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Items: 44

1.

diploS/HIC: An Updated Approach to Classifying Selective Sweeps.

Kern AD, Schrider DR.

G3 (Bethesda). 2018 Apr 6. pii: g3.200262.2018. doi: 10.1534/g3.118.200262. [Epub ahead of print]

2.

Supervised Machine Learning for Population Genetics: A New Paradigm.

Schrider DR, Kern AD.

Trends Genet. 2018 Apr;34(4):301-312. doi: 10.1016/j.tig.2017.12.005. Epub 2018 Jan 10. Review.

3.
4.

Exact Calculation of the Joint Allele Frequency Spectrum for Isolation with Migration Models.

Kern AD, Hey J.

Genetics. 2017 Sep;207(1):241-253. doi: 10.1534/genetics.116.194019. Epub 2017 Jul 10.

5.

Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome.

Schrider DR, Kern AD.

Mol Biol Evol. 2017 Aug 1;34(8):1863-1877. doi: 10.1093/molbev/msx154.

6.

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection.

Schrider DR, Shanku AG, Kern AD.

Genetics. 2016 Nov;204(3):1207-1223. doi: 10.1534/genetics.116.190223. Epub 2016 Sep 7.

7.

Discoal: flexible coalescent simulations with selection.

Kern AD, Schrider DR.

Bioinformatics. 2016 Dec 15;32(24):3839-3841. Epub 2016 Aug 24.

8.

S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning.

Schrider DR, Kern AD.

PLoS Genet. 2016 Mar 15;12(3):e1005928. doi: 10.1371/journal.pgen.1005928. eCollection 2016 Mar.

9.

Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain.

Schrider DR, Kern AD.

Genome Biol Evol. 2015 Nov 19;7(12):3511-28. doi: 10.1093/gbe/evv228.

10.

Myristoylated CIL-7 regulates ciliary extracellular vesicle biogenesis.

Maguire JE, Silva M, Nguyen KC, Hellen E, Kern AD, Hall DH, Barr MM.

Mol Biol Cell. 2015 Aug 1;26(15):2823-32. doi: 10.1091/mbc.E15-01-0009. Epub 2015 Jun 3.

11.

Soft shoulders ahead: spurious signatures of soft and partial selective sweeps result from linked hard sweeps.

Schrider DR, Mendes FK, Hahn MW, Kern AD.

Genetics. 2015 May;200(1):267-84. doi: 10.1534/genetics.115.174912. Epub 2015 Feb 25.

12.

The role of DNA insertions in phenotypic differentiation between humans and other primates.

Hellen EH, Kern AD.

Genome Biol Evol. 2015 Jan 28;7(4):1168-78. doi: 10.1093/gbe/evv012.

13.

Highly constrained intergenic Drosophila ultraconserved elements are candidate ncRNAs.

Kern AD, Barbash DA, Chang Mell J, Hupalo D, Jensen A.

Genome Biol Evol. 2015 Jan 23;7(3):689-98. doi: 10.1093/gbe/evv011.

14.

Discovering functional DNA elements using population genomic information: a proof of concept using human mtDNA.

Schrider DR, Kern AD.

Genome Biol Evol. 2014 Jun 9;6(7):1542-8. doi: 10.1093/gbe/evu116.

15.

Parallel geographic variation in Drosophila melanogaster.

Reinhardt JA, Kolaczkowski B, Jones CD, Begun DJ, Kern AD.

Genetics. 2014 May;197(1):361-73. doi: 10.1534/genetics.114.161463. Epub 2014 Mar 7.

16.

Conservation and functional element discovery in 20 angiosperm plant genomes.

Hupalo D, Kern AD.

Mol Biol Evol. 2013 Jul;30(7):1729-44. doi: 10.1093/molbev/mst082. Epub 2013 May 2.

PMID:
23640124
17.

Functional Annotation and Comparative Analysis of a Zygopteran Transcriptome.

Shanku AG, McPeek MA, Kern AD.

G3 (Bethesda). 2013 Apr 9;3(4):763-770. doi: 10.1534/g3.113.005637.

18.

Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes.

Kritsas K, Wuest SE, Hupalo D, Kern AD, Wicker T, Grossniklaus U.

Genome Res. 2012 Dec;22(12):2455-66. doi: 10.1101/gr.129346.111. Epub 2012 Sep 17.

19.

Genomic variation in natural populations of Drosophila melanogaster.

Langley CH, Stevens K, Cardeno C, Lee YC, Schrider DR, Pool JE, Langley SA, Suarez C, Corbett-Detig RB, Kolaczkowski B, Fang S, Nista PM, Holloway AK, Kern AD, Dewey CN, Song YS, Hahn MW, Begun DJ.

