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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Displaying 26 - 50 of 69

  1. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/27799563
  2. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/27768889
  3. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/27725671
  4. Strauli NB, Hernandez RD. Statistical inference of a convergent antibody repertoire response to influenza vaccine. Genome Med. 2016 06 03; 8(1):60.
    http://www.ncbi.nlm.nih.gov/pubmed/27255379
  5. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/27197206
  6. Z.A. Szpiech, R.D. Hernandez. Selective Sweeps. Encyclopedia of Evolutionary Biology. 2016 Jan 1; 23-32.
  7. Z.A. Szpiech, R.D. Hernandez. Selective Sweeps. Encyclopedia of Evolutionary Biology. 2016 Jan 1; 23-32.
    http://www.ncbi.nlm.nih.gov/pubmed/26587832
  8. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/25780776
  9. Maher MC, Hernandez RD. CauseMap: fast inference of causality from complex time series. PeerJ. 2015; 3:e824.
    http://www.ncbi.nlm.nih.gov/pubmed/25711833
  10. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/25544563
  11. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/25488688
  12. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/25417809
  13. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/25371374
  14. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/25015648
  15. Hanna RF, Ward TJ, Chow DS, Lagana SM, Moreira RK, Emond JC, Weintraub JL, Prince MR. An evaluation of the sensitivity of MRI at detecting hepatocellular carcinoma in cirrhotic patients utilizing an explant reference standard. Clin Imaging. 2014 Sep-Oct; 38(5):693-7.
    http://www.ncbi.nlm.nih.gov/pubmed/24561480
  16. Uricchio LH, Hernandez RD. Robust forward simulations of recurrent hitchhiking. Genetics. 2014 May; 197(1):221-36.
    http://www.ncbi.nlm.nih.gov/pubmed/24197012
  17. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/23992748
  18. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/23875710
  19. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/23843452
  20. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/23594490
  21. Dara G. Torgerson, Ryan D. Hernandez. Evolutionary signatures in non-coding DNA. Rapidly Evolving Genes and Genetic Systems. 2012 Jun 28; 115-124.
  22. Maher MC, Uricchio LH, Torgerson DG, Hernandez RD. Population genetics of rare variants and complex diseases. Hum Hered. 2012; 74(3-4):118-28.
    http://www.ncbi.nlm.nih.gov/pubmed/22502797
  23. Dara G. Torgerson, Ryan D. Hernandez. Evolutionary signatures in non-coding DNA. Rapidly Evolving Genes and Genetic Systems. 2012 Jun 28; 115-124.
    http://www.ncbi.nlm.nih.gov/pubmed/22422862
  24. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/22325360
  25. 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.
    http://www.ncbi.nlm.nih.gov/pubmed/22190034