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Ryan Hernandez, PhD

TitleAssociate Professor
InstitutionUniversity of California San Francisco
DepartmentBioengineering
Address1700 4th Street
San Francisco CA 94158
Phone415-514-9813
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    Collapse Biography 
    Collapse Awards and Honors
    Cornell University2007Outstanding Teaching Assistant
    Alfred P. Sloan Foundation2013  - 2016Sloan Research Fellow
    Gladstone Center For AIDS Research2014  - 2015Basic Science Award in HIV/AIDS

    Collapse Overview 
    Collapse Overview
    Dr. Ryan Hernandez’ research focuses on computational genomics and complements the department’s emerging strengths in quantitative sciences and genomics: First, he seeks to characterize the patterns of genetic variation within and between populations using large-scale genome resequencing data. A second branch of research in his lab focuses on developing novel population genetic simulation techniques. Such simulations are used to lend insight into the plausible evolutionary forces that have shaped patterns of genetic variation, including the implications of complex interactions among selected alleles in non-stationary demographic environments. His third branch of research seeks to exploit population genetic models of demographic history and natural selection to interrogate the genetic basis of disease. By capitalizing on recent theoretical advances, Dr. Hernandez is constructing models of population dynamics that will utilize genomic re-sequencing data to discover novel regions of the genome that underlie genetic susceptibility to disease and drug response.


    Collapse Research 
    Collapse Research Activities and Funding
    Powerful Simulation Tools for the Genomics Age
    NIH/NHGRI R01HG007644Jun 19, 2014 - Apr 30, 2019
    Role: Principal Investigator
    Accurate, long-read sequencing with droplet-microfluidic barcoding
    NIH/NHGRI R21HG007233Aug 1, 2013 - Jun 30, 2015
    Role: Co-Principal Investigator
    Retention of somatic mutations in cancers by changes in pH sensing
    NIH/NCI R21CA178706Jul 1, 2013 - Jun 30, 2015
    Role: Co-Principal Investigator
    BMI Bioinformatics Training Grant
    NIH/NIGMS T32GM067547Jul 1, 2003 - Jun 30, 2018
    Role: Principal Investigator
    Maximizing Opportunities for Research Excellence
    NIH/NIGMS R25GM056847Jan 1, 1998 - Jan 31, 2019
    Role: Co-Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse Featured Videos

