemulapalli, J. M. Daza, C. Feschotte, and D. D. Pollock. “Discovery of highly divergent repeat landscapes in snake genomes using high throughput sequencing.” Genome Biology and Evolution, 3:641-653. (2011).

13. T. A. Castoe, S. E. Fox, A. P. J. de Koning, A. W. Poole, J. M. Daza, E. N. Smith, T. Mockler, S. Secor, and D. D. Pollock. “A multi-organ transcriptome resource for the Burmese python (Python molurus bivittatus).” BMC Research Notes, 4:310, (2011).

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

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

12. D. D. Pollock, A. P. J. de Koning, H. Kim, T. A. Castoe, M. Churchill, and K. J. Kechris. “Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions.” PLoS ONE, 6(11) e26105, (2011).

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. The tangled bank of amino acids. Protein Sci. 2016 Jul;25(7):1354-62. PubMed PMID: 27028523

11. Alföldi, J., …, T. A. Castoe, D. D Pollock, ..., K. Linblad-Toh. “The genome of Anolis carolinensis, the green anole lizard, and a comparative analysis with birds and mammals.” Nature, 477(7366):587-91 (2011).

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

10. A.P.J. de Koning, W. Gu, T.A. Castoe, M. A. Batzer, and D. D. Pollock. “Repetitive elements may comprise over two-thirds of the human genome.” PLoS Genetics, Dec; 7(12):e1002384, (2011).

Nature Ecology & Evolution 1, Article number: 0059 (2017) doi:10.1038/s41559-016-0059

9. C. Sun, D. B. Shepard, A. J. López Arriaza, K. Hall, T. A. Castoe, C. Feschotte, D. D. Pollock, and R. L. Mueller, “LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders.” Genome Biology and Evolution, 4(2):168-83 (2012).

8. J. A. St. John, E. L Braun, ..., T.A Castoe, ..., D. D. Pollock, ..., [47 total authors], E. L. Green, and D. A. Ray, “Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.” Genome Biology Jan 31; 13(1):415 (2012).

7. T. A. Castoe, A. W. Poole, A. P. J. de Koning, K. L. Jones, D. F. Tomback, S. J. Oyler-McCance, J. A. Fike, S. L. Lance, J. W. Streicher, E. N. Smith and D. D. Pollock. “Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake.” PLoS One, 7(2):e30953, (2012).

3. B. Wang, R. Ekblom, T.A. Castoe, E. P. Jones, R. Kozma, E. Bongcam-Rudloff, D. D. Pollock, and J. Höglund. “Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development.” BMC Genomics, in press, (2012).

2. M. Nakayama, T.A. Castoe, T. Sosinowski, X. L. He, K. Johnson, K. Haskins, D. A. Vignali, L. Gapin, D. D. Pollock, and G. Eisenbarth. “Germline TRAV5D-4 T Cell Receptor Sequence Targets a Primary Insulin Peptide of NOD Mice.” Diabetes, (epub ahead of print Feb 7, 2012), (2012).

1. D. D. Pollock, Grant Thiltgen, and R. A. Goldstein, “Amino acid coevolution induces an evolutionary Stokes shift.” Proceeding of the National Academy of Sciences Plus, in press, (2012).

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Abramyan J, 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, Hillier LH, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning J, Li Y, Literman R, Mardis ER, McGaugh SE, Minx P, Mork L, O 8217 Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Shaffer B, Shedlock AM, Spinks PQ, Storey KB, Thane N, Thomson RC, Valenzuela N, Vinar T, Warren DE, Warren WC, Wilson RK, Zimmerman LM, Hernandez O, Amemiya CT. Genome Biol. 2013 Mar 28;14(3):R28. [Epub ahead of print] PMID: 23537068

Report from the first snake genomics and integrative biology meeting. 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. Stand Genomic Sci. 2012 Oct 10;7(1):150-2. doi: 10.4056/sigs.3106480. Epub 2012 Sep 24. PMID: 23451292

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

D. D. Pollock, “Society for Molecular Biology and Evolution, council and business meetings, Austin TX.” Molecular Biology and Evolution 35(1):259-261, January, (2018). Published 22 Dec., 2017.

