Ryan D Hernandez

Ryan D Hernandez

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Ryan D Hernandez

Ryan D Hernandez

Publications by authors named "Ryan D Hernandez"

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Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity.

Am J Hum Genet 2019 Oct 19;105(4):747-762. Epub 2019 Sep 19.

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada; Genome Quebec Innovation Center, McGill University, Montreal, QC H3A 0G1, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2019.08.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6817522PMC
October 2019

Population genetic simulation study of power in association testing across genetic architectures and study designs.

Genet Epidemiol 2019 Oct 6. Epub 2019 Oct 6.

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California.

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https://onlinelibrary.wiley.com/doi/abs/10.1002/gepi.22264
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http://dx.doi.org/10.1002/gepi.22264DOI Listing
October 2019

Ultrarare variants drive substantial cis heritability of human gene expression.

Nat Genet 2019 Sep 2;51(9):1349-1355. Epub 2019 Sep 2.

Institute for Human Genetics, UCSF, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41588-019-0487-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6730564PMC
September 2019

Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations.

Nat Commun 2019 Sep 4;10(1):4082. Epub 2019 Sep 4.

Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA.

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http://dx.doi.org/10.1038/s41467-019-12158-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6726619PMC
September 2019

An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos.

J Allergy Clin Immunol 2019 Mar 7;143(3):957-969. Epub 2018 Sep 7.

Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, Calif; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif; Department of Medicine, University of California, San Francisco, San Francisco, Calif.

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https://linkinghub.elsevier.com/retrieve/pii/S00916749183127
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http://dx.doi.org/10.1016/j.jaci.2016.08.057DOI Listing
March 2019

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. Epub 2019 Feb 20.

Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA.

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http://dx.doi.org/10.1038/s41467-019-08469-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6382865PMC
February 2019

Human demographic history has amplified the effects of background selection across the genome.

PLoS Genet 2018 06 18;14(6):e1007387. Epub 2018 Jun 18.

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, United States of America.

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https://dx.plos.org/10.1371/journal.pgen.1007387
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http://dx.doi.org/10.1371/journal.pgen.1007387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056204PMC
June 2018

Prominent features of the amino acid mutation landscape in cancer.

PLoS One 2017 24;12(8):e0183273. Epub 2017 Aug 24.

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183273PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570307PMC
October 2017

Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins.

Sci Signal 2017 Sep 5;10(495). Epub 2017 Sep 5.

Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1126/scisignal.aam9931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022362PMC
September 2017

Functional Segregation of Overlapping Genes in HIV.

Cell 2016 Dec;167(7):1762-1773.e12

Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.11.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5287106PMC
December 2016

Global environmental drivers of influenza.

Proc Natl Acad Sci U S A 2016 11 31;113(46):13081-13086. Epub 2016 Oct 31.

Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093;

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http://dx.doi.org/10.1073/pnas.1607747113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5135382PMC
November 2016

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens.

Cell 2016 Oct;167(3):657-669.e21

Department of Genetics, CHU Sainte-Justine Research Center, Montreal, QC H3T1C5, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montreal, QC H3T1J4, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.09.025DOI Listing
October 2016

Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants.

Genome Res 2016 07 18;26(7):863-73. Epub 2016 May 18.

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94143, USA; Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, California 94143, USA;

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http://dx.doi.org/10.1101/gr.202440.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937562PMC
July 2016

Statistical inference of a convergent antibody repertoire response to influenza vaccine.

Genome Med 2016 06 3;8(1):60. Epub 2016 Jun 3.

Department of Bioengineering and Therapeutic Sciences, University of California, Byers Hall, 1700 4th Street, San Francisco, CA, 94158, USA.

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http://dx.doi.org/10.1186/s13073-016-0314-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891843PMC
June 2016

CauseMap: fast inference of causality from complex time series.

PeerJ 2015 5;3:e824. Epub 2015 Mar 5.

Department of Bioengineering and Therapeutic Sciences , USA ; Institute for Human Genetics , USA ; Institute for Quantitative Biosciences (QB3), University of California , San Francisco, CA , USA.

