Publications

2018

Mittnik A, Wang CC, Pfrengle S, Daubaras M, Zarina G, Hallgren F, Allmae R, Khartanovich V, Moiseyev V, Torv M, Furtwangler A, Andrades Valtuena AA, Feldman M, Economou C, Oinonen M, Vasks A, Balanovska E, Reich D, Jankauskas R, Haak W, Schiffels S, Krause J (2018) The genetic prehistory of the Baltic Sea region. Nature Communnications 9:442. doi: 10.1038/s41467-018-02825-9


2017

Gymrek M, Willems T, Reich D, Erlich Y (2017) Interpreting short tandem repeat variations in humans using mutational constraint. Nature Genetics 49, 1495-501. (Supplementary Materials). PMCID: PMC5679271

Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlević P, Hajdinjak M, Vernot B, Skov L, Hsieh P, Peyrégne S, Reher D, Hopfe C, Nagel S, Maricic T, Fu Q, Theunert C, Rogers R, Skoglund P, Chintalapati M, Dannemann M, Nelson BJ, Key FM, Rudan P, Kućan Ž, Gušić I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andrés AM, Kelso J, Meyer M, Pääbo S (2017) A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358:655-8. doi: 10.1126/science.aao1887

Lipson M, Szécsényi-Nagy A, Mallick S, Pósa A, Stégmár B, Keerl V, Rohland N, Stewardson K, Ferry M, Michel M, Oppenheimer J, Broomandkhoshbacht N, Harney E, Nordenfelt S, Llamas B, Mende GB, Köhler K, Oross K, Bondár M, Marton T, Osztás A, Jakucs J, Paluch T, Horváth F, Csengeri P, Koós J, Sebők K, Anders A, Raczky P, Regenye J, Barna JP, Fábián S, Serlegi G, Toldi Z, Nagy EG, Dani J, Molnár E, Pálfi G, Márk L, Melegh B, Bánfai Z, Domboróczki L, Fernández-Eraso J, Antonio Mujika-Alustiza J, Fernández CA, Echevarría JJ, Bollongino R, Orschiedt J, Schierhold K, Meller H, Cooper A, Burger J, Bánffy E, Alt KW, Lalueza-Fox C, Haak W, Reich D (2017) Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature 551, 368-72. (Supplementary Materials). doi: 10.1038/nature24476

Skoglund P, Thompson JC, Prendergast ME, Mittnik A, Sirak K, Hajdinjak M, Salie T, Rohland N, Mallick S, Peltzer A, Heinze A, Olalde I, Ferry M, Harney E, Michel M, Stewardson K, Cerezo-Roman JI, Chiumia C, Crowther A, Gomani-Chindebvu E, Gidna AO, Grillo KM, Helenius IT, Hellenthal G, Helm R, Horton M, Lopez S, Mabulla AZP, Parkington J, Shipton C, Thomas MG, Tibesasa R, Welling M, Hayes VM, Kennett DJ, Ramesar R, Meyer M, Paabo S, Patterson N, Morris AG, Boivin N, Pinhasi R, Krause J, Reich D (2017) Reconstructing Prehistoric African Population Structure. Cell 171, 59-71. PMCID: PMC5679310

Hellwege JN, Jeff JM, Wise LA, Gallagher CS, Wellons M, Hartmann KE, Jones SF, Torstenson ES, Dickinson S, Ruiz-Narváez EA, Rohland N, Allen A, Reich D, Tandon A, Pasaniuc B, Mancuso N, Im HK, Hinds DA, Palmer JR, Rosenberg L, Denny JC, Roden DM, Stewart EA, Morton CC, Kenny EE, Edwards TL, Velez Edwards DR (2017) A multi-stage genome-wide association study of uterine fibroids in African Americans. Hum Genet 136, 1363-73. PMCID: PMC5628188

Lazaridis I, Mittnik A, Patterson N, Mallick S, Rohland N, Pfrengle S, Anja Furtwängler A, Peltzer A, Posth C, Vasilakis A, McGeorge PJP, Konsolaki-Yannopoulou E, Korres G, Martlew H, Michalodimitrakis M, Özsait M, Özsait N, Papathanasiou A, Richards M, Roodenberg SA, Tzedakis Y, Arnott R, Fernandes DM, Hughey JR, Lotakis DM, Navas PA, Maniatis Y, Stamatoyannopoulos JA, Stewardson K, Stockhammer P, Pinhasi R, Reich D, Krause J, Stamatoyannopoulos G (2017) Genetic origins of the Minoans and Mycenaeans. Nature 548. 214-8. (Supplementary Materials). PMCID: PMC5565772

Nakatsuka N, Moorjani P, Rai N, Sarkar B, Tandon A, Patterson N, Bhavani GS, Girisha KM , Mustak MS, Srinivasan S , Kaushik A, Vahab SA, Jagadeesh SM, Satyamoorthy K, Singh S, Reich D*, Thangaraj K* (2017) The promise of discovering population-specific disease-associated genes in South Asia. Nature Genetics 49. 1403-7. (Supplementary Materials). PMCID: PMC5675555

Lazaridis I, Reich D (2017) Failure to replicate a genetic signal for sex bias in the steppe migration into central Europe. Proceedings of the National Academy of Sciences 114 (20) E3873-4. PMCID: PMC5441797

Unterländer M, Palstra F, Lazaridis I, Pilipenko A, Hofmanová Z, Groß M, Sell C, Blöcher J, Kirsanow K, Rohland N, Rieger B, Kaiser E, Schier W, Pozdniakov D, Khokhlov A, Georges M, Wilde S, Powell A, Heyer E, Currat M, Reich D, Samashev Z, Parzinger H, Molodin VI, Burger J (2017) Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe. Nature Communications 8, 14615. PMCID: PMC5337992

Mathieson I, Reich D (2017) Differences in the rare variant spectrum among human populations. PLoS Genet 13, e1006581. PMCID: PMC5310914 

Lipson M, Reich D (2017) A working model of the deep relationships of diverse modern human genetic lineages outside of Africa. Molecular Biology and Evolution 34, 889-902. PMCID: PMC5400393

Tassi F, Vai S, Ghirotto S, Lari M, Modi A, Pilli E, Brunelli A, Susca RR, Budnik A, Labuda D, Alberti F, Lalueza-Fox C, Reich D, Caramelli D, Barbujani G (2017) Genome diversity in the Neolithic Globular Amphorae culture and the spread of Indo-European languages. Proc Biol Sci. 284:20171540. PMCID: PMC5719168 


2016

Reich D, Stewardson K, Lazaridis I, Mallick S, Rohland N, Owsley D (2016) Ancient DNA analysis of St. Mary’s City Lead Coffins Burial. Technical report.

Skoglund P, Posth C, Sirak K, Spriggs M, Valentin F, Bedford S, Clark GR, Reepmeyer C, Petchey F, Fernandes D, Fu Q, Harney H, Lipson M, Mallick S, Novak M, Rohland N, Stewardson K, Abdullah S, Cox MP, Friedlaender FR, Friedlaender JS, Kivisild T, Koki F, Kusuma P, Merriwether DA, Ricaut F-X, Wee JTS, Patterson N, Krause J, Pinhasi R, Reich D (2016) Genomic insights into the peopling of the Southwest Pacific. Nature 538, 510-3. PMCID: PMC5515717

