Hernandez Lab - Publications

Google Scholar

Former Members

Statistical inference of a convergent antibody repertoire response to influenza vaccine.

Strauli NB, Hernandez RD.
Genome Medicine (2016).
PMID: 27255379 doi:10.1186/s13073-016-0314-z

Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants.

Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez RD.
Genome Research (2016).
PMID: 27197206 doi:10.1101/gr.202440.115

Dumpster diving in RNA-sequencing to find the source of every last read

Mangul S, Yang HT, Strauli N, Gruhl F, Daley T, Christenson S, Wesolowska Andersen A, Spreafico R, Rios C, Eng C, Smith AD, Hernandez RD, Ophoff RA, Santana JR, Woodruff PG, Burchard E, Seibold MA, Shifman S, Eskin E, Zaitlen N.
bioRxiv (2016).
doi:10.1101/053041

Pooled Sequencing of Candidate Genes Implicates Rare Variants in the Development of Asthma Following Severe RSV Bronchiolitis in Infancy.

Torgerson DG, Giri T, Druley TE, Zheng J, Huntsman S, Seibold MA, Young AL, Schweiger T, Yin-Declue H, Sajol GD, Schechtman KB, Hernandez RD, Randolph AG, Bacharier LB, Castro M.
PloS One (2015).
PMID: 26587832 doi:10.1371/journal.pone.0142649

A global reference for human genetic variation.

1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR.
Nature (2015).
PMID: 26432245 doi:10.1038/nature15393

SFS_CODE: More Efficient and Flexible Forward Simulations

Hernandez RD, Uricchio LH.
bioRxiv (2015).
doi:10.1101/025064

Statistical Inference of a Convergent Antibody Repertoire Response to Influenza Vaccine

Strauli N, Hernandez R.
bioRxiv (2015).
doi:10.1101/025098

Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos.

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, Padhukasahasram B, Moreno-Estrada A, Sandoval K, Winkler CA, Lurmann F, Davis A, Farber HJ, Meade K, Avila PC, Serebrisky D, Chapela R, Ford JG, Lenoir MA, Thyne SM, Brigino-Buenaventura E, Borrell LN, Rodriguez-Cintron W, Sen S, Kumar R, Rodriguez-Santana JR, Bustamante CD, Martinez FD, Raby BA, Weiss ST, Nicolae DL, Ober C, Meyers DA, Bleecker ER, Mack SJ, Hernandez RD, Eichler EE, Barnes KC, Williams LK, Torgerson DG, Burchard EG.
The Journal of Allergy and Clinical Immunology (2015).
PMID: 25488688 doi:10.1016/j.jaci.2014.10.033

Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference.

Maher MC, Hernandez RD.
G3 (Bethesda, Md.) (2015).
PMID: 25711833 doi:10.1534/g3.115.017095

CauseMap: fast inference of causality from complex time series.

Maher MC, Hernandez RD.
PeerJ (2015).
PMID: 25780776 doi:10.7717/peerj.824

Selection and explosive growth may hamper the performance of rare variant association tests

Uricchio LH, Witte JS, Hernandez RD.
bioRxiv (2015).
doi:10.1101/015917

Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes.

Davis ZH, Verschueren E, Jang GM, Kleffman K, Johnson JR, Park J, Von Dollen J, Maher MC, Johnson T, Newton W, Jager S, Shales M, Horner J, Hernandez RD, Krogan NJ, Glaunsinger BA.
Molecular Cell (2015).
PMID: 25544563 doi:10.1016/j.molcel.2014.11.026

Genetic simulation tools for post-genome wide association studies of complex diseases.

Chen HS, Hutter CM, Mechanic LE, Amos CI, Bafna V, Hauser ER, Hernandez RD, Li C, Liberles DA, McAllister K, Moore JH, Paltoo DN, Papanicolaou GJ, Peng B, Ritchie MD, Rosenfeld G, Witte JS, Gillanders EM, Feuer EJ.
Genetic Epidemiology (2015).
PMID: 25371374 doi:10.1002/gepi.21870

Population genetic simulations of complex phenotypes with implications for rare variant association tests.

Uricchio LH, Torres R, Witte JS, Hernandez RD.
Genetic Epidemiology (2015).
PMID: 25417809 doi:10.1002/gepi.21866

selscan: an efficient multithreaded program to perform EHH-based scans for positive selection.

