Carlos Bustamante

Publications

• Melanesian blond hair is caused by an amino acid change in TYRP1. Kenny EE, Timpson NJ, Sikora M, Yee MC, Moreno-Estrada A, Eng C, Huntsman S, Burchard EG, Stoneking M, Bustamante CD, Myles S. Science. 2012; 336 (6081): 554
• Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. 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. Am J Hum Genet. 2012; 91 (4): 660-71
• Demographic history and rare allele sharing among human populations. Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, Bustamante CD. Proc Natl Acad Sci U S A. 2011; 108 (29): 11983-8
• Genomics for the world. Bustamante CD, Burchard EG, De la Vega FM. Nature. 2011; 475 (7355): 163-5
• Genome-wide patterns of population structure and admixture in West Africans and African Americans. Bryc K, Auton A, Nelson MR, Oksenberg JR, Hauser SL, Williams S, Froment A, Bodo JM, Wambebe C, Tishkoff SA, Bustamante CD. Proc Natl Acad Sci U S A. 2010; 107 (2): 786-91
• Genes mirror geography within Europe. Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD. Nature. 2008; 456 (7218): 98-101
• Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Cornejo OE, Lefébure T, Bitar PD, Lang P, Richards VP, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ, Burne RA, Siepel A, Bustamante CD, Stanhope MJ. Mol Biol Evol. 2013; 30 (4): 881-93
• High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development. Clark RT, Famoso AN, Zhao K, Shaff JE, Craft EJ, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV. Plant Cell Environ. 2013; 36 (2): 454-66
• Detecting and annotating genetic variations using the HugeSeq pipeline. Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M, Gerstein MB, Kidd JM, Bustamante CD, Snyder M. Nat Biotechnol. 2012; 30 (3): 226-9
• Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM. Science. 2012; 337 (6090): 64-9
• Genomic ancestry of North Africans supports back-to-Africa migrations. Henn BM, Botigué LR, Gravel S, Wang W, Brisbin A, Byrnes JK, Fadhlaoui-Zid K, Zalloua PA, Moreno-Estrada A, Bertranpetit J, Bustamante CD, Comas D. PLoS Genet. 2012; 8 (1): e1002397
• Limited evidence for classic selective sweeps in African populations. Granka JM, Henn BM, Gignoux CR, Kidd JM, Bustamante CD, Feldman MW. Genetics. 2012; 192 (3): 1049-64
• Mutation hot spots in yeast caused by long-range clustering of homopolymeric sequences. Ma X, Rogacheva MV, Nishant KT, Zanders S, Bustamante CD, Alani E. Cell Rep. 2012; 1 (1): 36-42
• New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, Leidinger P, Backes C, Khairat R, Forster M, Stade B, Franke A, Mayer J, Spangler J, McLaughlin S, Shah M, Lee C, Harkins TT, Sartori A, Moreno-Estrada A, Henn B, Sikora M, Semino O, Chiaroni J, Rootsi S, Myres NM, Cabrera VM, Underhill PA, Bustamante CD, Vigl EE, Samadelli M, Cipollini G, Haas J, Katus H, O'Connor BD, Carlson MR, Meder B, Blin N, Meese E, Pusch CM, Zink A. Nat Commun. 2012: 3 698
• North African Jewish and non-Jewish populations form distinctive, orthogonal clusters. Campbell CL, Palamara PF, Dubrovsky M, Botigué LR, Fellous M, Atzmon G, Oddoux C, Pearlman A, Hao L, Henn BM, Burns E, Bustamante CD, Comas D, Friedman E, Pe'er I, Ostrer H. Proc Natl Acad Sci U S A. 2012; 109 (34): 13865-70
• North African populations carry the signature of admixture with Neandertals. Sánchez-Quinto F, Botigué LR, Civit S, Arenas C, Avila-Arcos MC, Bustamante CD, Comas D, Lalueza-Fox C. PLoS One. 2012; 7 (10): e47765
