Carlos D. Bustamante, Ph.D. - Publications

Affiliations: 
Genetics  Stanford University, Palo Alto, CA 
Area:
Population Genetics, human genetics, evolutionary bilology
Website:
http://bustamantelab.stanford.edu/

173 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Schroeder H, Sikora M, Gopalakrishnan S, Cassidy LM, Maisano Delser P, Sandoval Velasco M, Schraiber JG, Rasmussen S, Homburger JR, Ávila-Arcos MC, Allentoft ME, Moreno-Mayar JV, Renaud G, Gómez-Carballa A, Laffoon JE, ... ... Bustamante CD, et al. Origins and genetic legacies of the Caribbean Taino. Proceedings of the National Academy of Sciences of the United States of America. PMID 29463742 DOI: 10.1073/pnas.1716839115  1
2016 Mathias RA, Taub MA, Gignoux CR, Fu W, Musharoff S, O'Connor TD, Vergara C, Torgerson DG, Pino-Yanes M, Shringarpure SS, Huang L, Rafaels N, Boorgula MP, Johnston HR, Ortega VE, ... ... Bustamante CD, et al. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nature Communications. 7: 12522. PMID 27725671 DOI: 10.1038/ncomms12522  1
2016 Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, Musolf A, Li Q, Holzinger E, Karyadi D, Cannon-Albright LA, Teerlink CC, Stanford JL, Isaacs WB, Xu J, ... ... Bustamante CD, et al. REVEL: an Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. American Journal of Human Genetics. PMID 27666373 DOI: 10.1016/j.ajhg.2016.08.016  1
2016 Homburger JR, Green EM, Caleshu C, Sunitha MS, Taylor RE, Ruppel KM, Metpally RP, Colan SD, Michels M, Day SM, Olivotto I, Bustamante CD, Dewey FE, Ho CY, Spudich JA, et al. Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation. Proceedings of the National Academy of Sciences of the United States of America. PMID 27247418 DOI: 10.1073/pnas.1606950113  1
2016 Baharian S, Barakatt M, Gignoux CR, Shringarpure S, Errington J, Blot WJ, Bustamante CD, Kenny EE, Williams SM, Aldrich MC, Gravel S. The Great Migration and African-American Genomic Diversity. Plos Genetics. 12: e1006059. PMID 27232753 DOI: 10.1371/journal.pgen.1006059  1
2016 Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, ... ... Bustamante CD, et al. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nature Genetics. PMID 27111036 DOI: 10.1038/ng.3559  1
2016 Shannon LM, Boyko RH, Castelhano M, Corey E, Hayward JJ, McLean C, White ME, Abi Said MR, Anita BA, Bondjengo NI, Calero J, Galov A, Hedimbi M, Imam B, Khalap R, ... ... Bustamante CD, et al. Reply to Wang et al.: Sequencing datasets do not refute Central Asian domestication origin of dogs. Proceedings of the National Academy of Sciences of the United States of America. PMID 27099288 DOI: 10.1073/pnas.1600618113  1
2016 Mendez FL, Poznik GD, Castellano S, Bustamante CD. The Divergence of Neandertal and Modern Human Y Chromosomes. American Journal of Human Genetics. 98: 728-34. PMID 27058445 DOI: 10.1016/j.ajhg.2016.02.023  1
2016 Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vilà C, ... ... Bustamante CD, et al. Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. Plos Genetics. 12: e1005851. PMID 26943675 DOI: 10.1371/journal.pgen.1005851  1
2016 Kelley JL, Arias-Rodriguez L, Martin DP, Yee MC, Bustamante CD, Tobler M. Mechanisms underlying adaptation to life in hydrogen sulfide rich environments. Molecular Biology and Evolution. PMID 26861137 DOI: 10.1093/molbev/msw020  1
2016 Cooke TF, Yee MC, Muzzio M, Sockell A, Bell R, Cornejo OE, Kelley JL, Bailliet G, Bravi CM, Bustamante CD, Kenny EE. GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data. Plos Genetics. 12: e1005631. PMID 26828719 DOI: 10.1371/journal.pgen.1005631  1
2015 Henn BM, Botigué LR, Peischl S, Dupanloup I, Lipatov M, Maples BK, Martin AR, Musharoff S, Cann H, Snyder MP, Excoffier L, Kidd JM, Bustamante CD. Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. Proceedings of the National Academy of Sciences of the United States of America. PMID 26712023 DOI: 10.1073/pnas.1510805112  1
2015 Homburger JR, Moreno-Estrada A, Gignoux CR, Nelson D, Sanchez E, Ortiz-Tello P, Pons-Estel BA, Acevedo-Vasquez E, Miranda P, Langefeld CD, Gravel S, Alarcón-Riquelme ME, Bustamante CD. Genomic Insights into the Ancestry and Demographic History of South America. Plos Genetics. 11: e1005602. PMID 26636962 DOI: 10.1371/journal.pgen.1005602  1
2015 Shringarpure SS, Bustamante CD. Privacy Risks from Genomic Data-Sharing Beacons. American Journal of Human Genetics. 97: 631-46. PMID 26522470 DOI: 10.1016/j.ajhg.2015.09.010  1
2015 Shannon LM, Boyko RH, Castelhano M, Corey E, Hayward JJ, McLean C, White ME, Abi Said M, Anita BA, Bondjengo NI, Calero J, Galov A, Hedimbi M, Imam B, Khalap R, ... ... Bustamante CD, et al. Genetic structure in village dogs reveals a Central Asian domestication origin. Proceedings of the National Academy of Sciences of the United States of America. PMID 26483491 DOI: 10.1073/pnas.1516215112  1
2015 Shringarpure SS, Carroll A, De La Vega FM, Bustamante CD. Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes. Plos One. 10: e0129277. PMID 26110529 DOI: 10.1371/journal.pone.0129277  1
2015 Rasmussen M, Sikora M, Albrechtsen A, Korneliussen TS, Moreno-Mayar JV, Poznik GD, Zollikofer CP, Ponce de León MS, Allentoft ME, Moltke I, Jónsson H, Valdiosera C, Malhi RS, Orlando L, Bustamante CD, et al. The ancestry and affiliations of Kennewick Man. Nature. PMID 26087396 DOI: 10.1038/nature14625  1
2015 Bustamante CD, Rasmussen M. Beyond the reference genome. Nature Biotechnology. 33: 605-6. PMID 26057977 DOI: 10.1038/nbt.3249  1
