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Joshua Akey

Research Profile

Genes & Molecular Sequences

Occupations

Genetics, Population

Phenomena

Evolution, Molecular

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Procedures

Physiology

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Genetic Markers

Co-author Network

Publications

TOP 3
Wenqing Fu; Stacey Gabriel; Goo Jun; Hyun Min Kang; Suzanne M Leal; Deborah A Nickerson; Timothy D O'Connor; Jay Shendure; Mark J Rieder; Goncalo Abecasis; David Altshuler; Michael Bamshad; Joshua M Akey
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.
Brian J O'Roak; Ian G Phelps; Ian B Stanaway; Emily H Turner; Laura Vives; Joshua M Akey; Katy Ankenman; Raphael Bernier; Elhanan Borenstein; Gemma Carvill; Bradley P Coe; Dan Doherty; Jarrett D Egertson; Evan E Eichler; Wenqing Fu; Joseph B Hiatt; Niklas Krumm; Akash Kumar; Choli Lee; Roie Levy; Beth K Martin; Heather C Mefford; Jeff Munson; Deborah A Nickerson; Diana R O'Day; Jay Shendure
Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders.
Benjamin Vernot; Jeff Vierstra; Matthew T Maurano; Shane Neph; John A Stamatoyannopoulos; Andrew B Stergachis; Robert E Thurman; Joshua M Akey
Personal and population genomics of human regulatory variation.