Mallick SM, Li HL, Lipson ML, Mathieson IM, Gymrek MG, Racimo FR, Zhao MZ, Chennagiri NC, Nordenfelt SN, Tandon AT, Skoglund PS, Lazaridis IL, Sankararaman SS, Fu QF, Rohland NR, Renaud GR, Erlich YE, Willems TW, Gallo CG, Spence JS, Song YSS, Poletti GP, Balloux FB, Driem GD, de Knijff PK, Gallego Romero IGR, Jha ARJ, Behar DMB, Bravi CMB, Capelli CC, Hervig TH, Moreno-Estrada AM-E, Posukh OLP, Balanovska EB, Balanovsky OB, Karachanak-Yankova SK-Y, Sahakyan HS, Toncheva DT, Yepiskoposyan LY, Tyler-Smith CT-S, Xue YX, Abdullah MSA, Ruiz-Linares AR-L, Beall CB, Di Rienzo ADR, Jeong CJ, Starikovskaya EBS, Metspalu EM, Parik JP, Villems RV, Henn BMH, Hodoglugil UH, Mahley RWM, Sajantila AS, Stamatoyannopoulos GS, Wee JTSW, Khusainova RK, Khusnutdinova EK, Litvinov SL, Ayodo GA, Comas DC, Hammer MH, Kivisild TK, Klitz WK, Winkler CW, Labuda DL, Bamshad MB, Jorde LBJ, Tishkoff SAT, Watkins WSW, Metspalu MM, Dryomov SD, Sukernik RS, Singh LS, Thangaraj KT, Pääbo SP, Kelso JK, Patterson NP, Reich DR (2016) The Simons Genome Diversity Project: 300 genomes from 142 diverse populations, Nature 538, 201-6. (Supplementary Materials). PMCID: PMC5161557

Skoglund P, Reich D (2016) A genomic view of the peopling of the Americas. Current Opinion in Genetics & Development 41, 27-35. PMCID: PMC5161672

Lazaridis I, Nadel D, Rollefson G, Merrett DC, Rohland N, Mallick S, Fernandes D, Novak M, Gamarra B, Sirak K, Connell S, Stewardson K, Harney E, Fu Q, Gonzalez-Fortes G, Jones ER, Roodenberg SA, Lengyel G, Bocquentin F, Gasparian B, Monge JM, Gregg M, Eshed V, Mizrahi A, Meiklejohn C, Gerritsen F, Bejenaru L, Blüher M, Campbell A, Cavalleri G, Comas D, Froguel P, Gilbert E, Kerr SM, Kovacs P, Krause J, McGettigan D, Merrigan M, Merriwether DA, O'Reilly S, Richards MB, Semino O, Shamoon-Pour M, Stefanescu G, Stumvoll M, Tönjes A, Torroni A, Wilson JF, Yengo L, Hovhannisyan NA, Patterson N, Pinhasi R, Reich D (2016) Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419-24. (Supplemantary Materials) PMCID:PMC5003663

Fu Q, Posth C, Hajdinjak M, Petr M, Mallick S, Fernandes C, Furtwängler A, Haak W, Meyer M, Mittnik A, Nickel B, Peltzer A, Rohland N, Slon V, Talamo S, Lazaridis I , Lipson M , Mathieson I, Schiffels S, Skoglund P, Derevianko AP, Drozdov N, Slavinsky V, Tsybankov A, Cremonesi RG, Mallegni F, Gély B, Vacca E, González Morales MR, Straus LG, Neugebauer-Maresch C, Teschler-Nicola M, Constantin S, Moldovan OT, Benazzi S, Peresani M, Coppola D, Lari M, Ricci S, Ronchitelli A, Valentin F, Thevenet C, Wehrberger K, Grigorescu D, Rougier H, CREVECOEUR I, Flas E, Semal P, Mannino MA, Cupillard C, Bocherens H, Conard NJ, Harvati K, Moiseyev V, Drucker DG, Svoboda J, Richards MP, Caramelli C, Pinhasi R, Kelso J, Patterson N, Krause J, Pääbo S, Reich D (2016) The genetic history of Ice Age Europe. Nature 534, 200-5. (Supplementary Materials) PMCID:PMC4943878

Moorjani M, Sankararaman S, Fu Q, Przeworski M, Patterson N, Reich D (2016) A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. Proceedings of the National Academy of Sciences of the USA 113, 5652-7. PMCID:PMC4878468

Llamas B, Fehren-Schmitz L, Valverde G, Soubrier J, Mallick S, Rohland N, Nordenfelt S, Valdiosera C, Richards SM, Rohrlach A, Romero MI, Espinoza IF, Cagigao ET, Jiménez LW, Makowski K, Reyna IS, Lory JM, Torrez JA, Rivera MA, Burger RL, Ceruti MC, Reinhard J, Wells RS, Politis G, Santoro CM, Standen VG, Smith C, Reich D, Ho SY, Cooper A, Haak W (2016) Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas. Science Advances 2, e1501385. PMCID:PMC4820370

Sankararaman S, Patterson N, Reich D (2016) The combined landscape of Denisovan and Neanderthal ancestry in present-day humans. Current Biology 26, 1-7. PMCID:PMC4864120


2015

Mathieson I, Lazaridis I, Rohland N, Mallick S, Patterson N, Roodenberg SA, Harney E, Stewardson K, Fernandes D, Novak M, Sirak K, Gamba C, Jones ER, Llamas B, Dryomov S, Pickrell J, Arsuaga JL, Bermúdez de Castro JM, Carbonell E, Gerritsen F, Khokhlov A, Kuznetsov P, Lozano M, Meller H, Mochalov O, Moiseyev V, Rojo Guerra MA, Roodenberg J, Maria Vergès JM, Krause J, Cooper A, Alt KW, Brown D, Anthony D, Lalueza-Fox C, Haak W, Pinhasi R, Reich D (2015) Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499-503. PMCID:PMC4918750

Mancuso N, Rohland N, Rand KA, Tandon A, Allen A, Quinque D, Mallick S, Li H, Stram A, Sheng X, Kote-Jarai Z, Easton DF, Eeles RA, the PRACTICAL consortium, Le Marchand L, Lubwama A, Stram D, Watya S,Conti DV, Henderson B, Haiman CA, Pasaniuc B, Reich D (2015) The contribution of rare variation to prostate cancer heritability. Nature Genetics 48, 30-5. (Supplementary Materials)

Lipson M, Loh PR, Sankararaman S, Patterson N, Berger B, Reich D (2015) Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes. PLoS Genet. 11, e1005550. PMCID:PMC4642934

Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, Coe BP, Baker C, Nordenfelt S, Bamshad M, Jorde LB, Posukh OL, Sahakyan H, Watkins WS, Yepiskoposyan L, Abdullah MS, Bravi CM, Capelli C, Hervig T, Wee JT, Tyler-Smith C, van Driem G, Romero IG, Jha AR, Karachanak-Yankova S, Toncheva D, Comas D, Henn B, Kivisild T, Ruiz-Linares A, Sajantila A, Metspalu E, Parik J, Villems R, Starikovskaya EB, Ayodo G, Beall CM, Di Rienzo A, Hammer MF, Khusainova R, husnutdinova E, Klitz W, Winkler C, Labuda D, Metspalu M, Tishkoff SA, Dryomov S, Sukernik R, Patterson N, Reich D, Eichler EE (2015) Global diversity, population stratification, and selection of human copy-number variation. Science 349, aab3761. (Supplementary Materials) PMCID:PMC4568308

Skoglund P, Mallick S, Bortolini MC, Chennagiri N, Hünemeier T, Petzl-Erler ML, Salzano FM, Patterson N, Reich D (2015) Genetic evidence for two founding populations of the Americas. Nature 525, 104-8. (Supplementary Materials) PMCID:PMC4982469

Fu Q, Hajdinjak M, Moldovan OT, Constantin S, Mallick S, Skoglund P, Patterson N, Rohland N, Lazaridis I, Nickel B, Viola B, Prüfer K, Meyer M, Kelso J, Reich D, Pääbo S (2015) An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216-9. (Supplementary Materials). PMCID:PMC4537386

Skoglund P, Ersmark E, Palkopoulou E, Dalen L (2015) Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds. Curr. Biol. 25,1515-9.

Palkopoulou E, Mallick S, Skoglund P, Enk J, Rohland N, Li H, Omrak A, Vartanyan S, Poinar H, Götherström A, Reich D & Dalén L (2015) Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth. Curr. Biol 25, 1395-1400 (Supplementary Materials). PMCID:PMC4439331

Li H (2015) BFC: correcting Illumina sequencing errors. Bioinformatics 31, 2885-7.

Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S, Llamas B, Brandt G, Nordenfelt S, Harney E, Stewardson K, Fu Q, Mittnik A, Bánffy E, Economou C, Francken M, Friederich S, Pena RG, Hallgren F, Khartanovich V, Khokhlov A, Kunst M, Kuznetsov P, Meller H, Mochalov O, Moiseyev V, Nicklisch N, Pichler S, Risch R, Guerra MAR, Roth C, Szécsényi-Nagy A, Wahl J, Meyer M, Krause J, Brown D, Anthony D, Cooper A, Alt KW & Reich D (2015) Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207-11 (Supplementary Materials). PMCID:PMC5048219

Williams AL, Genovese G, Dyer T, Altemose N, Truax K, Jun G, Patterson N, Myers SR, Curran JE, Duggirala R, Blangero J, Reich D, Przeworski M (2015) Non-crossover gene conversions show strong GC bias and unexpected clustering in humans. Elife 2015;4:e04637. PMCID:PMC4404656

Do R, Balick D, Li H, Adzhubei A, Sunyaev S & Reich D (2015) No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans. Nature Genetics 47, 126-31. PMCID:PMC4310772

Bryc K, Durand EY, Macpherson M, Reich D & Mountain JL (2015) The genetic ancestry of African Americans, Latinos, and European American across the United States. AJHG 96, 37-53. PMCID:PMC4289685


2014

Rohland N, Harney E, Mallick S, Nordenfelt S & Reich D (2014) Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. B 370. PMCID:PMC4275898

Fu Q, Li H, Moorjani P, Jay F, Slepchenko SM, Bondarev AA, Johnson PLF, Aximu-Petri A, Prüfer K, Filippo C, Meyer M, Zwyns N, Salazar-Garcia D, Kuzmin YV, Keates SG, Kosintsev P, Razhev DI, Richards MP, Peristov NV, Lachmann M, Douka K, Higham TFG, Slatkin M, Hublin JJ, Reich D, Kelso J, Viola TB & Pääbo S (2014) Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445-50 (Supplementary Materials). PMCID:PMC4753769

Bhatia G, Tandon A, Patterson N, Aldrich MC, Ambrosone CB, Amos C, Bandera EV, Berndt SI, Bernstein L, Blot WJ, Bock CH, Caporaso N, Casey G, Deming SL, Diver WR, Gapstur SM, Gillanders EM, Harris CC, Henderson BE, Ingles SA, Isaacs W, De Jager P, John EM, Kittles RA, Larkin E, McNeill LH, Millikan RC, Murphy A, Neslund-Dudas C, Nyante S, Press MF, Rodriguez-Gil J, Rybicki BA, Schwartz AG, Signorello LB, Spitz M, Strom SS, Tucker MA, Wiencke JK, Witte JS, Wu X, Yamamura Y, Zanetti KA, Zheng W, Ziegler RG, Chanock SJ, Haiman CA, Reich D & Price AL (2014) Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture. AJHG 95, 1-8. PMCID:PMC4185117

Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant P, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, Nordenfelt S, Li H, Filippo Cd, Prüfer K, Sawyer S, Posth C, Haak W, Hallgren F, Fornander E, Rohland N, Delsate D, Francken M, Guinet JM, Wahl J, Ayodo G, Babiker HA, Bailliet G, Balanovska E, Balanovsky O, Barrantes R, Bedoya G, Ben-Ami H, Bene J, Berrada F, Bravi CM, Brisighelli F, Busby GBJ, Cali F, Churnosov M, Cole DEC, Corach D, Damba L, Driem GV, Dryomov S, Dugoujon JM, Fedorova SA, Romero IG, Gubina M, Hammer M, Henn BM, Hervig T, Hodoglugil U, Jha AR, Karachanak-Yankova S, Khusainova R, Khusnutdinova E, Kittles R, Kivisild T, Klitz W, Kucinskas V, Kushniarevich A, Laredj L, Litvinov S, Loukidis T, Mahley RW, Melegh B, Metspalu E, Molina J, Mountain J, Nakkalajarvi K, Nesheva D, Nyambo T, Osipova L, Park J, Platonov F, Posukh O, Romano V, Rothhammer F, Rudan I, Ruizbakiev R, Sahakyan H, Sajantila A, Salas A, Starikovskaya EB, Tarekegn A,Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Vasquez R, Villena M, Voevoda M, Winkler CA, Yepiskoposyan L, Zalloua P, Zemunik T, Cooper A, Capelli C, Thomas MG, Ruiz-Linares A, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Pääbo S, Kelso J, Reich D & Krause J (2014) Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409-13 (Supplementary Materials). PMCID:PMC4170574

Pickrell JK & Reich D (2014) Toward a new history and geography of human genes informed by ancient DNA. Trends in Genetics Sep;30(9): 377-89. PMCID:PMC4163019

Lipson M, Loh PR, Patterson N, Moorjani P, Ko YC, Stoneking M, Berger B & Reich D (2014) Reconstructing Austronesian population history in Island Southeast Asia. Nature Communications 5 4689. PMCID:PMC4143916

Pickrell JK, Patterson N, Loh PR, Lipson M, Berger B, Stoneking M, Pakendorff B & Reich D (2014) Ancient west Eurasian ancestry in southern and eastern Africa. PNAS 111, 2632-7 (Supplementary Materials). PMCID:PMC3932865

Sankararaman S, Mallick S, Dannemann M, Prüfer K, Kelso J, Pääbo S, Patteron N & Reich D (2014) The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507, 354-7 (Supplementary Materials). PMCID:PMC4072735

The SIGMA Type 2 Diabetes Consortium (2014) Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature 506, 97-101 (Supplementary Materials). PMCID:PMC4127086


2013

Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant P, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PLF, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J & Pääbo S (2013) The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43-9 (Supplementary Materials). PMCID:PMC4031459

Bryc K, Patterson N, Reich D (2013) A novel approach to estimating heterozygosity from low-coverage genome sequence. Genetics 195, 553-61. PMCID:PMC3781980

Brandt G, Haak W, Adler CJ, Roth C, Szecsenyi-Nagy A, Karimnia S., Moller-Rieker S, Meller H, Ganslmeier R, Friedrich S, Dresely V, Nicklisch N, Pickrell JK, Siroko F, Reich D, Cooper A, Alt KW; Genographic Consortium (2013) Ancient DNA reveals key stages in the formation of central European mitochondrial genetics diversity. Science 341, 257-61 (Supplementary Materials). PMCID:PMC4039305

Moorjani P, Thangaraj K, Patterson N, Lipson M, Loh PR, Govindaraj P, Berger B, Reich D, Singh L (2013) Genetic evidence for recent population mixture in India. AJHG 93, 1-17 (Supplementary Materials). PMCID:PMC3769933

Lipson M, Loh PR, Levin A, Reich D, Patterson N, Berger B (2013) Efficient moment-based inference of admixture parameters and sources of gene flow. Mol Biol Evol 30, 1788-802 (Supplementary Materials). PMCID:PMC3708505

Loh PR, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D and Berger B (2013) Inferring admixture histories of human populations using linkage disequilibrium. Genetics 193, 1233-54 (Supplementary Materials). PMCID:PMC3606100

Moorjani P, Patterson N, Loh PR, Lipson M, Kisfali P, Melegh BI, Bonin M, Kadasi L, Riess O, Berger B, Reich D, Melegh B (2013) Reconstructing Roma history from genome-wide data. PLoS One 8, e58633. PMCID:PMC3596272

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 (2013) Great ape genetic diversity and population history. Nature 499, 471-5 (Supplementary Materials). PMCID:PMC3822165