2015 Henn BM, Botigué LR, Bustamante CD, Clark AG, Gravel S. Estimating the mutation load in human genomes. Nature Reviews. Genetics. 16: 333-43. PMID 25963372 DOI: 10.1038/nrg3931  1
2015 Schroeder H, Ávila-Arcos MC, Malaspinas AS, Poznik GD, Sandoval-Velasco M, Carpenter ML, Moreno-Mayar JV, Sikora M, Johnson PL, Allentoft ME, Samaniego JA, Haviser JB, Dee MW, Stafford TW, Salas A, ... ... Bustamante CD, et al. Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean. Proceedings of the National Academy of Sciences of the United States of America. 112: 3669-73. PMID 25755263 DOI: 10.1073/pnas.1421784112  1
2015 Pino-Yanes M, Gignoux CR, Galanter JM, Levin AM, Campbell CD, Eng C, Huntsman S, Nishimura KK, Gourraud PA, Mohajeri K, O'Roak BJ, Hu D, Mathias RA, Nguyen EA, Roth LA, ... ... Bustamante CD, et al. Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos. The Journal of Allergy and Clinical Immunology. 135: 1502-10. PMID 25488688 DOI: 10.1016/j.jaci.2014.10.033  1
2015 Pino-Yanes M, Thakur N, Gignoux CR, Galanter JM, Roth LA, Eng C, Nishimura KK, Oh SS, Vora H, Huntsman S, Nguyen EA, Hu D, Drake KA, Conti DV, Moreno-Estrada A, ... ... Bustamante CD, et al. Genetic ancestry influences asthma susceptibility and lung function among Latinos. The Journal of Allergy and Clinical Immunology. 135: 228-35. PMID 25301036 DOI: 10.1016/j.jaci.2014.07.053  1
2015 Underhill PA, Poznik GD, Rootsi S, Järve M, Lin AA, Wang J, Passarelli B, Kanbar J, Myres NM, King RJ, Di Cristofaro J, Sahakyan H, Behar DM, Kushniarevich A, Sarac J, ... ... Bustamante CD, et al. The phylogenetic and geographic structure of Y-chromosome haplogroup R1a. European Journal of Human Genetics : Ejhg. 23: 124-31. PMID 24667786 DOI: 10.1038/ejhg.2014.50  1
2015 Ávila-Arcos MC, Sandoval-Velasco M, Schroeder H, Carpenter ML, Malaspinas AS, Wales N, Peñaloza F, Bustamante CD, Gilbert MTP. Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries Methods in Ecology and Evolution. 6: 725-734. DOI: 10.1111/2041-210X.12353  1
2014 Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, Skoglund P, Korneliussen TS, Grønnow B, Appelt M, Gulløv HC, Friesen TM, Fitzhugh W, Malmström H, Rasmussen S, Olsen J, Melchior L, ... ... Bustamante C, et al. The genetic prehistory of the New World Arctic. Science (New York, N.Y.). 345: 1255832. PMID 25170159 DOI: 10.1126/science.1255832  1
2014 Martin AR, Costa HA, Lappalainen T, Henn BM, Kidd JM, Yee MC, Grubert F, Cann HM, Snyder M, Montgomery SB, Bustamante CD. Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture. Plos Genetics. 10: e1004549. PMID 25121757 DOI: 10.1371/journal.pgen.1004549  1
2014 Kelley JL, Peyton JT, Fiston-Lavier AS, Teets NM, Yee MC, Johnston JS, Bustamante CD, Lee RE, Denlinger DL. Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. Nature Communications. 5: 4611. PMID 25118180 DOI: 10.1038/ncomms5611  1
2014 Daneshjou R, Gamazon ER, Burkley B, Cavallari LH, Johnson JA, Klein TE, Limdi N, Hillenmeyer S, Percha B, Karczewski KJ, Langaee T, Patel SR, Bustamante CD, Altman RB, Perera MA. Genetic variant in folate homeostasis is associated with lower warfarin dose in African Americans. Blood. 124: 2298-305. PMID 25079360 DOI: 10.1182/blood-2014-04-568436  1
2014 Gardner KM, Brown P, Cooke TF, Cann S, Costa F, Bustamante C, Velasco R, Troggio M, Myles S. Fast and cost-effective genetic mapping in apple using next-generation sequencing. G3 (Bethesda, Md.). 4: 1681-7. PMID 25031181 DOI: 10.1534/g3.114.011023  1
2014 Moreno-Estrada A, Gignoux CR, Fernández-López JC, Zakharia F, Sikora M, Contreras AV, Acuña-Alonzo V, Sandoval K, Eng C, Romero-Hidalgo S, Ortiz-Tello P, Robles V, Kenny EE, Nuño-Arana I, Barquera-Lozano R, ... ... Bustamante CD, et al. Human genetics. The genetics of Mexico recapitulates Native American substructure and affects biomedical traits. Science (New York, N.Y.). 344: 1280-5. PMID 24926019 DOI: 10.1126/science.1251688  1
2014 Sikora M, Carpenter ML, Moreno-Estrada A, Henn BM, Underhill PA, Sánchez-Quinto F, Zara I, Pitzalis M, Sidore C, Busonero F, Maschio A, Angius A, Jones C, Mendoza-Revilla J, Nekhrizov G, ... ... Bustamante CD, et al. Population genomic analysis of ancient and modern genomes yields new insights into the genetic ancestry of the Tyrolean Iceman and the genetic structure of Europe. Plos Genetics. 10: e1004353. PMID 24809476 DOI: 10.1371/journal.pgen.1004353  1
2014 Kidd JM, Sharpton TJ, Bobo D, Norman PJ, Martin AR, Carpenter ML, Sikora M, Gignoux CR, Nemat-Gorgani N, Adams A, Guadalupe M, Guo X, Feng Q, Li Y, Liu X, ... ... Bustamante CD, et al. Exome capture from saliva produces high quality genomic and metagenomic data. Bmc Genomics. 15: 262. PMID 24708091 DOI: 10.1186/1471-2164-15-262  1
2014 Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas AS, White SS, ... ... Bustamante CD, et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 506: 225-9. PMID 24522598 DOI: 10.1038/nature13025  1
2014 Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vilà C, ... ... Bustamante CD, et al. Genome sequencing highlights the dynamic early history of dogs. Plos Genetics. 10: e1004016. PMID 24453982 DOI: 10.1371/journal.pgen.1004016  1
2014 Galanter JM, Gignoux CR, Torgerson DG, Roth LA, Eng C, Oh SS, Nguyen EA, Drake KA, Huntsman S, Hu D, Sen S, Davis A, Farber HJ, Avila PC, Brigino-Buenaventura E, ... ... Bustamante C, et al. Genome-wide association study and admixture mapping identify different asthma-associated loci in Latinos: the Genes-environments & Admixture in Latino Americans study. The Journal of Allergy and Clinical Immunology. 134: 295-305. PMID 24406073 DOI: 10.1016/j.jaci.2013.08.055  1