Szpiech ZA, Hernandez RD.
Molecular Biology and Evolution (2014).
PMID: 25015648 doi:10.1093/molbev/msu211

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.
Genome Biology (2014).
PMID: 24980144 doi:10.1186/gb-2014-15-6-r88

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.

Delaneau O, Marchini J, 1000 Genomes Project Consortium, 1000 Genomes Project Consortium.
Nature Communications (2014).
PMID: 25653097 doi:10.1038/ncomms4934

Robust forward simulations of recurrent hitchhiking.

Uricchio LH, Hernandez RD.
Genetics (2014).
PMID: 24561480 doi:10.1534/genetics.113.156935

Comparing Evolutionary Rates Using An Exact Test for 2x2 Tables with Continuous Cell Entries

Thompson AM, Maher MC, Uricchio LH, Szpiech ZA, Hernandez RD.
ArXiv e-prints (2014).
arXiv:1404.2992

A genome-wide association study of bronchodilator response in Latinos implicates rare variants.

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, Farber HJ, Kumar R, Avila PC, Brigino-Buenaventura E, Chapela R, Ford JG, Lenoir MA, Lurmann F, Meade K, Serebrisky D, Thyne S, Rodriguez-Cintron W, Sen S, Rodriguez-Santana JR, Hernandez RD, Giacomini KM, Burchard EG.
The Journal of Allergy and Clinical Immunology (2014).
PMID: 23992748 doi:10.1016/j.jaci.2013.06.043

High-resolution network biology: connecting sequence with function.

Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ.
Nature Reviews. Genetics (2013).
PMID: 24197012 doi:10.1038/nrg3574

Integrative annotation of variants from 1092 humans: application to cancer genomics.

Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gumus ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M.
Science (New York, N.Y.) (2013).
PMID: 24092746 doi:10.1126/science.1235587

Selective constraint, background selection, and mutation accumulation variability within and between human populations.

Hodgkinson A, Casals F, Idaghdour Y, Grenier JC, Hernandez RD, Awadalla P.
BMC Genomics (2013).
PMID: 23875710 doi:10.1186/1471-2164-14-495

Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism.

Vujkovic-Cvijin I, Dunham RM, Iwai S, Maher MC, Albright RG, Broadhurst MJ, Hernandez RD, Lederman MM, Huang Y, Somsouk M, Deeks SG, Hunt PW, Lynch SV, McCune JM.
Science Translational Medicine (2013).
PMID: 23843452 doi:10.1126/scitranslmed.3006438

Population genetics of rare variants and complex diseases.

Maher MC, Uricchio LH, Torgerson DG, Hernandez RD.
Human Heredity (2013).
PMID: 23594490 doi:000346826

An integrated map of genetic variation from 1,092 human genomes.

1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.
Nature (2012).
PMID: 23128226 doi:10.1038/nature11632

SNP discovery, expression and cis-regulatory variation in the UGT2B genes.

Sun C, Southard C, Huo D, Hernandez RD, Witonsky DB, Olopade OI, Di Rienzo A.
The Pharmacogenomics Journal (2012).
PMID: 21358749 doi:10.1038/tpj.2011.2

Case-control admixture mapping in Latino populations enriches for known asthma-associated genes.

Torgerson DG, Gignoux CR, Galanter JM, Drake KA, Roth LA, Eng C, Huntsman S, Torres R, Avila PC, Chapela R, Ford JG, Rodriguez-Santana JR, Rodriguez-Cintron W, Hernandez RD, Burchard EG.
The Journal of Allergy and Clinical Immunology (2012).
PMID: 22502797 doi:10.1016/j.jaci.2012.02.040

The 1000 Genomes Project: data management and community access.

Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P, 1000 Genomes Project Consortium.
Nature Methods (2012).
PMID: 22543379 doi:10.1038/nmeth.1974

A fine-scale chimpanzee genetic map from population sequencing.

Auton A, Fledel-Alon A, Pfeifer S, Venn O, Segurel L, Street T, Leffler EM, Bowden R, Aneas I, Broxholme J, Humburg P, Iqbal Z, Lunter G, Maller J, Hernandez RD, Melton C, Venkat A, Nobrega MA, Bontrop R, Myers S, Donnelly P, Przeworski M, McVean G.
Science (New York, N.Y.) (2012).
PMID: 22422862 doi:10.1126/science.1216872

Resequencing candidate genes implicates rare variants in asthma susceptibility.

