Phone
608-263-3308Website
View WebsiteOffice Location
1675 Observatory Dr
436 Animal Sciences
Madison, WI 53706
Francisco Peñagaricano is originally from Uruguay, where he earned his BS (2005) in Biology and Biochemistry and his MS (2010) in Animal Science, all from Universidad de la República. He continued his graduate studies at the University of Wisconsin where he earned his MS (2014) in Statistics and Ph.D. (2014) in Animal Science. Before joining UW, Francisco was a faculty member (2015-2020) in the Department of Animal Sciences at the University of Florida.
His research interests are in quantitative genomics and computational biology. His research program focuses on the development and application of methods to dissect the genetic architecture of economically relevant traits in livestock. He typically combines large, nationwide phenotypic datasets or field experiments, with high–throughput genomic technologies, and advanced statistical and computational methods in order to elucidate the connection between genome and phenotype. His research involves gene mapping, gene-set analysis, genomic prediction, methylome and transcriptome analysis, multi-omics data integration, and network modeling.
Selected Peer-Reviewed Articles
L Cavani, FS Reyes, JMC Van Os, KA Weigel, HM White, and F Peñagaricano (2025) Social dominance and feed efficiency: genetic analysis of latency to first meal after fresh feed delivery and residual feed intake in dairy cows. JDS Communications (in press)
FL Guinan, RH Fourdraine, F Peñagaricano, and KA Weigel (2025) Genetic parameters for alternative resilience phenotypes in Holstein cows. JDS Communications (in press)
P Nuñez, C Casto-Rebollo, G Martinez-Boggio, S Negro Rama, J Casellas, L Varona, R Pena, F Peñagaricano, and N Ibáñez-Escriche (2025) The gut microbiota as a predictor of feed efficiency and feeding behavior in Iberian pigs. Journal of Animal Science 103: skaf268.
FL Guinan, RH Fourdraine, F Peñagaricano, and KA Weigel (2025) Dairy cow resilience: data driven detection and quantification of perturbations using daily milk weights. Journal of Dairy Science 108: 11173-11185.
L Liu and F Peñagaricano (2025) EnrichKit: a multi-omics tool for livestock research. Frontiers in Genetics 16: 1573374.
BM Nascimento, KL Parker Gaddis, JE Koltes, RJ Tempelman, MJ VandeHaar, HM White, F Peñagaricano, and KA Weigel (2025) Impact of heat stress on dry matter intake and residual feed intake in mid-lactation dairy cows. Journal of Dairy Science 108: 7345-7353.
J Townsend, N Gross, Z Peng, F Peñagaricano, Z Yang, N Ahsan, and H Khatib (2025) The embryonic DPPA3 gene stimulates the expression of pregnancy-related genes in bovine endometrial cells. Journal of Dairy Science 108: 6471-6487.
P Nuñez, G Martinez-Boggio, J Casellas, L Varona, F Peñagaricano, and N Ibáñez-Escriche (2025) Applying recursive modeling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs. Animal 19: 101453.
J Laporta, B Dado-Senn, A Guadagnin, L Liu, and F Peñagaricano (2025) Pre-weaning heat stress alters liver transcriptome and DNA methylation in dairy calves. Journal of Dairy Science 108: 4390-4402.
JG Cortes-Hernández, A García-Ruiz, F Peñagaricano, HH Montaldo, and FJ Ruiz-López (2025) Uncovering the genetic basis of milk production traits in Mexican Holstein cattle based on individual markers and genomic windows. PLoS One 20: e0314888.
L Cavani, LC Novo, FS Reyes, BM Nascimento, MJ VandeHaar, RJ Tempelman, KL Parker Gaddis, RL Baldwin, JEP Santos, JE Koltes, HM White, KA Weigel, and F Peñagaricano (2025) Associations between body temperature and feed efficiency traits in lactating Holstein cows. JDS Communications 6: 256-260.
G Martinez Boggio, P Lutz, M Harrison, KA Weigel, and F Peñagaricano (2025) greenfeedr: an R-package for processing and reporting GreenFeed data. JDS Communications 6: 227-230.
L Cavani, KL Parker Gaddis, RL Baldwin, JEP Santos, JE Koltes, RJ Tempelman, MJ VandeHaar, HM White, F Peñagaricano, and KA Weigel (2025) Genetic characterization of feeding patterns in lactating Holstein cows and their association with feed efficiency traits. Journal of Animal Breeding and Genetics 142: 373–380.
FL Guinan, RH Fourdraine, F Peñagaricano, and KA Weigel (2025) Genetic analysis of daily milk weights in U.S. Holsteins using pen-based contemporary groups. JDS Communications 6: 237-240.
LT Casarotto, HN Jones, P Chavatte-Palmer, J Laporta, F Peñagaricano, V Ouellet, JJ Bromfield, and GE Dahl (2025) Late gestation heat stress alters placental structure and function in multiparous dairy cows. Journal of Dairy Science 108: 1125-1137.
AN SCI 366 Concepts in Genomics (3 credits, Fall)
Description: Basic overview of the latest concepts in genomics, including genome organization, the importance of genome annotation, the use of genomic testing in plant and animal breeding, the potential of genomic prediction on human medicine, and the latest advances in omics integration.
AN SCI 865 Design and Analysis of Biological Studies (4 credits, Spring)
Description: The fundamentals of linear models, generalized linear models, experimental design, and data analysis using common examples from biological studies.
Section Editor Journal of Dairy Science
Associate Editor BMC Genomics
Associate Editor Frontiers in Genetics
Judge John J. Crown Chair in Dairy Genetics (2025-2030)
Excellence Award for Assistant Professors, University of Florida (2019)