Ryan Hernandez, PhD

Professor
Bioengineering
+1 415 514-9813

Dr. Ryan Hernandez co-leads the Torgerson-Hernandez Lab (THeLab) along with Dr. Dara Torgerson at UCSF. THeLab is a highly collaborative group that uses machine learning and artificial intelligence to unravel the complex interplay of how genes and the environment contribute to complex traits across the continuum of human populations. Our work is centered on the importance of involving diverse populations, empowering us to pave the way toward innovative, equitable advancements in human health.

Dr. Hernandez also serves as:
(1) Co-Lead of UCSF's Advancing the Research Careers of Historically Excluded Scholars (ARCHES) Program, an initiative focused on supporting and advancing the career development of historically excluded research faculty, where he focuses on the development of community and scientific networks.
(2) Co-Director of the Biological and Medical Informatics (BMI) graduate program
(3) Co-Director of the Post-baccalaureate Research Opportunities to Promote Equity in Learning (PROPEL) and NIH-funded Post-baccalaureate Research Education Program (PREP).
(4) Director of the Genentech-UCSF School of Pharmacy PhD Student Diversity Fellowship Program.

Publications: 

Urinary Acetaminophen Metabolites and Clinical Outcomes in Extremely Premature Infants.

American journal of perinatology

Guardado M, Torgerson D, Chapin C, Atum A, Hernandez RD, Clyman R, Simmons R, Parry S, Ballard PL

Genetics of Latin American Diversity Project: Insights into population genetics and association studies in admixed groups in the Americas.

Cell genomics

Borda V, Loesch DP, Guo B, Laboulaye R, Veliz-Otani D, French JN, Leal TP, Gogarten SM, Ikpe S, Gouveia MH, Mendes M, Abecasis GR, Alvim I, Arboleda-Bustos CE, Arboleda G, Arboleda H, Barreto ML, Barwick L, Bezzera MA, Blangero J, Borges V, Caceres O, Cai J, Chana-Cuevas P, Chen Z, Custer B, Dean M, Dinardo C, Domingos I, Duggirala R, Dieguez E, Fernandez W, Ferraz HB, Gilliland F, Guio H, Horta B, Curran JE, Johnsen JM, Kaplan RC, Kelly S, Kenny EE, Konkle BA, Kooperberg C, Lescano A, Lima-Costa MF, Loos RJF, Manichaikul A, Meyers DA, Naslavsky MS, Nickerson DA, North KE, Padilla C, Preuss M, Raggio V, Reiner AP, Rich SS, Rieder CR, Rienstra M, Rotter JI, Rundek T, Sacco RL, Sanchez C, Sankaran VG, Santos-Lobato BL, Schumacher-Schuh AF, Scliar MO, Silverman EK, Sofer T, Lasky-Su J, Tumas V, Weiss ST, Latin American Research Consortium on the Genetics of Parkinson’s Disease (LARGE-PD), National Institute of Neurological Disorders and Stroke (NINDS) Stroke Genetics Network (SiGN) Conso, Trans-Omics for Precision Medicine (TOPMed) Population Genetics Working Group, Mata IF, Hernandez RD, Tarazona-Santos E, O'Connor TD

PROPEL: a scalable model for postbaccalaureate training to promote diversity in the biomedical workforce.

Journal of microbiology & biology education

Allen J, Abdiwahab E, Morris MD, Le Saux CJ, Betancur P, Ansel KM, Hernandez RD, Nystul TG

py_ped_sim - A flexible forward genetic simulator for complex family pedigree analysis.

bioRxiv : the preprint server for biology

Guardado M, Perez C, Jackson S, Magaña J, Campana S, Samperio E, Rojas BC, Hernandez S, Syas K, Hernandez R, Zavala EI, Rohlfs R

Effect of different ankle joint positions on medial gastrocnemius muscle fiber strains during isometric plantarflexion.

Scientific reports

Cunnane BT, Sinha U, Malis V, Hernandez RD, Smitaman E, Sinha S

The Urinary Metabolomic Fingerprint in Extremely Preterm Infants on Total Parenteral Nutrition vs. Enteral Feeds.