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All Publications

2013: Wenqing Fu; Stacey Gabriel; Goo Jun; Hyun Min Kang; Suzanne M Leal; Deborah A Nickerson; Timothy D O'Connor; Jay Shendure; Mark J Rieder; Goncalo Abecasis; David Altshuler; Michael Bamshad; Joshua M Akey
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.
Nature 2013;493(7431):216-20.
2012: Brian J O'Roak; Ian G Phelps; Ian B Stanaway; Emily H Turner; Laura Vives; Joshua M Akey; Katy Ankenman; Raphael Bernier; Elhanan Borenstein; Gemma Carvill; Bradley P Coe; Dan Doherty; Jarrett D Egertson; Evan E Eichler; Wenqing Fu; Joseph B Hiatt; Niklas Krumm; Akash Kumar; Choli Lee; Roie Levy; Beth K Martin; Heather C Mefford; Jeff Munson; Deborah A Nickerson; Diana R O'Day; Jay Shendure
Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders.
Science (New York, N.Y.) 2012;338(6114):1619-22.
2012: Benjamin Vernot; Jeff Vierstra; Matthew T Maurano; Shane Neph; John A Stamatoyannopoulos; Andrew B Stergachis; Robert E Thurman; Joshua M Akey
Personal and population genomics of human regulatory variation.
Genome research 2012;22(9):1689-97.
2012: Dennis C Ko; Joshua M Akey; Mitchell Brittnacher; M Eileen Dolan; Christine Fong; Eric Gamazon; Tarah D Holden; Cassandra Ogohara; Richard A Pfuetzner; Matthew Radey; Kajal P Shukla; Amy L Stark; Dale Whittington; Mark M Wurfel; Samuel I Miller
Functional genetic screen of human diversity reveals that a methionine salvage enzyme regulates inflammatory cell death.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(35):E2343-52.
2012: Joseph Lachance; Godfrey Lema; Thomas B Nyambo; Timothy R Rebbeck; Joshua M Akey; Jean-Marie Bodo; Clara C Elbers; Bart Ferwerda; Alain Froment; Wenqing Fu; Benjamin Vernot; Kun Zhang; Sarah A Tishkoff
Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers.
Cell 2012;150(3):457-69.
2012: Caitlin F Connelly; Joshua M Akey
On the prospects of whole-genome association mapping in Saccharomyces cerevisiae.
Genetics 2012;191(4):1345-53.
2012: Jacob A Tennessen; Goncalo Abecasis; Joshua M Akey; David Altshuler; Michael Bamshad; Abigail W Bigham; Eric Boerwinkle; Carlos D Bustamante; Ron Do; Wenqing Fu; Stacey Gabriel; Simon Gravel; Daniel Jordan; Goo Jun; Hyun Min Kang; Eimear E Kenny; Suzanne M Leal; Xiaoming Liu; Sean McGee; Deborah A Nickerson; Timothy D O'Connor; Mark J Rieder; Shamil Sunyaev
Evolution and functional impact of rare coding variation from deep sequencing of human exomes.
Science (New York, N.Y.) 2012;337(6090):64-9.
2012: Joshua M Akey
Parallel selection: evolution's surprising predictability.
Current biology : CB 2012;22(10):R407-9.
2012: Brian J O'Roak; Beau Reilly; Mark J Rieder; Jay Shendure; Joshua D Smith; Ian B Stanaway; Emily H Turner; Benjamin Vernot; Laura Vives; Santhosh Girirajan; Emre Karakoc; Arthur Ko; Niklas Krumm; Choli Lee; Roie Levy; Maika Malig; Deborah A Nickerson; Joshua M Akey; Carl Baker; Raphael Bernier; Elhanan Borenstein; Bradley P Coe; Evan E Eichler
Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations.
Nature 2012;485(7397):246-50.
2012: Aaron K Wong; Kathryn R Robertson; Alison L Ruhe; Joshua M Akey; Ammar Ali; Shameek Biswas; Mark Neff
Marker panels for genealogy-based mapping, breed demographics, and inference-of-ancestry in the dog.
Animal biotechnology 2012;23(4):241-52.
2012: Joshua M Akey
Understanding human evolutionary history: a meeting report of the Swedish Royal Academy of Sciences symposium of modern human genetic variation.
Investigative genetics 2012;3():7.
2012: Jason D Christie; Mitchell J Cohen; Rui Feng; Hakon Hakonarson; Cecilia Kim; Paul N Lanken; Mingyao Li; James P Maloney; Michael Matthay; Addison K May; Nuala J Meyer; Grant E O'Keefe; Jonathan Sevransky; Lorraine B Ware; Mark M Wurfel; Joshua M Akey; Richard Aplenc; Kathleen C Barnes; Jonathan Bradfield; Carolyn S Calfee; David C Christiani
