Ryan D. Hernandez - Publications

Affiliations: 
Epidemiology and Translational Science University of California, San Francisco, San Francisco, CA 
Area:
Genetics, Statistics, Computer Science

51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 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. 9. PMID 33372659 DOI: 10.7554/eLife.56029  0.6
2019 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, ... ... Hernandez RD, et al. Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nature Communications. 10: 4082. PMID 31484942 DOI: 10.1038/S41467-019-12158-W  0.6
2019 Hernandez RD, Uricchio LH, Hartman K, Ye C, Dahl A, Zaitlen N. Ultrarare variants drive substantial cis heritability of human gene expression. Nature Genetics. 51: 1349-1355. PMID 31477931 DOI: 10.1038/S41588-019-0487-7  0.76
2019 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, ... ... Hernandez RD, et al. Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nature Communications. 10: 880. PMID 30787307 DOI: 10.1038/S41467-019-08469-7  0.6
2018 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, ... ... Hernandez RD, et al. A genome-wide association and admixture mapping study of bronchodilator drug response in African Americans with asthma. The Pharmacogenomics Journal. PMID 30206298 DOI: 10.1038/S41397-018-0042-4  0.6
2018 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, ... ... Hernandez RD, et al. An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos. The Journal of Allergy and Clinical Immunology. PMID 30201514 DOI: 10.1016/J.Jaci.2016.08.057  0.76
2018 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, ... ... Hernandez RD, et al. Whole Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. American Journal of Respiratory and Critical Care Medicine. PMID 29509491 DOI: 10.1164/Rccm.201712-2529Oc  0.56
2016 Shringarpure SS, Mathias RA, Hernandez RD, 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 (Oxford, England). PMID 28171482 DOI: 10.1093/bioinformatics/btw786  0.48
2016 Shringarpure SS, Mathias RA, Hernandez RD, 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 (Oxford, England). PMID 28035032 DOI: 10.1093/Bioinformatics/Btw786  0.48
2016 Deyle ER, Maher MC, Hernandez RD, Basu S, Sugihara G. Global environmental drivers of influenza. Proceedings of the National Academy of Sciences of the United States of America. PMID 27799563 DOI: 10.1073/Pnas.1607747113  0.6
2016 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, ... ... Hernandez RD, et al. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nature Communications. 7: 12522. PMID 27725671 DOI: 10.1038/Ncomms12522  0.76
2016 Strauli NB, Hernandez RD. Statistical inference of a convergent antibody repertoire response to influenza vaccine. Genome Medicine. 8: 60. PMID 27255379 DOI: 10.1186/S13073-016-0314-Z  0.76
2016 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 Research. PMID 27197206 DOI: 10.1101/Gr.202440.115  0.76
2015 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. 10: e0142649. PMID 26587832 DOI: 10.1371/Journal.Pone.0142649  0.76
2015 Maher MC, Hernandez RD. CauseMap: fast inference of causality from complex time series. Peerj. 3: e824. PMID 25780776 DOI: 10.7717/Peerj.824  0.76
2015 Maher MC, Hernandez RD. Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. G3 (Bethesda, Md.). 5: 629-38. PMID 25711833 DOI: 10.1534/G3.115.017095  0.76
2015 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, et al. Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Molecular Cell. 57: 349-60. PMID 25544563 DOI: 10.1016/J.Molcel.2014.11.026  0.76
2015 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, ... ... Hernandez RD, et al. Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos. The Journal of Allergy and Clinical Immunology. 135: 1502-10. PMID 25488688 DOI: 10.1016/J.Jaci.2014.10.033  0.76
2015 Uricchio LH, Torres R, Witte JS, Hernandez RD. Population genetic simulations of complex phenotypes with implications for rare variant association tests. Genetic Epidemiology. 39: 35-44. PMID 25417809 DOI: 10.1002/Gepi.21866  0.76
2015 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, et al. Genetic simulation tools for post-genome wide association studies of complex diseases. Genetic Epidemiology. 39: 11-9. PMID 25371374 DOI: 10.1002/Gepi.21870  0.76
2014 Szpiech ZA, Hernandez RD. selscan: an efficient multithreaded program to perform EHH-based scans for positive selection. Molecular Biology and Evolution. 31: 2824-7. PMID 25015648 DOI: 10.1093/Molbev/Msu211  0.76
2014 Uricchio LH, Hernandez RD. Robust forward simulations of recurrent hitchhiking. Genetics. 197: 221-36. PMID 24561480 DOI: 10.1534/Genetics.113.156935  0.76
2014 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, ... ... Hernandez RD, et al. A genome-wide association study of bronchodilator response in Latinos implicates rare variants. The Journal of Allergy and Clinical Immunology. 133: 370-8. PMID 23992748 DOI: 10.1016/J.Jaci.2013.06.043  0.76
