Carlos D. Bustamante, Ph.D. - Publications

Affiliations: 
2002-2009 Cornell University, Ithaca, NY, United States 
 2009- Genetics Stanford University, Palo Alto, CA 
Area:
Population Genetics, human genetics, evolutionary bilology
Website:
http://bustamantelab.stanford.edu/

238 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, 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
2021 Venkataraman GR, DeBoever C, Tanigawa Y, Aguirre M, Ioannidis AG, Mostafavi H, Spencer CCA, Poterba T, Bustamante CD, Daly MJ, Pirinen M, Rivas MA. Bayesian model comparison for rare-variant association studies. American Journal of Human Genetics. PMID 34822764 DOI: 10.1016/j.ajhg.2021.11.005  0.314
2021 Ioannidis AG, Blanco-Portillo J, Sandoval K, Hagelberg E, Barberena-Jonas C, Hill AVS, Rodríguez-Rodríguez JE, Fox K, Robson K, Haoa-Cardinali S, Quinto-Cortés CD, Miquel-Poblete JF, Auckland K, Parks T, Sofro ASM, ... ... Bustamante CD, et al. Paths and timings of the peopling of Polynesia inferred from genomic networks. Nature. 597: 522-526. PMID 34552258 DOI: 10.1038/s41586-021-03902-8  0.811
2020 Ioannidis AG, Blanco-Portillo J, Sandoval K, Hagelberg E, Miquel-Poblete JF, Moreno-Mayar JV, Rodríguez-Rodríguez JE, Quinto-Cortés CD, Auckland K, Parks T, Robson K, Hill AVS, Avila-Arcos MC, Sockell A, Homburger JR, ... ... Bustamante CD, et al. Native American gene flow into Polynesia predating Easter Island settlement. Nature. PMID 32641827 DOI: 10.1038/S41586-020-2487-2  0.812
2020 Popejoy AB, Crooks KR, Fullerton SM, Hindorff LA, Hooker GW, Koenig BA, Pino N, Ramos EM, Ritter DI, Wand H, Wright MW, Yudell M, Zou JY, Plon SE, Bustamante CD, et al. Clinical Genetics Lacks Standard Definitions and Protocols for the Collection and Use of Diversity Measures. American Journal of Human Genetics. PMID 32504544 DOI: 10.1016/J.Ajhg.2020.05.005  0.335
2020 Verdugo RA, Di Genova A, Herrera L, Moraga M, Acuña M, Berríos S, Llop E, Valenzuela CY, Bustamante ML, Digman D, Symon A, Asenjo S, López P, Blanco A, Suazo J, ... ... Bustamante CD, et al. Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components. Biological Research. 53: 15. PMID 32299502 DOI: 10.1186/S40659-020-00284-5  0.416
2019 Grabek KR, Cooke TF, Epperson LE, Spees KK, Cabral GF, Sutton SC, Merriman DK, Martin SL, Bustamante CD. Genetic variation drives seasonal onset of hibernation in the 13-lined ground squirrel. Communications Biology. 2: 478. PMID 31925301 DOI: 10.1038/s42003-019-0719-5  0.339
2019 Grabek KR, Cooke TF, Epperson LE, Spees KK, Cabral GF, Sutton SC, Merriman DK, Martin SL, Bustamante CD. Genetic variation drives seasonal onset of hibernation in the 13-lined ground squirrel. Communications Biology. 2: 478. PMID 31886416 DOI: 10.1038/s42003-019-0719-5  0.343
2019 Ávila-Arcos MC, McManus KF, Sandoval K, Rodríguez-Rodríguez JE, Villa-Islas V, Martin AR, Luisi P, Peñaloza-Espinosa RI, Eng C, Huntsman S, Burchard EG, Gignoux CR, Bustamante CD, Moreno-Estrada A. Population history and gene divergence in Native Mexicans inferred from 76 human exomes. Molecular Biology and Evolution. PMID 31848607 DOI: 10.1093/Molbev/Msz282  0.499
2019 Nieves-Colón MA, Pestle WJ, Reynolds AW, Llamas B, de la Fuente C, Fowler K, Skerry KM, Crespo-Torres E, Bustamante CD, Stone AC. Ancient DNA reconstructs the genetic legacies of pre-contact Puerto Rico communities. Molecular Biology and Evolution. PMID 31710665 DOI: 10.1093/Molbev/Msz267  0.416
2019 Daya M, Rafaels N, Brunetti TM, Chavan S, Levin AM, Shetty A, Gignoux CR, Boorgula MP, Wojcik G, Campbell M, Vergara C, Torgerson DG, Ortega VE, Doumatey A, Johnston HR, ... ... Bustamante C, et al. Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nature Communications. 10: 4082. PMID 31484942 DOI: 10.1038/S41467-019-12158-W  0.65
2019 Lopez M, Choin J, Sikora M, Siddle K, Harmant C, Costa HA, Silvert M, Mouguiama-Daouda P, Hombert JM, Froment A, Le Bomin S, Perry GH, Barreiro LB, Bustamante CD, Verdu P, et al. Genomic Evidence for Local Adaptation of Hunter-Gatherers to the African Rainforest. Current Biology : Cb. PMID 31402299 DOI: 10.1016/J.Cub.2019.07.013  0.425
2019 Wojcik GL, Graff M, Nishimura KK, Tao R, Haessler J, Gignoux CR, Highland HM, Patel YM, Sorokin EP, Avery CL, Belbin GM, Bien SA, Cheng I, Cullina S, Hodonsky CJ, ... ... Bustamante CD, et al. Genetic analyses of diverse populations improves discovery for complex traits. Nature. PMID 31217584 DOI: 10.1038/S41586-019-1310-4  0.834
