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Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia.

Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE.

Science. 2018 Aug 3;361(6401):511-516. doi: 10.1126/science.aar8486.


Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana.

Press MO, McCoy RC, Hall AN, Akey JM, Queitsch C.

Genome Res. 2018 Aug;28(8):1169-1178. doi: 10.1101/gr.231753.117. Epub 2018 Jul 3.


Outstanding questions in the study of archaic hominin admixture.

Wolf AB, Akey JM.

PLoS Genet. 2018 May 31;14(5):e1007349. doi: 10.1371/journal.pgen.1007349. eCollection 2018 May. Review.


Evolution of DNAase I Hypersensitive Sites in MHC Regulatory Regions of Primates.

Jin Y, Gittelman RM, Lu Y, Liu X, Li MD, Ling F, Akey JM.

Genetics. 2018 Jun;209(2):579-589. doi: 10.1534/genetics.118.301028. Epub 2018 Apr 18.


Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture.

Browning SR, Browning BL, Zhou Y, Tucci S, Akey JM.

Cell. 2018 Mar 22;173(1):53-61.e9. doi: 10.1016/j.cell.2018.02.031. Epub 2018 Mar 15.


Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation.

McCoy RC, Akey JM.

Genome Biol. 2017 Aug 1;18(1):139. doi: 10.1186/s13059-017-1280-5.


Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression.

McCoy RC, Wakefield J, Akey JM.

Cell. 2017 Feb 23;168(5):916-927.e12. doi: 10.1016/j.cell.2017.01.038.


Tracing the peopling of the world through genomics.

Nielsen R, Akey JM, Jakobsson M, Pritchard JK, Tishkoff S, Willerslev E.

Nature. 2017 Jan 18;541(7637):302-310. doi: 10.1038/nature21347. Review.


Editorial overview: Genetics of human origin: New horizons in human population genetics.

Akey JM, Di Rienzo A.

Curr Opin Genet Dev. 2016 Dec;41:v-vi. doi: 10.1016/j.gde.2016.11.002. Epub 2016 Nov 23. No abstract available.


Human RECQ Helicase Pathogenic Variants, Population Variation and "Missing" Diseases.

Fu W, Ligabue A, Rogers KJ, Akey JM, Monnat RJ Jr.

Hum Mutat. 2017 Feb;38(2):193-203. doi: 10.1002/humu.23148. Epub 2016 Dec 9.


Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments.

Gittelman RM, Schraiber JG, Vernot B, Mikacenic C, Wurfel MM, Akey JM.

Curr Biol. 2016 Dec 19;26(24):3375-3382. doi: 10.1016/j.cub.2016.10.041. Epub 2016 Nov 10.


Robust Inference of Identity by Descent from Exome-Sequencing Data.

Fu W, Browning SR, Browning BL, Akey JM.

Am J Hum Genet. 2016 Nov 3;99(5):1106-1116. doi: 10.1016/j.ajhg.2016.09.011. Epub 2016 Oct 13.


Detecting Sources of Transcriptional Heterogeneity in Large-Scale RNA-Seq Data Sets.

Searle BC, Gittelman RM, Manor O, Akey JM.

Genetics. 2016 Dec;204(4):1391-1396. Epub 2016 Oct 11.


Population genetics: A map of human wanderlust.

Tucci S, Akey JM.

Nature. 2016 Oct 13;538(7624):179-180. doi: 10.1038/nature19472. Epub 2016 Sep 21. No abstract available.


Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.

Nuttle X, Giannuzzi G, Duyzend MH, Schraiber JG, Narvaiza I, Sudmant PH, Penn O, Chiatante G, Malig M, Huddleston J, Benner C, Camponeschi F, Ciofi-Baffoni S, Stessman HA, Marchetto MC, Denman L, Harshman L, Baker C, Raja A, Penewit K, Janke N, Tang WJ, Ventura M, Banci L, Antonacci F, Akey JM, Amemiya CT, Gage FH, Reymond A, Eichler EE.

Nature. 2016 Aug 11;536(7615):205-9. Epub 2016 Aug 3.


Human Diversity in a Cell Surface Receptor that Inhibits Autophagy.

Chaudhary A, Leite M, Kulasekara BR, Altura MA, Ogahara C, Weiss E, Fu W, Blanc MP, O'Keeffe M, Terhorst C, Akey JM, Miller SI.

Curr Biol. 2016 Jul 25;26(14):1791-801. doi: 10.1016/j.cub.2016.05.003. Epub 2016 Jun 23.


A flexible method for estimating the fraction of fitness influencing mutations from large sequencing data sets.

Moon S, Akey JM.

Genome Res. 2016 Jun;26(6):834-43. doi: 10.1101/gr.203059.115. Epub 2016 Apr 14.


Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.

