Ryan Hernandez, PhD

Professor
Department of Bioengineering and Therapeutic Sciences
hernandez
[email protected]
Phone: +1 415 514-9813
600 16th Street, Rm N472F
UCSF Box 2240
San Francisco, CA 94158
United States

Links

Hernandez Lab UCSF Profiles

Affiliations

Education programs

UCSF - UC Berkeley Joint Graduate Group in Bioengineering
Pharmaceutical Sciences and Pharmacogenomics Graduate Program (PSPG)
Director, Biological and Medical Informatics Graduate Program (BMI)

UCSF centers, institutes, and research programs

Quantitative Biosciences Institute (QBI)

What I do

I am a professor studying patterns of human genetic variation from global populations using large-scale whole genome sequencing data in order to understand genetic susceptibility to disease and drug response.

Departmental research area

pharmacogenomics and genomics
computational biology and systems pharmacology

My research expertise

population genetics, computational biology

Professional background

Degrees

PhD, Biometry, Cornell University, 2007
BA, Mathematics, Pitzer College, 2003
MS, Biometry, Cornell University

Biography

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-Director BMI: Biological and Medical Informatics Graduate Program
(2) Co-Director PROPEL: Post-baccalaureate Research Training Program
(3) Co-Director UCSF PREP: Post-baccalaureate Research Education Program
(4) Development Core for ARCHES: Building bridges to connect and support UCSF research faculty
(5) Director Genentech-UCSF School of Pharmacy Fellowship Program

Research keywords

  • evolutionary genomics
  • statistical genetics/genomics
  • computational biology and bioinformatics
  • population structure and admixture
  • Population genetics
  • human evolution
  • Mexican Americans
  • Genetics, Population
  • Genome-Wide Association Study
  • Isometric Contraction
  • Homozygote
  • Polymorphism, Single Nucleotide
  • Genetic Variation
  • Demography
  • Human Genome
  • Models, Genetic
  • Selection, Genetic
  • Haplotypes
  • Molecular Evolution
  • Multifactorial Inheritance
  • Ankle