Genome wide association identifies PPFIA1 as a candidate gene for acute lung injury risk following major trauma.
PloS one 2012;7(1):e28268.
2011: Daniel A Skelly; Jon Wakefield; Marnie Johansson; Jennifer Madeoy; Joshua M Akey
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data.
Genome research 2011;21(10):1728-37.
2011: Jacob A Tennessen; Joshua M Akey
Parallel adaptive divergence among geographically diverse human populations.
PLoS genetics 2011;7(6):e1002127.
2011: Laura B Scheinfeldt; Shameek Biswas; Caitlin F Connelly; Jennifer Madeoy; Joshua M Akey
Clusters of adaptive evolution in the human genome.
Frontiers in genetics 2011;2():50.
2011: Joshua M Akey; Mark D Shriver
A Grand Challenge in Evolutionary and Population Genetics: New Paradigms for Exploring the Past and Charting the Future in the Post-Genomic era.
Frontiers in genetics 2011;2():47.
2011: Jacob A Tennessen; Michael J Bamshad; Timothy D O'Connor; Joshua M Akey
The promise and limitations of population exomics for human evolution studies.
Genome biology 2011;12(9):127.
2011: Thomas J Nicholas; Carl Baker; Evan E Eichler; Joshua M Akey
A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog.
BMC genomics 2011;12():414.
2010: Leslie S Emery; Joseph Felsenstein; Joshua M Akey
Estimators of the human effective sex ratio detect sex biases on different timescales.
American journal of human genetics 2010;87(6):848-56.
2010: Jacob A Tennessen; Jennifer Madeoy; Joshua M Akey
Signatures of positive selection apparent in a small sample of human exomes.
Genome research 2010;20(10):1327-34.
2010: Abigail Bigham; Marc Bauchet; Dalila Pinto; Xianyun Mao; Joshua M Akey; Rui Mei; Stephen W Scherer; Colleen G Julian; Megan J Wilson; David López Herráez; Tom D Brutsaert; Esteban J Parra; Lorna G Moore; Mark D Shriver
Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data.
PLoS genetics 2010;6(9):.
2010: Joshua M Akey; Alison L Ruhe; Dayna T Akey; Aaron K Wong; Caitlin F Connelly; Jennifer Madeoy; Thomas J Nicholas; Mark Neff
Tracking footprints of artificial selection in the dog genome.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(3):1160-5.
2010: Charla A Lambert; Caitlin F Connelly; Jennifer Madeoy; Ruolan Qiu; Maynard V Olson; Joshua M Akey
Highly punctuated patterns of population structure on the X chromosome and implications for African evolutionary history.
American journal of human genetics 2010;86(1):34-44.
2009: Abigail W Bigham; Xianyun Mao; Rui Mei; Tom Brutsaert; Megan J Wilson; Colleen Glyde Julian; Esteban J Parra; Joshua M Akey; Lorna G Moore; Mark D Shriver
Identifying positive selection candidate loci for high-altitude adaptation in Andean populations.
Human genomics 2009;4(2):79-90.
2009: Dennis C Ko; Kajal P Shukla; Christine Fong; Michael Wasnick; Mitchell Brittnacher; Mark M Wurfel; Tarah D Holden; Grant E O'Keefe; Brian Van Yserloo; Joshua M Akey; Samuel I Miller
A genome-wide in vitro bacterial-infection screen reveals human variation in the host response associated with inflammatory disease.
American journal of human genetics 2009;85(2):214-27.
2009: Laura B Scheinfeldt; Shameek Biswas; Jennifer Madeoy; Caitlin F Connelly; Eric E Schadt; Joshua M Akey
Population genomic analysis of ALMS1 in humans reveals a surprisingly complex evolutionary history.
Molecular biology and evolution 2009;26(6):1357-67.
2009: Shameek Biswas; Laura B Scheinfeldt; Joshua M Akey
Genome-wide insights into the patterns and determinants of fine-scale population structure in humans.
American journal of human genetics 2009;84(5):641-50.
2009: Joshua M Akey
Constructing genomic maps of positive selection in humans: where do we go from here?
Genome research 2009;19(5):711-22.
2009: Thomas J Nicholas; Ze Cheng; ventura Mario; Katrina Mealey; Evan E Eichler; Joshua M Akey
The genomic architecture of segmental duplications and associated copy number variants in dogs.