Vernot B, Tucci S, Kelso J, Schraiber JG, Wolf AB, Gittelman RM, Dannemann M, Grote S, McCoy RC, Norton H, Scheinfeldt LB, Merriwether DA, Koki G, Friedlaender JS, Wakefield J, Pääbo S, Akey JM.

Science. 2016 Apr 8;352(6282):235-9. doi: 10.1126/science.aad9416. Epub 2016 Mar 17.


The phenotypic legacy of admixture between modern humans and Neandertals.

Simonti CN, Vernot B, Bastarache L, Bottinger E, Carrell DS, Chisholm RL, Crosslin DR, Hebbring SJ, Jarvik GP, Kullo IJ, Li R, Pathak J, Ritchie MD, Roden DM, Verma SS, Tromp G, Prato JD, Bush WS, Akey JM, Denny JC, Capra JA.

Science. 2016 Feb 12;351(6274):737-41. doi: 10.1126/science.aad2149.


Patterns of deleterious variation between human populations reveal an unbalanced load.

McCoy RC, Akey JM.

Proc Natl Acad Sci U S A. 2016 Jan 26;113(4):809-11. doi: 10.1073/pnas.1524016113. Epub 2016 Jan 19. No abstract available.


Methods and models for unravelling human evolutionary history.

Schraiber JG, Akey JM.

Nat Rev Genet. 2015 Dec;16(12):727-40. doi: 10.1038/nrg4005. Epub 2015 Nov 10. Review.


Small Amounts of Archaic Admixture Provide Big Insights into Human History.

Vattathil S, Akey JM.

Cell. 2015 Oct 8;163(2):281-4. doi: 10.1016/j.cell.2015.09.042. Review.


The origins, determinants, and consequences of human mutations.

Shendure J, Akey JM.

Science. 2015 Sep 25;349(6255):1478-83. doi: 10.1126/science.aaa9119. Epub 2015 Sep 24. Review.


Comprehensive identification and analysis of human accelerated regulatory DNA.

Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins RD, Akey JM.

Genome Res. 2015 Sep;25(9):1245-55. doi: 10.1101/gr.192591.115. Epub 2015 Jun 23.


Complex history of admixture between modern humans and Neandertals.

Vernot B, Akey JM.

Am J Hum Genet. 2015 Mar 5;96(3):448-53. doi: 10.1016/j.ajhg.2015.01.006. Epub 2015 Feb 12.


Estimates of continental ancestry vary widely among individuals with the same mtDNA haplogroup.

Emery LS, Magnaye KM, Bigham AW, Akey JM, Bamshad MJ.

Am J Hum Genet. 2015 Feb 5;96(2):183-93. doi: 10.1016/j.ajhg.2014.12.015. Epub 2015 Jan 22.


Rare variation facilitates inferences of fine-scale population structure in humans.

O'Connor TD, Fu W; NHLBI GO Exome Sequencing Project; ESP Population Genetics and Statistical Analysis Working Group, Emily Turner, Mychaleckyj JC, Logsdon B, Auer P, Carlson CS, Leal SM, Smith JD, Rieder MJ, Bamshad MJ, Nickerson DA, Akey JM.

Mol Biol Evol. 2015 Mar;32(3):653-60. doi: 10.1093/molbev/msu326. Epub 2014 Nov 21.


Characteristics of neutral and deleterious protein-coding variation among individuals and populations.

Fu W, Gittelman RM, Bamshad MJ, Akey JM.

Am J Hum Genet. 2014 Oct 2;95(4):421-36. doi: 10.1016/j.ajhg.2014.09.006.


Heritable variation of mRNA decay rates in yeast.

Andrie JM, Wakefield J, Akey JM.

Genome Res. 2014 Dec;24(12):2000-10. doi: 10.1101/gr.175802.114. Epub 2014 Sep 25.


Human evolution: genomic gifts from archaic hominins.

Vernot B, Akey JM.

Curr Biol. 2014 Sep 22;24(18):R845-R848. doi: 10.1016/j.cub.2014.07.079.


Global and disease-associated genetic variation in the human Fanconi anemia gene family.

Rogers KJ, Fu W, Akey JM, Monnat RJ Jr.

Hum Mol Genet. 2014 Dec 20;23(25):6815-25. doi: 10.1093/hmg/ddu400. Epub 2014 Aug 7.


Evolution and genetic architecture of chromatin accessibility and function in yeast.

Connelly CF, Wakefield J, Akey JM.

PLoS Genet. 2014 Jul 3;10(7):e1004427. doi: 10.1371/journal.pgen.1004427. eCollection 2014 Jul.


Resurrecting surviving Neandertal lineages from modern human genomes.

Vernot B, Akey JM.