Genetics. 2012 Oct;192(2):533-98. doi: 10.1534/genetics.112.142018. Epub 2012 Jun 5.

20.

Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster.

Kolaczkowski B, Kern AD, Holloway AK, Begun DJ.

Genetics. 2011 Jan;187(1):245-60. doi: 10.1534/genetics.110.123059. Epub 2010 Nov 8.

21.

Recurrent adaptation in RNA interference genes across the Drosophila phylogeny.

Kolaczkowski B, Hupalo DN, Kern AD.

Mol Biol Evol. 2011 Feb;28(2):1033-42. doi: 10.1093/molbev/msq284. Epub 2010 Oct 22.

PMID:
20971974
22.

Kinetic and structural characterization of DmpI from Helicobacter pylori and Archaeoglobus fulgidus, two 4-oxalocrotonate tautomerase family members.

Almrud JJ, Dasgupta R, Czerwinski RM, Kern AD, Hackert ML, Whitman CP.

Bioorg Chem. 2010 Dec;38(6):252-9. doi: 10.1016/j.bioorg.2010.07.002. Epub 2010 Jul 18.

23.

GC-biased evolution near human accelerated regions.

Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D.

PLoS Genet. 2010 May 20;6(5):e1000960. doi: 10.1371/journal.pgen.1000960.

24.

A population genetic hidden Markov model for detecting genomic regions under selection.

Kern AD, Haussler D.

Mol Biol Evol. 2010 Jul;27(7):1673-85. doi: 10.1093/molbev/msq053. Epub 2010 Feb 25.

25.

Correcting the site frequency spectrum for divergence-based ascertainment.

Kern AD.

PLoS One. 2009;4(4):e5152. doi: 10.1371/journal.pone.0005152. Epub 2009 Apr 16.

26.
27.

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.

Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH.

PLoS Biol. 2007 Nov 6;5(11):e310.

28.

Human genome ultraconserved elements are ultraselected.

Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D.

Science. 2007 Aug 17;317(5840):915.

29.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

30.

Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade.

Begun DJ, Lindfors HA, Kern AD, Jones CD.

Genetics. 2007 Jun;176(2):1131-7. Epub 2007 Apr 15.

31.

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.

32.

Variation resources at UC Santa Cruz.

Thomas DJ, Trumbower H, Kern AD, Rhead BL, Kuhn RM, Haussler D, Kent WJ.

Nucleic Acids Res. 2007 Jan;35(Database issue):D716-20. Epub 2006 Dec 6.

33.

Forces shaping the fastest evolving regions in the human genome.

Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D.

PLoS Genet. 2006 Oct 13;2(10):e168. Epub 2006 Aug 23.

34.

An RNA gene expressed during cortical development evolved rapidly in humans.

Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, Haussler D.

Nature. 2006 Sep 14;443(7108):167-72. Epub 2006 Aug 16.

PMID:
16915236
35.

Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression.

Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ.

Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9935-9. Epub 2006 Jun 15.

36.

Evolutionary genomics: codon bias and selection on single genomes.

Hahn MW, Mezey JG, Begun DJ, Gillespie JH, Kern AD, Langley CH, Moyle LC.

Nature. 2005 Jan 20;433(7023):E5-6; discussion E7-8.

PMID:
15662370
37.

Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks.

Hahn MW, Kern AD.

Mol Biol Evol. 2005 Apr;22(4):803-6. Epub 2004 Dec 22.

PMID:
15616139
38.

Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs.

Kern AD, Kondrashov FA.

Nat Genet. 2004 Nov;36(11):1207-12. Epub 2004 Oct 24.

PMID:
15502829
39.
40.
41.

Genomic effects of nucleotide substitutions in Drosophila simulans.

Kern AD, Jones CD, Begun DJ.

Genetics. 2002 Dec;162(4):1753-61.

42.

The crystal structure of YdcE, a 4-oxalocrotonate tautomerase homologue from Escherichia coli, confirms the structural basis for oligomer diversity.

Almrud JJ, Kern AD, Wang SC, Czerwinski RM, Johnson WH Jr, Murzin AG, Hackert ML, Whitman CP.

Biochemistry. 2002 Oct 8;41(40):12010-24.

PMID:
12356301
43.

Crystal structure of human ornithine decarboxylase at 2.1 A resolution: structural insights to antizyme binding.

Almrud JJ, Oliveira MA, Kern AD, Grishin NV, Phillips MA, Hackert ML.

J Mol Biol. 2000 Jan 7;295(1):7-16.

PMID:
10623504
44.

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