2014 Martin AR, Tse G, Bustamante CD, Kenny EE. Imputation-based assessment of next generation rare exome variant arrays. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 241-52. PMID 24297551  1
2014 Daneshjou R, Zappala Z, Kukurba K, Boyle SM, Ormond KE, Klein TE, Snyder M, Bustamante CD, Altman RB, Montgomery SB. PATH-SCAN: a reporting tool for identifying clinically actionable variants. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 229-40. PMID 24297550  1
2014 Drake KA, Torgerson DG, Gignoux CR, Galanter JM, Roth LA, Huntsman S, Eng C, Oh SS, Yee SW, Lin L, Bustamante CD, Moreno-Estrada A, Sandoval K, Davis A, Borrell LN, et al. A genome-wide association study of bronchodilator response in Latinos implicates rare variants. The Journal of Allergy and Clinical Immunology. 133: 370-8. PMID 23992748 DOI: 10.1016/j.jaci.2013.06.043  1
2013 Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, Allentoft ME, Sikora M, Rasmussen M, Gravel S, Guillén S, Nekhrizov G, Leshtakov K, Dimitrova D, Theodossiev N, Pettener D, Luiselli D, ... ... Bustamante CD, et al. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. American Journal of Human Genetics. 93: 852-64. PMID 24568772 DOI: 10.1016/j.ajhg.2013.10.002  1
2013 Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, ... ... Bustamante CD, et al. Reconstructing Native American migrations from whole-genome and whole-exome data. Plos Genetics. 9: e1004023. PMID 24385924 DOI: 10.1371/journal.pgen.1004023  1
2013 Auton A, Rui Li Y, Kidd J, Oliveira K, Nadel J, Holloway JK, Hayward JJ, Cohen PE, Greally JM, Wang J, Bustamante CD, Boyko AR. Genetic recombination is targeted towards gene promoter regions in dogs. Plos Genetics. 9: e1003984. PMID 24348265 DOI: 10.1371/journal.pgen.1003984  1
2013 Rootsi S, Behar DM, Järve M, Lin AA, Myres NM, Passarelli B, Poznik GD, Tzur S, Sahakyan H, Pathak AK, Rosset S, Metspalu M, Grugni V, Semino O, Metspalu E, ... Bustamante CD, et al. Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites. Nature Communications. 4: 2928. PMID 24346185 DOI: 10.1038/ncomms3928  1
2013 Simões HG, Asano RY, Sales MM, Browne RA, Arsa G, Motta-Santos D, Puga GM, Lima LC, Campbell CS, Franco OL. Type 2 diabetes elicits lower nitric oxide, bradykinin concentration and kallikrein activity together with higher DesArg(9)-BK and reduced post-exercise hypotension compared to non-diabetic condition. Plos One. 8: e80348. PMID 24265812 DOI: 10.1371/journal.pone.0080348  1
2013 Moreno-Estrada A, Gravel S, Zakharia F, McCauley JL, Byrnes JK, Gignoux CR, Ortiz-Tello PA, Martínez RJ, Hedges DJ, Morris RW, Eng C, Sandoval K, Acevedo-Acevedo S, Norman PJ, Layrisse Z, ... ... Bustamante CD, et al. Reconstructing the population genetic history of the Caribbean. Plos Genetics. 9: e1003925. PMID 24244192 DOI: 10.1371/journal.pgen.1003925  1
2013 Ma X, Kelley JL, Eilertson K, Musharoff S, Degenhardt JD, Martins AL, Vinar T, Kosiol C, Siepel A, Gutenkunst RN, Bustamante CD. Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii). Plos One. 8: e77175. PMID 24194868 DOI: 10.1371/journal.pone.0077175  1
2013 Goldstein O, Mezey JG, Schweitzer PA, Boyko AR, Gao C, Bustamante CD, Jordan JA, Aguirre GD, Acland GM. IQCB1 and PDE6B mutations cause similar early onset retinal degenerations in two closely related terrier dog breeds. Investigative Ophthalmology & Visual Science. 54: 7005-19. PMID 24045995 DOI: 10.1167/iovs.13-12915  1
2013 Maples BK, Gravel S, Kenny EE, Bustamante CD. RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. American Journal of Human Genetics. 93: 278-88. PMID 23910464 DOI: 10.1016/j.ajhg.2013.06.020  1
2013 Poznik GD, Henn BM, Yee MC, Sliwerska E, Euskirchen GM, Lin AA, Snyder M, Quintana-Murci L, Kidd JM, Underhill PA, Bustamante CD. Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science (New York, N.Y.). 341: 562-5. PMID 23908239 DOI: 10.1126/science.1237619  1
2013 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, ... ... Bustamante CD, et al. Great ape genetic diversity and population history. Nature. 499: 471-5. PMID 23823723 DOI: 10.1038/nature12228  1
2013 Botigué LR, Henn BM, Gravel S, Maples BK, Gignoux CR, Corona E, Atzmon G, Burns E, Ostrer H, Flores C, Bertranpetit J, Comas D, Bustamante CD. Gene flow from North Africa contributes to differential human genetic diversity in southern Europe. Proceedings of the National Academy of Sciences of the United States of America. 110: 11791-6. PMID 23733930 DOI: 10.1073/pnas.1306223110  1
2013 Motamayor JC, Mockaitis K, Schmutz J, Haiminen N, Livingstone D, Cornejo O, Findley SD, Zheng P, Utro F, Royaert S, Saski C, Jenkins J, Podicheti R, Zhao M, Scheffler BE, ... ... Bustamante CD, et al. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biology. 14: r53. PMID 23731509 DOI: 10.1186/gb-2013-14-6-r53  1
2013 Corona E, Chen R, Sikora M, Morgan AA, Patel CJ, Ramesh A, Bustamante CD, Butte AJ. Analysis of the genetic basis of disease in the context of worldwide human relationships and migration. Plos Genetics. 9: e1003447. PMID 23717210 DOI: 10.1371/journal.pgen.1003447  1
