Ryan Hernandez, PhD

Ryan Hernandez, PhD

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Professor, School of Pharmacy
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Biography

My focus is on the development of population genetic models that can best explain observed data. Most recently, I have been evaluating models of background selection under parameters that are realistic for humans. My scientific approach tends to be highly computational, often involving a thorough analysis of detailed simulations.

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  1. 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.
  2. 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 03; 54(3):263-273.
  3. 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 08 27; 373(6558):1030-1035.
  4. 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 02; 590(7845):290-299.
  5. 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.
  6. 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).
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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).
  23. 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.
  24. 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.
  25. 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.