Science. 2014 Feb 28;343(6174):1017-21. doi: 10.1126/science.1245938. Epub 2014 Jan 29.


Exonic transcription factor binding directs codon choice and affects protein evolution.

Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM, Stamatoyannopoulos JA.

Science. 2013 Dec 13;342(6164):1367-72. doi: 10.1126/science.1243490.


Genetic architecture of quantitative traits and complex diseases.

Fu W, O'Connor TD, Akey JM.

Curr Opin Genet Dev. 2013 Dec;23(6):678-83. doi: 10.1016/j.gde.2013.10.008. Epub 2013 Nov 26. Review.


Signatures of natural selection on genetic variants affecting complex human traits.

Zhang G, Muglia LJ, Chakraborty R, Akey JM, Williams SM.

Appl Transl Genom. 2013 Nov 7;2:78-94. eCollection 2013 Dec 1.


Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.

Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R, Haugen E, Heimfeld S, Murry CE, Akey JM, Stamatoyannopoulos JA.

Cell. 2013 Aug 15;154(4):888-903. doi: 10.1016/j.cell.2013.07.020.


Fine-scale patterns of population stratification confound rare variant association tests.

O'Connor TD, Kiezun A, Bamshad M, Rich SS, Smith JD, Turner E; NHLBIGO Exome Sequencing Project; ESP Population Genetics, Statistical Analysis Working Group, Leal SM, Akey JM.

PLoS One. 2013 Jul 4;8(7):e65834. doi: 10.1371/journal.pone.0065834. Print 2013.


Exploring signatures of positive selection in pigmentation candidate genes in populations of East Asian ancestry.

Hider JL, Gittelman RM, Shah T, Edwards M, Rosenbloom A, Akey JM, Parra EJ.

BMC Evol Biol. 2013 Jul 12;13:150. doi: 10.1186/1471-2148-13-150.


Selection and adaptation in the human genome.

Fu W, Akey JM.

Annu Rev Genomics Hum Genet. 2013;14:467-89. doi: 10.1146/annurev-genom-091212-153509. Epub 2013 Jul 3. Review.


Great ape genetic diversity and population history.

Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T.

Nature. 2013 Jul 25;499(7459):471-5. doi: 10.1038/nature12228. Epub 2013 Jul 3.


Identification and antiviral activity of common polymorphisms in the APOBEC3 locus in human populations.

Duggal NK, Fu W, Akey JM, Emerman M.

Virology. 2013 Sep 1;443(2):329-37. doi: 10.1016/j.virol.2013.05.016. Epub 2013 Jun 10.


Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast.

Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, Johansson M, Jaschob D, Graczyk B, Shulman NJ, Wakefield J, Cooper SJ, Fields S, Noble WS, Muller EG, Davis TN, Dunham MJ, Maccoss MJ, Akey JM.

Genome Res. 2013 Sep;23(9):1496-504. doi: 10.1101/gr.155762.113. Epub 2013 May 29.


Population genomics and transcriptional consequences of regulatory motif variation in globally diverse Saccharomyces cerevisiae strains.

Connelly CF, Skelly DA, Dunham MJ, Akey JM.

Mol Biol Evol. 2013 Jul;30(7):1605-13. doi: 10.1093/molbev/mst073. Epub 2013 Apr 25.


Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.

Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ; NHLBI Exome Sequencing Project, Akey JM.

Nature. 2013 Jan 10;493(7431):216-20. doi: 10.1038/nature11690. Epub 2012 Nov 28. Erratum in: Nature. 2013 Mar 14;495(7440):270. Rieder, Mark J [added].


Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders.

O'Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O'Day DR, Krumm N, Coe BP, Martin BK, Borenstein E, Nickerson DA, Mefford HC, Doherty D, Akey JM, Bernier R, Eichler EE, Shendure J.

Science. 2012 Dec 21;338(6114):1619-22. doi: 10.1126/science.1227764. Epub 2012 Nov 15.


Marker panels for genealogy-based mapping, breed demographics, and inference-of-ancestry in the dog.

Wong AK, Ruhe AL, Biswas S, Robertson KR, Ali A, Akey JM, Neff MW.

Anim Biotechnol. 2012;23(4):241-52. doi: 10.1080/10495398.2012.717151.


Adaptive evolution of the FADS gene cluster within Africa.

Mathias RA, Fu W, Akey JM, Ainsworth HC, Torgerson DG, Ruczinski I, Sergeant S, Barnes KC, Chilton FH.

PLoS One. 2012;7(9):e44926. doi: 10.1371/journal.pone.0044926. Epub 2012 Sep 19.


Personal and population genomics of human regulatory variation.

Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, Akey JM.

Genome Res. 2012 Sep;22(9):1689-97. doi: 10.1101/gr.134890.111.


An expansive human regulatory lexicon encoded in transcription factor footprints.

Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212.

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