Ryan Hernandez, PhD
Professor
Bioengineering
School of Pharmacy

In parallel with his active, federally funded research program, Dr. Hernandez designs and leads training initiatives that expand access to scientific careers and develop the next generation of scientific leaders. He co-directs the Biological and Medical Informatics (BMI) PhD program, the PROPEL post-baccalaureate research training program, and the UCSF PREP program, and co-leads the community building pillar of the ARCHES faculty development program. Across these roles, he builds and integrates training systems that broaden participation in science and support more inclusive scientific leadership.

• py_ped_sim - A flexible forward genetic simulator for complex family pedigree analysis.
  bioRxiv : the preprint server for biology 2024 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 2023 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 2023 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 2023 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, …
• The hydrocortisone-responsive urinary metabolome of premature infants.
  Pediatric research 2023 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 2023 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.) 2023 Hernandez R, Sinha U, Malis V, Cunnane B, Smitaman E, Sinha S
• MRI Based Fiber Strain Mapping of the Medial Gastrocnemius Muscle at Submaximal Isometric Contractions at Different Ankle Angles.
  Research square 2023 Cunnane B, Sinha U, Malis V, Hernandez R, Smitaman E, Sinha S
• Correlations between complex human phenotypes vary by genetic background, gender, and environment.
  Cell reports. Medicine 2022 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 …
• Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data.
  Nature genetics 2022 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 …
• Population sequencing data reveal a compendium of mutational processes in the human germ line.
  Science (New York, N.Y.) 2021 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…
• Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program.
  Nature 2021 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…
• Recent shifts in the genomic ancestry of Mexican Americans may alter the genetic architecture of biomedical traits.
  eLife 2020 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 2020 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 2020 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 2020 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, …
• Population genetic simulation study of power in association testing across genetic architectures and study designs.
  Genetic epidemiology 2019 Tong DMH, Hernandez RD
• Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity.
  American journal of human genetics 2019 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 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, Acevedo N, Araujo MI, Avila PC…
• Ultrarare variants drive substantial cis heritability of human gene expression.
  Nature genetics 2019 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 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, Acevedo N, Araujo MI, Avila PC…
• Correction: Human demographic history has amplified the effects of background selection across the genome.
  PLoS genetics 2019 Torres R, Szpiech ZA, Hernandez RD
• Ebola virus, but not Marburg virus, replicates efficiently and without required adaptation in snake cells.
  Virus evolution 2018 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 2018 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…
• An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos.
  The Journal of allergy and clinical immunology 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, McGarry M, Moreno-Estrada A, …
• An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses.
  Molecular cell 2018 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, …
• Human demographic history has amplified the effects of background selection across the genome.
  PLoS genetics 2018 Torres R, Szpiech ZA, Hernandez RD
• Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma.
  American journal of respiratory and critical care medicine 2018 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…
• ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues.
  Genome biology 2018 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,…
• Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins.
  Science signaling 2017 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 2017 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) 2017 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 2016 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 2016 Deyle ER, Maher MC, Hernandez RD, Basu S, Sugihara G
• Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens.
  Cell 2016 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 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, Levin AM, Song W, …
• Statistical inference of a convergent antibody repertoire response to influenza vaccine.
  Genome medicine 2016 Strauli NB, Hernandez RD
• Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants.
  Genome research 2016 Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez RD
• Selective Sweeps.
  Encyclopedia of Evolutionary Biology 2016 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 2015 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
• CauseMap: fast inference of causality from complex time series.
  PeerJ 2015 Maher MC, Hernandez RD
• Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference.
  G3 (Bethesda, Md.) 2015 Maher MC, Hernandez RD
• Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes.
  Molecular cell 2014 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 2014 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-…
• Population genetic simulations of complex phenotypes with implications for rare variant association tests.
  Genetic epidemiology 2014 Uricchio LH, Torres R, Witte JS, Hernandez RD
• Genetic simulation tools for post-genome wide association studies of complex diseases.
  Genetic epidemiology 2014 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…
• selscan: an efficient multithreaded program to perform EHH-based scans for positive selection.
  Molecular biology and evolution 2014 Szpiech ZA, Hernandez RD
• Robust forward simulations of recurrent hitchhiking.
  Genetics 2014 Uricchio LH, Hernandez RD
• High-resolution network biology: connecting sequence with function.
  Nature reviews. Genetics 2013 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 2013 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, …
• Selective constraint, background selection, and mutation accumulation variability within and between human populations.
  BMC genomics 2013 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 2013 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 2013 Maher MC, Uricchio LH, Torgerson DG, Hernandez RD
• Evolutionary signatures in non-coding DNA.
  Rapidly Evolving Genes and Genetic Systems 2012 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 2012 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.) 2012 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, …
• Resequencing candidate genes implicates rare variants in asthma susceptibility.
  American journal of human genetics 2012 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 2011 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…
• A population genetics-phylogenetics approach to inferring natural selection in coding sequences.
  PLoS genetics 2011 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 2011 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, …
• Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.
  PloS one 2011 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.) 2011 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 2010 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 2009 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 2009 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.) 2009 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, …
• A flexible forward simulator for populations subject to selection and demography.
  Bioinformatics (Oxford, England) 2008 Hernandez RD
• Assessing the evolutionary impact of amino acid mutations in the human genome.
  PLoS genetics 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
• Proportionally more deleterious genetic variation in European than in African populations.
  Nature 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
• Genome-wide patterns of nucleotide polymorphism in domesticated rice.
  PLoS genetics 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
• Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans.
  Molecular biology and evolution 2007 Hernandez RD, Williamson SH, Zhu L, Bustamante CD
• Context dependence, ancestral misidentification, and spurious signatures of natural selection.
  Molecular biology and evolution 2007 Hernandez RD, Williamson SH, Bustamante CD
• Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques.
  Science (New York, N.Y.) 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
• Evolutionary and biomedical insights from the rhesus macaque genome.
  Science (New York, N.Y.) 2007 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 …
• Natural selection on protein-coding genes in the human genome.
  Nature 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
• 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 2005 Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, Bustamante CD
• Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice.
  PLoS Genetics 2005 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