| Year |
Citation |
Score |
| 2022 |
Wainschtein P, Jain D, Zheng Z, Cupples LA, Shadyab AH, McKnight B, Shoemaker BM, Mitchell BD, Psaty BM, Kooperberg C, Liu CT, Albert CM, Roden D, Chasman DI, Darbar D, ... ... Hernandez RD, et al. Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data. Nature Genetics. PMID 35256806 DOI: 10.1038/s41588-021-00997-7 |
0.382 |
|
| 2021 |
Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, Taliun SAG, Corvelo A, Gogarten SM, Kang HM, Pitsillides AN, LeFaive J, Lee SB, Tian X, Browning BL, ... ... Hernandez RD, et al. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature. 590: 290-299. PMID 33568819 DOI: 10.1038/s41586-021-03205-y |
0.405 |
|
| 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 |
0.397 |
|
| 2020 |
Torres R, Stetter MG, Hernandez RD, Ross-Ibarra J. The Temporal Dynamics of Background Selection in Non-equilibrium Populations. Genetics. PMID 32071195 DOI: 10.1534/Genetics.119.302892 |
0.494 |
|
| 2020 |
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, ... ... Hernandez R, et al. De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population. Proceedings of the National Academy of Sciences of the United States of America. PMID 31964835 DOI: 10.1073/Pnas.1902766117 |
0.497 |
|
| 2019 |
Tong DMH, Hernandez RD. Population genetic simulation study of power in association testing across genetic architectures and study designs. Genetic Epidemiology. PMID 31587362 DOI: 10.1002/Gepi.22264 |
0.486 |
|
| 2019 |
Szpiech ZA, Mak ACY, White MJ, Hu D, Eng C, Burchard EG, Hernandez RD. Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity. American Journal of Human Genetics. PMID 31543216 DOI: 10.1016/J.Ajhg.2019.08.011 |
0.514 |
|
| 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 |
0.51 |
|
| 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 |
0.755 |
|
| 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 |
0.531 |
|
| 2019 |
Torres R, Szpiech ZA, Hernandez RD. Correction: Human demographic history has amplified the effects of background selection across the genome. Plos Genetics. 15: e1007898. PMID 30601801 DOI: 10.1371/Journal.Pgen.1007898 |
0.388 |
|
| 2018 |
Fedewa G, Radoshitzky SR, Chī X, Dǒng L, Zeng X, Spear M, Strauli N, Ng M, Chandran K, Stenglein MD, Hernandez RD, Jahrling PB, Kuhn JH, DeRisi JL. Ebola virus, but not Marburg virus, replicates efficiently and without required adaptation in snake cells. Virus Evolution. 4: vey034. PMID 30524754 DOI: 10.1093/Ve/Vey034 |
0.316 |
|
| 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 |
0.446 |
|
| 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 |
0.727 |
|
| 2018 |
Torres R, Szpiech ZA, Hernandez RD. Human demographic history has amplified the effects of background selection across the genome. Plos Genetics. 14: e1007387. PMID 29912945 DOI: 10.1371/Journal.Pgen.1007387 |
0.541 |
|
| 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 |
0.486 |
|
| 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 |
0.484 |
|
| 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 |
0.562 |
|
| 2016 |
Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD. Functional Segregation of Overlapping Genes in HIV. Cell. 167: 1762-1773.e12. PMID 27984726 DOI: 10.1016/J.Cell.2016.11.031 |
0.352 |
|
| 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 |
0.469 |
|
| 2016 |
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, et al. Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens. Cell. 167: 657-669.e21. PMID 27768889 DOI: 10.1016/J.Cell.2016.09.025 |
0.427 |
|
| 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 |
0.625 |
|
| 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 |
0.761 |
|
| 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 |
0.334 |
|
| 2015 |
Maher MC, Hernandez RD. CauseMap: fast inference of causality from complex time series. Peerj. 3: e824. PMID 25780776 DOI: 10.7717/Peerj.824 |
0.473 |
|
| 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 |
0.56 |
|
| 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 |
0.472 |
|
| 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 |
0.5 |
|
| 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 |
0.779 |
|
| 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 |
0.421 |
|
| 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 |
0.421 |
|
| 2014 |
Uricchio LH, Hernandez RD. Robust forward simulations of recurrent hitchhiking. Genetics. 197: 221-36. PMID 24561480 DOI: 10.1534/Genetics.113.156935 |
0.742 |
|
| 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 |
0.599 |
|
| 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 |
0.302 |
|
| 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 |
0.471 |
|
| 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 |
0.449 |
|
| 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 |
0.795 |
|
| 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 |
0.392 |
|
| 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 |
0.404 |
|
| 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 |
0.389 |
|
| 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 |
0.362 |
|
| 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 |
0.681 |
|
| 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 |
0.487 |
|
| 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 |
0.398 |
|
| 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 |
0.592 |
|
| 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 |
0.517 |
|
| 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 |
0.549 |
|
| 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 |
0.592 |
|
| 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 |
0.62 |
|
| 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 |
0.553 |
|
| 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 |
0.784 |
|
| 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 |
0.443 |
|
| 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 |
0.787 |
|
| 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 |
0.72 |
|
| 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 |
0.591 |
|
| 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 |
0.603 |
|
| 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 |
0.584 |
|
| 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 |
0.561 |
|
| 2007 |
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, ... ... Hernandez RD, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/Science.1139247 |
0.774 |
|
| 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 |
0.573 |
|
| 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 |
0.593 |
|
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