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Ryan Hernandez, PhD

Title(s)Associate Professor, Bioengineering
SchoolSchool of Pharmacy
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, 2023
    Role: Principal Investigator
    Maximizing Opportunities for Research Excellence
    NIH/NIGMS R25GM056847Jan 1, 1998 - Jan 31, 2019
    Role: Co-Principal Investigator

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    Collapse Academic Senate

    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. The Temporal Dynamics of Background Selection in Nonequilibrium Populations. Genetics. 2020 Apr; 214(4):1019-1030. Torres R, Stetter MG, Hernandez RD, Ross-Ibarra J. PMID: 32071195.
      View in: PubMed   Mentions: 1     Fields:    
    2. 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. 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, O'Connor TD. PMID: 31964835.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    3. Population genetic simulation study of power in association testing across genetic architectures and study designs. Genet Epidemiol. 2020 01; 44(1):90-103. Tong DMH, Hernandez RD. PMID: 31587362.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    4. Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity. Am J Hum Genet. 2019 10 03; 105(4):747-762. Szpiech ZA, Mak ACY, White MJ, Hu D, Eng C, Burchard EG, Hernandez RD. PMID: 31543216.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    5. 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. 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. PMID: 31484942.
      View in: PubMed   Mentions:    Fields:    
    6. Ultrarare variants drive substantial cis heritability of human gene expression. Nat Genet. 2019 09; 51(9):1349-1355. Hernandez RD, Uricchio LH, Hartman K, Ye C, Dahl A, Zaitlen N. PMID: 31477931.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    7. 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. 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. PMID: 30787307.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    8. Correction: Human demographic history has amplified the effects of background selection across the genome. PLoS Genet. 2019 01; 15(1):e1007898. Torres R, Szpiech ZA, Hernandez RD. PMID: 30601801.
      View in: PubMed   Mentions:    Fields:    
    9. Ebola virus, but not Marburg virus, replicates efficiently and without required adaptation in snake cells. Virus Evol. 2018 Jul; 4(2):vey034. 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. PMID: 30524754.
      View in: PubMed   Mentions:
    10. 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. 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. PMID: 30206298.
      View in: PubMed   Mentions: 10     Fields:    
    11. 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. 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. PMID: 30201514.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    12. 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. 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. PMID: 30118682.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    13. Human demographic history has amplified the effects of background selection across the genome. PLoS Genet. 2018 06; 14(6):e1007387. Torres R, Szpiech ZA, Hernandez RD. PMID: 29912945.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    14. Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. Am J Respir Crit Care Med. 2018 06 15; 197(12):1552-1564. 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 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 RD, Burchard EG. PMID: 29509491.
      View in: PubMed   Mentions: 22     Fields:    Translation:Humans
    15. 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. 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. PMID: 29548336.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    16. Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Sci Signal. 2017 Sep 05; 10(495). White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL. PMID: 28874603.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    17. Prominent features of the amino acid mutation landscape in cancer. PLoS One. 2017; 12(8):e0183273. Szpiech ZA, Strauli NB, White KA, Ruiz DG, Jacobson MP, Barber DL, Hernandez RD. PMID: 28837668.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    18. 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. Shringarpure SS, Mathias RA, Hernandez RD, O'Connor TD, Szpiech ZA, Torres R, De La Vega FM, Bustamante CD, Barnes KC, Taub MA. PMID: 28035032.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    19. Functional Segregation of Overlapping Genes in HIV. Cell. 2016 Dec 15; 167(7):1762-1773.e12. Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD. PMID: 27984726.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    20. Global environmental drivers of influenza. Proc Natl Acad Sci U S A. 2016 11 15; 113(46):13081-13086. Deyle ER, Maher MC, Hernandez RD, Basu S, Sugihara G. PMID: 27799563.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansPHPublic Health
    21. Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens. Cell. 2016 Oct 20; 167(3):657-669.e21. 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. PMID: 27768889.
      View in: PubMed   Mentions: 76     Fields:    
    22. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nat Commun. 2016 10 11; 7:12522. 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, Barnes KC. PMID: 27725671.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    23. Statistical inference of a convergent antibody repertoire response to influenza vaccine. Genome Med. 2016 06 03; 8(1):60. Strauli NB, Hernandez RD. PMID: 27255379.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    24. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants. Genome Res. 2016 07; 26(7):863-73. Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez RD. PMID: 27197206.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    25. Selective Sweeps. Encyclopedia of Evolutionary Biology. 2016 Jan 1; 23-32. Z.A. Szpiech, R.D. Hernandez. .