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Mak AC, 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 R, Burchard EG. Whole Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. Am J Respir Crit Care Med. 2018 Mar 06. PMID: 29509491.
      View in: PubMed
    2. 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 R, 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 Feb 15; 19(1):36. PMID: 29548336.
      View in: PubMed
    3. White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez R, 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). PMID: 28874603.
      View in: PubMed
    4. Szpiech ZA, Strauli NB, White KA, Ruiz DG, Jacobson MP, Barber DL, Hernandez R. Prominent features of the amino acid mutation landscape in cancer. PLoS One. 2017; 12(8):e0183273. PMID: 28837668.
      View in: PubMed
    5. Shringarpure SS, Mathias RA, Hernandez R, O'Connor TD, Szpiech ZA, Torres R, De La Vega FM, Bustamante CD, Barnes KC, Taub MA. 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 Apr 15; 33(8):1147-1153. PMID: 28035032.
      View in: PubMed
    6. Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez R, Frankel AD. Functional Segregation of Overlapping Genes in HIV. Cell. 2016 Dec 15; 167(7):1762-1773.e12. PMID: 27984726.
      View in: PubMed
    7. Deyle ER, Maher MC, Hernandez R, Basu S, Sugihara G. Global environmental drivers of influenza. Proc Natl Acad Sci U S A. 2016 11 15; 113(46):13081-13086. PMID: 27799563.
      View in: PubMed
    8. 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 R, 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. PMID: 27768889.
      View in: PubMed
    9. 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 R, Beaty TH, Ruczinski I, Akey J. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nat Commun. 2016 Oct 11; 7:12522. PMID: 27725671.
      View in: PubMed
    10. Strauli NB, Hernandez R. Statistical inference of a convergent antibody repertoire response to influenza vaccine. Genome Med. 2016 06 03; 8(1):60. PMID: 27255379; PMCID: PMC4891843.
    11. Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez R. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants. Genome Res. 2016 07; 26(7):863-73. PMID: 27197206; PMCID: PMC4937562.
    12. Torgerson DG, Giri T, Druley TE, Zheng J, Huntsman S, Seibold MA, Young AL, Schweiger T, Yin-Declue H, Sajol GD, Schechtman KB, Hernandez R, 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. PMID: 26587832; PMCID: PMC4654486.
    13. Maher MC, Hernandez R. CauseMap: fast inference of causality from complex time series. PeerJ. 2015; 3:e824. PMID: 25780776; PMCID: PMC4359046.
    14. Maher MC, Hernandez R. Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. G3 (Bethesda). 2015 Feb 23; 5(4):629-38. PMID: 25711833; PMCID: PMC4390578.
    15. 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 R, 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. PMID: 25544563; PMCID: PMC4305015.
    16. 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 R, 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. PMID: 25488688.
      View in: PubMed
    17. Uricchio LH, Torres R, Witte JS, Hernandez R. Population genetic simulations of complex phenotypes with implications for rare variant association tests. Genet Epidemiol. 2015 Jan; 39(1):35-44. PMID: 25417809; PMCID: PMC4270825.
    18. Chen HS, Hutter CM, Mechanic LE, Amos CI, Bafna V, Hauser ER, Hernandez R, 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. PMID: 25371374.
      View in: PubMed
    19. Szpiech ZA, Hernandez R. selscan: an efficient multithreaded program to perform EHH-based scans for positive selection. Mol Biol Evol. 2014 Oct; 31(10):2824-7. PMID: 25015648; PMCID: PMC4166924.
    20. Uricchio LH, Hernandez R. Robust forward simulations of recurrent hitchhiking. Genetics. 2014 May; 197(1):221-36. PMID: 24561480; PMCID: PMC4012482.
    21. Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez R, Krogan NJ. High-resolution network biology: connecting sequence with function. Nat Rev Genet. 2013 Dec; 14(12):865-79. PMID: 24197012; PMCID: PMC4023809.
    22. 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 R, 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. PMID: 23992748.
      View in: PubMed
    23. Hodgkinson A, Casals F, Idaghdour Y, Grenier JC, Hernandez R, Awadalla P. Selective constraint, background selection, and mutation accumulation variability within and between human populations. BMC Genomics. 2013 Jul 23; 14:495. PMID: 23875710; PMCID: PMC3727949.
    24. Vujkovic-Cvijin I, Dunham RM, Iwai S, Maher MC, Albright RG, Broadhurst MJ, Hernandez R, 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. PMID: 23843452; PMCID: PMC4094294.
    25. Maher MC, Uricchio LH, Torgerson DG, Hernandez R. Population genetics of rare variants and complex diseases. Hum Hered. 2012; 74(3-4):118-28. PMID: 23594490; PMCID: PMC3698246.
    26. 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 R, 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. PMID: 22502797; PMCID: PMC3593143.
    27. 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 R, 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. PMID: 22422862.
      View in: PubMed
    28. Torgerson DG, Capurso D, Mathias RA, Graves PE, Hernandez R, 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. PMID: 22325360; PMCID: PMC3276672.
    29. 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 R, 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. PMID: 22190034; PMCID: PMC3310911.
    30. Wilson DJ, Hernandez R, Andolfatto P, Przeworski M. A population genetics-phylogenetics approach to inferring natural selection in coding sequences. PLoS Genet. 2011 Dec; 7(12):e1002395. PMID: 22144911; PMCID: PMC3228810.
    31. 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 R, 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. Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations. Nat Genet. 2011 Jul 31; 43(9):887-92. PMID: 21804549.
      View in: PubMed
    32. 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. PMID: 21674010; PMCID: PMC3108957.
    33. Hernandez R, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G. Classic selective sweeps were rare in recent human evolution. Science. 2011 Feb 18; 331(6019):920-4. PMID: 21330547.
      View in: PubMed
    34. Zanders S, Ma X, Roychoudhury A, Hernandez R, 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. PMID: 20660644; PMCID: PMC2954485.
    35. Gutenkunst RN, Hernandez R, Williamson SH, Bustamante CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 2009 Oct; 5(10):e1000695. PMID: 19851460; PMCID: PMC2760211.
    36. Torgerson DG, Boyko AR, Hernandez R, 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. PMID: 19662163; PMCID: PMC2714078.
    37. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009 Apr 24; 324(5926):528-32. PMID: 19390050; PMCID: PMC2735092.
    38. Hernandez R. A flexible forward simulator for populations subject to selection and demography. Bioinformatics. 2008 Dec 01; 24(23):2786-7. PMID: 18842601; PMCID: PMC2639268.
    39. Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez R, 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. PMID: 18516229; PMCID: PMC2377339.
    40. Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez R, 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. PMID: 18288194; PMCID: PMC2923434.
    41. Caicedo AL, Williamson SH, Hernandez R, 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. PMID: 17907810; PMCID: PMC1994709.
    42. Hernandez R, 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. PMID: 17656634.
      View in: PubMed
    43. Hernandez R, Williamson SH, Bustamante CD. Context dependence, ancestral misidentification, and spurious signatures of natural selection. Mol Biol Evol. 2007 Aug; 24(8):1792-800. PMID: 17545186.
      View in: PubMed
    44. Hernandez R, 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. PMID: 17431170.
      View in: PubMed
    45. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13; 316(5822):222-34. PMID: 17431167.
      View in: PubMed
    46. Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum DM, White TJ, Sninsky JJ, Hernandez R, 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. PMID: 16237444.
      View in: PubMed
    47. 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. PMID: 15905331; PMCID: PMC1142382.