Metabolites

Guardado M, Steurer M, Chapin C, Hernandez RD, Ballard PL, Torgerson D

Efficacy of National Comprehensive Cancer Network Guidelines in Identifying Pathogenic Germline Variants Among Unselected Patients with Prostate Cancer: The PROCLAIM Trial.

European urology oncology

Shore N, Gazi M, Pieczonka C, Heron S, Modh R, Cahn D, Belkoff LH, Berger A, Mazzarella B, Veys J, Idom C, Morris D, Jayram G, Engelman A, Bukkapatnam R, Dato P, Bevan-Thomas R, Cornell R, Wise DR, Hardwick MK, Hernandez RD, Rojahn S, Layman P, Hatchell KE, Heald B, Nussbaum RL, Nielsen SM, Esplin ED

The hydrocortisone-responsive urinary metabolome of premature infants.

Pediatric research

Torgerson D, Guardado M, Steurer M, Chapin C, Hernandez RD, Ballard PL

Effect of Ocrelizumab on B- and T-Cell Receptor Repertoire Diversity in Patients With Relapsing Multiple Sclerosis From the Randomized Phase III OPERA Trial.

Neurology(R) neuroimmunology & neuroinflammation

Laurent SA, Strauli NB, Eggers EL, Wu H, Michel B, Demuth S, Palanichamy A, Wilson MR, Sirota M, Hernandez RD, Cree BAC, Herman AE, von Büdingen HC

Strain and Strain Rate Tensor Mapping of Medial Gastrocnemius at Submaximal Isometric Contraction and Three Ankle Angles.

Tomography (Ann Arbor, Mich.)

Hernandez R, Sinha U, Malis V, Cunnane B, Smitaman E, Sinha S

Correlations between complex human phenotypes vary by genetic background, gender, and environment.

Cell reports. Medicine

Elgart M, Goodman MO, Isasi C, Chen H, Morrison AC, de Vries PS, Xu H, Manichaikul AW, Guo X, Franceschini N, Psaty BM, Rich SS, Rotter JI, Lloyd-Jones DM, Fornage M, Correa A, Heard-Costa NL, Vasan RS, Hernandez R, Kaplan RC, Redline S, Trans-Omics for Precision Medicine (TOPMed) Consortium, Sofer T

Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data.

Nature genetics

Wainschtein P, Jain D, Zheng Z, TOPMed Anthropometry Working Group, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Cupples LA, Shadyab AH, McKnight B, Shoemaker BM, Mitchell BD, Psaty BM, Kooperberg C, Liu CT, Albert CM, Roden D, Chasman DI, Darbar D, Lloyd-Jones DM, Arnett DK, Regan EA, Boerwinkle E, Rotter JI, O'Connell JR, Yanek LR, de Andrade M, Allison MA, McDonald MN, Chung MK, Fornage M, Chami N, Smith NL, Ellinor PT, Vasan RS, Mathias RA, Loos RJF, Rich SS, Lubitz SA, Heckbert SR, Redline S, Guo X, Chen Y-I, Laurie CA, Hernandez RD, McGarvey ST, Goddard ME, Laurie CC, North KE, Lange LA, Weir BS, Yengo L, Yang J, Visscher PM

Population sequencing data reveal a compendium of mutational processes in the human germ line.

Science (New York, N.Y.)

Seplyarskiy VB, Soldatov RA, Koch E, McGinty RJ, Goldmann JM, Hernandez RD, Barnes K, Correa A, Burchard EG, Ellinor PT, McGarvey ST, Mitchell BD, Vasan RS, Redline S, Silverman E, Weiss ST, Arnett DK, Blangero J, Boerwinkle E, He J, Montgomery C, Rao DC, Rotter JI, Taylor KD, Brody JA, Chen YI, de Las Fuentes L, Hwu CM, Rich SS, Manichaikul AW, Mychaleckyj JC, Palmer ND, Smith JA, Kardia SLR, Peyser PA, Bielak LF, O'Connor TD, Emery LS, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Population Genetics Working Group, Gilissen C, Wong WSW, Kharchenko PV, Sunyaev S

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program.