Fu Q, Mittnik A, Johnson PL, Bos K, Lari M, Bollongino R, Sun C, Giemsch L, Schmitz R, Burger J, Ronchitelli AM, Martini F, Cremonesi RG, Svoboda J, Bauer P, Caramelli D, Castellano S, Reich D, Pääbo S, Krause J (2013) A revised timescale for human evolution based on ancient mitochondrial genomes. Curr Biol. 23: 553-9 (Supplementary Materials). PMCID:PMC5036973

Genovese G, Handsaker RE, Li H, Altemose N, Lindgren AM, Chambert K, Pasaniuc B, Price AL, Reich D, Morton CC, Pollak MR, Wilson JG, McCarroll SA (2013) Using population admixture to help complete maps of the human genome. Nat Genet 45: 406-14 (Supplementary Materials). PMCID:PMC3683849


2012

Wise LA, Ruiz-Narvaez EA, Palmer JR, Cozier YC, Tandon A, Patterson N, Radin RG, Rosenberg L, Reich D (2012) African ancestry and genetics risk for uterine leiomyomata. Am J Epidemiol 176, 1159-68. PMCID:PMC3571235

Pickrell JK, Patterson N, Barbieri C, Berthold F, Gerlach L, Güldemann T, Kure B, Mpoloka SW, Nakagawa H, Naumann C, Lipson M, Loh PR, Lachance J, Mountain J, Bustamante CD, Berger B, Tishkoff SA, Henn BM, Stoneking M, Reich D, Pakendorf B (2012) The genetic prehistory of southern Africa. Nature Communications 3 1143. (Supplementary Materials). PMCID:PMC3493647

Sankararaman S, Patterson N, Li H, Pääbo S, Reich D (2012) The Date of Interbreeding between Neandertals and Modern Humans. PLoS Genet 8, e1002947 (Supplementary Materials). PMCID:PMC3464203

Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D (2012) Ancient admixture in human history. Genetics 192, 1065-93 (Supplementary Materials). PMCID:PMC3522152

Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Pruefer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV Derevianko AP, Patterson N, Andres AM, Eichler EE, Slatkin M, Reich D*, Kelso J*, Paabo S* (2012) A high coverage genome sequence from an archaic Denisovan individual. Science 338, 222-6. (Supplementary Materials). PMCID:PMC3617501

Sun JX, Helgason A, Masson G, Ebenesersdottir SS, Li H, Mallick S, Gnerre S, Patterson N, Kong A Reich D & Stefansson K (2012) A direct characterization of human mutation based on microsatellites. Nat Genet 44, 1161-5 (Supplementary Materials). PMCID:PMC3459271

Turchin MC, Chiang CWK, Palmer CD, Sankararaman S, Reich D, Genetic Investigation of ANthropomorphic Traits (GIANT) Consortium, Hirschhorn JN (2012) Evidence of widespread selection on standing variation in Europe at height-associated SNPs. Nat Genet 44, 1015-9 (Supplementary Materials). PMCID:PMC3480734

Williams AL, Patterson N, Glessner J, Hakonarson H, Reich D (2012) Phasing many thousands of genotyped samples. Am J Hum Gen 91, 238-51. PMCID:PMC3415548

Reich DE, Patterson N, Campbell D, Tandon A, Mazieres S, Ray N, Parra MV, Rojas W, Duque C, Mesa N, Garcia LF, Triana O, Blair S, Maestre A, Dib JC, Bravi CM, Bailliet G, Corach D, Hunemeier T, Bortolini MC, Salzano FM, Petzl-Erler ML, Acuna-Alonza V, Aguilar-Salinas C, Canizales-Quinteros S, Tusie-Luna T, Riba L, Rogriguez-Cruz M, Lopez-Alarcon M, Coral-Vazquez R, Canto-Cetina T, Silva-Zolezzi I, Fernandez-Lopez JC, Contreras AV, Jimenez-Sanchez G, Gomez-Vazquez MJ, Molina J, Carrcedo A, Salas A. Gallo C, Poletti G, Witonsky DB, Alkorta-Aranburu G, Sukernik RI, Osipova L, Fedorova SA, Vasquez R, Villena M, Moreau C, Barrantes R, Pauls D, Excoffier L, Bedoya G, Rothhammer F, Dugoujon JM, Larrouy G, Klitz W, Labuda D, Kidd J, Kidd K, Di Rienzo A, Freimer NB, Price AL, Ruiz-Linares A (2012) Reconstructing Native American Population History. Nature 488, 37-4 (Supplementary Materials). PMCID:PMC3615710

Pasaniuc B, Rohland N, McClaren PJ, Garimella K, Zaitlen N, Li H, Gupta N, Neale BM, Daly MJ, Sklar P, Sullivan PF, Bergen S, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Purcell SM, Haas DW, Liang L, Sunyaev S, Patterson N, de Bakker PIW, Reich D & Price AL (2012) Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat. Genet 44, 631-5 (Supplementary Materials). PMCID:PMC3400344

Campbell DD, Parra MV, Duque C, Gallego N, Franco L, Tandon A, Hünemeier T, Bortolini C, Villegas A, Bedoya G, McCarthy MI, Prica A, Reich D, Ruiz-Linaresa (2012) Amerind Ancestry, Socioeconomic Status and the Genetics of Type 2 Diabetes in a Colombian Population. PLoS One 7, e33570. PMCID:PMC3328483

Cheng CY, Reich D, Haiman CA, Tandon A, Patterson N, Elizabeth S, Akylbekova EL, Brancati FL, Coresh J, Boerwinkle E, Altshuler D, Taylor HA, Henderson BE, Wilson JG, Kao WH (2012) African ancestry and its correlation to Type 2 Diabetes in African Americans: a genetic admixture analysis in three U.S. population cohorts. PLoS One 7, e32840 (Supplementary Materials). PMCID:PMC3306373

Rohland N. "DNA Extraction of Ancient Animal Hard Tissue Samples via Adsorption to Silica Particles", in Shapiro, Beth and Hofreiter, Michael, (eds). Ancient DNA Methods and Protocols, Methods in Molecular Biology, vol. 840, 21-28, Springer Science + Business Media, 2012.

Rohland N, Reich, D. Cost-effective high-throughput DNA sequencing libraries for multiplexed target capture (2012) Genome Research 5, 939-46 (Supplementary Materials). PMCID:PMC3337438

IL6R Genetics Consortium Emerging Risk Factors Collaboration, Sarwar N, Butterworth AS, Freitag DF, Gregson J, Willeit P, Gorman DN, Gao P, Saleheen D, Rendon A, Nelson CP, Braund PS, Hall AS, Chasman DI, Tybjærg-Hansen A, Chambers JC, Benjamin EJ, Franks PW, Clarke R, Wilde AA, Trip MD, Steri M, Witteman JC, Qi L, van der Schoot CE, de Faire U, Erdmann J, Stringham HM, Koenig W, Rader DJ, Melzer D, Reich D, Psaty BM, Kleber ME, Panagiotakos DB, Willeit J, Wennberg P, Woodward M, Adamovic S, Rimm EB, Meade TW, Gillum RF, Shaffer JA, Hofman A, Onat A, Sundström J, Wassertheil-Smoller S, Mellström D, Gallacher J, Cushman M, Tracy RP, Kauhanen J, Karlsson M, Salonen JT, Wilhelmsen L, Amouyel P, Cantin B, Best LG, Ben-Shlomo Y, Manson JE, Davey-Smith G, de Bakker PI, O'Donnell CJ, Wilson JF, Wilson AG, Assimes TL, Jansson JO, Ohlsson C, Tivesten Å, Ljunggren Ö, Reilly MP, Hamsten A, Ingelsson E, Cambien F, Hung J, Thomas GN, Boehnke M, Schunkert H, Asselbergs FW, Kastelein JJ, Gudnason V, Salomaa V, Harris TB, Kooner JS, Allin KH, Nordestgaard BG, Hopewell JC, Goodall AH, Ridker PM, Hólm H, Watkins H, Ouwehand WH, Samani NJ, Kaptoge S, Di Angelantonio E, Harari O, Danesh J (2012) Interleukin-6 receptor pathways in coronary heart disease: a collaborative meta-analysis of 82 studies. Lancet 379, 1205-13. PMCID:PMC3316940