2013 Kumar R, Nguyen EA, Roth LA, Oh SS, Gignoux CR, Huntsman S, Eng C, Moreno-Estrada A, Sandoval K, Peñaloza-Espinosa RI, López-López M, Avila PC, Farber HJ, Tcheurekdjian H, Rodriguez-Cintron W, ... ... Bustamante CD, et al. Factors associated with degree of atopy in Latino children in a nationwide pediatric sample: the Genes-environments and Admixture in Latino Asthmatics (GALA II) study. The Journal of Allergy and Clinical Immunology. 132: 896-905.e1. PMID 23684070 DOI: 10.1016/j.jaci.2013.02.046  1
2013 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. Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Molecular Biology and Evolution. 30: 881-93. PMID 23228887 DOI: 10.1093/molbev/mss278  1
2013 Clark RT, Famoso AN, Zhao K, Shaff JE, Craft EJ, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV. High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development. Plant, Cell & Environment. 36: 454-66. PMID 22860896 DOI: 10.1111/j.1365-3040.2012.02587.x  1
2012 Casto AM, Henn BM, Kidd JM, Bustamante CD, Feldman MW. A tale of two haplotypes: the EDA2R/AR Intergenic region is the most divergent genomic segment between Africans and East Asians in the human genome. Human Biology. 84: 641-94. PMID 23959643 DOI: 10.3378/027.084.0604  1
2012 Brisbin A, Bryc K, Byrnes J, Zakharia F, Omberg L, Degenhardt J, Reynolds A, Ostrer H, Mezey JG, Bustamante CD. PCAdmix: principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations. Human Biology. 84: 343-64. PMID 23249312 DOI: 10.3378/027.084.0401  1
2012 Eilertson KE, Booth JG, Bustamante CD. SnIPRE: selection inference using a Poisson random effects model. Plos Computational Biology. 8: e1002806. PMID 23236270 DOI: 10.1371/journal.pcbi.1002806  1
2012 Sánchez-Quinto F, Botigué LR, Civit S, Arenas C, Avila-Arcos MC, Bustamante CD, Comas D, Lalueza-Fox C. North African populations carry the signature of admixture with Neandertals. Plos One. 7: e47765. PMID 23082212 DOI: 10.1371/journal.pone.0047765  1
2012 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, et al. The genetic prehistory of southern Africa. Nature Communications. 3: 1143. PMID 23072811 DOI: 10.1038/ncomms2140  1
2012 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, ... ... Bustamante CD, et al. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. American Journal of Human Genetics. 91: 660-71. PMID 23040495 DOI: 10.1016/j.ajhg.2012.08.025  1
2012 Granka JM, Henn BM, Gignoux CR, Kidd JM, Bustamante CD, Feldman MW. Limited evidence for classic selective sweeps in African populations. Genetics. 192: 1049-64. PMID 22960214 DOI: 10.1534/genetics.112.144071  1
2012 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, et al. Variation of BMP3 contributes to dog breed skull diversity. Plos Genetics. 8: e1002849. PMID 22876193 DOI: 10.1371/journal.pgen.1002849  1
2012 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, et al. North African Jewish and non-Jewish populations form distinctive, orthogonal clusters. Proceedings of the National Academy of Sciences of the United States of America. 109: 13865-70. PMID 22869716 DOI: 10.1073/pnas.1204840109  1
2012 Ma X, Rogacheva MV, Nishant KT, Zanders S, Bustamante CD, Alani E. Mutation hot spots in yeast caused by long-range clustering of homopolymeric sequences. Cell Reports. 1: 36-42. PMID 22832106 DOI: 10.1016/j.celrep.2011.10.003  1
2012 Omberg L, Salit J, Hackett N, Fuller J, Matthew R, Chouchane L, Rodriguez-Flores JL, Bustamante C, Crystal RG, Mezey JG. Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations. Bmc Genetics. 13: 49. PMID 22734698 DOI: 10.1186/1471-2156-13-49  1
2012 Kelley JL, Yee MC, Lee C, Levandowsky E, Shah M, Harkins T, Earley RL, Bustamante CD. The possibility of de novo assembly of the genome and population genomics of the mangrove rivulus, Kryptolebias marmoratus. Integrative and Comparative Biology. 52: 737-42. PMID 22723055 DOI: 10.1093/icb/ics094  1
2012 Knowles JW, Assimes TL, Kiernan M, Pavlovic A, Goldstein BA, Yank V, McConnell MV, Absher D, Bustamante C, Ashley EA, Ioannidis JP. Randomized trial of personal genomics for preventive cardiology: design and challenges. Circulation. Cardiovascular Genetics. 5: 368-76. PMID 22715281 DOI: 10.1161/CIRCGENETICS.112.962746  1
2012 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, ... ... Bustamante CD, et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science (New York, N.Y.). 337: 64-9. PMID 22604720 DOI: 10.1126/science.1219240  1
2012 Kenny EE, Timpson NJ, Sikora M, Yee MC, Moreno-Estrada A, Eng C, Huntsman S, Burchard EG, Stoneking M, Bustamante CD, Myles S. Melanesian blond hair is caused by an amino acid change in TYRP1. Science (New York, N.Y.). 336: 554. PMID 22556244 DOI: 10.1126/science.1217849  1
2012 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, ... ... Bustamante CD, et al. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nature Communications. 3: 698. PMID 22426219 DOI: 10.1038/ncomms1701  1
2012 Galanter JM, Fernandez-Lopez JC, Gignoux CR, Barnholtz-Sloan J, Fernandez-Rozadilla C, Via M, Hidalgo-Miranda A, Contreras AV, Figueroa LU, Raska P, Jimenez-Sanchez G, Zolezzi IS, Torres M, Ponte CR, Ruiz Y, ... ... Bustamante C, et al. Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas. Plos Genetics. 8: e1002554. PMID 22412386 DOI: 10.1371/journal.pgen.1002554  1
2012 Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M, Gerstein MB, Kidd JM, Bustamante CD, Snyder M. Detecting and annotating genetic variations using the HugeSeq pipeline. Nature Biotechnology. 30: 226-9. PMID 22398614 DOI: 10.1038/nbt.2134  1