Publications

Guardado M, Perez C, Campana S, Chavez Rojas B, Magaña J, Jackson S, Samperio E, Hernandez S, Syas K, Hernandez RD, Zavala EI, Rohlfs RV. py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis. BMC Bioinformatics. 2025 May 07; 26(1):122.
T. Malave-Mendez, M. Guardado, C. Chapin, R.D. Hernandez, P. Ballard, D.G. Torgerson. Metabolomic Fingerprint of Bronchopulmonary Dysplasia in Extremely Premature Infants. American Journal of Respiratory and Critical Care Medicine. 2025 May 1; 211(Abstracts):a5432-a5432.
Guardado M, Torgerson D, Chapin C, Atum A, Hernandez RD, Clyman R, Simmons R, Parry S, Ballard PL. Urinary Acetaminophen Metabolites and Clinical Outcomes in Extremely Premature Infants. Am J Perinatol. 2025 Jan 31.
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. Genetics of Latin American Diversity Project: Insights into population genetics and association studies in admixed groups in the Americas. Cell Genom. 2024 Nov 13; 4(11):100692.
Allen J, Abdiwahab E, Morris MD, Le Saux CJ, Betancur P, Ansel KM, Hernandez RD, Nystul TG. PROPEL: a scalable model for postbaccalaureate training to promote diversity in the biomedical workforce. J Microbiol Biol Educ. 2024 Dec 12; 25(3):e0012224.
Guardado M, Perez C, Jackson S, Magaña J, Campana S, Samperio E, Rojas BC, Hernandez S, Syas K, Hernandez R, Zavala EI, Rohlfs R. py_ped_sim - A flexible forward genetic simulator for complex family pedigree analysis. bioRxiv. 2024 Mar 29.
Cunnane BT, Sinha U, Malis V, Hernandez RD, Smitaman E, Sinha S. Effect of different ankle joint positions on medial gastrocnemius muscle fiber strains during isometric plantarflexion. Sci Rep. 2023 09 11; 13(1):14986.
Guardado M, Steurer M, Chapin C, Hernandez RD, Ballard PL, Torgerson D. The Urinary Metabolomic Fingerprint in Extremely Preterm Infants on Total Parenteral Nutrition vs. Enteral Feeds. Metabolites. 2023 Aug 24; 13(9).
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. Efficacy of National Comprehensive Cancer Network Guidelines in Identifying Pathogenic Germline Variants Among Unselected Patients with Prostate Cancer: The PROCLAIM Trial. Eur Urol Oncol. 2023 10; 6(5):477-483.
Torgerson D, Guardado M, Steurer M, Chapin C, Hernandez RD, Ballard PL. The hydrocortisone-responsive urinary metabolome of premature infants. Pediatr Res. 2023 Oct; 94(4):1317-1326.
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. Effect of Ocrelizumab on B- and T-Cell Receptor Repertoire Diversity in Patients With Relapsing Multiple Sclerosis From the Randomized Phase III OPERA Trial. Neurol Neuroimmunol Neuroinflamm. 2023 07; 10(4).
Hernandez R, Sinha U, Malis V, Cunnane B, Smitaman E, Sinha S. Strain and Strain Rate Tensor Mapping of Medial Gastrocnemius at Submaximal Isometric Contraction and Three Ankle Angles. Tomography. 2023 04 11; 9(2):840-856.
Cunnane B, Sinha U, Malis V, Hernandez R, Smitaman E, Sinha S. MRI Based Fiber Strain Mapping of the Medial Gastrocnemius Muscle at Submaximal Isometric Contractions at Different Ankle Angles. Res Sq. 2023 Feb 09.
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. Correlations between complex human phenotypes vary by genetic background, gender, and environment. Cell Rep Med. 2022 12 20; 3(12):100844.
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. Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data. Nat Genet. 2022 Mar; 54(3):263-273.
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. Population sequencing data reveal a compendium of mutational processes in the human germ line. Science. 2021 Aug 27; 373(6558):1030-1035.
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. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature. 2021 Feb; 590(7845):290-299.
Spear ML, Diaz-Papkovich A, Ziv E, Yracheta JM, Gravel S, Torgerson DG, Hernandez RD. Recent shifts in the genomic ancestry of Mexican Americans may alter the genetic architecture of biomedical traits. Elife. 2020 12 29; 9.
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. A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles. Sci Transl Med. 2020 11 18; 12(570).
Torres R, Stetter MG, Hernandez RD, Ross-Ibarra J. The Temporal Dynamics of Background Selection in Nonequilibrium Populations. Genetics. 2020 04; 214(4):1019-1030.
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. De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population. Proc Natl Acad Sci U S A. 2020 02 04; 117(5):2560-2569.
Tong DMH, Hernandez RD. Population genetic simulation study of power in association testing across genetic architectures and study designs. Genet Epidemiol. 2020 01; 44(1):90-103.
Szpiech ZA, Mak ACY, White MJ, Hu D, Eng C, Burchard EG, Hernandez RD. Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity. Am J Hum Genet. 2019 10 03; 105(4):747-762.
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. Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nat Commun. 2019 Sep 04; 10(1):4082.
Hernandez RD, Uricchio LH, Hartman K, Ye C, Dahl A, Zaitlen N. Ultrarare variants drive substantial cis heritability of human gene expression. Nat Genet. 2019 09; 51(9):1349-1355.
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. Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nat Commun. 2019 02 20; 10(1):880.
Torres R, Szpiech ZA, Hernandez RD. Correction: Human demographic history has amplified the effects of background selection across the genome. PLoS Genet. 2019 01; 15(1):e1007898.
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. Ebola virus, but not Marburg virus, replicates efficiently and without required adaptation in snake cells. Virus Evol. 2018 Jul; 4(2):vey034.
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. A genome-wide association and admixture mapping study of bronchodilator drug response in African Americans with asthma. Pharmacogenomics J. 2019 06; 19(3):249-259.
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 admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos. J Allergy Clin Immunol. 2019 03; 143(3):957-969.
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. An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses. Mol Cell. 2018 08 16; 71(4):637-648.e5.
Torres R, Szpiech ZA, Hernandez RD. Human demographic history has amplified the effects of background selection across the genome. PLoS Genet. 2018 06; 14(6):e1007387.
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. Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. Am J Respir Crit Care Med. 2018 06 15; 197(12):1552-1564.
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. ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. Genome Biol. 2018 02 15; 19(1):36.
White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL. Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Sci Signal. 2017 Sep 05; 10(495).