2019 Bucio D, Ormond KE, Hernandez D, Bustamante CD, Lopez Pineda A. A genetic counseling needs assessment of Mexico. Molecular Genetics & Genomic Medicine. e668. PMID 30938092 DOI: 10.1002/Mgg3.668  0.37
2019 Fregel R, Ordóñez AC, Santana-Cabrera J, Cabrera VM, Velasco-Vázquez J, Alberto V, Moreno-Benítez MA, Delgado-Darias T, Rodríguez-Rodríguez A, Hernández JC, Pais J, González-Montelongo R, Lorenzo-Salazar JM, Flores C, Cruz-de-Mercadal MC, ... ... Bustamante CD, et al. Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands. Plos One. 14: e0209125. PMID 30893316 DOI: 10.1371/Journal.Pone.0209125  0.423
2019 Daya M, Rafaels N, Brunetti TM, Chavan S, Levin AM, Shetty A, Gignoux CR, Boorgula MP, Wojcik G, Campbell M, Vergara C, Torgerson DG, Ortega VE, Doumatey A, Johnston HR, ... ... Bustamante C, et al. Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nature Communications. 10: 880. PMID 30787307 DOI: 10.1038/S41467-019-08469-7  0.654
2019 Li Q, Zhao K, Bustamante CD, Ma X, Wong WH. Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 30675030 DOI: 10.1038/S41436-019-0439-8  0.324
2018 Troll CJ, Putnam NH, Hartley PD, Rice B, Blanchette M, Siddiqui S, Ganbat JO, Powers MP, Ramakrishnan R, Kunder CA, Bustamante CD, Zehnder JL, Green RE, Costa HA. Structural Variation Detection by Proximity Ligation from Formalin-Fixed, Paraffin-Embedded Tumor Tissue. The Journal of Molecular Diagnostics : Jmd. PMID 30605765 DOI: 10.1016/J.Jmoldx.2018.11.003  0.351
2018 De La Vega FM, Bustamante CD. Polygenic risk scores: a biased prediction? Genome Medicine. 10: 100. PMID 30591078 DOI: 10.1186/S13073-018-0610-X  0.308
2018 Lin M, Siford RL, Martin AR, Nakagome S, Möller M, Hoal EG, Bustamante CD, Gignoux CR, Henn BM. Rapid evolution of a skin-lightening allele in southern African KhoeSan. Proceedings of the National Academy of Sciences of the United States of America. 115: 13324-13329. PMID 30530665 DOI: 10.1073/Pnas.1801948115  0.403
2018 Huddart R, Fohner AE, Whirl-Carrillo M, Wojcik GL, Gignoux CR, Popejoy AB, Bustamante CD, Altman RB, Klein TE. Standardized biogeographic grouping system for annotating populations in pharmacogenetic research. Clinical Pharmacology and Therapeutics. PMID 30506572 DOI: 10.1002/Cpt.1322  0.384
2018 Jha AR, Davenport ER, Gautam Y, Bhandari D, Tandukar S, Ng KM, Fragiadakis GK, Holmes S, Gautam GP, Leach J, Sherchand JB, Bustamante CD, Sonnenburg JL. Gut microbiome transition across a lifestyle gradient in Himalaya. Plos Biology. 16: e2005396. PMID 30439937 DOI: 10.1371/Journal.Pbio.2005396  0.375
2018 Cornejo OE, Yee MC, Dominguez V, Andrews M, Sockell A, Strandberg E, Livingstone D, Stack C, Romero A, Umaharan P, Royaert S, Tawari NR, Ng P, Gutierrez O, Phillips W, ... ... Bustamante CD, et al. Population genomic analyses of the chocolate tree, L., provide insights into its domestication process. Communications Biology. 1: 167. PMID 30345393 DOI: 10.1038/s42003-018-0168-6  0.81
2018 Ioannidis NM, Wang W, Furlotte NA, Hinds DA, Bustamante CD, Jorgenson E, Asgari MM, Whittemore AS. Gene expression imputation identifies candidate genes and susceptibility loci associated with cutaneous squamous cell carcinoma. Nature Communications. 9: 4264. PMID 30323283 DOI: 10.1038/S41467-018-06149-6  0.797
2018 Popejoy AB, Ritter DI, Crooks K, Currey E, Fullerton SM, Hindorff LA, Koenig B, Ramos EM, Sorokin EP, Wand H, Wright MW, Zou J, Gignoux CR, Bonham VL, Plon SE, ... Bustamante CD, et al. The clinical imperative for inclusivity: Race, ethnicity, and ancestry (REA) in genomics. Human Mutation. 39: 1713-1720. PMID 30311373 DOI: 10.1002/Humu.23644  0.422
2018 Gignoux CR, Torgerson DG, Pino-Yanes M, Uricchio LH, Galanter J, Roth LA, Eng C, Hu D, Nguyen EA, Huntsman S, Mathias RA, Kumar R, Rodriguez-Santana J, Thakur N, Oh SS, ... ... Bustamante CD, et al. An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos. The Journal of Allergy and Clinical Immunology. PMID 30201514 DOI: 10.1016/J.Jaci.2016.08.057  0.776
2018 Wojcik GL, Fuchsberger C, Taliun D, Welch R, Martin AR, Shringarpure S, Carlson CS, Abecasis G, Kang HM, Boehnke M, Bustamante CD, Gignoux CR, Kenny EE. Imputation-Aware Tag SNP Selection To Improve Power for Large-Scale, Multi-ethnic Association Studies. G3 (Bethesda, Md.). PMID 30131328 DOI: 10.1534/G3.118.200502  0.442