      View in: Publisher Site   Mentions:
    26. 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. 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. PMID: 26587832.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    27. CauseMap: fast inference of causality from complex time series. PeerJ. 2015; 3:e824. Maher MC, Hernandez RD. PMID: 25780776.
      View in: PubMed   Mentions:
    28. Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. G3 (Bethesda). 2015 Feb 23; 5(4):629-38. Maher MC, Hernandez RD. PMID: 25711833.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimals
    29. Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Mol Cell. 2015 Jan 22; 57(2):349-60. 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. PMID: 25544563.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansCells
    30. 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. 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. PMID: 25488688.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    31. Population genetic simulations of complex phenotypes with implications for rare variant association tests. Genet Epidemiol. 2015 Jan; 39(1):35-44. Uricchio LH, Torres R, Witte JS, Hernandez RD. PMID: 25417809.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    32. Genetic simulation tools for post-genome wide association studies of complex diseases. Genet Epidemiol. 2015 Jan; 39(1):11-19. 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. PMID: 25371374.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    33. selscan: an efficient multithreaded program to perform EHH-based scans for positive selection. Mol Biol Evol. 2014 Oct; 31(10):2824-7. Szpiech ZA, Hernandez RD. PMID: 25015648.
      View in: PubMed   Mentions: 102     Fields:    Translation:HumansCells
    34. Robust forward simulations of recurrent hitchhiking. Genetics. 2014 May; 197(1):221-36. Uricchio LH, Hernandez RD. PMID: 24561480.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    35. High-resolution network biology: connecting sequence with function. Nat Rev Genet. 2013 Dec; 14(12):865-79. Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ. PMID: 24197012.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimalsCells
    36. A genome-wide association study of bronchodilator response in Latinos implicates rare variants. J Allergy Clin Immunol. 2014 Feb; 133(2):370-8. 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. PMID: 23992748.
      View in: PubMed   Mentions: 33     Fields:    Translation:Humans
    37. Selective constraint, background selection, and mutation accumulation variability within and between human populations. BMC Genomics. 2013 Jul 23; 14:495. Hodgkinson A, Casals F, Idaghdour Y, Grenier JC, Hernandez RD, Awadalla P. PMID: 23875710.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    38. Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism. Sci Transl Med. 2013 Jul 10; 5(193):193ra91. 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. PMID: 23843452.
      View in: PubMed   Mentions: 211     Fields:    Translation:HumansAnimalsCells
    39. Population genetics of rare variants and complex diseases. Hum Hered. 2012; 74(3-4):118-28. Maher MC, Uricchio LH, Torgerson DG, Hernandez RD. PMID: 23594490.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    40. Evolutionary signatures in non-coding DNA. Rapidly Evolving Genes and Genetic Systems. 2012 Jun 28; 115-124. Dara G. Torgerson, Ryan D. Hernandez. .
      View in: Publisher Site   Mentions:
    41. Case-control admixture mapping in Latino populations enriches for known asthma-associated genes. J Allergy Clin Immunol. 2012 Jul; 130(1):76-82.e12. 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. PMID: 22502797.
      View in: PubMed   Mentions: 30     Fields:    Translation:Humans
    42. A fine-scale chimpanzee genetic map from population sequencing. Science. 2012 Apr 13; 336(6078):193-8. 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. PMID: 22422862.
      View in: PubMed   Mentions: 137     Fields:    Translation:HumansAnimalsCells
    43. Resequencing candidate genes implicates rare variants in asthma susceptibility. Am J Hum Genet. 2012 Feb 10; 90(2):273-81. 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. PMID: 22325360.
      View in: PubMed   Mentions: 29     Fields:    Translation:Humans
    44. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21; 481(7381):365-70. 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. PMID: 22190034.
      View in: PubMed   Mentions: 260     Fields:    Translation:HumansCells
    45. A population genetics-phylogenetics approach to inferring natural selection in coding sequences. PLoS Genet. 2011 Dec; 7(12):e1002395. Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M. PMID: 22144911.
      View in: PubMed   Mentions: 46     Fields:    Translation:Animals
    46. Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations. Nat Genet. 2011 Jul 31; 43(9):887-92. 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, Gilliland FD, Burchard EG, Martinez FD, Weiss ST, Williams LK, Barnes KC, Ober C, Nicolae DL. PMID: 21804549.