Szpiech ZA, Strauli NB, White KA, Ruiz DG, Jacobson MP, Barber DL, Hernandez RD. Prominent features of the amino acid mutation landscape in cancer. PLoS One. 2017; 12(8):e0183273.
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. 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. 2017 04 15; 33(8):1147-1153.
Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD. Functional Segregation of Overlapping Genes in HIV. Cell. 2016 Dec 15; 167(7):1762-1773.e12.
Deyle ER, Maher MC, Hernandez RD, Basu S, Sugihara G. Global environmental drivers of influenza. Proc Natl Acad Sci U S A. 2016 11 15; 113(46):13081-13086.
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. Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens. Cell. 2016 Oct 20; 167(3):657-669.e21.
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. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nat Commun. 2016 10 11; 7:12522.
Strauli NB, Hernandez RD. Statistical inference of a convergent antibody repertoire response to influenza vaccine. Genome Med. 2016 06 03; 8(1):60.
Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez RD. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants. Genome Res. 2016 07; 26(7):863-73.
Z.A. Szpiech, R.D. Hernandez. Selective Sweeps. Encyclopedia of Evolutionary Biology. 2016 Jan 1; 23-32.
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. Pooled Sequencing of Candidate Genes Implicates Rare Variants in the Development of Asthma Following Severe RSV Bronchiolitis in Infancy. PLoS One. 2015; 10(11):e0142649.
Maher MC, Hernandez RD. CauseMap: fast inference of causality from complex time series. PeerJ. 2015; 3:e824.
Maher MC, Hernandez RD. Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. G3 (Bethesda). 2015 Feb 23; 5(4):629-38.
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. Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Mol Cell. 2015 Jan 22; 57(2):349-60.
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. Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos. J Allergy Clin Immunol. 2015 Jun; 135(6):1502-10.
Uricchio LH, Torres R, Witte JS, Hernandez RD. Population genetic simulations of complex phenotypes with implications for rare variant association tests. Genet Epidemiol. 2015 Jan; 39(1):35-44.
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 simulation tools for post-genome wide association studies of complex diseases. Genet Epidemiol. 2015 Jan; 39(1):11-19.
Szpiech ZA, Hernandez RD. selscan: an efficient multithreaded program to perform EHH-based scans for positive selection. Mol Biol Evol. 2014 Oct; 31(10):2824-7.
Uricchio LH, Hernandez RD. Robust forward simulations of recurrent hitchhiking. Genetics. 2014 May; 197(1):221-36.
Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ. High-resolution network biology: connecting sequence with function. Nat Rev Genet. 2013 Dec; 14(12):865-79.
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. A genome-wide association study of bronchodilator response in Latinos implicates rare variants. J Allergy Clin Immunol. 2014 Feb; 133(2):370-8.
Hodgkinson A, Casals F, Idaghdour Y, Grenier JC, Hernandez RD, Awadalla P. Selective constraint, background selection, and mutation accumulation variability within and between human populations. BMC Genomics. 2013 Jul 23; 14:495.
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. Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism. Sci Transl Med. 2013 Jul 10; 5(193):193ra91.
Maher MC, Uricchio LH, Torgerson DG, Hernandez RD. Population genetics of rare variants and complex diseases. Hum Hered. 2012; 74(3-4):118-28.
Dara G. Torgerson, Ryan D. Hernandez. Evolutionary signatures in non-coding DNA. Rapidly Evolving Genes and Genetic Systems. 2012 Jun 28; 115-124.
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. Case-control admixture mapping in Latino populations enriches for known asthma-associated genes. J Allergy Clin Immunol. 2012 Jul; 130(1):76-82.e12.
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. A fine-scale chimpanzee genetic map from population sequencing. Science. 2012 Apr 13; 336(6078):193-8.
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. Resequencing candidate genes implicates rare variants in asthma susceptibility. Am J Hum Genet. 2012 Feb 10; 90(2):273-81.
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. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21; 481(7381):365-70.
Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M. A population genetics-phylogenetics approach to inferring natural selection in coding sequences. PLoS Genet. 2011 Dec; 7(12):e1002395.
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. Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations. Nat Genet. 2011 Jul 31; 43(9):887-92.
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. 2011; 6(6):e20670.
Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, 1000 Genomes Project, Sella G, Przeworski M. Classic selective sweeps were rare in recent human evolution. Science. 2011 Feb 18; 331(6019):920-4.
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. 2010 Oct; 186(2):493-503.
Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 2009 Oct; 5(10):e1000695.
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 Genet. 2009 Aug; 5(8):e1000592.
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. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009 Apr 24; 324(5926):528-32.
Hernandez RD. A flexible forward simulator for populations subject to selection and demography. Bioinformatics. 2008 Dec 01; 24(23):2786-7.
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 Genet. 2008 May 30; 4(5):e1000083.
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. 2008 Feb 21; 451(7181):994-7.
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 Genet. 2007 Sep; 3(9):1745-56.
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. Mol Biol Evol. 2007 Oct; 24(10):2196-202.
Hernandez RD, Williamson SH, Bustamante CD. Context dependence, ancestral misidentification, and spurious signatures of natural selection. Mol Biol Evol. 2007 Aug; 24(8):1792-800.
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. 2007 Apr 13; 316(5822):240-3.
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. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13; 316(5822):222-34.
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. 2005 Oct 20; 437(7062):1153-7.
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. Proc Natl Acad Sci U S A. 2005 May 31; 102(22):7882-7.
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. Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice. PLoS Genetics. 2005 Jan 1; preprint(2007):e163.