Genome research 2009;19(3):491-9.
2009: Daniel A Skelly; James Ronald; Caitlin F Connelly; Joshua M Akey
Population genomics of intron splicing in 38 Saccharomyces cerevisiae genome sequences.
Genome biology and evolution 2009;1():466-78.
2009: Daniel A Skelly; James Ronald; Joshua M Akey
Inherited variation in gene expression.
Annual review of genomics and human genetics 2009;10():313-32.
2009: A S Yatsenko; M M Kucherenko; M Pantoja; Karin A Fischer; Jennifer Madeoy; Wu-Min Deng; M Schneider; Stefan Baumgartner; Joshua M Akey; Halyna R Shcherbata; T. Hannele Ruohola-Baker
The conserved WW-domain binding sites in Dystroglycan C-terminus are essential but partially redundant for Dystroglycan function.
BMC developmental biology 2009;9():18.
2008: Shameek Biswas; John D Storey; Joshua M Akey
Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis.
BMC bioinformatics 2008;9():244.
2007: Joshua M Akey; Shameek Biswas; Jeffrey T Leek; John D Storey
On the design and analysis of gene expression studies in human populations.
Nature genetics 2007;39(7):807-8; author reply 808-9.
2007: John D Storey; Jennifer Madeoy; Jeanna L Strout; Mark Wurfel; James Ronald; Joshua M Akey
Gene-expression variation within and among human populations.
American journal of human genetics 2007;80(3):502-9.
2007: James Ronald; Joshua M Akey
The evolution of gene expression QTL in Saccharomyces cerevisiae.
PloS one 2007;2(7):e678.
2006: Joanna L Kelley; Jennifer Madeoy; John C Calhoun; Willie J Swanson; Joshua M Akey
Genomic signatures of positive selection in humans and the limits of outlier approaches.
Genome research 2006;16(8):980-9.
2006: Shameek Biswas; Joshua M Akey
Genomic insights into positive selection.
Trends in genetics : TIG 2006;22(8):437-46.
2006: Joshua M Akey; Willie J Swanson; Jennifer Madeoy; Michael A Eberle; Mark D Shriver
TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations.
Human molecular genetics 2006;15(13):2106-13.
2006: Rachel Mackelprang; Robert Livingston; Michael A Eberle; Christopher S Carlson; Qian Yi; Joshua M Akey; Deborah A Nickerson
Sequence diversity, natural selection and linkage disequilibrium in the human T cell receptor alpha/delta locus.
Human genetics 2006;119(3):255-66.
2006: Tonibelle Gatbonton; Maria Imbesi; Melisa Nelson; Joshua M Akey; Douglas M Ruderfer; Leonid Kruglyak; Julian A Simon; Antonio Bedalov
Telomere length as a quantitative trait: genome-wide survey and genetic mapping of telomere length-control genes in yeast.
PLoS genetics 2006;2(3):e35.
2005: John D Storey; Joshua M Akey; Leonid Kruglyak
Multiple locus linkage analysis of genomewide expression in yeast.
PLoS biology 2005;3(8):e267.
2005: James Ronald; Joshua M Akey
Genome-wide scans for loci under selection in humans.
Human genomics 2005;2(2):113-25.
2005: Mark D Shriver; Rui Mei; Esteban J Parra; Vibhor Sonpar; INDRANI HALDER; Sarah A Tishkoff; Theodore G Schurr; Sergev I Zhadanov; Ludmila P Osipova; Tom D Brutsaert; Jonathan Friedlaender; Lynn B Jorde; W Scott Watkins; Michael Bamshad; Gerardo Gutierrez; Halina Loi; Hajime Matsuzaki; Rick Kittles; George Argyropoulos; Jose R Fernandez; Joshua M Akey; Keith W Jones
Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation.
Human genomics 2005;2(2):81-9.
2005: James Ronald; Joshua M Akey; Jacqueline Whittle; Erin N Smith; Gaël Yvert; Leonid Kruglyak
Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays.
Genome research 2005;15(2):284-91.
2004: Joshua M Akey; Michael A Eberle; Mark J Rieder; Christopher S Carlson; Mark D Shriver; Deborah A Nickerson; Leonid Kruglyak
Population history and natural selection shape patterns of genetic variation in 132 genes.
PLoS biology 2004;2(10):e286.
2004: Li Jin; Ge Zhang; Joshua M Akey; Jingchun Luo; Juwon Lee; Michael H Weisman; Jane Bruckel; Robert D Inman; Millicent A Stone; Muhammad A Khan; H Ralph Schumacher; Walter P Maksymowych; Maren L Mahowald; Allen D Sawitzke; Frank B Vasey; D T Y Yu; John D Reveille