2018 Cruz-Dávalos DI, Nieves-Colón MA, Sockell A, Poznik GD, Schroeder H, Stone AC, Bustamante CD, Malaspinas AS, Ávila-Arcos MC. In-solution Y-chromosome capture-enrichment on ancient DNA libraries. Bmc Genomics. 19: 608. PMID 30107783 DOI: 10.1186/S12864-018-4945-X  0.795
2018 Fregel R, Méndez FL, Bokbot Y, Martín-Socas D, Camalich-Massieu MD, Santana J, Morales J, Ávila-Arcos MC, Underhill PA, Shapiro B, Wojcik G, Rasmussen M, Soares AER, Kapp J, Sockell A, ... ... Bustamante CD, et al. Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. Proceedings of the National Academy of Sciences of the United States of America. PMID 29895688 DOI: 10.1073/Pnas.1800851115  0.817
2018 Waszak SM, Northcott PA, Buchhalter I, Robinson GW, Sutter C, Groebner S, Grund KB, Brugières L, Jones DTW, Pajtler KW, Morrissy AS, Kool M, Sturm D, Chavez L, Ernst A, ... ... Bustamante CD, et al. Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort. The Lancet. Oncology. PMID 29753700 DOI: 10.1016/S1470-2045(18)30242-0  0.315
2018 Muzzio M, Motti JMB, Paz Sepulveda PB, Yee MC, Cooke T, Santos MR, Ramallo V, Alfaro EL, Dipierri JE, Bailliet G, Bravi CM, Bustamante CD, Kenny EE. Population structure in Argentina. Plos One. 13: e0196325. PMID 29715266 DOI: 10.1371/Journal.Pone.0196325  0.371
2018 DeBoever C, Tanigawa Y, Lindholm ME, McInnes G, Lavertu A, Ingelsson E, Chang C, Ashley EA, Bustamante CD, Daly MJ, Rivas MA. Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study. Nature Communications. 9: 1612. PMID 29691392 DOI: 10.1038/S41467-018-03910-9  0.341
2018 de Freitas PD, Mendez FL, Chávez-Congrains K, Galetti PM, Coutinho LL, Pissinatti A, Bustamante CD. Next-Generation Sequencing of the Complete Mitochondrial Genome of the Endangered Species Black Lion Tamarin (Primates) and Mitogenomic Phylogeny Focusing on the Callitrichidae Family. G3 (Bethesda, Md.). PMID 29650540 DOI: 10.1534/G3.118.200153  0.357
2018 de la Fuente C, Ávila-Arcos MC, Galimany J, Carpenter ML, Homburger JR, Blanco A, Contreras P, Cruz Dávalos D, Reyes O, San Roman M, Moreno-Estrada A, Campos PF, Eng C, Huntsman S, Burchard EG, ... ... Bustamante CD, et al. Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia. Proceedings of the National Academy of Sciences of the United States of America. PMID 29632188 DOI: 10.1073/Pnas.1715688115  0.494
2018 Bhattacharya S, Li J, Sockell A, Kan MJ, Bava FA, Chen SC, Ávila-Arcos MC, Ji X, Smith E, Asadi NB, Lachman RS, Lam HYK, Bustamante CD, Butte AJ, Nolan GP. Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia. Genome Research. PMID 29567674 DOI: 10.1101/Gr.223693.117  0.819
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  0.605
2018 Rappoport N, Toung J, Hadley D, Wong RJ, Fujioka K, Reuter J, Abbott CW, Oh S, Hu D, Eng C, Huntsman S, Bodian DL, Niederhuber JE, Hong X, Zhang G, ... ... Bustamante CD, et al. A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth. Scientific Reports. 8: 226. PMID 29317701 DOI: 10.1038/S41598-017-18246-5  0.42
2017 Lins LSF, Trojahn S, Sockell A, Yee MC, Tatarenkov A, Bustamante CD, Earley RL, Kelley JL. Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate. Genome. PMID 29268023 DOI: 10.1139/Gen-2017-0188  0.828
2017 Martin AR, Lin M, Granka JM, Myrick JW, Liu X, Sockell A, Atkinson EG, Werely CJ, Möller M, Sandhu MS, Kingsley DM, Hoal EG, Liu X, Daly MJ, Feldman MW, ... ... Bustamante CD, et al. An Unexpectedly Complex Architecture for Skin Pigmentation in Africans. Cell. 171: 1340-1353.e14. PMID 29195075 DOI: 10.1016/J.Cell.2017.11.015  0.795
2017 Cooke TF, Fischer CR, Wu P, Jiang TX, Xie KT, Kuo J, Doctorov E, Zehnder A, Khosla C, Chuong CM, Bustamante CD. Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars. Cell. 171: 427-439.e21. PMID 28985565 DOI: 10.1016/J.Cell.2017.08.016  0.359
2017 Ioannidis NM, Davis JR, DeGorter MK, Larson NB, McDonnell SK, French AJ, Battle AJ, Hastie TJ, Thibodeau SN, Montgomery SB, Bustamante CD, Sieh W, Whittemore AS. FIRE: functional inference of genetic variants that regulate gene expression. Bioinformatics (Oxford, England). PMID 28961785 DOI: 10.1093/Bioinformatics/Btx534  0.82