Nature

Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, Taliun SAG, Corvelo A, Gogarten SM, Kang HM, Pitsillides AN, LeFaive J, Lee SB, Tian X, Browning BL, Das S, Emde AK, Clarke WE, Loesch DP, Shetty AC, Blackwell TW, Smith AV, Wong Q, Liu X, Conomos MP, Bobo DM, Aguet F, Albert C, Alonso A, Ardlie KG, Arking DE, Aslibekyan S, Auer PL, Barnard J, Barr RG, Barwick L, Becker LC, Beer RL, Benjamin EJ, Bielak LF, Blangero J, Boehnke M, Bowden DW, Brody JA, Burchard EG, Cade BE, Casella JF, Chalazan B, Chasman DI, Chen YI, Cho MH, Choi SH, Chung MK, Clish CB, Correa A, Curran JE, Custer B, Darbar D, Daya M, de Andrade M, DeMeo DL, Dutcher SK, Ellinor PT, Emery LS, Eng C, Fatkin D, Fingerlin T, Forer L, Fornage M, Franceschini N, Fuchsberger C, Fullerton SM, Germer S, Gladwin MT, Gottlieb DJ, Guo X, Hall ME, He J, Heard-Costa NL, Heckbert SR, Irvin MR, Johnsen JM, Johnson AD, Kaplan R, Kardia SLR, Kelly T, Kelly S, Kenny EE, Kiel DP, Klemmer R, Konkle BA, Kooperberg C, Köttgen A, Lange LA, Lasky-Su J, Levy D, Lin X, Lin KH, Liu C, Loos RJF, Garman L, Gerszten R, Lubitz SA, Lunetta KL, Mak ACY, Manichaikul A, Manning AK, Mathias RA, McManus DD, McGarvey ST, Meigs JB, Meyers DA, Mikulla JL, Minear MA, Mitchell BD, Mohanty S, Montasser ME, Montgomery C, Morrison AC, Murabito JM, Natale A, Natarajan P, Nelson SC, North KE, O'Connell JR, Palmer ND, Pankratz N, Peloso GM, Peyser PA, Pleiness J, Post WS, Psaty BM, Rao DC, Redline S, Reiner AP, Roden D, Rotter JI, Ruczinski I, Sarnowski C, Schoenherr S, Schwartz DA, Seo JS, Seshadri S, Sheehan VA, Sheu WH, Shoemaker MB, Smith NL, Smith JA, Sotoodehnia N, Stilp AM, Tang W, Taylor KD, Telen M, Thornton TA, Tracy RP, Van Den Berg DJ, Vasan RS, Viaud-Martinez KA, Vrieze S, Weeks DE, Weir BS, Weiss ST, Weng LC, Willer CJ, Zhang Y, Zhao X, Arnett DK, Ashley-Koch AE, Barnes KC, Boerwinkle E, Gabriel S, Gibbs R, Rice KM, Rich SS, Silverman EK, Qasba P, Gan W, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Papanicolaou GJ, Nickerson DA, Browning SR, Zody MC, Zöllner S, Wilson JG, Cupples LA, Laurie CC, Jaquish CE, Hernandez RD, O'Connor TD, Abecasis GR

Recent shifts in the genomic ancestry of Mexican Americans may alter the genetic architecture of biomedical traits.

eLife

Spear ML, Diaz-Papkovich A, Ziv E, Yracheta JM, Gravel S, Torgerson DG, Hernandez RD

A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles.

Science translational medicine

Claesen J, Spagnolo JB, Ramos SF, Kurita KL, Byrd AL, Aksenov AA, Melnik AV, Wong WR, Wang S, Hernandez RD, Donia MS, Dorrestein PC, Kong HH, Segre JA, Linington RG, Fischbach MA, Lemon KP

The Temporal Dynamics of Background Selection in Nonequilibrium Populations.

Genetics

Torres R, Stetter MG, Hernandez RD, Ross-Ibarra J

De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population.