2011

Reich D, Patterson N, Kircher M, Delfin F, Nandineni MR, Pugach I, Ko YC, Jinam TA, Phipps ME, Saitou N, Wollstein A, Kayser M, Pääbo S, Stoneking M. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania (2011) Am J Hum Genet 89, 516-28. (Supplementary Materials). PMCID:PMC3188841

Durand EY, Patterson N, Reich D, Slatkin M. Testing for ancient admixture between closely related populations (2011) Mol Bio Evol. 28, 2239-52 (Supplementary Materials). PMCID:PMC3144383

Deo RC, Wilson JG, Xing C, Lawson K, Kao WH, Reich D, Tandon A, Akylbekova E, Patterson N, Mosley TH Jr, Boerwinkle E, Taylor HA Jr. (2011) Single-nucleotide polymorphisms in LPA explain most of the ancestry-specific variation in Lp(a) levels in African Americans. PLoS One. 6, e14581 (Supplem139379.zipentary Materials). PMCID:PMC3025914

Bhatia G, Patterson N, Pasaniuc B, Zaitlen N, Genovese G, Pollack S, Mallick S, Myers S, Tandon A, Spencer C, Palmer CD, Adebowale AA, Akylbekova EL, Cupples A, Divers J, Fornage M, Kao LWH, Lange L, Li M, Musani S, Mychalecky JC, Ogunniyi A, Papanicolaou G, Rotimi CN, Rotter JI, Ruczinski I, Salako B, Siscovick DS, Tayo BO, Yang Q, McCarroll SA, Sabeti P, Lettre G, De Jager P, Hirschhorn J, Zhu X, Cooper R, Reich DE, Wilson J and Price AL. Genome-wide Comparison of African-Ancestry Populations from CARe and Other Cohorts Reveals Signals of Natural Selection (2011) Am J Hum Genet 89, 368-81. (Supplementary Materials). PMCID:PMC3169818

Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, Palmer CD, Chen GK, Wang K, Buxbaum SG, Akylbekova EL, Aldrich MC, Ambrosone CB, Amos C, Bandera AV, Berndt SI, Berstein L, Blot WJ, Bock CH, Boerwinkle E, Cai Q, Caporaso N, Casey G, Cupples AL, Deming SL, Diver WR, Divers J, Fornage M, Gillanders EM, Glessner J, Harris CC, Hu JJ, Ingles SA, Isaacs W, John EM, Kao LWH, Keating B, Kittles RA, Kolonel LN, Larkin E, Le Marchand L, McNeill LH, Millikan RC, Murphy, Musani S, Neslund-Dudas C, Nyante S, Papanicolaou GJ, Press MF, Psaty BM, Reiner AP, Rich SS, Rodriguez-Gil JL, Rotter JI, Rybicki BA, Schwartz AG, Signorello LB, Spitz M, Strom SS, Thun MJ, Tucker MA, Wang Z, Wiencke JK, Witte JS, Wrensch M, Wu X, Yamamura Y, Zanetti KA, Zheng W, Ziegler RG, Zhu Ziaofeng, Redline S, Hirschhorn JN, Henderson BE, Taylor HE, Price AL, Hakonarson H, Chanock SJ, Haiman CA, Wilson JG, Reich DL & Myers SR (2011) The landscape of recombination in African Americans. Nature 476, 170-5 (Supplementary Materials). PMCID:PMC3154982

Li, H, Durbin R (2011) Inferences of human population history from whole genome sequences. Nature 475, 493-6 (Supplementary Materials).

Shah AM, Tamang R, Moorjani P, Rani DS, Govindaraj P, Kulkami G, Bhattacharya T, Mustak MS, Bhaskar LV, Reddy AG, Gadhvi D, Gai PB, Chaubey G, Patterson N, Reich D, Tyler-Smith C, Singh L, Thangaraj K (2011) Indian Siddis: African Descendants with Indian Admixture. Am J Hum Genet 89, 154-61 (Supplementary Materials). PMCID:PMC3135801

Tandon A, Patterson N, Reich D (2011) Ancestry informative marker panels for African Americans based on subsets of commercially available SNP arrays. Genetic Epidemiology 35, 80-3. PMCID:PMC4386999

Moorjani P, Patterson N, Hirschhorn JN, Keinan A, Hao L, Atzmon G, Burns E, Ostrer H, Price AL, Reich D (2011) The History of African Gene Flow into Southern Europeans, Levantines, and Jews. PLoS Genetics 7, e1001373 (Supplementary Materials). PMCID:PMC3080861

Pasaniuc B, Zaitlen, N, Lettre G, Chen GK, Tandon A, Kao LWH, Ruczinski I, Fornage M, Siscovik DS, Zhu X, Larkin E, Lange LA, Cupples LA, Yang Qiong, Akylbekova EL, Musani SK, Divers J, Mychaleckj J, Mingyao L, Papanicolaou, Millikan RC, Ambrosone CB, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG Nyante SJ, Bandera EV, Ingles SA, Press MF, Chanock SJ, Deming SL, Rodriguez-Gil JL, Palmer CP, Buxbaum S, Ekunwe L, Hirschhorn JN, Henderson BE, Myers S, Haiman CA, Reich D, Patterson N, Wilson JG, Price AL (2011) Enhanced Statistical Tests for GWAS in Admixed Populations: Assessment using African Americans from CARe and a Breast Cancer Consortium. PLoS Genetics 7, e1001371 (Supplementary Materials). PMCID:PMC3080860


2010

Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PLF, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M & Pääbo S (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053-60 (Supplementary Materials). PMCID:PMC4306417

Rohland, N, Reich D, Mallick S, Meyer M, Green RE, et al. (2010) Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants. PLoS Biol 8, e1000564 (Supplementary Materials). PMCID:PMC3006346

Price AL, Zaitlen NA, Reich D, Patterson N (2010) New Approaches to population stratification in genome-wide association studies. Nat Rev Genet. 11, 459-63. PMCID:PMC2975875

Cheng CY, Reich D, Wong TY, Klein R, Klein BE, Patterson N, Tandon A, Li M, Boerwinkle E, Sharrett AR, Kao WH (2010) Admixture mapping scans identify a locus affecting retinal vascular caliber in hypertensive African Americans: the Atherschlerosis Risk in (ARIC) study. PLoS Genet. 6, e1000908 (Supplementary Materials). PMCID:PMC2855324

Patterson N, Petersen DC, van der Ross RE, Sudoyo H, Glashoff RH, Marsuki S, Reich D, Hayes VM (2010) Genetic structure of a unique admixed population: implications for medical research. Hum Mol Genet. 19, 411-19 (Supplementary Materials).

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kirchner M, Patterson N, Li H, Zhai W, Fritz MH-Y, Hansen NF, Durand EY, Malaspinas A-S, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer H, Burbano HA, Good JM, Schultz R, Axima-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan A, Gušic I, Doronichev VB, Golovanova Verna C, Lalueza-Fox C, Rasilla M, Fortea, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush E, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D*, Pääbo S* (2010) A draft sequence of the Neandertal genome. Science 328, 710-22 (Supplementary Materials).

Campbell KL, Roberts JEE, Watson LN, Stetefeld J, Sloan AM, Signore AV, Howatt JW, Jeremy RHT, Rohland N, Shen T, Austin JJ, Hofreiter Michael, Ho Chien, Weber RE, Cooper A (2010) Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance. Nature Genetics 42, 536-40 (Supplementary Materials).