• PCAdmix: principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations. Brisbin A, Bryc K, Byrnes J, Zakharia F, Omberg L, Degenhardt J, Reynolds A, Ostrer H, Mezey JG, Bustamante CD. Hum Biol. 2012; 84 (4): 343-64
• Randomized trial of personal genomics for preventive cardiology: design and challenges. Knowles JW, Assimes TL, Kiernan M, Pavlovic A, Goldstein BA, Yank V, McConnell MV, Absher D, Bustamante C, Ashley EA, Ioannidis JP. Circ Cardiovasc Genet. 2012; 5 (3): 368-76
• SnIPRE: selection inference using a poisson random effects model. Eilertson KE, Booth JG, Bustamante CD. PLoS Comput Biol. 2012; 8 (12): e1002806
• The genetic prehistory of southern Africa. 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. Nat Commun. 2012: 3 1143
• The possibility of de novo assembly of the genome and population genomics of the mangrove rivulus, Kryptolebias marmoratus. Kelley JL, Yee MC, Lee C, Levandowsky E, Shah M, Harkins T, Earley RL, Bustamante CD. Integr Comp Biol. 2012; 52 (6): 737-42
• Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases. Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD, Butte AJ. PLoS Genet. 2012; 8 (4): e1002621
• Variation of BMP3 contributes to dog breed skull diversity. Schoenebeck JJ, Hutchinson SA, Byers A, Beale HC, Carrington B, Faden DL, Rimbault M, Decker B, Kidd JM, Sood R, Boyko AR, Fondon JW, Wayne RK, Bustamante CD, Ciruna B, Ostrander EA. PLoS Genet. 2012; 8 (8): e1002849
• A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. vonHoldt BM, Pollinger JP, Earl DA, Knowles JC, Boyko AR, Parker H, Geffen E, Pilot M, Jedrzejewski W, Jedrzejewska B, Sidorovich V, Greco C, Randi E, Musiani M, Kays R, Bustamante CD, Ostrander EA, Novembre J, Wayne RK. Genome Res. 2011; 21 (8): 1294-305
• A population genetic approach to mapping neurological disorder genes using deep resequencing. Myers RA, Casals F, Gauthier J, Hamdan FF, Keebler J, Boyko AR, Bustamante CD, Piton AM, Spiegelman D, Henrion E, Zilversmit M, Hussin J, Quinlan J, Yang Y, Lafrenière RG, Griffing AR, Stone EA, Rouleau GA, Awadalla P. PLoS Genet. 2011; 7 (2): e1001318
• An Aboriginal Australian genome reveals separate human dispersals into Asia. Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega FM, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MT, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijff P, Migliano AB, Gallego Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Wang J, Willerslev E. Science. 2011; 334 (6052): 94-8
• Comparative and demographic analysis of orang-utan genomes. Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK. Nature. 2011; 469 (7331): 529-33
• Detecting directional selection in the presence of recent admixture in African-Americans. Lohmueller KE, Bustamante CD, Clark AG. Genetics. 2011; 187 (3): 823-35
• Fast, exact linkage analysis for categorical traits on arbitrary pedigree designs. Brisbin A, Cruickshank J, Moïse NS, Gunn T, Bustamante CD, Mezey JG. Genet Epidemiol. 2011; 35 (5): 371-80
• GENOME-WIDE ASSOCIATION MAPPING AND RARE ALLELES: FROM POPULATION GENOMICS TO PERSONALIZED MEDICINE - Session Introduction. DE LA Vega FM, Bustamante CD, Leal SM. Pac Symp Biocomput. 2011: 74-5