2017 Holl HM, Vanhnasy J, Everts RE, Hoefs-Martin K, Cook D, Brooks SA, Carpenter ML, Bustamante CD, Lafayette C. Single nucleotide polymorphisms for DNA typing in the domestic horse. Animal Genetics. PMID 28901559 DOI: 10.1111/Age.12608  0.351
2017 Migicovsky Z, Sawler J, Gardner KM, Aradhya MK, Prins BH, Schwaninger HR, Bustamante CD, Buckler ES, Zhong GY, Brown PJ, Myles S. Patterns of genomic and phenomic diversity in wine and table grapes. Horticulture Research. 4: 17035. PMID 28791127 DOI: 10.1038/Hortres.2017.35  0.418
2017 Passow CN, Brown AP, Arias-Rodriquez L, Yee MC, Sockell A, Schartl M, Warren WC, Bustamante C, Kelley JL, Tobler M. Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae). Molecular Ecology. PMID 28598519 DOI: 10.1111/Mec.14198  0.799
2017 Patin E, Lopez M, Grollemund R, Verdu P, Harmant C, Quach H, Laval G, Perry GH, Barreiro LB, Froment A, Heyer E, Massougbodji A, Fortes-Lima C, Migot-Nabias F, Bellis G, ... ... Bustamante CD, et al. Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America. Science (New York, N.Y.). 356: 543-546. PMID 28473590 DOI: 10.1126/Science.Aal1988  0.453
2017 Johnston HR, Hu YJ, Gao J, O'Connor TD, Abecasis GR, Wojcik GL, Gignoux CR, Gourraud PA, Lizee A, Hansen M, Genuario R, Bullis D, Lawley C, Kenny EE, Bustamante C, et al. Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome. Scientific Reports. 7: 46398. PMID 28429804 DOI: 10.1038/Srep46398  0.491
2017 Martin AR, Gignoux CR, Walters RK, Wojcik GL, Neale BM, Gravel S, Daly MJ, Bustamante CD, Kenny EE. Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations. American Journal of Human Genetics. PMID 28366442 DOI: 10.1016/J.Ajhg.2017.03.004  0.469
2017 Raisaro JL, Tramèr F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P, Shringarpure S, Bustamante C, Wang S, Jiang X, Ohno-Machado L, et al. Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks. Journal of the American Medical Informatics Association : Jamia. PMID 28339683 DOI: 10.1093/Jamia/Ocw167  0.393
2017 McManus KF, Taravella AM, Henn BM, Bustamante CD, Sikora M, Cornejo OE. Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans. Plos Genetics. 13: e1006560. PMID 28282382 DOI: 10.1371/Journal.Pgen.1006560  0.42
2016 Shringarpure SS, Mathias RA, Hernandez RD, O'Connor TD, Szpiech ZA, Torres R, De La Vega FM, Bustamante CD, Barnes KC, Taub MA. Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data. Bioinformatics (Oxford, England). PMID 28171482 DOI: 10.1093/bioinformatics/btw786  0.643
2016 Shringarpure SS, Mathias RA, Hernandez RD, O'Connor TD, Szpiech ZA, Torres R, De La Vega FM, Bustamante CD, Barnes KC, Taub MA. Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data. Bioinformatics (Oxford, England). PMID 28035032 DOI: 10.1093/Bioinformatics/Btw786  0.682
2016 Bien SA, Wojcik GL, Zubair N, Gignoux CR, Martin AR, Kocarnik JM, Martin LW, Buyske S, Haessler J, Walker RW, Cheng I, Graff M, Xia L, Franceschini N, Matise T, ... ... Bustamante CD, et al. Strategies for Enriching Variant Coverage in Candidate Disease Loci on a Multiethnic Genotyping Array. Plos One. 11: e0167758. PMID 27973554 DOI: 10.1371/Journal.Pone.0167758  0.469
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  0.737
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  0.78
2016 Daneshjou R, Cavallari LH, Weeke PE, Karczewski KJ, Drozda K, Perera MA, Johnson JA, Klein TE, Bustamante CD, Roden DM, Shaffer C, Denny JC, Zehnder JL, Altman RB. Population-specific single-nucleotide polymorphism confers increased risk of venous thromboembolism in African Americans. Molecular Genetics & Genomic Medicine. 4: 513-520. PMID 27652279 DOI: 10.1002/Mgg3.226  0.387
2016 Kelley JL, Yee MC, Brown AP, Richardson RR, Tatarenkov A, Lee CC, Harkins TT, Bustamante CD, Earley RL. The genome of the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus: a model for studying phenotypic plasticity and adaptations to extreme environments. Genome Biology and Evolution. PMID 27324916 DOI: 10.1093/Gbe/Evw145  0.418
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  0.359
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  0.366
2016 Shringarpure SS, Bustamante CD, Lange K, Alexander DH. Efficient analysis of large datasets and sex bias with ADMIXTURE. Bmc Bioinformatics. 17: 218. PMID 27216439 DOI: 10.1186/S12859-016-1082-X  0.396
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  0.593