2012 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. Genomic ancestry of North Africans supports back-to-Africa migrations. Plos Genetics. 8: e1002397. PMID 22253600 DOI: 10.1371/journal.pgen.1002397  1
2012 Thomson MJ, Zhao K, Wright M, McNally KL, Rey J, Tung CW, Reynolds A, Scheffler B, Eizenga G, McClung A, Kim H, Ismail AM, de Ocampo M, Mojica C, Reveche MY, ... ... Bustamante C, et al. High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform Molecular Breeding. 29: 875-886. DOI: 10.1007/s11032-011-9663-x  1
2012 Ostrander EA, Bustamante CD. Genetics of morphological traits in the domestic dog Genetics of the Dog: 2nd Edition. 359-374.  1
2011 Kenny EE, Bustamante CD. SnapShot: Human biomedical genomics. Cell. 147: 248-248.e1. PMID 21962520 DOI: 10.1016/j.cell.2011.09.020  1
2011 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, ... ... Bustamante CD, et al. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (New York, N.Y.). 334: 94-8. PMID 21940856 DOI: 10.1126/science.1211177  1
2011 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, ... ... Bustamante CD, et al. The functional spectrum of low-frequency coding variation. Genome Biology. 12: R84. PMID 21917140 DOI: 10.1186/gb-2011-12-9-r84  1
2011 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. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communications. 2: 467. PMID 21915109 DOI: 10.1038/ncomms1467  1
2011 Famoso AN, Zhao K, Clark RT, Tung CW, Wright MH, Bustamante C, Kochian LV, McCouch SR. Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. Plos Genetics. 7: e1002221. PMID 21829395 DOI: 10.1371/journal.pgen.1002221  1
2011 Bustamante CD, Burchard EG, De la Vega FM. Genomics for the world. Nature. 475: 163-5. PMID 21753830 DOI: 10.1038/475163a  1
2011 Gao H, Bryc K, Bustamante CD. On identifying the optimal number of population clusters via the deviance information criterion. Plos One. 6: e21014. PMID 21738600 DOI: 10.1371/journal.pone.0021014  1
2011 Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, Bustamante CD. Demographic history and rare allele sharing among human populations. Proceedings of the National Academy of Sciences of the United States of America. 108: 11983-8. PMID 21730125 DOI: 10.1073/pnas.1019276108  1
2011 Xie X, Molina J, Hernandez R, Reynolds A, Boyko AR, Bustamante CD, Purugganan MD. Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection. Plos One. 6: e20670. PMID 21674010 DOI: 10.1371/journal.pone.0020670  1
2011 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, et al. A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Research. 21: 1294-305. PMID 21566151 DOI: 10.1101/gr.116301.110  1
2011 Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Reynolds A, Huang P, Jackson S, Schaal BA, Bustamante CD, Boyko AR, Purugganan MD. Molecular evidence for a single evolutionary origin of domesticated rice. Proceedings of the National Academy of Sciences of the United States of America. 108: 8351-6. PMID 21536870 DOI: 10.1073/pnas.1104686108  1
2011 Brisbin A, Cruickshank J, Moïse NS, Gunn T, Bustamante CD, Mezey JG. Fast, exact linkage analysis for categorical traits on arbitrary pedigree designs. Genetic Epidemiology. 35: 371-80. PMID 21520271 DOI: 10.1002/gepi.20585  1
2011 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, et al. A population genetic approach to mapping neurological disorder genes using deep resequencing. Plos Genetics. 7: e1001318. PMID 21383861 DOI: 10.1371/journal.pgen.1001318  1
2011 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, ... ... Bustamante CD, et al. Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proceedings of the National Academy of Sciences of the United States of America. 108: 5154-62. PMID 21383195 DOI: 10.1073/pnas.1017511108  1
2011 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, ... ... Bustamante CD, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 469: 529-33. PMID 21270892 DOI: 10.1038/nature09687  1
2011 Myles S, Boyko AR, Owens CL, Brown PJ, Grassi F, Aradhya MK, Prins B, Reynolds A, Chia JM, Ware D, Bustamante CD, Buckler ES. Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences of the United States of America. 108: 3530-5. PMID 21245334 DOI: 10.1073/pnas.1009363108  1
2011 Lohmueller KE, Bustamante CD, Clark AG. Detecting directional selection in the presence of recent admixture in African-Americans. Genetics. 187: 823-35. PMID 21196524 DOI: 10.1534/genetics.110.122739  1
2011 Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Reynolds A, Huang P, Jackson SA, Schaal BA, Bustamante CD, Boyko AR, Purugganan MD. Reply to Ge and Sang: A single origin of domesticated rice Proceedings of the National Academy of Sciences of the United States of America. 108: E756. DOI: 10.1073/pnas.1112466108  1
2011 Henn BM, Bustamante CD, Mountain JL, Feldman MW. Reply to Hublin and Klein: Locating a geographic point of dispersion in Africa for contemporary humans Proceedings of the National Academy of Sciences of the United States of America. 108: E278. DOI: 10.1073/pnas.1107300108  1
2010 Bustamante CD, Henn BM. Human origins: Shadows of early migrations. Nature. 468: 1044-5. PMID 21179156 DOI: 10.1038/4681044a  1
2010 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. Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation. Plos Genetics. 6: e1001157. PMID 20976248 DOI: 10.1371/journal.pgen.1001157  1
2010 Wright MH, Tung CW, Zhao K, Reynolds A, McCouch SR, Bustamante CD. ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics (Oxford, England). 26: 2952-60. PMID 20926420 DOI: 10.1093/bioinformatics/btq533  1