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http://dx.doi.org/10.7717/peerj.824DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359046PMC
March 2015

Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference.

G3 (Bethesda) 2015 Feb 23;5(4):629-38. Epub 2015 Feb 23.

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California Institute for Human Genetics, University of California, San Francisco, San Francisco, California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, California 94158

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http://dx.doi.org/10.1534/g3.115.017095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390578PMC
February 2015

Population genetic simulations of complex phenotypes with implications for rare variant association tests.

Genet Epidemiol 2015 Jan 21;39(1):35-44. Epub 2014 Nov 21.

Graduate Program in Bioinformatics, University of California, San Francisco, California, United States of America.

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http://dx.doi.org/10.1002/gepi.21866DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270825PMC
January 2015

selscan: an efficient multithreaded program to perform EHH-based scans for positive selection.

Mol Biol Evol 2014 Oct 10;31(10):2824-7. Epub 2014 Jul 10.

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco Institute for Human Genetics, University of California, San Francisco Institute for Quantitative Biosciences (QB3), University of California, San Francisco.

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http://dx.doi.org/10.1093/molbev/msu211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166924PMC
October 2014

Robust forward simulations of recurrent hitchhiking.

Genetics 2014 May 21;197(1):221-36. Epub 2014 Feb 21.

University of California, Berkeley, and University of California, San Francisco, Joint Graduate Group in Bioengineering, University of California, San Francisco, California 94158.

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http://dx.doi.org/10.1534/genetics.113.156935DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012482PMC
May 2014

High-resolution network biology: connecting sequence with function.

Nat Rev Genet 2013 Dec 7;14(12):865-79. Epub 2013 Nov 7.

1] School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland. [2] Complex and Adaptive Systems Laboratory, University College Dublin, Dublin 4, Ireland.

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http://dx.doi.org/10.1038/nrg3574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023809PMC
December 2013

Population genetics of rare variants and complex diseases.

Hum Hered 2012 11;74(3-4):118-28. Epub 2013 Apr 11.

Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1159/000346826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3698246PMC
October 2013

Selective constraint, background selection, and mutation accumulation variability within and between human populations.

BMC Genomics 2013 Jul 23;14:495. Epub 2013 Jul 23.

Sainte Justine Research Centre, Department of Pediatrics, University of Montreal, Montreal, Canada.

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http://dx.doi.org/10.1186/1471-2164-14-495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3727949PMC
July 2013

A population genetics-phylogenetics approach to inferring natural selection in coding sequences.

PLoS Genet 2011 Dec 1;7(12):e1002395. Epub 2011 Dec 1.

Department of Human Genetics and Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1371/journal.pgen.1002395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228810PMC
December 2011

Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations.

Nat Genet 2011 Jul 31;43(9):887-92. Epub 2011 Jul 31.

Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3445408PMC
http://dx.doi.org/10.1038/ng.888DOI Listing
July 2011

Classic selective sweeps were rare in recent human evolution.

Science 2011 Feb;331(6019):920-4

Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1126/science.1198878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669691PMC
February 2011

Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data.

PLoS Genet 2009 Oct 23;5(10):e1000695. Epub 2009 Oct 23.

Theoretical Biology and Biophysics and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.

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https://dx.plos.org/10.1371/journal.pgen.1000695
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http://dx.doi.org/10.1371/journal.pgen.1000695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760211PMC
October 2009

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.

Science 2009 Apr;324(5926):528-32

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http://dx.doi.org/10.1126/science.1167936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735092PMC
April 2009

A flexible forward simulator for populations subject to selection and demography.

Authors:
Ryan D Hernandez

Bioinformatics 2008 Dec 7;24(23):2786-7. Epub 2008 Oct 7.

Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639268PMC
December 2008

Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans.

Mol Biol Evol 2007 Oct 26;24(10):2196-202. Epub 2007 Jul 26.

Biological Statistics and Computational Biology, Cornell University, USA.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msm149DOI Listing
October 2007

Context dependence, ancestral misidentification, and spurious signatures of natural selection.

Mol Biol Evol 2007 Aug 1;24(8):1792-800. Epub 2007 Jun 1.