Lack of linkage of IL1RN genotypes with ankylosing spondylitis susceptibility.
Arthritis and rheumatism 2004;50(9):3047-8.
2004: Mark D Shriver; Giulia C Kennedy; Esteban J Parra; Heather A Lawson; Vibhor Sonpar; Jing Huang; Joshua M Akey; Keith W Jones
The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs.
Human genomics 2004;1(4):274-86.
2003: Gaël Yvert; Rachel B Brem; Jacqueline Whittle; Joshua M Akey; Eric Foss; Erin N Smith; Rachel Mackelprang; Leonid Kruglyak
Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors.
Nature genetics 2003;35(1):57-64.
2003: Kun Zhang; Joshua M Akey; Ning Wang; Momiao Xiong; Ranajit Chakraborty; Li Jin
Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drift.
Human genetics 2003;113(1):51-9.
2003: Joshua M Akey; Kun Zhang; Momiao Xiong; Li Jin
The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium.
Molecular biology and evolution 2003;20(2):232-42.
2003: Guangyun Sun; Stephen T McGarvey; Riad Bayoumi; Connie J Mulligan; Ramiro Barrantes; Salmo Raskin; Yixi Zhong; Joshua M Akey; Ranajit Chakraborty; Ranjan Deka
Global genetic variation at nine short tandem repeat loci and implications on forensic genetics.
European journal of human genetics : EJHG 2003;11(1):39-49.
2002: Joshua M Akey; Ge Zhang; Kun Zhang; Li Jin; Mark D Shriver
Interrogating a high-density SNP map for signatures of natural selection.
Genome research 2002;12(12):1805-14.
2002: Ning Wang; Joshua M Akey; Kun Zhang; Ranajit Chakraborty; Li Jin
Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation.
American journal of human genetics 2002;71(5):1227-34.
2002: Dayna T Akey; Joshua M Akey; Kun Zhang; Li Jin
Assaying DNA methylation based on high-throughput melting curve approaches.
Genomics 2002;80(4):376-84.
2001: Joshua M Akey; H Wang; M Xiong; H Wu; W Liu; Mark D Shriver; Li Jin
Interaction between the melanocortin-1 receptor and P genes contributes to inter-individual variation in skin pigmentation phenotypes in a Tibetan population.
Human genetics 2001;108(6):516-20.
2001: Joshua M Akey; K Zhang; M Xiong; P Doris; Li Jin
The effect that genotyping errors have on the robustness of common linkage-disequilibrium measures.
American journal of human genetics 2001;68(6):1447-56.
2001: Joshua M Akey; L Jin; Momiao Xiong
Haplotypes vs single marker linkage disequilibrium tests: what do we gain?
European journal of human genetics : EJHG 2001;9(4):291-300.
2001: Joshua M Akey; Donna M Sosnoski; E Parra; Sonia Dios; Kevin Hiester; B Su; Carolina Bonilla; L Jin; Mark D Shriver
Melting curve analysis of SNPs (McSNP): a gel-free and inexpensive approach for SNP genotyping.
BioTechniques 2001;30(2):358-62, 364, 366-7.
2000: Momiao Xiong; Joshua M Akey; L Jin
The haplotype linkage disequilibrium test for genome-wide screens: its power and study design.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2000;():675-86.
1999: Bing Su; J Xiao; Peter A Underhill; Ranjan Deka; W Zhang; Joshua M Akey; Wei Huang; D Shen; Daru Lu; J Luo; J Chu; J Tan; Peidong Shen; R Davis; L Luca Cavalli-Sforza; Ranajit Chakraborty; Momiao Xiong; R Du; Peter Oefner; Z Chen; Li Jin
Y-Chromosome evidence for a northward migration of modern humans into Eastern Asia during the last Ice Age.
American journal of human genetics 1999;65(6):1718-24.
1998: E J Parra; A Marcini; Joshua M Akey; Jeremy Martinson; M A Batzer; R Cooper; T Forrester; David Allison; Ranjan Deka; Robert E Ferrell; Mark D Shriver
Estimating African American admixture proportions by use of population-specific alleles.
American journal of human genetics 1998;63(6):1839-51.
1997: Mark D Shriver; M W Smith; Li Jin; A Marcini; Joshua M Akey; Ranjan Deka; Robert E Ferrell
Ethnic-affiliation estimation by use of population-specific DNA markers.
American journal of human genetics 1997;60(4):957-64.