2010 Henn BM, Gravel S, Moreno-Estrada A, Acevedo-Acevedo S, Bustamante CD. Fine-scale population structure and the era of next-generation sequencing. Human Molecular Genetics. 19: R221-6. PMID 20876616 DOI: 10.1093/hmg/ddq403  1
2010 Brisbin A, Weissman MM, Fyer AJ, Hamilton SP, Knowles JA, Bustamante CD, Mezey JG. Bayesian linkage analysis of categorical traits for arbitrary pedigree designs. Plos One. 5: e12307. PMID 20865038 DOI: 10.1371/journal.pone.0012307  1
2010 Nishant KT, Wei W, Mancera E, Argueso JL, Schlattl A, Delhomme N, Ma X, Bustamante CD, Korbel JO, Gu Z, Steinmetz LM, Alani E. The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis. Plos Genetics. 6: e1001109. PMID 20838597 DOI: 10.1371/journal.pgen.1001109  1
2010 Goldstein O, Mezey JG, Boyko AR, Gao C, Wang W, Bustamante CD, Anguish LJ, Jordan JA, Pearce-Kelling SE, Aguirre GD, Acland GM. An ADAM9 mutation in canine cone-rod dystrophy 3 establishes homology with human cone-rod dystrophy 9. Molecular Vision. 16: 1549-69. PMID 20806078  1
2010 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, ... ... Bustamante CD, et al. A simple genetic architecture underlies morphological variation in dogs. Plos Biology. 8: e1000451. PMID 20711490 DOI: 10.1371/journal.pbio.1000451  1
2010 Zanders S, Ma X, Roychoudhury A, Hernandez RD, Demogines A, Barker B, Gu Z, Bustamante CD, Alani E. Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach. Genetics. 186: 493-503. PMID 20660644 DOI: 10.1534/genetics.110.120105  1
2010 Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. Plos One. 5: e10780. PMID 20520727 DOI: 10.1371/journal.pone.0010780  1
2010 Bryc K, Velez C, Karafet T, Moreno-Estrada A, Reynolds A, Auton A, Hammer M, Bustamante CD, Ostrer H. Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proceedings of the National Academy of Sciences of the United States of America. 107: 8954-61. PMID 20445096 DOI: 10.1073/pnas.0914618107  1
2010 Brideau CM, Eilertson KE, Hagarman JA, Bustamante CD, Soloway PD. Successful computational prediction of novel imprinted genes from epigenomic features. Molecular and Cellular Biology. 30: 3357-70. PMID 20421412 DOI: 10.1128/MCB.01355-09  1
2010 Lohmueller KE, Bustamante CD, Clark AG. The effect of recent admixture on inference of ancient human population history. Genetics. 185: 611-22. PMID 20382834 DOI: 10.1534/genetics.109.113761  1
2010 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, ... ... Bustamante CD, et al. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature. 464: 898-902. PMID 20237475 DOI: 10.1038/nature08837  1
2010 Bryc K, Auton A, Nelson MR, Oksenberg JR, Hauser SL, Williams S, Froment A, Bodo JM, Wambebe C, Tishkoff SA, Bustamante CD. Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proceedings of the National Academy of Sciences of the United States of America. 107: 786-91. PMID 20080753 DOI: 10.1073/pnas.0909559107  1
2010 McCouch SR, Zhao K, Wright M, Tung CW, Ebana K, Thomson M, Reynolds A, Wang D, Declerck G, Ali ML, Mcclung A, Eizenga G, Bustamante C. Development of genome-wide SNP assays for rice Breeding Science. 60: 524-535. DOI: 10.1270/jsbbs.60.524  1
2010 Tung CW, Zhao K, Wright MH, Ali ML, Jung J, Kimball J, Tyagi W, Thomson MJ, McNally K, Leung H, Kim H, Ahn SN, Reynolds A, Scheffler B, Eizenga G, ... ... Bustamante C, et al. Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.) Rice. 3: 205-217. DOI: 10.1007/s12284-010-9056-5  1
2010 Ramachandran S, Tang H, Gutenkunst RN, Bustamante CD. Genetics and genomics of human population structure Vogel and Motulsky's Human Genetics: Problems and Approaches (Fourth Edition). 589-615. DOI: 10.1007/978-3-540-37654-5_22  1
2009 Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. Plos Genetics. 5: e1000695. PMID 19851460 DOI: 10.1371/journal.pgen.1000695  1
2009 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, ... ... Bustamante CD, et al. Coat variation in the domestic dog is governed by variants in three genes. Science (New York, N.Y.). 326: 150-3. PMID 19713490 DOI: 10.1126/science.1177808  1
2009 Andrés AM, Hubisz MJ, Indap A, Torgerson DG, Degenhardt JD, Boyko AR, Gutenkunst RN, White TJ, Green ED, Bustamante CD, Clark AG, Nielsen R. Targets of balancing selection in the human genome. Molecular Biology and Evolution. 26: 2755-64. PMID 19713326 DOI: 10.1093/molbev/msp190  1
2009 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. Complex population structure in African village dogs and its implications for inferring dog domestication history. Proceedings of the National Academy of Sciences of the United States of America. 106: 13903-8. PMID 19666600 DOI: 10.1073/pnas.0902129106  1
2009 Torgerson DG, Boyko AR, Hernandez RD, Indap A, Hu X, White TJ, Sninsky JJ, Cargill M, Adams MD, Bustamante CD, Clark AG. Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. Plos Genetics. 5: e1000592. PMID 19662163 DOI: 10.1371/journal.pgen.1000592  1
2009 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, et al. An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs. Science (New York, N.Y.). 325: 995-8. PMID 19608863 DOI: 10.1126/science.1173275  1
2009 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, et al. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences of the United States of America. 106: 12273-8. PMID 19597147 DOI: 10.1073/pnas.0900992106  1
