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Items: 36

1.

Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry.

Lewis JJ, Geltman RC, Pollak PC, Rondem KE, Van Belleghem SM, Hubisz MJ, Munn PR, Zhang L, Benson C, Mazo-Vargas A, Danko CG, Counterman BA, Papa R, Reed RD.

Proc Natl Acad Sci U S A. 2019 Nov 11. pii: 201907068. doi: 10.1073/pnas.1907068116. [Epub ahead of print]

PMID:
31712408
2.

SweepFinder2: increased sensitivity, robustness and flexibility.

DeGiorgio M, Huber CD, Hubisz MJ, Hellmann I, Nielsen R.

Bioinformatics. 2016 Jun 15;32(12):1895-7. doi: 10.1093/bioinformatics/btw051. Epub 2016 Feb 15.

PMID:
27153702
3.

Ancient gene flow from early modern humans into Eastern Neanderthals.

Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado-Martinez J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Marques-Bonet T, Andrés AM, Viola B, Pääbo S, Meyer M, Siepel A, Castellano S.

Nature. 2016 Feb 25;530(7591):429-33. doi: 10.1038/nature16544. Epub 2016 Feb 17.

4.

A method for calculating probabilities of fitness consequences for point mutations across the human genome.

Gulko B, Hubisz MJ, Gronau I, Siepel A.

Nat Genet. 2015 Mar;47(3):276-83. doi: 10.1038/ng.3196. Epub 2015 Jan 19.

5.

Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution.

Hubisz MJ, Pollard KS.

Curr Opin Genet Dev. 2014 Dec;29:15-21. doi: 10.1016/j.gde.2014.07.005. Epub 2014 Aug 23. Review.

6.

Genome-wide inference of ancestral recombination graphs.

Rasmussen MD, Hubisz MJ, Gronau I, Siepel A.

PLoS Genet. 2014 May 15;10(5):e1004342. doi: 10.1371/journal.pgen.1004342. eCollection 2014.

7.

A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes.

Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A.

PLoS Genet. 2013;9(8):e1003684. doi: 10.1371/journal.pgen.1003684. Epub 2013 Aug 15.

8.

Genome-wide inference of natural selection on human transcription factor binding sites.

Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A.

Nat Genet. 2013 Jul;45(7):723-9. doi: 10.1038/ng.2658. Epub 2013 Jun 9.

9.

Replacing and additive horizontal gene transfer in Streptococcus.

Choi SC, Rasmussen MD, Hubisz MJ, Gronau I, Stanhope MJ, Siepel A.

Mol Biol Evol. 2012 Nov;29(11):3309-20. doi: 10.1093/molbev/mss138. Epub 2012 May 21.

10.

The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome.

Kostka D, Hubisz MJ, Siepel A, Pollard KS.

Mol Biol Evol. 2012 Mar;29(3):1047-57. doi: 10.1093/molbev/msr279. Epub 2011 Nov 10.

11.

A high-resolution map of human evolutionary constraint using 29 mammals.

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.

Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.

12.

Bayesian inference of ancient human demography from individual genome sequences.

Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A.

Nat Genet. 2011 Sep 18;43(10):1031-4. doi: 10.1038/ng.937.

13.

Error and error mitigation in low-coverage genome assemblies.

Hubisz MJ, Lin MF, Kellis M, Siepel A.

PLoS One. 2011 Feb 14;6(2):e17034. doi: 10.1371/journal.pone.0017034.

14.

Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution.

Suzuki H, Lefébure T, Hubisz MJ, Pavinski Bitar P, Lang P, Siepel A, Stanhope MJ.

Genome Biol Evol. 2011;3:168-85. doi: 10.1093/gbe/evr006. Epub 2011 Jan 31.

15.

PHAST and RPHAST: phylogenetic analysis with space/time models.

Hubisz MJ, Pollard KS, Siepel A.

Brief Bioinform. 2011 Jan;12(1):41-51. doi: 10.1093/bib/bbq072. Epub 2010 Dec 21.

16.

A simple genetic architecture underlies morphological variation in dogs.

Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, vonHoldt BM, Cargill M, Auton A, Reynolds A, Elkahloun AG, Castelhano M, Mosher DS, Sutter NB, Johnson GS, Novembre J, Hubisz MJ, Siepel A, Wayne RK, Bustamante CD, Ostrander EA.

PLoS Biol. 2010 Aug 10;8(8):e1000451. doi: 10.1371/journal.pbio.1000451.