• Genetic structure and domestication history of the grape. Myles S, Boyko AR, Owens CL, Brown PJ, Grassi F, Aradhya MK, Prins B, Reynolds A, Chia JM, Ware D, Bustamante CD, Buckler ES. Proc Natl Acad Sci U S A. 2011; 108 (9): 3530-5
• Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR. Nat Commun. 2011: 2 467
• Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Henn BM, Gignoux CR, Jobin M, Granka JM, Macpherson JM, Kidd JM, Rodríguez-Botigué L, Ramachandran S, Hon L, Brisbin A, Lin AA, Underhill PA, Comas D, Kidd KK, Norman PJ, Parham P, Bustamante CD, Mountain JL, Feldman MW. Proc Natl Acad Sci U S A. 2011; 108 (13): 5154-62
• Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection. Xie X, Molina J, Hernandez R, Reynolds A, Boyko AR, Bustamante CD, Purugganan MD. PLoS One. 2011; 6 (6): e20670
• Molecular evidence for a single evolutionary origin of domesticated rice. Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Reynolds A, Huang P, Jackson S, Schaal BA, Bustamante CD, Boyko AR, Purugganan MD. Proc Natl Acad Sci U S A. 2011; 108 (20): 8351-6
• On identifying the optimal number of population clusters via the deviance information criterion. Gao H, Bryc K, Bustamante CD. PLoS One. 2011; 6 (6): e21014
• Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB, Klein TE, Butte AJ, Ashley EA. PLoS Genet. 2011; 7 (9): e1002280
• SnapShot: Human biomedical genomics. Kenny EE, Bustamante CD. Cell. 2011; 147 (1): 248-248.e1
• The functional spectrum of low-frequency coding variation. Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R. Genome Biol. 2011; 12 (9): R84
• A genome-wide linkage scan in German shepherd dogs localizes canine platelet procoagulant deficiency (Scott syndrome) to canine chromosome 27. Brooks M, Etter K, Catalfamo J, Brisbin A, Bustamante C, Mezey J. Gene. 2010; 450 (1-2): 70-5
• A simple genetic architecture underlies morphological variation in dogs. Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, vonHoldt BM, Cargill M, Auton A, Reynolds A, Elkahloun AG, Castelhano M, Mosher DS, Sutter NB, Johnson GS, Novembre J, Hubisz MJ, Siepel A, Wayne RK, Bustamante CD, Ostrander EA. PLoS Biol. 2010; 8 (8): e1000451
• ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Wright MH, Tung CW, Zhao K, Reynolds A, McCouch SR, Bustamante CD. Bioinformatics. 2010; 26 (23): 2952-60
• An ADAM9 mutation in canine cone-rod dystrophy 3 establishes homology with human cone-rod dystrophy 9. Goldstein O, Mezey JG, Boyko AR, Gao C, Wang W, Bustamante CD, Anguish LJ, Jordan JA, Pearce-Kelling SE, Aguirre GD, Acland GM. Mol Vis. 2010: 16 1549-69
• Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation. Andrés AM, Dennis MY, Kretzschmar WW, Cannons JL, Lee-Lin SQ, Hurle B, Schwartzberg PL, Williamson SH, Bustamante CD, Nielsen R, Clark AG, Green ED. PLoS Genet. 2010; 6 (10): e1001157
• Bayesian linkage analysis of categorical traits for arbitrary pedigree designs. Brisbin A, Weissman MM, Fyer AJ, Hamilton SP, Knowles JA, Bustamante CD, Mezey JG. PLoS One. 2010; 5 (8): e12307
• Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Bryc K, Velez C, Karafet T, Moreno-Estrada A, Reynolds A, Auton A, Hammer M, Bustamante CD, Ostrer H. Proc Natl Acad Sci U S A. 2010: 107 Suppl 2 8954-61
• Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach. Zanders S, Ma X, Roychoudhury A, Hernandez RD, Demogines A, Barker B, Gu Z, Bustamante CD, Alani E. Genetics. 2010; 186 (2): 493-503