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  0.337
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  0.389
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  0.361
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  0.829
2015 Davis JR, Fresard L, Knowles DA, Pala M, Bustamante CD, Battle A, Montgomery SB. An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants. American Journal of Human Genetics. PMID 26749306 DOI: 10.1016/J.Ajhg.2015.11.021  0.302
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  0.437
2015 Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Bustamante CD, Hammer MF, Wall JD. The Time-Scale Of Recombination Rate Evolution In Great Apes. Molecular Biology and Evolution. PMID 26671457 DOI: 10.1093/Molbev/Msv331  0.391
2015 Valenzano DR, Benayoun BA, Singh PP, Zhang E, Etter PD, Hu CK, Clément-Ziza M, Willemsen D, Cui R, Harel I, Machado BE, Yee MC, Sharp SC, Bustamante CD, Beyer A, et al. The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan. Cell. 163: 1539-54. PMID 26638078 DOI: 10.1016/J.Cell.2015.11.008  0.436
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  0.427
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  0.441
2015 Costa HA, Leitner MG, Sos ML, Mavrantoni A, Rychkova A, Johnson JR, Newton BW, Yee MC, De La Vega FM, Ford JM, Krogan NJ, Shokat KM, Oliver D, Halaszovich CR, Bustamante CD. Discovery and functional characterization of a neomorphic PTEN mutation. Proceedings of the National Academy of Sciences of the United States of America. 112: 13976-81. PMID 26504226 DOI: 10.1073/Pnas.1422504112  0.32
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  0.416
2015 Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, et al. Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell. PMID 26300125 DOI: 10.1016/J.Cell.2015.07.048  0.399
2015 Patwardhan A, Harris J, Leng N, Bartha G, Church DM, Luo S, Haudenschild C, Pratt M, Zook J, Salit M, Tirch J, Morra M, Chervitz S, Li M, Clark M, ... ... Bustamante C, et al. Achieving high-sensitivity for clinical applications using augmented exome sequencing. Genome Medicine. 7: 71. PMID 26269718 DOI: 10.1186/S13073-015-0197-4  0.39
2015 Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, ... ... Bustamante CD, et al. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science (New York, N.Y.). PMID 26198033 DOI: 10.1126/Science.Aab3884  0.566
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  0.433
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  0.577
2015 Bustamante CD, Rasmussen M. Beyond the reference genome. Nature Biotechnology. 33: 605-6. PMID 26057977 DOI: 10.1038/Nbt.3249  0.413
2015 Rehm HL, Berg JS, Brooks LD, Bustamante CD, Evans JP, Landrum MJ, Ledbetter DH, Maglott DR, Martin CL, Nussbaum RL, Plon SE, Ramos EM, Sherry ST, Watson MS. ClinGen--the Clinical Genome Resource. The New England Journal of Medicine. 372: 2235-42. PMID 26014595 DOI: 10.1056/Nejmsr1406261  0.307
2015 Tilgner H, Jahanbani F, Blauwkamp T, Moshrefi A, Jaeger E, Chen F, Harel I, Bustamante CD, Rasmussen M, Snyder MP. Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events. Nature Biotechnology. PMID 25985263 DOI: 10.1038/Nbt.3242  0.308
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  0.555
2015 Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, ... ... Bustamante CD, et al. Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science (New York, N.Y.). 348: 666-9. PMID 25954003 DOI: 10.1126/Science.1261877  0.413
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  0.435
2015 McManus KF, Kelley JL, Song S, Veeramah KR, Woerner AE, Stevison LS, Ryder OA, Ape Genome Project G, Kidd JM, Wall JD, Bustamante CD, Hammer MF. Inference of gorilla demographic and selective history from whole-genome sequence data. Molecular Biology and Evolution. 32: 600-12. PMID 25534031 DOI: 10.1093/Molbev/Msu394  0.478
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  0.643
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  0.37
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  0.587
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  0.468
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  0.388
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  0.325
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  0.425