17.

Detection of nonneutral substitution rates on mammalian phylogenies.

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A.

Genome Res. 2010 Jan;20(1):110-21. doi: 10.1101/gr.097857.109. Epub 2009 Oct 26.

18.

Inferring weak population structure with the assistance of sample group information.

Hubisz MJ, Falush D, Stephens M, Pritchard JK.

Mol Ecol Resour. 2009 Sep;9(5):1322-32. doi: 10.1111/j.1755-0998.2009.02591.x. Epub 2009 Apr 1.

19.

Targets of balancing selection in the human genome.

Andrés AM, Hubisz MJ, Indap A, Torgerson DG, Degenhardt JD, Boyko AR, Gutenkunst RN, White TJ, Green ED, Bustamante CD, Clark AG, Nielsen R.

Mol Biol Evol. 2009 Dec;26(12):2755-64. doi: 10.1093/molbev/msp190. Epub 2009 Aug 27.

20.

Darwinian and demographic forces affecting human protein coding genes.

Nielsen R, Hubisz MJ, Hellmann I, Torgerson D, Andrés AM, Albrechtsen A, Gutenkunst R, Adams MD, Cargill M, Boyko A, Indap A, Bustamante CD, Clark AG.

Genome Res. 2009 May;19(5):838-49. doi: 10.1101/gr.088336.108. Epub 2009 Mar 11.

21.

Patterns of positive selection in six Mammalian genomes.

Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A.

PLoS Genet. 2008 Aug 1;4(8):e1000144. doi: 10.1371/journal.pgen.1000144.

22.

Proportionally more deleterious genetic variation in European than in African populations.

Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD.

Nature. 2008 Feb 21;451(7181):994-7. doi: 10.1038/nature06611.

23.

Patterns of mutation and selection at synonymous sites in Drosophila.

Singh ND, Bauer DuMont VL, Hubisz MJ, Nielsen R, Aquadro CF.

Mol Biol Evol. 2007 Dec;24(12):2687-97. Epub 2007 Nov 13.

PMID:
18000010
24.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
25.

Localizing recent adaptive evolution in the human genome.

Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, Nielsen R.

PLoS Genet. 2007 Jun;3(6):e90. Epub 2007 Apr 20.

26.

Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques.

Hernandez RD, Hubisz MJ, Wheeler DA, Smith DG, Ferguson B, Rogers J, Nazareth L, Indap A, Bourquin T, McPherson J, Muzny D, Gibbs R, Nielsen R, Bustamante CD.

Science. 2007 Apr 13;316(5822):240-3.

27.

Evolutionary and biomedical insights from the rhesus macaque genome.

Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS.

Science. 2007 Apr 13;316(5822):222-34.

28.

Adaptive genic evolution in the Drosophila genomes.

Shapiro JA, Huang W, Zhang C, Hubisz MJ, Lu J, Turissini DA, Fang S, Wang HY, Hudson RR, Nielsen R, Chen Z, Wu CI.

Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2271-6. Epub 2007 Feb 6.

29.

Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila.

Nielsen R, Bauer DuMont VL, Hubisz MJ, Aquadro CF.

Mol Biol Evol. 2007 Jan;24(1):228-35. Epub 2006 Oct 13.

PMID:
17041152
30.

Genomic scans for selective sweeps using SNP data.

Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C.

Genome Res. 2005 Nov;15(11):1566-75.

31.

Ascertainment bias in studies of human genome-wide polymorphism.

Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R.

Genome Res. 2005 Nov;15(11):1496-502.

32.

Detecting coevolving amino acid sites using Bayesian mutational mapping.

Dimmic MW, Hubisz MJ, Bustamante CD, Nielsen R.

Bioinformatics. 2005 Jun;21 Suppl 1:i126-35.

PMID:
15961449
33.

A scan for positively selected genes in the genomes of humans and chimpanzees.

Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, J Sninsky J, Adams MD, Cargill M.

PLoS Biol. 2005 Jun;3(6):e170. Epub 2005 May 3.

34.

Evolutionary genomics: detecting selection needs comparative data.

Nielsen R, Hubisz MJ.

Nature. 2005 Jan 20;433(7023):E6; discussion E7-8.

PMID:
15662372
35.

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.

Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MA, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA.

Genome Res. 2005 Jan;15(1):1-18.

36.

Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data.

Nielsen R, Hubisz MJ, Clark AG.

Genetics. 2004 Dec;168(4):2373-82. Epub 2004 Sep 15.

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