Publications — Peñagaricano Lab

For a complete and up-to-date list, visit Google Scholar.

Selected Publications

Representative work across the lab's research themes

Rezende, F. M., Nani, J. P., and Peñagaricano, F. (2019). Genomic prediction of bull fertility in US Jersey dairy cattle. Journal of Dairy Science, 102(4), 3230–3240.
Liu, L. & Peñagaricano, F. (2025). EnrichKit: A multi-omics tool for livestock research. Frontiers in Genetics, 16, 1573374.
Martinez-Boggio, G., Lutz, P., Harrison, M., Weigel, K. A., & Peñagaricano, F. (2025). greenfeedr: An R package for processing and reporting GreenFeed data. JDS Communications, 6(2), 227–230.
Martinez-Boggio, G. et al. (2024). Revealing host genome–microbiome networks underlying feed efficiency in dairy cows. Scientific Reports, 14, 26060.
Amorín, R., Liu, L. et al. (2023). Maternal diet induces persistent DNA methylation changes in the muscle of beef calves. Scientific Reports, 13, 1587.
Laporta, J., Dado-Senn, B., Guadagnin, A. R., Liu, L., & Peñagaricano, F. (2025). Preweaning heat stress alters liver transcriptome and DNA methylation in dairy calves. Journal of Dairy Science, 108(4), 4390–4402.

2026 2

Cortes-Hernández, J. G., Ruiz-López, F. J., Peñagaricano, F., Montaldo, H. H., et al. (2026). SNPs with high linkage disequilibrium increase the explained genetic variance and the reliability of genomic predictions. Animals, 16(2), 337.
Guinan, F. L., Fourdraine, R. H., Peñagaricano, F., & Weigel, K. A. (2026). Genetic parameters for alternative resilience phenotypes in Holstein cows. JDS Communications.