2013 Ryan CJ, Cimerman?i? P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ. High-resolution network biology: connecting sequence with function. Nature Reviews. Genetics. 14: 865-79. PMID 24197012 DOI: 10.1038/Nrg3574  0.76
2013 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. 14: 495. PMID 23875710 DOI: 10.1186/1471-2164-14-495  0.76
2013 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. Science Translational Medicine. 5: 193ra91. PMID 23843452 DOI: 10.1126/Scitranslmed.3006438  0.76
2012 Maher MC, Uricchio LH, Torgerson DG, Hernandez RD. Population genetics of rare variants and complex diseases. Human Heredity. 74: 118-28. PMID 23594490 DOI: 10.1159/000346826  0.76
2012 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. The Journal of Allergy and Clinical Immunology. 130: 76-82.e12. PMID 22502797 DOI: 10.1016/J.Jaci.2012.02.040  0.76
2012 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, et al. A fine-scale chimpanzee genetic map from population sequencing. Science (New York, N.Y.). 336: 193-8. PMID 22422862 DOI: 10.1126/Science.1216872  0.76
2012 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. American Journal of Human Genetics. 90: 273-81. PMID 22325360 DOI: 10.1016/J.Ajhg.2012.01.008  0.76
2012 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, ... ... Hernandez RD, et al. Global landscape of HIV-human protein complexes. Nature. 481: 365-70. PMID 22190034 DOI: 10.1038/Nature10719  0.76
2012 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. The Pharmacogenomics Journal. 12: 287-96. PMID 21358749 DOI: 10.1038/Tpj.2011.2  0.76
2012 Perdry H, Müller-Myhsok B, Clerget-Darpoux F, Génin E, Sahbatou M, Kim W, Londono D, Kazma R, Cardin NJ, Witte JS, Asimit JL, Zeggini E, Jouan L, Gauthier J, Dion PA, ... ... Hernandez RD, et al. Contents Vol. 74, 2012 Human Heredity. 74. DOI: 10.1159/000346894  0.76
2011 Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M. A population genetics-phylogenetics approach to inferring natural selection in coding sequences. Plos Genetics. 7: e1002395. PMID 22144911 DOI: 10.1371/Journal.Pgen.1002395  0.76
2011 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, ... ... Hernandez RD, et al. Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations. Nature Genetics. 43: 887-92. PMID 21804549 DOI: 10.1038/Ng.888  0.76
2011 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. 6: e20670. PMID 21674010 DOI: 10.1371/Journal.Pone.0020670  0.76
2011 Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, Sella G, Przeworski M. Classic selective sweeps were rare in recent human evolution. Science (New York, N.Y.). 331: 920-4. PMID 21330547 DOI: 10.1126/Science.1198878  0.76
2010 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. 186: 493-503. PMID 20660644 DOI: 10.1534/Genetics.110.120105  0.76
2010 Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Diffusion Approximations for Demographic Inference: DaDi Nature Precedings. 1-1. DOI: 10.1038/Npre.2010.4594.1  0.48
2009 Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. Plos Genetics. 5: e1000695. PMID 19851460 DOI: 10.1371/Journal.Pgen.1000695  0.76
2009 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 Genetics. 5: e1000592. PMID 19662163 DOI: 10.1371/Journal.Pgen.1000592  0.76
2009 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, ... ... Hernandez RD, et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science (New York, N.Y.). 324: 528-32. PMID 19390050 DOI: 10.1126/Science.1167936  0.76
2008 Hernandez RD. A flexible forward simulator for populations subject to selection and demography. Bioinformatics (Oxford, England). 24: 2786-7. PMID 18842601 DOI: 10.1093/Bioinformatics/Btn522  0.76
2008 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 Genetics. 4: e1000083. PMID 18516229 DOI: 10.1371/Journal.Pgen.1000083  0.76
2008 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. 451: 994-7. PMID 18288194 DOI: 10.1038/Nature06611  0.76
2007 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 Genetics. 3: 1745-56. PMID 17907810 DOI: 10.1371/Journal.Pgen.0030163  0.76
2007 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. Molecular Biology and Evolution. 24: 2196-202. PMID 17656634 DOI: 10.1093/Molbev/Msm149  0.76
2007 Hernandez RD, Williamson SH, Bustamante CD. Context dependence, ancestral misidentification, and spurious signatures of natural selection. Molecular Biology and Evolution. 24: 1792-800. PMID 17545186 DOI: 10.1093/Molbev/Msm108  0.76
2007 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 (New York, N.Y.). 316: 240-3. PMID 17431170 DOI: 10.1126/Science.1140462  0.76
2005 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. 437: 1153-7. PMID 16237444 DOI: 10.1038/Nature04240  0.76
2005 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. Proceedings of the National Academy of Sciences of the United States of America. 102: 7882-7. PMID 15905331 DOI: 10.1073/Pnas.0502300102  0.76
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