Ryan Hernandez, PhD

Associate Professor
Department of Bioengineering and Therapeutic Sciences
+1 415 514-9813

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.

Primary Thematic Area: 
Human Genetics
Secondary Thematic Area: 
None
Research Summary: 
Human population genomics

Websites

Publications: 

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)

Shringarpure SS, Mathias RA, Hernandez RD, O'Connor TD, Szpiech ZA, Torres R, De La Vega FM, Bustamante CD, Barnes KC, Taub MA

Functional Segregation of Overlapping Genes in HIV.

Cell

Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD

Global environmental drivers of influenza.

Proceedings of the National Academy of Sciences of the United States of America

Deyle ER, Maher MC, Hernandez RD, Basu S, Sugihara G

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

Cell

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

A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome.

Nature communications

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