 Connection
David Pollock to Phylogeny
This is a "connection" page, showing publications David Pollock has written about Phylogeny.
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Connection Strength |
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3.020 |
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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: 0.365
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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: 0.355
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de Koning AP, Gu W, Castoe TA, Pollock DD. Phylogenetics, likelihood, evolution and complexity. Bioinformatics. 2012 Nov 15; 28(22):2989-90.
Score: 0.320
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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: 0.269
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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: 0.192
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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: 0.163
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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: 0.141
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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: 0.139
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Goldstein RA, Pollock DD. The tangled bank of amino acids. Protein Sci. 2016 07; 25(7):1354-62.
Score: 0.103
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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: 0.095
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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: 0.083
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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: 0.078
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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: 0.076
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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: 0.065
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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: 0.063
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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: 0.057
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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: 0.056
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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: 0.055
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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.
Score: 0.046
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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: 0.045
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Faith JJ, Pollock DD. Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics. 2003 Oct; 165(2):735-45.
Score: 0.043
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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.
Score: 0.040
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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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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: 0.036
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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: 0.035
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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: 0.023
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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: 0.019
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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: 0.014
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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.
Score: 0.006
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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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