Keinan A, Reich D (2010) Human Population Differentiation Is Strongly Correlated with Local Recombination Rate. PLoS Genetics 6, e1000886 (Supplementary Materials). PMCID:PMC2845648

Schuster, SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oustuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Kekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE Hardison RC, Gibbs RA, Harkins TT, Hayes VM (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature 463, 942-7 (Supplementary Materials). PMCID:PMC3890430

Chen H, Patterson N, Reich D (2010) Population differentiation as a test for selective sweeps. Genome Res. 20, 393-402 (Supplementary Materials). PMCID:PMC2840981

Keinan A, Reich D. Can a sex-biased human demography account for the reduced effective population size of chromosome X in non-Africans? (2010) Mol Biol Evol. 27, 2312-21 (Supplementary Materials). PMCID:PMC2944028

Rohland N, Siedel H, Hofreiter M (2010) A rapid column-based ancient DNA extraction method for increased sample throughput. Molecular Ecology Resources 10, 677-83.


2009

Yu F, Keinan A, Chen H, Ferland RJ, Hill RS, Mignault AA, Walsh CA, Reich D. (2009) Detecting natural selection by empirical comparison to random regions of the genome. Human Molecular Genetics 18, 4853-67 (Supplementary Materials). PMCID:PMC2778377

Reich D, Thangaraj K, Patterson N, Price AL, Singh L (2009) Reconstructing Indian population history. Nature 461, 489-94 (Mathematical Appendix) (Supplementary Materials). PMCID:PMC2842210

Florez JC, Price AL, Campbell D, Riba L, Parra MV, Yu F, Duque C, Saxena R, Gallego N, Tello-Ruiz M, Franco L, Rodríguez-Torres M, Villegas A, Bedoya G, Aguilar-Salinas CA, Tusié-Luna MT, Ruiz-Linares A, Reich D (2009) Strong association of socioeconomic status with genetic ancestry in Latinos: implications for admixture studies of type 2 diabetes. Diabetologia 52, 1528-36 (Supplementary Materials). PMCID:PMC3113605

Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, Beaty TH, Mathias R, Reich D, Myers S (2009) Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet 5, e1000519 (Supplementary Materials). PMCID:PMC2689842

Price AL, Helgason A, P Snaebjorn, S Hreinn, St. Clair D, Andreassen OA, Reich D, Kong A, Stefansson K (2009) The impact of divergence time on the nature of population structure: An example from Iceland. PLoS Genet 5, e1000505 (Supplementary Materials). PMCID:PMC2684636

Cheng CY, Kao WH, Patterson N, Tandon A, Haiman CA, Harris TB, Xing C, John EM, Ambrosone CB, Brancati FL, Coresh J, Press MF, Parekh RS, Klag MJ, Meoni LA, Hsueh WC, Fejerman L, Pawlikowska L, Freedman ML, Jandorf LH, Bandera EV, Ciupak GL, Nalls MA, Akylbekova EL, Orwoll ES, Leak TS, Miljkovic I, Li R, Ursin G, Bernstein L, Ardlie K, Taylor HA, Boerwinckle E, Zmuda JM, Henderson BE, Wilson JG, Reich D (2009) Admixture mapping of 15,280 African Americans identifies obesity susceptibility Loci on chromosomes 5 and X. PLoS Genet. 5, e1000490 (Supplementary Materials). PMCID:PMC2679192

Sun JX, Mullikin JC, Patterson N, Reich DE (2009) Microsatellites are molecular clocks that support accurate inferences about history. Mol Biol Evol. 26, 1017-27. PMCID:PMC2734136

Mallick S, Gnerre S, Muller P, Reich D (2009) The difficulty of avoiding false positives in genome scans for natural selection. Genome Research 19, 922-33 (Supplementary Materials). PMCID:PMC2675981

De Jager PL, Baecher-Allan C, Maier LM, Arthur AT, Ottoboni L, Barcellos L, McCauley JL, Sawcer S, Goris A, Saarela J, Yelensky R, Price A, Leppa V, Patterson N, de Bakker PI, Tran D, Aubin C, Pobywajlo S, Rossin E, Hu X, Ashley CW, Choy E, Rioux JD, Pericak-Vance MA, Ivinson A, Booth DR, Stewart GJ, Palotie A, Peltonen L, Dubois B, Haines JL, Weiner HL, Compston A, Hauser SL, Daly MJ, Reich D, Oksenberg JR, Hafler DA (2009) The role of the CD58 locus in multiple sclerosis. Proc Natl Acad Sci USA, 106, 5264-9 (Supplementary Materials). PMCID:PMC2664005

Reich D, Nalls MA, Kao WHL, Akylbekova EL, Tandon A, Patterson N, Mullikin J, Hsueh W-C, Cheng C-Y, Coresh J, Boerwinkle B, Li M, Waliszewska A, Neubauer J, Li R, Leak TS, Ekunwe L, Files JC, Hardy CL, Zmuda JM, Taylor HA, Ziv E, Harris TB, Wilson JG (2009) Reduced neutrophil count in people of African descent is due to a regulatory variant in the Duffy Antigen Receptor for Chemokines gene. PLoS Genetics 5, e1000360 (Materials and Methods). PMCID:PMC2628742

Dhandapany PS, Sadayappan S, Xue Y, Powell GT, Rani DS, Nallari P, Rai TS, Khullar M, Soares P, Bahl A, Tharkan JM, Vaideeswar P, Rathinavel A, Narasimhan C, Ayapati DR, Ayub Q, Mehdi SQ, Oppenheimer S, Richards MB, Price AL, Patterson N, Reich D, Singh L, Tyler-Smith C, Thangaraj K (2009) A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia. Nature Genetics 41, 187-91 (Supplementary Materials). PMCID:PMC2697598

Deo RC, Reich D, Tandon A, Akylbekova E, Patterson N, Waliszewska A, Kathiresan S, Sarpong D, Taylor HA Jr, Wilson JG (2009) Genetic differences between the determinants of lipid profile phenotypes in African and European Americans: the Jackson Heart Study. PLoS Genet. 5, e1000342 (Supplementary Materials). PMCID:PMC2613537

Keinan A, Mullikin JC, Patterson N, Reich D (2009) Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nature Genetics 41, 66-70 (Supplementary Materials). PMCID:PMC2612098

Fejerman L, Haiman CA, Reich D, Tandon A, Deo RC, John EM, Ingles SA, Ambrosone CB, Bovbjerg DH, Jandorf LH, Davis W, Ciupak G, Whittemore AS, Press MF, Ursin G, Bernstein L, Huntsman S, Henderson BE, Ziv E, Freedman ML (2009) An admixture scan in 1,484 African American women with breast cancer. Cancer Epidemiol Biomarkers Prev. 11, 3110-7 (Supplementary Materials). PMCID:PMC2783219

Cheng CY, Reich D, Coresh J, Boerwinkle E, Patterson N, Li M, North KE, Tandon A, Bailey-Wilson JE, Wilson JG, Kao WH. Admixture mapping of obesity-related traits in African Americans: the Atherosclerosis Risk in Communities (ARIC) Study. (2009) Obesity 3, 563-72 (Supplementary Materials). PMCID:PMC2866099

Jia L, Landan G, Pomerantz M, Jaschek R, Herman P, Reich D, Yan C, Khalid O, Kantoff P, Oh W, Manak JR, Berman BP, Henderson BE, Frenkel B, Haiman CA, Freedman M, Tanay A, Coetzee GA (2009) Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet. 8, e1000597 (Supplementary Materials). PMCID:PMC2717370

Bock CH, Schwartz AG, Ruterbusch JJ, Levin AM, Neslund-Dudas C, Land SJ, Wenzlaff AS, Reich D, McKeigue P, Chen W, Heath EI, Powell IJ, Kittles RA, Rybicki BA. Results from a prostate cancer admixture mapping study in African-American men. (2009) Hum Genet. 11, 637-42. PMCID:PMC2975267

Cree BA, Reich DE, Khan O, De Jager PL, Nakashima I, Takahashi T, Bar-Or A, Tong C, Hauser SL, Oksenberg JR. Modification of multiple sclerosis phenotypes by African Ancestry at HLA. (2009) Arch Neurol. 2, 226-33. PMCID:PMC4334456


