 Connection
David Pollock to Evolution, Molecular
This is a "connection" page, showing publications David Pollock has written about Evolution, Molecular.
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Connection Strength |
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7.207 |
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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.
Score: 0.645
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Fukushima K, Pollock DD. Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution. Nat Commun. 2020 09 08; 11(1):4459.
Score: 0.549
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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.
Score: 0.450
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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.
Score: 0.374
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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.
Score: 0.360
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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.
Score: 0.350
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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.
Score: 0.343
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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.
Score: 0.307
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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.
Score: 0.265
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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.
Score: 0.250
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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.
Score: 0.234
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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.
Score: 0.225
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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.
Score: 0.221
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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.
Score: 0.216
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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.
Score: 0.208
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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.
Score: 0.203
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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.
Score: 0.194
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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.
Score: 0.189
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Wang ZO, Pollock DD. Context dependence and coevolution among amino acid residues in proteins. Methods Enzymol. 2005; 395:779-90.
Score: 0.185
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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.
Score: 0.179
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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.
Score: 0.141
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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.
Score: 0.139
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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.
Score: 0.139
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Goldstein RA, Pollock DD. The tangled bank of amino acids. Protein Sci. 2016 07; 25(7):1354-62.
Score: 0.102
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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.
Score: 0.092
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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.
Score: 0.086
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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.
Score: 0.077
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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.
Score: 0.075
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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.
Score: 0.073
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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.
Score: 0.064
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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.
Score: 0.054
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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.
Score: 0.054
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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.
Score: 0.051
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Pollock DD. Genomic biodiversity, phylogenetics and coevolution in proteins. Appl Bioinformatics. 2002; 1(2):81-92.
Score: 0.038
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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).
Score: 0.036
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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.
Score: 0.020
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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.
Score: 0.017
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Connection Strength
The connection strength for concepts is the sum of the scores for each matching publication.
Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.
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