Proceedings of the National Academy of Sciences of the United States of America

Kessler MD, Loesch DP, Perry JA, Heard-Costa NL, Taliun D, Cade BE, Wang H, Daya M, Ziniti J, Datta S, Celedón JC, Soto-Quiros ME, Avila L, Weiss ST, Barnes K, Redline SS, Vasan RS, Johnson AD, Mathias RA, Hernandez R, Wilson JG, Nickerson DA, Abecasis G, Browning SR, Zöllner S, O'Connell JR, Mitchell BD, National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Population Genetics Working Group, O'Connor TD

Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity.

American journal of human genetics

Szpiech ZA, Mak ACY, White MJ, Hu D, Eng C, Burchard EG, Hernandez RD

Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations.

Nature communications

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, Acevedo N, Araujo MI, Avila PC, Belbin G, Bleecker E, Bustamante C, Caraballo L, Cruz A, Dunston GM, Eng C, Faruque MU, Ferguson TS, Figueiredo C, Ford JG, Gan W, Gourraud PA, Hansel NN, Hernandez RD, Herrera-Paz EF, Jiménez S, Kenny EE, Knight-Madden J, Kumar R, Lange LA, Lange EM, Lizee A, Maul P, Maul T, Mayorga A, Meyers D, Nicolae DL, O'Connor TD, Oliveira RR, Olopade CO, Olopade O, Qin ZS, Rotimi C, Vince N, Watson H, Wilks RJ, Wilson JG, Salzberg S, Ober C, Burchard EG, Williams LK, Beaty TH, Taub MA, Ruczinski I, Mathias RA, Barnes KC, CAAPA

Ultrarare variants drive substantial cis heritability of human gene expression.

Nature genetics

Hernandez RD, Uricchio LH, Hartman K, Ye C, Dahl A, Zaitlen N

Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations.

Nature communications

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, Acevedo N, Araujo MI, Avila PC, Belbin G, Bleecker E, Bustamante C, Caraballo L, Cruz A, Dunston GM, Eng C, Faruque MU, Ferguson TS, Figueiredo C, Ford JG, Gan W, Gourraud PA, Hansel NN, Hernandez RD, Herrera-Paz EF, Jiménez S, Kenny EE, Knight-Madden J, Kumar R, Lange LA, Lange EM, Lizee A, Maul P, Maul T, Mayorga A, Meyers D, Nicolae DL, O'Connor TD, Oliveira RR, Olopade CO, Olopade O, Qin ZS, Rotimi C, Vince N, Watson H, Wilks RJ, Wilson JG, Salzberg S, Ober C, Burchard EG, Williams LK, Beaty TH, Taub MA, Ruczinski I, Mathias RA, Barnes KC, CAAPA

Ebola virus, but not Marburg virus, replicates efficiently and without required adaptation in snake cells.

Virus evolution

Fedewa G, Radoshitzky SR, Chi X, Dong L, Zeng X, Spear M, Strauli N, Ng M, Chandran K, Stenglein MD, Hernandez RD, Jahrling PB, Kuhn JH, DeRisi JL

A genome-wide association and admixture mapping study of bronchodilator drug response in African Americans with asthma.

The pharmacogenomics journal

Spear ML, Hu D, Pino-Yanes M, Huntsman S, Eng C, Levin AM, Ortega VE, White MJ, McGarry ME, Thakur N, Galanter J, Mak ACY, Oh SS, Ampleford E, Peters SP, Davis A, Kumar R, Farber HJ, Meade K, Avila PC, Serebrisky D, Lenoir MA, Brigino-Buenaventura E, Cintron WR, Thyne SM, Rodriguez-Santana JR, Ford JG, Chapela R, Estrada AM, Sandoval K, Seibold MA, Winkler CA, Bleecker ER, Myers DA, Williams LK, Hernandez RD, Torgerson DG, Burchard EG

An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos.