2009 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, ... ... Bustamante CD, et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science (New York, N.Y.). 324: 528-32. PMID 19390050 DOI: 10.1126/science.1167936  1
2009 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. Darwinian and demographic forces affecting human protein coding genes. Genome Research. 19: 838-49. PMID 19279335 DOI: 10.1101/gr.088336.108  1
2009 Santos VJ, Bustamante CD, Valero-Cuevas FJ. Improving the fitness of high-dimensional biomechanical models via data-driven stochastic exploration. Ieee Transactions On Bio-Medical Engineering. 56: 552-64. PMID 19272906 DOI: 10.1109/TBME.2008.2006033  1
2009 Lohmueller KE, Bustamante CD, Clark AG. Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data. Genetics. 182: 217-31. PMID 19255370 DOI: 10.1534/genetics.108.099275  1
2009 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. Global distribution of genomic diversity underscores rich complex history of continental human populations Genome Research. 19: 795-803. PMID 19218534 DOI: 10.1101/gr.088898.108  1
2009 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. Molecular and evolutionary history of melanism in North American gray wolves. Science (New York, N.Y.). 323: 1339-43. PMID 19197024 DOI: 10.1126/science.1165448  1
2009 Gray MM, Granka JM, Bustamante CD, Sutter NB, Boyko AR, Zhu L, Ostrander EA, Wayne RK. Linkage disequilibrium and demographic history of wild and domestic canids. Genetics. 181: 1493-505. PMID 19189949 DOI: 10.1534/genetics.108.098830  1
2009 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, et al. Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta). Plos Genetics. 5: e1000346. PMID 19165326 DOI: 10.1371/journal.pgen.1000346  1
2009 Bustamante CD, Ramachandran S. Evaluating signatures of sex-specific processes in the human genome. Nature Genetics. 41: 8-10. PMID 19112457 DOI: 10.1038/ng0109-8  1
2009 Barsh GS, Anderson TM, Vonholdt BM, Candille SI, Musiani M, Stahler DR, Leonard JA, Padhukasahasram B, Randi E, Bustamante CD, Ostrander EA, Tang H, Wayne RK. Response Science. 325: 34. DOI: 10.1126/science.325_34  1
2008 Brooks MB, Catalfamo JL, Etter K, Brisbin A, Bustamante CD. Exclusion of ABCA-1 as a candidate gene for canine Scott syndrome Journal of Thrombosis and Haemostasis. 6: 1608-1610. PMID 18844827 DOI: 10.1111/j.1538-7836.2008.03068.x  1
2008 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, ... ... Bustamante CD, et al. The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research. American Journal of Human Genetics. 83: 347-58. PMID 18760391 DOI: 10.1016/j.ajhg.2008.08.005  1
2008 Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD. Genes mirror geography within Europe. Nature. 456: 98-101. PMID 18758442 DOI: 10.1038/nature07331  1
2008 Kosiol C, Vinař T, Da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A. Patterns of positive selection in six mammalian genomes Plos Genetics. 4. PMID 18670650 DOI: 10.1371/journal.pgen.1000144  1
2008 Blekhman R, Man O, Herrmann L, Boyko AR, Indap A, Kosiol C, Bustamante CD, Teshima KM, Przeworski M. Natural selection on genes that underlie human disease susceptibility. Current Biology : Cb. 18: 883-9. PMID 18571414 DOI: 10.1016/j.cub.2008.04.074  1
2008 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. Assessing the evolutionary impact of amino acid mutations in the human genome. Plos Genetics. 4: e1000083. PMID 18516229 DOI: 10.1371/journal.pgen.1000083  1
2008 Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M. Exploring population genetic models with recombination using efficient forward-time simulations. Genetics. 178: 2417-27. PMID 18430959 DOI: 10.1534/genetics.107.085332  1
2008 Shimizu KK, Reininga JM, Caicedo AL, Mays CA, Moore RC, Olsen KM, Ruzsa S, Coop G, Bustamante CD, Purugganan MD. Retraction. Science (New York, N.Y.). 320: 176. PMID 18403691 DOI: 10.1126/science.320.5873.176a  1
2008 Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD. Proportionally more deleterious genetic variation in European than in African populations. Nature. 451: 994-7. PMID 18288194 DOI: 10.1038/nature06611  1
2008 Huerta-Sanchez E, Durrett R, Bustamante CD. Population genetics of polymorphism and divergence under fluctuating selection. Genetics. 178: 325-37. PMID 17947441 DOI: 10.1534/genetics.107.073361  1
2008 Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD. Genes mirror geography within Europe (Nature (2008) 456, (98-101)) Nature. 456: 274. DOI: 10.1038/nature07566  1
2007 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. Genome-wide patterns of nucleotide polymorphism in domesticated rice. Plos Genetics. 3: 1745-56. PMID 17907810 DOI: 10.1371/journal.pgen.0030163  1
2007 Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, Bustamante CD, McCouch SR. Global dissemination of a single mutation conferring white pericarp in rice. Plos Genetics. 3: e133. PMID 17696613 DOI: 10.1371/journal.pgen.0030133  1
2007 Hernandez RD, Williamson SH, Zhu L, Bustamante CD. Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans. Molecular Biology and Evolution. 24: 2196-202. PMID 17656634 DOI: 10.1093/molbev/msm149  1
2007 Jensen JD, Thornton KR, Bustamante CD, Aquadro CF. On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations. Genetics. 176: 2371-9. PMID 17565955 DOI: 10.1534/genetics.106.069450  1
2007 Hernandez RD, Williamson SH, Bustamante CD. Context dependence, ancestral misidentification, and spurious signatures of natural selection. Molecular Biology and Evolution. 24: 1792-800. PMID 17545186 DOI: 10.1093/molbev/msm108  1