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  0.477
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  0.499
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  0.454
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  0.573
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  0.425
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  0.384
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  0.355
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  0.312
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  0.699
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  0.405
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  0.473
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  0.422
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  0.474
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  0.816
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  0.318
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  0.366
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  0.352
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  0.461
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  0.427
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  0.408
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  0.38
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  0.452
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  0.466
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  0.814
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  0.379
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  0.431
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  0.489
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  0.831
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  0.471
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  0.43
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  0.378
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  0.374
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  0.474
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  0.478
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  0.368
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  0.439
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  0.335
2012 Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD, Butte AJ. Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases. Plos Genetics. 8: e1002621. PMID 22511877 DOI: 10.1371/Journal.Pgen.1002621  0.393
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  0.398
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  0.455
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  0.351
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  0.796
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  0.375
2011 Kenny EE, Bustamante CD. SnapShot: Human biomedical genomics. Cell. 147: 248-248.e1. PMID 21962520 DOI: 10.1016/J.Cell.2011.09.020  0.356
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  0.737
2011 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, ... ... Bustamante CD, et al. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. Plos Genetics. 7: e1002280. PMID 21935354 DOI: 10.1371/Journal.Pgen.1002280  0.418
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  0.565
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  0.696
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  0.642
2011 Bustamante CD, Burchard EG, De la Vega FM. Genomics for the world. Nature. 475: 163-5. PMID 21753830 DOI: 10.1038/475163A  0.341
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  0.778
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  0.61
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  0.703
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  0.455
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  0.406
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  0.753
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  0.414
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  0.796
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  0.8
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  0.411
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  0.73
2011 DE LA Vega FM, Bustamante CD, Leal SM. GENOME-WIDE ASSOCIATION MAPPING AND RARE ALLELES: FROM POPULATION GENOMICS TO PERSONALIZED MEDICINE - Session Introduction. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 74-5. PMID 21121034  0.338