• Fine-scale population structure and the era of next-generation sequencing. Henn BM, Gravel S, Moreno-Estrada A, Acevedo-Acevedo S, Bustamante CD. Hum Mol Genet. 2010; 19 (R2): R221-6
• Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Vonholdt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG, Quignon P, Degenhardt JD, Boyko AR, Earl DA, Auton A, Reynolds A, Bryc K, Brisbin A, Knowles JC, Mosher DS, Spady TC, Elkahloun A, Geffen E, Pilot M, Jedrzejewski W, Greco C, Randi E, Bannasch D, Wilton A, Shearman J, Musiani M, Cargill M, Jones PG, Qian Z, Huang W, Ding ZL, Zhang YP, Bustamante CD, Ostrander EA, Novembre J, Wayne RK. Nature. 2010; 464 (7290): 898-902
• Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR. PLoS One. 2010; 5 (5): e10780
• Human origins: Shadows of early migrations. Bustamante CD, Henn BM. Nature. 2010; 468 (7327): 1044-5
• SNP identification, verification, and utility for population genetics in a non-model genus. Williams LM, Ma X, Boyko AR, Bustamante CD, Oleksiak MF. BMC Genet. 2010: 11 32
• Successful computational prediction of novel imprinted genes from epigenomic features. Brideau CM, Eilertson KE, Hagarman JA, Bustamante CD, Soloway PD. Mol Cell Biol. 2010; 30 (13): 3357-70
• The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis. Nishant KT, Wei W, Mancera E, Argueso JL, Schlattl A, Delhomme N, Ma X, Bustamante CD, Korbel JO, Gu Z, Steinmetz LM, Alani E. PLoS Genet. 2010; 6 (9)
• The effect of recent admixture on inference of ancient human population history. Lohmueller KE, Bustamante CD, Clark AG. Genetics. 2010; 185 (2): 611-22
• An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs. Parker HG, VonHoldt BM, Quignon P, Margulies EH, Shao S, Mosher DS, Spady TC, Elkahloun A, Cargill M, Jones PG, Maslen CL, Acland GM, Sutter NB, Kuroki K, Bustamante CD, Wayne RK, Ostrander EA. Science. 2009; 325 (5943): 995-8
• Coat variation in the domestic dog is governed by variants in three genes. Cadieu E, Neff MW, Quignon P, Walsh K, Chase K, Parker HG, Vonholdt BM, Rhue A, Boyko A, Byers A, Wong A, Mosher DS, Elkahloun AG, Spady TC, André C, Lark KG, Cargill M, Bustamante CD, Wayne RK, Ostrander EA. Science. 2009; 326 (5949): 150-3
• Complex population structure in African village dogs and its implications for inferring dog domestication history. Boyko AR, Boyko RH, Boyko CM, Parker HG, Castelhano M, Corey L, Degenhardt JD, Auton A, Hedimbi M, Kityo R, Ostrander EA, Schoenebeck J, Todhunter RJ, Jones P, Bustamante CD. Proc Natl Acad Sci U S A. 2009; 106 (33): 13903-8
• Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta). Degenhardt JD, de Candia P, Chabot A, Schwartz S, Henderson L, Ling B, Hunter M, Jiang Z, Palermo RE, Katze M, Eichler EE, Ventura M, Rogers J, Marx P, Gilad Y, Bustamante CD. PLoS Genet. 2009; 5 (1): e1000346
• Darwinian and demographic forces affecting human protein coding genes. Nielsen R, Hubisz MJ, Hellmann I, Torgerson D, Andrés AM, Albrechtsen A, Gutenkunst R, Adams MD, Cargill M, Boyko A, Indap A, Bustamante CD, Clark AG. Genome Res. 2009; 19 (5): 838-49
• Evaluating signatures of sex-specific processes in the human genome. Bustamante CD, Ramachandran S. Nat Genet. 2009; 41 (1): 8-10
• Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. Torgerson DG, Boyko AR, Hernandez RD, Indap A, Hu X, White TJ, Sninsky JJ, Cargill M, Adams MD, Bustamante CD, Clark AG. PLoS Genet. 2009; 5 (8): e1000592
• Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, Gill CA, Green RD, Hamernik DL, Kappes SM, Lien S, Matukumalli LK, McEwan JC, Nazareth LV, Schnabel RD, Weinstock GM, Wheeler DA, Ajmone-Marsan P, Boettcher PJ, Caetano AR, Garcia JF, Hanotte O, Mariani P, Skow LC, Sonstegard TS, Williams JL, Diallo B, Hailemariam L, Martinez ML, Morris CA, Silva LO, Spelman RJ, Mulatu W, Zhao K, Abbey CA, Agaba M, Araujo FR, Bunch RJ, Burton J, Gorni C, Olivier H, Harrison BE, Luff B, Machado MA, Mwakaya J, Plastow G, Sim W, Smith T, Thomas MB, Valentini A, Williams P, Womack J, Woolliams JA, Liu Y, Qin X, Worley KC, Gao C, Jiang H, Moore SS, Ren Y, Song XZ, Bustamante CD, Hernandez RD, Muzny DM, Patil S, San Lucas A, Fu Q, Kent MP, Vega R, Matukumalli A, McWilliam S, Sclep G, Bryc K, Choi J, Gao H, Grefenstette JJ, Murdoch B, Stella A, Villa-Angulo R, Wright M, Aerts J, Jann O, Negrini R, Goddard ME, Hayes BJ, Bradley DG, Barbosa da Silva M, Lau LP, Liu GE, Lynn DJ, Panzitta F, Dodds KG. Science. 2009; 324 (5926): 528-32
• Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Rätsch G, Buell CR, Leung H, Leach JE. Proc Natl Acad Sci U S A. 2009; 106 (30): 12273-8
• Global distribution of genomic diversity underscores rich complex history of continental human populations. Auton A, Bryc K, Boyko AR, Lohmueller KE, Novembre J, Reynolds A, Indap A, Wright MH, Degenhardt JD, Gutenkunst RN, King KS, Nelson MR, Bustamante CD. Genome Res. 2009; 19 (5): 795-803
• Improving the fitness of high-dimensional biomechanical models via data-driven stochastic exploration. Santos VJ, Bustamante CD, Valero-Cuevas FJ. IEEE Trans Biomed Eng. 2009; 56 (3): 552-64
• Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. PLoS Genet. 2009; 5 (10): e1000695
• Linkage disequilibrium and demographic history of wild and domestic canids. Gray MM, Granka JM, Bustamante CD, Sutter NB, Boyko AR, Zhu L, Ostrander EA, Wayne RK. Genetics. 2009; 181 (4): 1493-505
• Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data. Lohmueller KE, Bustamante CD, Clark AG. Genetics. 2009; 182 (1): 217-31
• Molecular and evolutionary history of melanism in North American gray wolves. Anderson TM, vonHoldt BM, Candille SI, Musiani M, Greco C, Stahler DR, Smith DW, Padhukasahasram B, Randi E, Leonard JA, Bustamante CD, Ostrander EA, Tang H, Wayne RK, Barsh GS. Science. 2009; 323 (5919): 1339-43
• Targets of balancing selection in the human genome. Andrés AM, Hubisz MJ, Indap A, Torgerson DG, Degenhardt JD, Boyko AR, Gutenkunst RN, White TJ, Green ED, Bustamante CD, Clark AG, Nielsen R. Mol Biol Evol. 2009; 26 (12): 2755-64
• Assessing the evolutionary impact of amino acid mutations in the human genome. Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, Lohmueller KE, Adams MD, Schmidt S, Sninsky JJ, Sunyaev SR, White TJ, Nielsen R, Clark AG, Bustamante CD. PLoS Genet. 2008; 4 (5): e1000083
• Exclusion of ABCA-1 as a candidate gene for canine Scott syndrome. Brooks MB, Catalfamo JL, Etter K, Brisbin A, Bustamante CD. J Thromb Haemost. 2008; 6 (9): 1608-10
• Exploring population genetic models with recombination using efficient forward-time simulations. Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M. Genetics. 2008; 178 (4): 2417-27
• Natural selection on genes that underlie human disease susceptibility. Blekhman R, Man O, Herrmann L, Boyko AR, Indap A, Kosiol C, Bustamante CD, Teshima KM, Przeworski M. Curr Biol. 2008; 18 (12): 883-9
