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    Ryan Hernandez, PhD

    TitleAssistant Professor
    SchoolUCSF School of Pharmacy
    Address1700 4th Street
    San Francisco CA 94158
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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 Interests
      Population and evolutionary genetics/genomics, computational biology and bioinformatics, population structure and admixture, statistical genetics/genomics, bioengineering, human evolution, 1,000 Genomes Project

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      Collapse NIH Awarded Grants
      Collapse Global Health
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      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.
      List All   |   Timeline
      1. Maher MC, Hernandez RD. CauseMap: fast inference of causality from complex time series. PeerJ. 2015; 3:e824.
        View in: PubMed
      2. Maher MC, Hernandez RD. Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. G3 (Bethesda). 2015; 5(4):629-38.
        View in: PubMed
      3. 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.
        View in: PubMed
      4. 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.
        View in: PubMed
      5. 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.
        View in: PubMed
      6. 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):11-9.
        View in: PubMed
      7. 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.
        View in: PubMed PMC4166924
      8. Uricchio LH, Hernandez RD. Robust forward simulations of recurrent hitchhiking. Genetics. 2014 May; 197(1):221-36.
        View in: PubMed PMC4012482
      9. 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.
        View in: PubMed PMC4023809
      10. 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.
        View in: PubMed PMC3938989
      11. 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; 14:495.
        View in: PubMed PMC3727949
      12. 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.
        View in: PubMed PMC4094294
      13. Maher MC, Uricchio LH, Torgerson DG, Hernandez RD. Population genetics of rare variants and complex diseases. Hum Hered. 2012; 74(3-4):118-28.
        View in: PubMed PMC3698246
      14. 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.
        View in: PubMed PMC3593143
      15. 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.
        View in: PubMed PMC3532813
      16. 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.
        View in: PubMed PMC3276672
      17. 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. 2012 Jan 19; 481(7381):365-70.
        View in: PubMed PMC3310911
      18. 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.
        View in: PubMed PMC3228810
      19. 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. Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations. Nat Genet. 2011 Sep; 43(9):887-92.
        View in: PubMed PMC3445408
      20. 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.
        View in: PubMed PMC3108957
      21. Sun C, Southard C, Huo D, Hernandez RD, Witonsky DB, Olopade OI, Di Rienzo A. SNP discovery, expression and cis-regulatory variation in the UGT2B genes. Pharmacogenomics J. 2012 Aug; 12(4):287-96.
        View in: PubMed
      22. Hernandez RD, 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.
        View in: PubMed PMC3669691
      23. 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.
        View in: PubMed PMC2954485
      24. 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.
        View in: PubMed PMC2760211
      25. 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.
        View in: PubMed PMC2714078
      26. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009 Apr 24; 324(5926):528-32.
        View in: PubMed PMC2735092
      27. Hernandez RD. A flexible forward simulator for populations subject to selection and demography. Bioinformatics. 2008 Dec 1; 24(23):2786-7.
        View in: PubMed PMC2639268
      28. 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; 4(5):e1000083.
        View in: PubMed PMC2377339
      29. 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.
        View in: PubMed PMC2923434
      30. 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.
        View in: PubMed PMC1994709
      31. 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.
        View in: PubMed
      32. 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.
        View in: PubMed
      33. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13; 316(5822):222-34.
        View in: PubMed
      34. 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.
        View in: PubMed
      35. 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.
        View in: PubMed
      36. 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.
        View in: PubMed PMC1142382
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