Biological Statistics and Computational Biology, Cornell University, NY, USA.

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http://dx.doi.org/10.1093/molbev/msm108DOI Listing
August 2007

Evolutionary and biomedical insights from the rhesus macaque genome.

Authors:
Richard A Gibbs Jeffrey Rogers Michael G Katze Roger Bumgarner George M Weinstock Elaine R Mardis Karin A Remington Robert L Strausberg J Craig Venter Richard K Wilson Mark A Batzer Carlos D Bustamante Evan E Eichler Matthew W Hahn Ross C Hardison Kateryna D Makova Webb Miller Aleksandar Milosavljevic Robert E Palermo Adam Siepel James M Sikela Tony Attaway Stephanie Bell Kelly E Bernard Christian J Buhay Mimi N Chandrabose Marvin Dao Clay Davis Kimberly D Delehaunty Yan Ding Huyen H Dinh Shannon Dugan-Rocha Lucinda A Fulton Ramatu Ayiesha Gabisi Toni T Garner Jennifer Godfrey Alicia C Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan Ewen F Kirkness Andrew Cree R Gerald Fowler Sandra Lee Lora R Lewis Zhangwan Li Yih-Shin Liu Stephanie M Moore Donna Muzny Lynne V Nazareth Dinh Ngoc Ngo Geoffrey O Okwuonu Grace Pai David Parker Heidie A Paul Cynthia Pfannkoch Craig S Pohl Yu-Hui Rogers San Juana Ruiz Aniko Sabo Jireh Santibanez Brian W Schneider Scott M Smith Erica Sodergren Amanda F Svatek Teresa R Utterback Selina Vattathil Wesley Warren Courtney Sherell White Asif T Chinwalla Yucheng Feng Aaron L Halpern Ladeana W Hillier Xiaoqiu Huang Pat Minx Joanne O Nelson Kymberlie H Pepin Xiang Qin Granger G Sutton Eli Venter Brian P Walenz John W Wallis Kim C Worley Shiaw-Pyng Yang Steven M Jones Marco A Marra Mariano Rocchi Jacqueline E Schein Robert Baertsch Laura Clarke Miklós Csürös Jarret Glasscock R Alan Harris Paul Havlak Andrew R Jackson Huaiyang Jiang Yue Liu David N Messina Yufeng Shen Henry Xing-Zhi Song Todd Wylie Lan Zhang Ewan Birney Kyudong Han Miriam K Konkel Jungnam Lee Arian F A Smit Brygg Ullmer Hui Wang Jinchuan Xing Richard Burhans Ze Cheng John E Karro Jian Ma Brian Raney Xinwei She Michael J Cox Jeffery P Demuth Laura J Dumas Sang-Gook Han Janet Hopkins Anis Karimpour-Fard Young H Kim Jonathan R Pollack Tomas Vinar Charles Addo-Quaye Jeremiah Degenhardt Alexandra Denby Melissa J Hubisz Amit Indap Carolin Kosiol Bruce T Lahn Heather A Lawson Alison Marklein Rasmus Nielsen Eric J Vallender Andrew G Clark Betsy Ferguson Ryan D Hernandez Kashif Hirani Hildegard Kehrer-Sawatzki Jessica Kolb Shobha Patil Ling-Ling Pu Yanru Ren David Glenn Smith David A Wheeler Ian Schenck Edward V Ball Rui Chen David N Cooper Belinda Giardine Fan Hsu W James Kent Arthur Lesk David L Nelson William E O'brien Kay Prüfer Peter D Stenson James C Wallace Hui Ke Xiao-Ming Liu Peng Wang Andy Peng Xiang Fan Yang Galt P Barber David Haussler Donna Karolchik Andy D Kern Robert M Kuhn Kayla E Smith Ann S Zwieg

Science 2007 Apr;316(5822):222-34

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/science.1139247DOI Listing
April 2007

Natural selection on protein-coding genes in the human genome.

Nature 2005 Oct;437(7062):1153-7

Department of Biological Statistics and Computational Biology, 101 Biotechnology Building, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1038/nature04240DOI Listing
October 2005