A. C. Wacholder and D. D. Pollock, “PRDM9 and an epidemic of gene conversion and nonhomologous recombination among Alu elements in ancestral gorillas.” BioRxiv, 241356, Dec. 31, (2017).

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

SP transcription factor paralogs and DNA-binding sites coevolve and adaptively converge in mammals and birds. Yokoyama KD, Pollock DD. Genome Biol Evol. 2012;4(11):1102-17. doi: 10.1093/gbe/evs085. PMID: 23019068

Phylogenetics, likelihood, evolution and complexity. de Koning AP, Gu W, Castoe TA, Pollock DD. Bioinformatics. 2012 Nov 15;28(22):2989-90. doi: 10.1093/bioinformatics/bts555. Epub 2012 Sep 12. PMID: 22976081

Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species. Castoe TA, Streicher JW, Meik JM, Ingrasci MJ, Poole AW, de Koning AP, Campbell JA, Parkinson CL, Smith EN, Pollock DD. Mol Ecol Resour. 2012 Nov;12(6):1105-13. doi: 10.1111/1755-0998.12000. Epub 2012 Sep 1. PMID: 22938699

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

Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development. Wang B, Ekblom R, Castoe TA, Jones EP, Kozma R, Bongcam-Rudloff E, Pollock DD, Höglund J. Open Biol. 2012 Apr;2(4):120054. doi: 10.1098/rsob.120054. PMID: 22724064

Amino acid coevolution induces an evolutionary Stokes shift. Pollock DD, Thiltgen G, Goldstein RA. Proc Natl Acad Sci U S A. 2012 May 22;109(21):E1352-9. doi: 10.1073/pnas.1120084109. Epub 2012 Apr 30. PMID: 22547823

The interface of protein structure, protein biophysics, and molecular evolution. 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, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review. PMID: 22528593

Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. Castoe TA, Poole AW, de Koning AP, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, Pollock DD. PLoS One. 2012;7(2):e30953. doi: 10.1371/journal.pone.0030953. Epub 2012 Feb 14. PMID: 22348032

10. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. 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 Jr, Glenn TC, Green RE, Ray DA. Genome Biol. 2012 Jan 31;13(1):415. doi: 10.1186/gb-2012-13-1-415. PMID: 22293439

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

11. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Sun C, Shepard DB, Chong RA, López Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL. Genome Biol Evol. 2012;4(2):168-83. doi: 10.1093/gbe/evr139. Epub 2011 Dec 26. PMID: 22200636

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

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 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

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

Fukushima K, Pollock DD. Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence. Nat Ecol Evol. 2023 Jan;7(1):155-170. PubMed PMID: 36604553

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. PubMed PMID: 36194597

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 Aug 30;11. PubMed PMID: 36040013

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. PubMed PMID: 35864233

Nikolakis ZL, Carlton EJ, Pollock DD, Castoe TA. A genomic can of worms for schistosome host-specificity. Trends Parasitol. 2022 Jul;38(7):496-497. PubMed PMID: 35504822

Prospects for genomic surveillance for selection in schistosome parasites, Zachary L. Nikolakis, Richard H. Adams, Kristen J. Wade, Andrea J. Lund, Elizabeth J. Carlton, Todd A. Castoe and David D. Pollock, 29 September 2022, Sec. Infectious Disease Epidemiology Volume 2 - 2022 | https://doi.org/10.3389/fepid.2022.932021

Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence. Fukushima K, Pollock DD. Nat Ecol Evol. 2023 Jan;7(1):155-170. doi: 10.1038/s41559-022-01932-7. Epub 2023 Jan 5. PMID: 36604553

Professor, Biochemistry & Molecular Genetics

Department

Publications

School of Medicine

CU Anschutz

Fitzsimons Building