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  0.344
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  0.362
2010 Bustamante CD, Henn BM. Human origins: Shadows of early migrations. Nature. 468: 1044-5. PMID 21179156 DOI: 10.1038/4681044A  0.393
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  0.622
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  0.59
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  0.502
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  0.766
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  0.337
2010 Awadalla P, Gauthier J, Myers RA, Casals F, Hamdan FF, Griffing AR, Côté M, Henrion E, Spiegelman D, Tarabeux J, Piton A, Yang Y, Boyko A, Bustamante C, Xiong L, et al. Direct measure of the de novo mutation rate in autism and schizophrenia cohorts. American Journal of Human Genetics. 87: 316-24. PMID 20797689 DOI: 10.1016/J.Ajhg.2010.07.019  0.349
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  0.813
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  0.674
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  0.72
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  0.823
2010 Williams LM, Ma X, Boyko AR, Bustamante CD, Oleksiak MF. SNP identification, verification, and utility for population genetics in a non-model genus. Bmc Genetics. 11: 32. PMID 20433726 DOI: 10.1186/1471-2156-11-32  0.449
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  0.35
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  0.749
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  0.832
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  0.813
2010 Brooks M, Etter K, Catalfamo J, Brisbin A, Bustamante C, Mezey J. A genome-wide linkage scan in German shepherd dogs localizes canine platelet procoagulant deficiency (Scott syndrome) to canine chromosome 27 Gene. 450: 70-75. PMID 19854246 DOI: 10.1016/J.Gene.2009.09.016  0.765
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  0.414
2010 De La Vega FM, Bryc K, Degehnardt JD, Musharoff S, Kidd JM, Seth V, Stanley S, Brisbin A, Keinan A, Clark A, Bustamante CD. Genome sequencing and analysis of admixed genomes of African and Mexican ancestry: implications for personal ancestry reconstruction and multi-ethnic medical genomics Genome Biology. 11. DOI: 10.1186/Gb-2010-11-S1-O4  0.819
2010 Ostrander EA, Boyko A, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, Holdt BMV, Cargill M, Auton A, Reynolds A, Elkahloun AG, ... ... Bustamante CD, et al. Tracking genes and finding mutations: finding genes for complex traits in the domestic dog (Canis familiaris) Genome Biology. 11: 1-1. DOI: 10.1186/Gb-2010-11-S1-I23  0.818
2010 Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Diffusion Approximations for Demographic Inference: DaDi Nature Precedings. 1-1. DOI: 10.1038/Npre.2010.4594.1  0.704
2010 Wen J, Lancaster L, Noller H, Bustamante C, Tinoco I. Single-Molecule Study of Programmed Ribosomal Frameshifting Biophysical Journal. 98: 260a. DOI: 10.1016/J.Bpj.2009.12.1416  0.311
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  0.635
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  0.72
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  0.339
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  0.835
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  0.773
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  0.721
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  0.392
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  0.436
2009 Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamante C, Yoshimura A, Doi K, McCouch S. Evolutionary history of GS3, a gene conferring grain length in rice. Genetics. 182: 1323-34. PMID 19506305 DOI: 10.1534/Genetics.109.103002  0.325
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  0.835
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  0.649
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  0.73
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  0.824
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  0.353
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  0.466
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  0.754
