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Items: 1 to 20 of 35

1.

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
2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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