Torgerson DG, Capurso D, Mathias RA, Graves PE, Hernandez RD, Beaty TH, Bleecker ER, Raby BA, Meyers DA, Barnes KC, Weiss ST, Martinez FD, Nicolae DL, Ober C.
American Journal of Human Genetics (2012).
PMID: 22325360 doi:10.1016/j.ajhg.2012.01.008

Resequencing candidate genes implicates rare variants in asthma susceptibility.

Global landscape of HIV-human protein complexes.

Jager S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ.
Nature (2012).
PMID: 22190034 doi:10.1038/nature10719

Evolutionary signatures in non-coding DNA

Torgerson DG, Hernandez RD.
Rapidly Evolving Genes and Genetic Systems (2012).

A population genetics-phylogenetics approach to inferring natural selection in coding sequences.

Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M.
PLoS Genetics (2011).
PMID: 22144911 doi:10.1371/journal.pgen.1002395

The functional spectrum of low-frequency coding variation.

Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R, 1000 Genomes Project.
Genome Biology (2011).
PMID: 21917140 doi:10.1186/gb-2011-12-9-r84

Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations.

Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR, Graves PE, Himes BE, Levin AM, Mathias RA, Hancock DB, Baurley JW, Eng C, Stern DA, Celedon JC, Rafaels N, Capurso D, Conti DV, Roth LA, Soto-Quiros M, Togias A, Li X, Myers RA, Romieu I, Van Den Berg DJ, Hu D, Hansel NN, Hernandez RD, Israel E, Salam MT, Galanter J, Avila PC, Avila L, Rodriquez-Santana JR, Chapela R, Rodriguez-Cintron W, Diette GB, Adkinson NF, Abel RA, Ross KD, Shi M, Faruque MU, Dunston GM, Watson HR, Mantese VJ, Ezurum SC, Liang L, Ruczinski I, Ford JG, Huntsman S, Chung KF, Vora H, Li X, Calhoun WJ, Castro M, Sienra-Monge JJ, del Rio-Navarro B, Deichmann KA, Heinzmann A, Wenzel SE, Busse WW, Gern JE, Lemanske RF Jr, Beaty TH, Bleecker ER, Raby BA, Meyers DA, London SJ, Mexico City Childhood Asthma Study (MCAAS), Gilliland FD, Children's Health Study (CHS) and HARBORS study, Burchard EG, Genetics of Asthma in Latino Americans (GALA) Study, Study of Genes-Environment, Martinez FD, Childhood Asthma Research and Education (CARE) Network, Weiss ST, Childhood Asthma Management Program (CAMP), Williams LK, Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity, Barnes KC, Genetic Research on Asthma in African Diaspora (GRAAD) Study, Ober C, Nicolae DL.
Nature Genetics (2011).
PMID: 21804549 doi:10.1038/ng.888

The variant call format and VCFtools.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group.
Bioinformatics (Oxford, England) (2011).
PMID: 21653522 doi:10.1093/bioinformatics/btr330

Demographic history and rare allele sharing among human populations.

Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, 1000 Genomes Project, Bustamante CD.
Proceedings of the National Academy of Sciences of the United States of America (2011).
PMID: 21730125 doi:10.1073/pnas.1019276108

Variation in genome-wide mutation rates within and between human families.

Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P, 1000 Genomes Project.
Nature Genetics (2011).
PMID: 21666693 doi:10.1038/ng.862

Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.

Xie X, Molina J, Hernandez R, Reynolds A, Boyko AR, Bustamante CD, Purugganan MD.
PloS One (2011).
PMID: 21674010 doi:10.1371/journal.pone.0020670

Classic selective sweeps were rare in recent human evolution.

Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, 1000 Genomes Project, Sella G, Przeworski M.
Science (New York, N.Y.) (2011).
PMID: 21330547 doi:10.1126/science.1198878

Mapping copy number variation by population-scale genome sequencing.

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stutz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project.
Nature (2011).
PMID: 21293372 doi:10.1038/nature09708

Diversity of human copy number variation and multicopy genes.

Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, 1000 Genomes Project, Eichler EE.
Science (New York, N.Y.) (2010).
PMID: 21030649 doi:10.1126/science.1197005

A map of human genome variation from population-scale sequencing.

1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA.
Nature (2010).
PMID: 20981092 doi:10.1038/nature09534

Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach.

Zanders S, Ma X, Roychoudhury A, Hernandez RD, Demogines A, Barker B, Gu Z, Bustamante CD, Alani E.
Genetics (2010).
PMID: 20660644 doi:10.1534/genetics.110.120105

Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data.

Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD.
PLoS Genetics (2009).
PMID: 19851460 doi:10.1371/journal.pgen.1000695

Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence.

Torgerson DG, Boyko AR, Hernandez RD, Indap A, Hu X, White TJ, Sninsky JJ, Cargill M, Adams MD, Bustamante CD, Clark AG.
PLoS Genetics (2009).
PMID: 19662163 doi:10.1371/journal.pgen.1000592

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.

Bovine HapMap Consortium, Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, Gill CA, Green RD, Hamernik DL, Kappes SM, Lien S, Matukumalli LK, McEwan JC, Nazareth LV, Schnabel RD, Weinstock GM, Wheeler DA, Ajmone-Marsan P, Boettcher PJ, Caetano AR, Garcia JF, Hanotte O, Mariani P, Skow LC, Sonstegard TS, Williams JL, Diallo B, Hailemariam L, Martinez ML, Morris CA, Silva LO, Spelman RJ, Mulatu W, Zhao K, Abbey CA, Agaba M, Araujo FR, Bunch RJ, Burton J, Gorni C, Olivier H, Harrison BE, Luff B, Machado MA, Mwakaya J, Plastow G, Sim W, Smith T, Thomas MB, Valentini A, Williams P, Womack J, Woolliams JA, Liu Y, Qin X, Worley KC, Gao C, Jiang H, Moore SS, Ren Y, Song XZ, Bustamante CD, Hernandez RD, Muzny DM, Patil S, San Lucas A, Fu Q, Kent MP, Vega R, Matukumalli A, McWilliam S, Sclep G, Bryc K, Choi J, Gao H, Grefenstette JJ, Murdoch B, Stella A, Villa-Angulo R, Wright M, Aerts J, Jann O, Negrini R, Goddard ME, Hayes BJ, Bradley DG, Barbosa da Silva M, Lau LP, Liu GE, Lynn DJ, Panzitta F, Dodds KG.
Science (New York, N.Y.) (2009).
PMID: 19390050 doi:10.1126/science.1167936

A flexible forward simulator for populations subject to selection and demography.

Hernandez RD.
Bioinformatics (Oxford, England) (2008).
PMID: 18842601 doi:10.1093/bioinformatics/btn522

Assessing the evolutionary impact of amino acid mutations in the human genome.

Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, Lohmueller KE, Adams MD, Schmidt S, Sninsky JJ, Sunyaev SR, White TJ, Nielsen R, Clark AG, Bustamante CD.
PLoS Genetics (2008).
PMID: 18516229 doi:10.1371/journal.pgen.1000083

Proportionally more deleterious genetic variation in European than in African populations.

Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD.
Nature (2008).
PMID: 18288194 doi:10.1038/nature06611

Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans.

Hernandez RD, Williamson SH, Zhu L, Bustamante CD.
Molecular Biology and Evolution (2007).
PMID: 17656634 doi:10.1093/molbev/msm149

Genome-wide patterns of nucleotide polymorphism in domesticated rice.

Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD.
PLoS Genetics (2007).
PMID: 17907810 doi:10.1371/journal.pgen.0030163

Context dependence, ancestral misidentification, and spurious signatures of natural selection.

Hernandez RD, Williamson SH, Bustamante CD.
Molecular Biology and Evolution (2007).
PMID: 17545186 doi:10.1093/molbev/msm108

Evolutionary and biomedical insights from the rhesus macaque genome.

Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csuros M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prufer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS.
Science (New York, N.Y.) (2007).
PMID: 17431167 doi:10.1126/science.1139247

Evolutionary and biomedical insights from the rhesus macaque genome.

Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques.

Hernandez RD, Hubisz MJ, Wheeler DA, Smith DG, Ferguson B, Rogers J, Nazareth L, Indap A, Bourquin T, McPherson J, Muzny D, Gibbs R, Nielsen R, Bustamante CD.
Science (New York, N.Y.) (2007).
PMID: 17431170 doi:10.1126/science.1140462

Natural selection on protein-coding genes in the human genome.

Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum DM, White TJ, Sninsky JJ, Hernandez RD, Civello D, Adams MD, Cargill M, Clark AG.
Nature (2005).
PMID: 16237444 doi:10.1038/nature04240

Simultaneous inference of selection and population growth from patterns of variation in the human genome.

Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, Bustamante CD.
Proceedings of the National Academy of Sciences of the United States of America (2005).
PMID: 15905331 doi:10.1073/pnas.0502300102