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  0.367
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  0.363
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  0.733
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  0.821
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  0.812
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  0.564
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  0.348
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  0.824
2008 Ptacin JL, Nollmann M, Becker EC, Cozzarelli NR, Pogliano K, Bustamante C. Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilis. Nature Structural & Molecular Biology. 15: 485-93. PMID 18391964 DOI: 10.1038/Nsmb.1412  0.31
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  0.817
2008 Comolli LR, Spakowitz AJ, Siegerist CE, Jardine PJ, Grimes S, Anderson DL, Bustamante C, Downing KH. Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging process. Virology. 371: 267-77. PMID 18001811 DOI: 10.1016/J.Virol.2007.07.035  0.328
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  0.36
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  0.759
2007 Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG. Recent and ongoing selection in the human genome. Nature Reviews. Genetics. 8: 857-68. PMID 17943193 DOI: 10.1038/Nrg2187  0.674
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  0.74
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  0.325
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  0.698
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  0.746
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  0.686
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  0.674
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  0.402
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  0.74
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  0.821
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  0.418
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  0.444
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  0.406
2005 Levy O, Ptacin JL, Pease PJ, Gore J, Eisen MB, Bustamante C, Cozzarelli NR. Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase. Proceedings of the National Academy of Sciences of the United States of America. 102: 17618-23. PMID 16301526 DOI: 10.1073/Pnas.0508932102  0.327
2005 Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C. Genomic scans for selective sweeps using SNP data. Genome Research. 15: 1566-75. PMID 16251466 DOI: 10.1101/Gr.4252305  0.633
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  0.651
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  0.759
2005 Chemla YR, Aathavan K, Michaelis J, Grimes S, Jardine PJ, Anderson DL, Bustamante C. Mechanism of force generation of a viral DNA packaging motor. Cell. 122: 683-92. PMID 16143101 DOI: 10.1016/J.Cell.2005.06.024  0.305
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  0.471
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  0.716
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  0.737
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  0.356
2005 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. A scan for positively selected genes in the genomes of humans and chimpanzees. Plos Biology. 3: e170. PMID 15869325 DOI: 10.1371/Journal.Pbio.0030170  0.776
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  0.358
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  0.353
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  0.749
2003 Gilad Y, Bustamante CD, Lancet D, Pääbo S. Natural selection on the olfactory receptor gene family in humans and chimpanzees. American Journal of Human Genetics. 73: 489-501. PMID 12908129 DOI: 10.1086/378132  0.35
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  0.648
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  0.673
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 DOI: 10.1093/Oxfordjournals.Molbev.A003975  0.648
2001 Bustamante CD, Wakeley J, Sawyer S, Hartl DL. Directional selection and the site-frequency spectrum. Genetics. 159: 1779-88. PMID 11779814  0.451
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  0.755
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 DOI: 10.1093/Oxfordjournals.Molbev.A026310  0.657
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