2008

Price AL, Patterson N, Hancks DC, Myers S, Reich D, Cheung VG, Spielman RS (2008) Effects of cis and trans genetic ancestry on gene expression in African Americans. PLoS Genetics 4, e1000294 (Supplementary Materials). PMCID:PMC2586034

Kao WH, Klag MJ, Meoni LA, Reich D, Berthier-Schaad Y, Li M, Coresh J, Patterson N, Tandon A, Powe NR, Fink NE, Sadler JH, Weir MR, Abboud HE, Adler SG, Divers J, Iyengar SK, Freedman BI, Kimmel PL, Knowler WC, Kohn OF, Kramp K, Leehey DJ, Nicholas SB, Pahl MV, Schelling JR, Sedor JR, Thornley-Brown D, Winkler CA, Smith MW, Parekh RS; Family Investigation of Nephropathy and Diabetes Research Group (2008) MYH9 is associated with nondiabetic end-stage renal disease in African Americans. Nature Genetics 40, 1185-92 (Supplementary Materials). PMCID:PMC2614692

Price AL, Weale ME, Patterson N, Myers SR, Need AC, Shianna KV, Ge D, Rotter JI, Torres E, Taylor KD, Goldstein DB, Reich D (2008) Long-range LD can confound genome scans in admixed populations. Am J Hum Genet. 83, 132-5. PMCID:PMC2443852

Reich D, Price AL, Patterson N (2008) Principal component analysis of genetic data. Nature Genetics 40, 491-2.

Caswell JL, Mallick S, Richter DJ, Neubauer J, Schirmer C, Gnerre S, Reich D (2008) Analysis of chimpanzee history based on genome sequence alignments. PLoS Genetics 4, e1000057 (Supplementary Materials). PMCID:PMC2278377

Myers S, Fefferman C, Patterson N (2008) Can one learn history from the allelic spectrum? Theoretical Population Biology 73, 342-8.

Nalls MA, Wilson JG, Patterson NJ, Tandon A, Zmuda JM, Huntsman S, Garcia M, Hu D, Li R, Beamer BA, Patel KV, Akylbekova EL, Files JC, Hardy CL, Buxbaum SG, Taylor HA, Reich D, Harris TB, Ziv E (2008) Admixture mapping of white cell count: genetic locus responsible for lower white blood cell count in the health ABC and Jackson Heart Studies. Am J Hum Genet. 82, 81-7. PMCID:PMC2253985

Seldin MF, Price AL (2008) Application of ancestry informative markers to association studies in European Americans. PLoS Genetics 4, e5. PMCID:PMC2211545

Price AL, Butler J, Patterson N, Capelli C, Pascali VL, Scarnicci F, Ruiz-Linares A, Groop L, Saetta AA, Korkolopoulou P, Seligsohn U, Waliszewska A, Schirmer C, Ardlie K, Ramos A, Nemesh J, Arbeitman L, Goldstein DB, Reich D, Hirschhorn JN (2008) Discerning the ancestry of European Americans in genetic association studies. PLoS Genetics 4, e236. PMCID:PMC2211542


2007

Deo R, Patterson N, Tandon A, McDonald G, Haiman CA, Ardlie K, Henderson BE, Henderson SO, Reich D (2007) A high-density admixture scan in 1,670 African Americans with hypertension. PLoS Genetics 3, e196. PMCID:PMC2077893

Keinan A, Mullikin JC, Patterson N, Reich D (2007) Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than Europeans. Nature Genetics 39, 1251-5 (Supplementary Materials). PMCID:PMC3586588

Haiman CA, Le Marchand L, Yamamato J, Stram DO, Sheng X, Kolonel LN, Wu AH, Reich D, Henderson BE (2007) A common genetic risk factor for colorectal and prostate cancer. Nature Genetics 39, 954-6 (Supplementary Materials). PMCID:PMC2391283

Ayodo G, Price AL, Keinan A, Ajwang A, Otieno MF, Orago ASS, Patterson N, Reich D (2007) Combining evidence of natural selection with association analysis increases power to detect malaria-resistance variants. Am J Hum Genet. 81, 234-42. PMCID:PMC1950820

Yu F, Hill RS, Schaffner SF, Sabeti PC, Wang ET, Mignault AA, Ferland RJ, Moyzis RK, Walsh CA, Reich D (2007) Technical comment on ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Science 316, 370 (Supplementary Materials).

Becquet C, Patterson N, Stone AC, Przeworski M, Reich D (2007) Genetic structure of chimpanzee populations. PLoS Genetics 3, e66. PMCID:PMC1853122

Price AL, Patterson N, Yu F, Cox DR, Waliszewska A, McDonald GJ, Tandon A, Schirmer C, Neubauer J, Bedoya G, Duque C, Villegas A, Bortolini MC, Salzano FM, Gallo C, Mazzotti G, Tello-Ruiz M, Riba L, Aguilar-Salinas CA, Canizales-Quinteros S, Menjivar M, Klitz W, Henderson B, Haiman CA, Winkler C, Tusie-Luna T, Ruiz-Linares A, Reich D (2007) A genomewide admixture map for Latino populations. Am J Hum Genet. 80, 1024-36 (Supplementary Materials). PMCID:PMC1867092

Haiman CA, Patterson N, Freedman ML, Myers SR, Pike MC, Waliszewska A, Neubauer J, Tandon A, Schirmer C, McDonald GJ, Greenway SC, Stram DO, Le Marchand L, Kolonel LN, Frasco M, Wong D, Pooler LC, Ardlie K, Oakley-Girvan I, Whittemore AS, Cooney KA, John EM, Ingles SA, Altshuler D, Henderson BE, Reich D (2007) Multiple regions within 8q24 independently affect risk for prostate cancer. Nature Genetics 39, 638-44 (Supplementary Materials). PMCID:PMC2638766

Reich D, Patterson N, Ramesh V, De Jager PL, McDonald GJ, Tandon A, Choy E, Hu D, Tamraz B, Pawlikowska L, Wassel-Fyr C, Huntsman S, Waliszewska A, Rossin E, Li R, Garcia M, Reiner A, Ferrell R, Cummings S, Kwok PY, Harris T, Zmuda JM, Ziv E; Health, Aging and Body Composition (Health ABC) Study (2007) Admixture mapping of an allele affecting interleukin 6 soluble receptor and interleukin 6 levels. Am J Hum Genet. 80, 716-26 (Supplementary Materials). PMCID:PMC1852718

Wassel Fyr CL, Kanaya AM, Cummings SR, Reich D, Hsueh WC, Reiner AP, Harris TB, Moffett S, Li R, Ding J, Miljkovic-Gacic I, Ziv E for the Health, Aging, Body Composition Study (2007) Genetic admixture, adipocytokines, and adiposity in Black Americans: the Health, Aging, and Body Composition study. Human Genetics 121, 615-24.

Shaffer JR, Kammerer CM, Reich D, McDonald G, Patterson N, Goodpaster B, Bauer DC, Li J, Newman AB, Cauley JA, Harris TB, Tylavsky F, Ferrell RE, Zmuda JM; for the Health ABC study (2007) Genetic markers for ancestry are correlated with body composition traits in older African Americans. Osteoporosis International 18, 733-41.


2006

Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genetics 2, e190. PMCID:PMC1713260

Freedman ML, Haiman CA, Patterson N, McDonald GJ, Tandon A, Waliszewska A, Penney K, Steen RG, Ardlie K, John EM, Oakley-Girvan I, Whittemore AS, Cooney KA, Ingles SA, Altshuler D, Henderson BE, Reich D (2006) Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc. Natl. Acad. Sci. USA 103, 14068-73 (Supplementary Notes). PMCID:PMC1499913

Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics 38, 904-9 (Supplementary Materials) (EIGENSTRAT software).

Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D (2006) Genetic evidence for complex speciation of humans and chimpanzees. Nature 441, 1103-8 (Supplementary Materials) (Raw Data Available Online) (Correspondence with John Wakeley March 2008).