2007 Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, Nielsen R. Localizing recent adaptive evolution in the human genome. Plos Genetics. 3: e90. PMID 17542651 DOI: 10.1371/journal.pgen.0030090  1
2007 Mosher DS, Quignon P, Bustamante CD, Sutter NB, Mellersh CS, Parker HG, Ostrander EA. A mutation in the myostatin gene increases muscle mass and enhances racing performance in heterozygote dogs. Plos Genetics. 3: e79. PMID 17530926 DOI: 10.1371/journal.pgen.0030079  1
2007 Gao H, Williamson S, Bustamante CD. A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data. Genetics. 176: 1635-51. PMID 17483417 DOI: 10.1534/genetics.107.072371  1
2007 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. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science (New York, N.Y.). 316: 240-3. PMID 17431170 DOI: 10.1126/science.1140462  1
2007 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, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/science.1139247  1
2007 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, et al. A single IGF1 allele is a major determinant of small size in dogs. Science (New York, N.Y.). 316: 112-5. PMID 17412960 DOI: 10.1126/science.1137045  1
2007 Abecasis G, Tam PKH, Bustamante CD, Ostrander EA, Scherer SW, Chanock SJ, Kwok PY, Brookes AJ. Human genome variation 2006: Emerging views on structural variation and large-scale SNP analysis Nature Genetics. 39: 153-155. PMID 17262030 DOI: 10.1038/ng0207-153  1
2005 Pollinger JP, Bustamante CD, Fledel-Alon A, Schmutz S, Gray MM, Wayne RK. Selective sweep mapping of genes with large phenotypic effects. Genome Research. 15: 1809-19. PMID 16339379 DOI: 10.1101/gr.4374505  1
2005 Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R. Ascertainment bias in studies of human genome-wide polymorphism. Genome Research. 15: 1496-502. PMID 16251459 DOI: 10.1101/gr.4107905  1
2005 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. Natural selection on protein-coding genes in the human genome. Nature. 437: 1153-7. PMID 16237444 DOI: 10.1038/nature04240  1
2005 Dimmic MW, Hubisz MJ, Bustamante CD, Nielsen R. Detecting coevolving amino acid sites using Bayesian mutational mapping. Bioinformatics (Oxford, England). 21: i126-35. PMID 15961449 DOI: 10.1093/bioinformatics/bti1032  1
2005 Jensen JD, Kim Y, DuMont VB, Aquadro CF, Bustamante CD. Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics. 170: 1401-10. PMID 15911584 DOI: 10.1534/genetics.104.038224  1
2005 Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, Bustamante CD. Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 102: 7882-7. PMID 15905331 DOI: 10.1073/pnas.0502300102  1
2005 Zhu L, Bustamante CD. A composite-likelihood approach for detecting directional selection from DNA sequence data Genetics. 170: 1411-1421. PMID 15879513 DOI: 10.1534/genetics.104.035097  1
2005 Dimmic MW, Sunyaev S, Bustamante CD. Inferring SNP function using evolutionary, structural, and computational methods. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 382-4. PMID 15759643  1
2005 Williamson S, Perry SM, Bustamante CD, Orive ME, Stearns MN, Kelly JK. A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients. Molecular Biology and Evolution. 22: 456-68. PMID 15509726 DOI: 10.1093/molbev/msi029  1
2005 Dimmic MW, Hubisz MJ, Bustamante CD, Nielsen R. Detecting coevolving amino acid sites using Bayesian mutational mapping Ismb 2005 Proceedings - 13th International Conference On Intelligent Systems For Molecular Biology. i126-i135.  1
2004 Shimizu KK, Cork JM, Caicedo AL, Mays CA, Moore RC, Olsen KM, Ruzsa S, Coop G, Bustamante CD, Awadalla P, Purugganan MD. Darwinian selection on a selfing locus. Science (New York, N.Y.). 306: 2081-4. PMID 15604405 DOI: 10.1126/science.1103776  1
2004 Williamson S, Fledel-Alon A, Bustamante CD. Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominance. Genetics. 168: 463-75. PMID 15454557 DOI: 10.1534/genetics.103.024745  1
2003 Sawyer SA, Kulathinal RJ, Bustamante CD, Hartl DL. Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection. Journal of Molecular Evolution. 57: S154-64. PMID 15008412 DOI: 10.1007/s00239-003-0022-3  1
2003 Barrier M, Bustamante CD, Yu J, Purugganan MD. Selection on rapidly evolving proteins in the Arabidopsis genome. Genetics. 163: 723-33. PMID 12618409  1
2003 Bustamante CD, Nielsen R, Hartl DL. Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Theoretical Population Biology. 63: 91-103. PMID 12615493 DOI: 10.1016/S0040-5809(02)00050-3  1
2002 Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, Hartl DL. The cost of inbreeding in Arabidopsis. Nature. 416: 531-4. PMID 11932744 DOI: 10.1038/416531a  1
2002 Bustamante CD, Nielsen R, Hartl DL. A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Molecular Biology and Evolution. 19: 110-7. PMID 11752196  1
2001 Bustamante CD, Wakeley J, Sawyer S, Hartl DL. Directional selection and the site-frequency spectrum. Genetics. 159: 1779-88. PMID 11779814  1
2001 Nurminsky D, Aguiar DD, Bustamante CD, Hartl DL. Chromosomal effects of rapid gene evolution in Drosophila melanogaster. Science (New York, N.Y.). 291: 128-30. PMID 11141564 DOI: 10.1126/science.291.5501.128  1
2000 Bustamante CD, Townsend JP, Hartl DL. Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Molecular Biology and Evolution. 17: 301-8. PMID 10677853  1
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