The Journal of allergy and clinical immunology

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, McGarry M, Moreno-Estrada A, Sandoval K, Winkler CA, Seibold MA, Padhukasahasram B, Conti DV, Farber HJ, Avila P, Brigino-Buenaventura E, Lenoir M, Meade K, Serebrisky D, Borrell LN, Rodriguez-Cintron W, Thyne S, Joubert BR, Romieu I, Levin AM, Sienra-Monge JJ, Del Rio-Navarro BE, Gan W, Raby BA, Weiss ST, Bleecker E, Meyers DA, Martinez FJ, Gauderman WJ, Gilliland F, London SJ, Bustamante CD, Nicolae DL, Ober C, Sen S, Barnes K, Williams LK, Hernandez RD, Burchard EG

An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses.

Molecular cell

Penn BH, Netter Z, Johnson JR, Von Dollen J, Jang GM, Johnson T, Ohol YM, Maher C, Bell SL, Geiger K, Golovkine G, Du X, Choi A, Parry T, Mohapatra BC, Storck MD, Band H, Chen C, Jäger S, Shales M, Portnoy DA, Hernandez R, Coscoy L, Cox JS, Krogan NJ

Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma.

American journal of respiratory and critical care medicine

Mak ACY, White MJ, Eckalbar WL, Szpiech ZA, Oh SS, Pino-Yanes M, Hu D, Goddard P, Huntsman S, Galanter J, Wu AC, Himes BE, Germer S, Vogel JM, Bunting KL, Eng C, Salazar S, Keys KL, Liberto J, Nuckton TJ, Nguyen TA, Torgerson DG, Kwok PY, Levin AM, Celedón JC, Forno E, Hakonarson H, Sleiman PM, Dahlin A, Tantisira KG, Weiss ST, Serebrisky D, Brigino-Buenaventura E, Farber HJ, Meade K, Lenoir MA, Avila PC, Sen S, Thyne SM, Rodriguez-Cintron W, Winkler CA, Moreno-Estrada A, Sandoval K, Rodriguez-Santana JR, Kumar R, Williams LK, Ahituv N, Ziv E, Seibold MA, Darnell RB, Zaitlen N, Hernandez RD, Burchard EG, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium

ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues.

Genome biology

Mangul S, Yang HT, Strauli N, Gruhl F, Porath HT, Hsieh K, Chen L, Daley T, Christenson S, Wesolowska-Andersen A, Spreafico R, Rios C, Eng C, Smith AD, Hernandez RD, Ophoff RA, Santana JR, Levanon EY, Woodruff PG, Burchard E, Seibold MA, Shifman S, Eskin E, Zaitlen N

Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins.

Science signaling

White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL

Prominent features of the amino acid mutation landscape in cancer.

PloS one

Szpiech ZA, Strauli NB, White KA, Ruiz DG, Jacobson MP, Barber DL, Hernandez RD

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)

Shringarpure SS, Mathias RA, Hernandez RD, O'Connor TD, Szpiech ZA, Torres R, De La Vega FM, Bustamante CD, Barnes KC, Taub MA, CAAPA Consortium

Functional Segregation of Overlapping Genes in HIV.

Cell

Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD

Global environmental drivers of influenza.

Proceedings of the National Academy of Sciences of the United States of America

Deyle ER, Maher MC, Hernandez RD, Basu S, Sugihara G

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens.

Cell

Nédélec Y, Sanz J, Baharian G, Szpiech ZA, Pacis A, Dumaine A, Grenier JC, Freiman A, Sams AJ, Hebert S, Pagé Sabourin A, Luca F, Blekhman R, Hernandez RD, Pique-Regi R, Tung J, Yotova V, Barreiro LB

A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome.

Nature communications

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, Levin AM, Song W, Torres R, Padhukasahasram B, Eng C, Mejia-Mejia DA, Ferguson T, Qin ZS, Scott AF, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Kumar R, Avila PC, Williams LK, Watson H, Ware LB, Olopade C, Olopade O, Oliveira R, Ober C, Nicolae DL, Meyers D, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker E, Araujo MI, Herrera-Paz EF, Gietzen K, Grus WE, Bamshad M, Bustamante CD, Kenny EE, Hernandez RD, Beaty TH, Ruczinski I, Akey J, CAAPA, Barnes KC

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

Genome research

Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez RD

Selective Sweeps.