      View in: PubMed   Mentions: 286     Fields:    Translation:Humans
    47. Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection. PLoS One. 2011; 6(6):e20670. Xie X, Molina J, Hernandez R, Reynolds A, Boyko AR, Bustamante CD, Purugganan MD. PMID: 21674010.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    48. Classic selective sweeps were rare in recent human evolution. Science. 2011 Feb 18; 331(6019):920-4. Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, Sella G, Przeworski M. PMID: 21330547.
      View in: PubMed   Mentions: 180     Fields:    Translation:HumansCells
    49. Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach. Genetics. 2010 Oct; 186(2):493-503. Zanders S, Ma X, Roychoudhury A, Hernandez RD, Demogines A, Barker B, Gu Z, Bustamante CD, Alani E. PMID: 20660644.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    50. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 2009 Oct; 5(10):e1000695. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. PMID: 19851460.
      View in: PubMed   Mentions: 437     Fields:    Translation:Humans
    51. Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet. 2009 Aug; 5(8):e1000592. Torgerson DG, Boyko AR, Hernandez RD, Indap A, Hu X, White TJ, Sninsky JJ, Cargill M, Adams MD, Bustamante CD, Clark AG. PMID: 19662163.
      View in: PubMed   Mentions: 62     Fields:    Translation:HumansAnimalsCells
    52. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009 Apr 24; 324(5926):528-32. 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, Weinstock GM, Wheeler DA, Ajmone-Marsan P, Boettcher PJ, Caetano AR, Garcia JF, Hanotte O, Mariani P, Skow LC, Sonstegard TS, Williams JL, Diallo B, Hailemariam L, Martinez ML, Morris CA, Silva LO, Spelman RJ, Mulatu W, Zhao K, Abbey CA, Agaba M, Araujo FR, Bunch RJ, Burton J, Gorni C, Olivier H, Harrison BE, Luff B, Machado MA, Mwakaya J, Plastow G, Sim W, Smith T, Thomas MB, Valentini A, Williams P, Womack J, Woolliams JA, Liu Y, Qin X, Worley KC, Gao C, Jiang H, Moore SS, Ren Y, Song XZ, Bustamante CD, Hernandez RD, Muzny DM, Patil S, San Lucas A, Fu Q, Kent MP, Vega R, Matukumalli A, McWilliam S, Sclep G, Bryc K, Choi J, Gao H, Grefenstette JJ, Murdoch B, Stella A, Villa-Angulo R, Wright M, Aerts J, Jann O, Negrini R, Goddard ME, Hayes BJ, Bradley DG, Barbosa da Silva M, Lau LP, Liu GE, Lynn DJ, Panzitta F, Dodds KG. PMID: 19390050.
      View in: PubMed   Mentions: 292     Fields:    Translation:Animals
    53. A flexible forward simulator for populations subject to selection and demography. Bioinformatics. 2008 Dec 01; 24(23):2786-7. Hernandez RD. PMID: 18842601.
      View in: PubMed   Mentions: 106     Fields:    Translation:Humans
    54. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet. 2008 May 30; 4(5):e1000083. 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. PMID: 18516229.
      View in: PubMed   Mentions: 288     Fields:    Translation:HumansAnimals
    55. Proportionally more deleterious genetic variation in European than in African populations. Nature. 2008 Feb 21; 451(7181):994-7. Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD. PMID: 18288194.
      View in: PubMed   Mentions: 175     Fields:    Translation:Humans
    56. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet. 2007 Sep; 3(9):1745-56. 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. PMID: 17907810.
      View in: PubMed   Mentions: 158     Fields:    Translation:AnimalsCells
    57. 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. Hernandez RD, Williamson SH, Zhu L, Bustamante CD. PMID: 17656634.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimals
    58. Context dependence, ancestral misidentification, and spurious signatures of natural selection. Mol Biol Evol. 2007 Aug; 24(8):1792-800. Hernandez RD, Williamson SH, Bustamante CD. PMID: 17545186.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansAnimals
    59. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13; 316(5822):222-34. Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS. PMID: 17431167.
      View in: PubMed   Mentions: 579     Fields:    Translation:HumansAnimals
    60. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science. 2007 Apr 13; 316(5822):240-3. 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. PMID: 17431170.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansAnimals
    61. Natural selection on protein-coding genes in the human genome. Nature. 2005 Oct 20; 437(7062):1153-7. 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. PMID: 16237444.
      View in: PubMed   Mentions: 358     Fields:    Translation:HumansAnimalsCells
    62. 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. Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, Bustamante CD. PMID: 15905331.
      View in: PubMed   Mentions: 146     Fields:    Translation:Humans
    63. Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice. PLoS Genetics. 2005 Jan 1; preprint(2007):e163. 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. .
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