Please see complete listing on myNCBI or Google Scholar. Manuscript preprints for many current projects are posted on bioRxiv.

2016 

Song S, Sliwerska E, Emery S, Kidd JM Modeling human population separation history using physically phased genomes.  Genetics.  2016 November 9; DOI: 10.1534/genetics.116.192963.  Data available at  data dryad

 

Oetjens MT, Shen F, Emery SB, Zou Z, Kidd JM Y-chromosome structural diversity in the bonobo and chimpanzee lineages. Genome Biol Evol. 2016 Aug 3;8(7):2231-40.  PMC4987114   Data available at data dryad.

 

Zhao X, Emery SB, Myers B, Kidd JM, Mills RE Resolving complex structural genomic rearrangements using a randomized approach. Genome Biol. 2016 Jun 10;17(1):126. PMC4901421

 

Wildschutte* JH, Williams* ZH, Montesion M, Subramanian RP, Kidd JM, Coffin JM Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):E2326-34 PMC4843416

2015 

Henn* BM, Botigué* LR, Peischl* S, Dupanloup I, Lipatov M, Maples BK, Martin AR, Musharoff S, Cann H, Snyder MP, Excoffier* L, Kidd* JM, Bustamante* CD.  Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. Proc Natl Acad Sci U S A. 2015 Dec 28. pii: 201510805 PMC4743782

 

Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Great Ape Genome Project, Bustamante CD, Hammer MF, Wall JD.  The time-scale of recombination rate evolution in great apes. Mol Biol Evol. 2015 Dec 15. pii: msv331.

 

Wildschutte JH, Baron A, Diroff NM, Kidd JM. Discovery and characterization of Alu repeat sequences via precise local read assembly. Nucleic Acids Res. 2015 Oct 25. pii: gkv1089

 

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang  Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.

 

1000 Genomes Project Consortium. A global reference for human genetic variation.  Nature, 2015 Oct 1;526(7571):68-74

2014 

McManus* KF, Kelley* JL, Song* S, Veeramah KR, Woerner AE, Stevison LS, Ryder OA, Great Ape Genome Project, Kidd# JM, Wall JD, Bustamante CD, Hammer# MF. Inference of gorilla demographic and selective history from whole-genome sequence data.  Mol Biol Evol 2014 Dec 21. 21. pii: msu394.

 

Dayama G, Emery SB, Kidd JM, Mills RE. The genomic landscape of polymorphic human nuclear mitochondrial insertions. Nucleic Acids Research. 2014 Nov 10;42(20):12640-9. PMC4227756

 

Martin AR, Costa HA, Lappalainen T, Henn BM, Kidd JM, Yee MC,Grubert F, Cann HM, Snyder M, Montgomery SB, Bustamante CD Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture. PLoS Genet. 2014 Aug 14;10(8):e1004549 PMC4133153

 

Kidd* JM, Sharpton* TJ, Bobo D, Norman PJ, Martin AR, Carpenter ML, Sikora M, Gignoux CR, Nemat-Gorgani N, Adams A, Guadalupe M, Guo X, Feng Q, Li Y, Liu X, Parham P, Hoal EG, Feldman MW, Pollard KS, Wall JD, Bustamante CD, Henn BM Exome capture from saliva produces high quality genomic and metagenomic data. BMC Genomics. 2014 Apr 4;15(1):262

2013

Auton A, Rui Li Y, Kidd J, Oliveira K, Nadel J, Holloway JK, Hayward JJ, Cohen PE, Greally JM, Wang J, Bustamante CD, Boyko AR Genetic recombination is targeted towards gene promoter regions in dogs. PLoS Genet. 2013 Dec;9(12):e1003984

 

Poznik GD, Henn BM, Yee MC, Sliwerska E, Euskirchen GM, Lin AA, Snyder M, Quintana-Murci L, Kidd JM, Underhill PA, Bustamante CD. Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science. 2013 Aug 2;341(6145):562-5.

 

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. Great ape genetic diversity and population history. Nature. 2013 Jul 3.

2012 

1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1;491(7422):56-65.

 

Casto AM, Henn BM, Kidd JM, Bustamante CD, Feldman MW. A tale of two haplotypes: the EDA2R/AR Intergenic region is the most divergent genomic segment between Africans and East Asians in the human genome. Hum Biol. 2012 Dec;84(6):641-94.

 

Kidd* JM, Gravel* S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, Degenhardt JD, Brisbin A, Sheth V, Chen R, McLaughlin SF, Peckham HE, Omberg L, Bormann Chung CA, Stanley S, Pearlstein K, Levandowsky E, Acevedo-Acevedo S, Auton A, Keinan A, Acuña-Alonzo V, Barquera-Lozano R, Canizales-Quinteros S, Eng C, Burchard EG, Russell A, Reynolds A, Clark AG, Reese MG, Lincoln SE, Butte AJ, De La Vega FM, Bustamante CD. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet. 2012 Oct 5;91(4):660-71

 

Granka JM, Henn BM, Gignoux CR, Kidd JM, Bustamante CD, Feldman MW. Limited Evidence for Classic Selective Sweeps in African Populations. Genetics. 2012 Sep 7

 

Schoenebeck JJ, Hutchinson SA, Byers A, Beale HC, Carrington B, Faden DL, Rimbault M, Decker B, Kidd JM, Sood R, Boyko AR, Fondon JW 3rd, Wayne RK, Bustamante CD, Ciruna B, Ostrander EA. Variation of BMP3 Contributes to Dog Breed Skull Diversity. PLoS Genet. 2012 Aug;8(8):e1002849

 

Steinberg* KM, Antonacci* F, Sudmant PH, Kidd JM, Campbell CD, Vives L, Malig M, Scheinfeldt L, Beggs W, Ibrahim M, Lema G, Nyambo TB, Omar SA, Bodo JM, Froment A, Donnelly MP, Kidd KK, Tishkoff SA, Eichler EE. Structural diversity and African origin of the 17q21.31 inversion polymorphism. Nat Genetic. 2012 Jul 1. doi:10.1038/ng.2335

 

Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M,Gerstein MB, Kidd JM, Bustamante CD, Snyder M Detecting and annotating genetic variations using the HugeSeq pipeline. Nat Biotechnol. 2012 Mar 7;30(3):226-9