Encyclopedia of Evolutionary Biology

Z.A. Szpiech, R.D. Hernandez

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

PloS one

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

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

Molecular cell

Davis ZH, Verschueren E, Jang GM, Kleffman K, Johnson JR, Park J, Von Dollen J, Maher MC, Johnson T, Newton W, Jäger S, Shales M, Horner J, Hernandez RD, Krogan NJ, Glaunsinger BA

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

The Journal of allergy and clinical immunology

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

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

Genetic epidemiology

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

Robust forward simulations of recurrent hitchhiking.

Genetics

Uricchio LH, Hernandez RD

High-resolution network biology: connecting sequence with function.

Nature reviews. Genetics

Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ

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

The Journal of allergy and clinical immunology

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, Rodríguez-Cintrón W, Sen S, Rodríguez-Santana JR, Hernandez RD, Giacomini KM, Burchard EG

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

BMC genomics

Hodgkinson A, Casals F, Idaghdour Y, Grenier JC, Hernandez RD, Awadalla P

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

Science translational medicine

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

Population genetics of rare variants and complex diseases.

Human heredity

Maher MC, Uricchio LH, Torgerson DG, Hernandez RD

Evolutionary signatures in non-coding DNA.

Rapidly Evolving Genes and Genetic Systems

Dara G. Torgerson, Ryan D. Hernandez

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

The Journal of allergy and clinical immunology

Torgerson DG, Gignoux CR, Galanter JM, Drake KA, Roth LA, Eng C, Huntsman S, Torres R, Avila PC, Chapela R, Ford JG, Rodríguez-Santana JR, Rodríguez-Cintrón W, Hernandez RD, Burchard EG

A fine-scale chimpanzee genetic map from population sequencing.

Science (New York, N.Y.)

Auton A, Fledel-Alon A, Pfeifer S, Venn O, Ségurel 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

Resequencing candidate genes implicates rare variants in asthma susceptibility.

American journal of human genetics

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

Global landscape of HIV-human protein complexes.

Nature

Jäger 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

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

PLoS genetics

Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M

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

Nature genetics

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, Celedón 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, 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 and Admixture in Lat, 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 (SAPPHIRE), Barnes KC, Genetic Research on Asthma in African Diaspora (GRAAD) Study, Ober C, Nicolae DL

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

PloS one

Xie X, Molina J, Hernandez R, Reynolds A, Boyko AR, Bustamante CD, Purugganan MD

Classic selective sweeps were rare in recent human evolution.

Science (New York, N.Y.)

Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, 1000 Genomes Project, Sella G, Przeworski M

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

Genetics

Zanders S, Ma X, Roychoudhury A, Hernandez RD, Demogines A, Barker B, Gu Z, Bustamante CD, Alani E

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

PLoS genetics

Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD

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

PLoS genetics

Torgerson DG, Boyko AR, Hernandez RD, Indap A, Hu X, White TJ, Sninsky JJ, Cargill M, Adams MD, Bustamante CD, Clark AG

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

Science (New York, N.Y.)

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

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

PLoS genetics

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

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

Nature

Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD

Genome-wide patterns of nucleotide polymorphism in domesticated rice.

PLoS genetics

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

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

Molecular biology and evolution

Hernandez RD, Williamson SH, Zhu L, Bustamante CD

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

Molecular biology and evolution

Hernandez RD, Williamson SH, Bustamante CD

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

Science (New York, N.Y.)

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

Evolutionary and biomedical insights from the rhesus macaque genome.

Science (New York, N.Y.)

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, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS

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

Nature

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

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

Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, Bustamante CD

Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice.

PLoS genetics

Ana Caicedo, Scott Williamson, Ryan D Hernandez, Adam Boyko, Adi Fledel-Alon, Thomas York, Nicholas Polato, Ken Olsen, Rasmus Nielsen, Susan R. McCouch, Carlos D. Bustamante, Michael D. Purugganan