• Patterns of positive selection in six Mammalian genomes. Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A. PLoS Genet. 2008; 4 (8): e1000144
• Population genetics of polymorphism and divergence under fluctuating selection. Huerta-Sanchez E, Durrett R, Bustamante CD. Genetics. 2008; 178 (1): 325-37
• Proportionally more deleterious genetic variation in European than in African populations. Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD. Nature. 2008; 451 (7181): 994-7
• The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research. Nelson MR, Bryc K, King KS, Indap A, Boyko AR, Novembre J, Briley LP, Maruyama Y, Waterworth DM, Waeber G, Vollenweider P, Oksenberg JR, Hauser SL, Stirnadel HA, Kooner JS, Chambers JC, Jones B, Mooser V, Bustamante CD, Roses AD, Burns DK, Ehm MG, Lai EH. Am J Hum Genet. 2008; 83 (3): 347-58
• A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data. Gao H, Williamson S, Bustamante CD. Genetics. 2007; 176 (3): 1635-51
• A mutation in the myostatin gene increases muscle mass and enhances racing performance in heterozygote dogs. Mosher DS, Quignon P, Bustamante CD, Sutter NB, Mellersh CS, Parker HG, Ostrander EA. PLoS Genet. 2007; 3 (5): e79
• A single IGF1 allele is a major determinant of small size in dogs. Sutter NB, Bustamante CD, Chase K, Gray MM, Zhao K, Zhu L, Padhukasahasram B, Karlins E, Davis S, Jones PG, Quignon P, Johnson GS, Parker HG, Fretwell N, Mosher DS, Lawler DF, Satyaraj E, Nordborg M, Lark KG, Wayne RK, Ostrander EA. Science. 2007; 316 (5821): 112-5
• Context dependence, ancestral misidentification, and spurious signatures of natural selection. Hernandez RD, Williamson SH, Bustamante CD. Mol Biol Evol. 2007; 24 (8): 1792-800
• Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans. Hernandez RD, Williamson SH, Zhu L, Bustamante CD. Mol Biol Evol. 2007; 24 (10): 2196-202
• Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Hernandez RD, Hubisz MJ, Wheeler DA, Smith DG, Ferguson B, Rogers J, Nazareth L, Indap A, Bourquin T, McPherson J, Muzny D, Gibbs R, Nielsen R, Bustamante CD. Science. 2007; 316 (5822): 240-3
• Evolutionary and biomedical insights from the rhesus macaque genome. Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS. Science. 2007; 316 (5822): 222-34
• Genome-wide patterns of nucleotide polymorphism in domesticated rice. Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD. PLoS Genet. 2007; 3 (9): 1745-56
• Global dissemination of a single mutation conferring white pericarp in rice. Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, Bustamante CD, McCouch SR. PLoS Genet. 2007; 3 (8): e133
• Human Genome Variation 2006: emerging views on structural variation and large-scale SNP analysis. Abecasis G, Tam PK, Bustamante CD, Ostrander EA, Scherer SW, Chanock SJ, Kwok PY, Brookes AJ. Nat Genet. 2007; 39 (2): 153-5
• Localizing recent adaptive evolution in the human genome. Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, Nielsen R. PLoS Genet. 2007; 3 (6): e90
• On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations. Jensen JD, Thornton KR, Bustamante CD, Aquadro CF. Genetics. 2007; 176 (4): 2371-9
• A composite-likelihood approach for detecting directional selection from DNA sequence data. Zhu L, Bustamante CD. Genetics. 2005; 170 (3): 1411-21