Lohmueller KE, Mauney MM, Reich D, Braverman JM (2006) Variants associated with common disease are not unusually differentiated in frequency across populations. Am J Hum Genet. 78, 130-6. PMCID:PMC1380210

Bonnen PE, Pe'er I, Plenge RM, Salit J, Lowe JK, Shapero MH, Lifton RP, Breslow JL, Daly MJ, Reich DE, Jones KW, Stoffel M, Altshuler D, Friedman JM (2006) Evaluating potential for whole-genome studies in Kosrae, an isolated population in Micronesia. Nature Genetics 38, 214-7.

2005

Reich D, Patterson N (2005) Will admixture mapping work to find disease genes? Philos Trans R Soc Lond B Biol Sci. 360, 1605-7. PMCID:PMC1609196

Reich D, Patterson N, Jager PL, McDonald GJ, Waliszewska A, Tandon A, Lincoln RR, Deloa C, Fruhan SA, Cabre P, Bera O, Semana G, Kelly MA, Francis DA, Ardlie K, Khan O, Cree BA, Hauser SL, Oksenberg JR, Hafler DA (2005) A whole-genome admixture scan finds a candidate gene for multiple sclerosis susceptibility. Nature Genetics 37, 1113-8.

Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87.

Winckler W, Myers SR, Richter DJ, Onofrio RC, McDonald GJ, Bontrop RE, McVean GA, Gabriel SB, Reich D, Donnelly P, Altshuler D (2005) Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308, 107-11.

Sabeti PC, Walsh E, Schaffner SF, Varilly P, Fry B, Hutcheson HB, Cullen M, Mikkelsen TS, Roy J, Patterson N, Cooper R, Reich D, Altshuler D, O'Brien S, Lander ES (2005) The case for selection at CCR5-Delta32. PLoS Biol. 3, e378. PMCID:PMC1275522

Patterson NJ (2005) How old is the most recent ancestor of two copies of an allele? Genetics 169, 1093-104. PMCID:PMC1449139

Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, Altshuler D (2005) Calibrating a coalescent simulation of human genome sequence variation. Genome Res. 15, 1576-83. PMCID:PMC1310645


2004

Freedman ML*, Reich D*, Penney KL, McDonald GJ, Mignault AA, Patterson N, Gabriel SB, Topol EJ, Smoller JW, Pato CN, Pato MT, Petryshen T, Kolonel LN, Lander ES, Sklar P, Henderson B, Hirschhorn J, Altshuler D (2004) Assessing the impact of population stratification on genetic association studies. Nature Genetics 36, 388-93. PMCID:PMC4406348

Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, Malasky MJ, Scafe C, Le E, De Jager P, Yi Z, DeThé G, Essex M, Kanki PJ, Moore JH, Poku K, Phair JP, Goedert JJ, Vlahov D, Williams SM, Tishkoff SA, Winkler CA, De La Vega FM, Woodage T, Sninsky JJ, Hafler DA, Altshuler D, Gilbert DA, O’Brien SJ, Reich D (2004) A high density admixture map for disease gene discovery in African Americans. Am J Hum Genet. 74, 979-1000 (Online Table A) (Online Table B). PMCID:PMC1181963

Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Oksenberg JR, Hauser SL, Smith MW, O'Brien SJ, Altshuler D, Daly M, Reich D (2004) Methods for high-density admixture mapping of disease genes. Am J Hum Genet. 74, 1001-13 (ANCESTRYMAP software). PMCID:PMC1181990

Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, Drake JA, Rhodes M, Reich DE, Hirschhorn JN (2004) Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet. 74, 1111-20. PMCID:PMC1182075

Cree BA, Khan O, Bourdette D, Goodin DS, Cohen JA, Marrie RA, Glidden D, Weinstock-Guttman B, Reich D, Patterson N, Haines JL, Pericak-Vance M, Deloa C, Oksenberg JR, Hauser SL (2004) Clinical characteristics of African Americans vs Caucasian Americans with multiple sclerosis. Neurology 63, 2039-45.

Oksenberg JR, Barcellos LF, Cree BA, Baranzini SE, Bugawan TL, Khan O, Lincoln RR, Swerdlin A, Mignot E, Lin L, Goodin D, Erlich HA, Schmidt S, Thomson G, Reich DE, Pericak-Vance MA, Haines JL, Hauser SL (2004) Mapping multiple sclerosis susceptibility to the HLA-DR locus in African Americans. Am. J. Hum. Genet. 74, 160-7. PMCID:PMC1181903


2003

Reich DE, Gabriel SB and Altshuler D (2003) Quality and completeness of SNP databases. Nature Genetics 33, 457-8.

2002

Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GM, Ackerman HC, Campbell SJ, Altshuler D, Kwiatkowski D, Ward R, Lander ES (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832-837, 2002.

Reich DE*, Schaffner, SF*, Daly, MJ, McVean, G. Mullikin, JC, Higgins, JM, Richter, DJ, Lander, ES, Altshuler, D (2002) Human genome sequence variation and the influence of gene history, mutation and recombination. Nature Genetics 32, 135-42.

Reich DE, Lander ES, Waterston R, Paabo S, Ruvolo M and Varki A (2002) Sequencing the chimpanzee genome, a white paper funded by the National Human Genome Research Institute.

2001

Reich DE, Lander ES (2001) On the allelic spectrum of human disease. Trends Genet 17, 502-10.

Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES (2001) Linkage Disequilibrium in the human genome. Nature 411, 199-204.

The International SNP Map Working Group (2001) A map of human genome sequence variation containing 1.4 million SNPs, Nature 409, 928-33.

Reich DE, Goldstein DB (2001) Detecting associations in case-control studies while correcting for population stratification, Genetic Epidemiology 20, 4-16.

2000

Lindblad-Toh K, Winchester E, Daly MJ, Wang DG, Hirschhorn JN, Laviolette JP, Ardlie K, Reich DE, Robinson E, Sklar P, Shah N, Thomas D, Fan JB, Gingeras T, Warrington J, Patil N, Hudson TJ, Lander ES (2000) Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nature Genetics 24, 381-6.

Goldstein DB, Reich, DE, Bradman N, Usher S, Seligsohn U, Peretz H. (1999) Age estimates for two common mutations causing Factor XI deficiency. Am. J. Hum. Genet. 64, 1071-5.

Goldstein DB, Roemer GW, Smith DA, Reich DE, Bergman A, Wayne RK (1999) The use of microsatellite variation to infer population structure and demographic history in a natural model system. Genetics 151, 797-801.

Reich DE, Feldman MW, Goldstein DB (1999) Statistical properties of two tests that use multilocus data sets to detect population expansions. Mol. Biol. Evol. 16, 453-66.

Reich DE, Goldstein DB (1999) Estimating the ages of mutations using variation at linked markers. in Microsatellites: Evolution & Applications, Oxford University Press, 129-38.

1998

Stephens JC, Reich DE, Goldstein DB, Shin HD, Smith MW, Carrington M, Winkler C, Huttley GA, Allikmets R, Schriml L, Gerrard B, Malasky M, Ramos MD, Morlot S, Tzetis M, Oddoux C, di Giovine FS, Nasioulas G, Chandler D, Aseev M, Hanson M, Kalaydjieva L, Glavac D, Gasparini P, Kanavakis E, Claustres M, Kambouris M, Ostrer H, Duff G, Baranov V, Sibul H, Metspalu A, Goldman D, Martin N, Duffy D, Schmidtke J, Estivill X, O'Brien SJ, Dean M (1998) Dating the origin of the CCR5-D32 AIDS resistance allele by the coalescence of haplotypes. Am. J. Hum. Genet. 62, 1507-15.

Reich DE, Goldstein DB (1998) Genetic evidence for a Paleolithic human population expansion in Africa. Proc. Natl. Acad. Sci. USA 95, 8119-23.

Reich DE, Wayne RK, Goldstein DB (1998) Genetic evidence for a recent origin by hybridization of red wolves. Molecular Ecology 8, 139-45.