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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, 1053-1060 (Supplementary Materials).
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(12): e1000564 (Supplementary Materials.)
Price AL, Zaitlen NA, Reich D, Patterson N (2010) New Approaches to population stratification in genome-wide association studies. Nat Rev Genet. Jun 15, 459-463.
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.
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, 411-419 (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, 710-722 (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, 536-540 (Supplementary Materials).
Keinan A, Reich D (2010) Human Population Differentiation Is Strongly Correlated with Local Recombination Rate. PLoS Genetics 6, e 1000886 (Supplementary Materials).
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, 942-947 (Supplementary Materials).
Chen H, Patterson N, Reich D (2010) Population differentiation as a test for selective sweeps. Genome Res. 20, 393-402 (Supplementary Materials).
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. Epub 2010 May 7. (Supplementary Data).
2009
Rohland N, Siedel H, Hofreiter M (2009) A rapid column-based ancient DNA extraction method for increased sample throughput. Molecular Ecology Resources.
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, 4853–4867.
Reich D, Thangaraj K, Patterson N, Price AL, Singh L (2009) Reconstructing Indian population history. Nature 461, 489-494 (Mathematical Appendix) (Supplementary Materials).
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(8): 1528-36.
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.
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.
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).
Sun JX, Mullikin JC, Patterson N, Reich DE (2009) Microsatellites are molecular clocks that support accurate inferences about history. Mol Biol Evol. 26, 1017-1027.
Mallick S, Gnerre S, Muller P, Reich D (2009) The difficulty of avoiding false positives in genome scans for natural selection. Genome Research 19, 922-933 (Supplementary Materials).
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, 5264-5269 (Supplementary Materials).
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.
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, 187-191 (Supplementary Materials).
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).
Keinan A, Mullikin JC, Patterson N, Reich D (2009) Accelerated genetic drift on chromosome X during the human dispersal out of Africa. (2009) Nature Genetics 41, 66-70 (Supplementary Materials).
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. An admixture scan in 1,484 African American women with breast cancer. (2009) Cancer Epidemiol Biomarkers Prev. 11 :3110-7 (Supplementary Materials).
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).
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. Functional enhancers at the gene-poor 8q24 cancer-linked locus. (2009) PLoS Genet. 8, e1000597 (Supplementary Materials).
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.
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.
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.
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, 1185-1192 (Supplementary Materials).
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, 132-135.
Reich D, Price AL, Patterson N (2008) Principal component analysis of genetic data. Nature Genetics 40, 491-492.
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).
Myers S, Fefferman C, Patterson N (2008) Can one learn history from the allelic spectrum? Theoretical Population Biology 73, 342-348.
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, 81–87.
Seldin MF, Price AL (2008) Application of Ancestry Informative Markers to Association Studies in European Americans. PLoS Genetics 4, e5.
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 (Supplementary Materials).
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.
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, 1251-1255 (Supplementary Materials, Raw Data Available Online).
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, 954-956 (Supplementary Materials).
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, 234-242.
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 (Supplementary Materials).
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, 1024-1036 (Supplementary Materials).
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, 638-644 (Supplementary Materials).
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, 716-726 (Supplementary Materials).
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, 615-624.
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, 733-741.
2006
Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genetics 2, e190.
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, 14068-14073 (Supplementary Notes) (Supplementary Tables).
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, 904-909 (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, 1103-1108 (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, 130-136.
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, 214-217.

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