• A scan for positively selected genes in the genomes of humans and chimpanzees. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, J Sninsky J, Adams MD, Cargill M. PLoS Biol. 2005; 3 (6): e170
• A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients. Williamson S, Perry SM, Bustamante CD, Orive ME, Stearns MN, Kelly JK. Mol Biol Evol. 2005; 22 (3): 456-68
• Ascertainment bias in studies of human genome-wide polymorphism. Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R. Genome Res. 2005; 15 (11): 1496-502
• Detecting coevolving amino acid sites using Bayesian mutational mapping. Dimmic MW, Hubisz MJ, Bustamante CD, Nielsen R. Bioinformatics. 2005: 21 Suppl 1 i126-35
• Distinguishing between selective sweeps and demography using DNA polymorphism data. Jensen JD, Kim Y, DuMont VB, Aquadro CF, Bustamante CD. Genetics. 2005; 170 (3): 1401-10
• Genomic scans for selective sweeps using SNP data. Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C. Genome Res. 2005; 15 (11): 1566-75
• Inferring SNP function using evolutionary, structural, and computational methods. Dimmic MW, Sunyaev S, Bustamante CD. Pac Symp Biocomput. 2005: 382-4
• Natural selection on protein-coding genes in the human genome. Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum DM, White TJ, Sninsky JJ, Hernandez RD, Civello D, Adams MD, Cargill M, Clark AG. Nature. 2005; 437 (7062): 1153-7
• Selective sweep mapping of genes with large phenotypic effects. Pollinger JP, Bustamante CD, Fledel-Alon A, Schmutz S, Gray MM, Wayne RK. Genome Res. 2005; 15 (12): 1809-19
• Simultaneous inference of selection and population growth from patterns of variation in the human genome. Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, Bustamante CD. Proc Natl Acad Sci U S A. 2005; 102 (22): 7882-7
• Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominance. Williamson S, Fledel-Alon A, Bustamante CD. Genetics. 2004; 168 (1): 463-75
• Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection. Sawyer SA, Kulathinal RJ, Bustamante CD, Hartl DL. J Mol Evol. 2003: 57 Suppl 1 S154-64
• Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Bustamante CD, Nielsen R, Hartl DL. Theor Popul Biol. 2003; 63 (2): 91-103
• Natural selection on the olfactory receptor gene family in humans and chimpanzees. Gilad Y, Bustamante CD, Lancet D, Pääbo S. Am J Hum Genet. 2003; 73 (3): 489-501
• Selection on rapidly evolving proteins in the Arabidopsis genome. Barrier M, Bustamante CD, Yu J, Purugganan MD. Genetics. 2003; 163 (2): 723-33
• A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Bustamante CD, Nielsen R, Hartl DL. Mol Biol Evol. 2002; 19 (1): 110-7
• The cost of inbreeding in Arabidopsis. Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, Hartl DL. Nature. 2002; 416 (6880): 531-4
• Chromosomal effects of rapid gene evolution in Drosophila melanogaster. Nurminsky D, Aguiar DD, Bustamante CD, Hartl DL. Science. 2001; 291 (5501): 128-30
• Directional selection and the site-frequency spectrum. Bustamante CD, Wakeley J, Sawyer S, Hartl DL. Genetics. 2001; 159 (4): 1779-88
• Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Bustamante CD, Townsend JP, Hartl DL. Mol Biol Evol. 2000; 17 (2): 301-8
• Pretreatment with 1,25(OH)2D3 protects from Cytoxan-induced alopecia without protecting the leukemic cells from Cytoxan. Jimenez JJ, Alvarez E, Bustamante CD, Yunis AA. Am J Med Sci. 1995; 310 (2): 43-7