2025 27

Cortes-Hernández, J. G., Martinez-Boggio, G., Peñagaricano, F., Montaldo, H. H., et al. (2025). Predicting productive, health, and reproductive traits in Mexican Holstein cattle using single nucleotide polymorphisms, haplotypes, and runs of homozygosity. JDS Communications.
Kendall, S. J., Martinez-Boggio, G., Arshad, U., Kennedy, K. M., Fukumori, R., et al. (2025). Mitochondrial function and nutrient partitioning in high and low feed efficient multiparous Holstein dairy cows. Journal of Dairy Science.
Fernandez-Wallace, T., Arshad, U., Mancheno, M., Praisler, G., de la Paz, M. C., et al. (2025). Metabolic and functional changes in T helper cells during the periparturient period of dairy cows. Journal of Dairy Science.
Cavani, L., Reyes, F. S., Van Os, J. M. C., Weigel, K. A., White, H. M., & Peñagaricano, F. (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.
Guinan, F. L., Fourdraine, R. H., Peñagaricano, F., & Weigel, K. A. (2025). Genetic parameters for alternative resilience phenotypes in Holstein cows. JDS Communications.
Chasi, B., Andrade, J. P., Monteiro, P. L. J., Castro, B., Moreno, E., Anta, E., Ali, N. N., et al. (2025). Association of fertility traits with markers of oocyte competence in dairy cattle. Journal of Dairy Science.
Rocha, C. C., Silva, F. A. C. C., Cavani, L., Cordeiro, A. L. L., Maldonado, M. B. C., et al. (2025). Endometrial gene expression predicts pregnancy outcome in Brahman cows. Molecular Reproduction and Development, 92(8), e70047.
Nascimento, B. M., Gaddis, K. L. P., Koltes, J. E., Tempelman, R. J., VandeHaar, M. J., et al. (2025). Impact of heat stress on dry matter intake and residual feed intake in mid-lactation dairy cows. Journal of Dairy Science, 108(7), 7345–7353.
Cavani, L., Parker Gaddis, K. L., Baldwin, R. L., Santos, J. E. P., Koltes, J. E., et al. (2025). Genetic characterisation of feeding patterns in lactating Holstein cows and their association with feed efficiency traits. Journal of Animal Breeding and Genetics, 142(4), 373–380.
Liu, L. & Peñagaricano, F. (2025). EnrichKit: A multi-omics tool for livestock research. Frontiers in Genetics, 16, 1573374.
Coelho Jr, W. M., Monteiro, H. F., Figueiredo, C. C., Mion, B., Santos, J. E. P., et al. (2025). Associations of serum fatty acids, serum urea nitrogen, and ruminal ammonia nitrogen with residual feed intake in lactating dairy cows. Journal of Dairy Science, 108(5), 4839–4850.
Townsend, J., Gross, N., Peng, Z., Peñagaricano, F., Yang, Z., Ahsan, N., et al. (2025). The embryonic DPPA3 gene stimulates the expression of pregnancy-related genes in bovine endometrial cells. Journal of Dairy Science.
Laporta, J., Dado-Senn, B., Guadagnin, A. R., Liu, L., & Peñagaricano, F. (2025). Preweaning heat stress alters liver transcriptome and DNA methylation in dairy calves. Journal of Dairy Science, 108(4), 4390–4402.
Nuñez, P., Martinez-Boggio, G., Casellas, J., Varona, L., Peñagaricano, F., et al. (2025). Applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs. animal, 19(3), 101453.
Cavani, L., Novo, L. C., Reyes, F. S., Nascimento, B. M., VandeHaar, M. J., et al. (2025). Associations between body temperature and feed efficiency traits in lactating Holstein cows. JDS Communications, 6(2), 256–260.
Martinez-Boggio, G., Lutz, P., Harrison, M., Weigel, K. A., & Peñagaricano, F. (2025). greenfeedr: An R package for processing and reporting GreenFeed data. JDS Communications, 6(2), 227–230.
Guinan, F. L., Fourdraine, R. H., Peñagaricano, F., & Weigel, K. A. (2025). Genetic analysis of daily milk weights in US Holsteins using pen-based contemporary groups. JDS Communications, 6(2), 237–240.
Nuñez Romano, P., Martinez-Boggio, G., Casellas, J., Varona, L., et al. (2025). Applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs. Cambridge University Press.
Cortes-Hernández, J. G., García-Ruiz, A., Peñagaricano, F., Montaldo, H. H., et al. (2025). Uncovering the genetic basis of milk production traits in Mexican Holstein cattle based on individual markers and genomic windows. PLoS ONE, 20(2), e0314888.
Nuñez, P., Casto-Rebollo, C., Martinez-Boggio, G., Negro Rama, S., et al. (2025). The gut microbiota as a predictor of feed efficiency and feeding behavior in Iberian pigs. Journal of Animal Science, 103, skaf268.
Heredia, D., Tarnonsky, F., Lopez-Duarte, M. C., Venturini, M., Podversich, F., et al. (2025). Impact of dietary supplementation of beef cows with rumen-protected methionine during the periconceptional period on prenatal growth and performance to weaning. Journal of Animal Science, 103, skae384.
Casarotto, L. T., Jones, H. N., Chavatte-Palmer, P., Laporta, J., Peñagaricano, F., et al. (2025). Late-gestation heat stress alters placental structure and function in multiparous dairy cows. Journal of Dairy Science, 108(1), 1125–1137.
Guinan, F. L., Fourdraine, R. H., Peñagaricano, F., & Weigel, K. A. (2025). Dairy cow resilience: data driven detection and quantification of perturbations using daily milk weights. Journal of Dairy Science, 108, 11173–11185.
Gonella-Diaza, A., Sponchiado, M., Rodrigues França, M., Liu, L., Pugliesi, G., et al. (2025). The metabolomic composition of the oviductal fluid is controlled by the periovulatory hormonal context in Bos indicus cows. Biology of Reproduction, 111(6), 1188–1201.

2024 20

Toledo-Alvarado, H. O., Tempelman, R. J., Lopez-Cruz, M., VandeHaar, M. J., et al. (2024). Selection indexes for residual feed intake derived from milk spectra. Journal of Dairy Science, 107(12), 11164–11179.
Pacheco, H. A., Rossoni, A., Cecchinato, A., & Peñagaricano, F. (2024). Genomic prediction of male fertility in Brown Swiss cattle. JDS Communications, 5(6), 568–571.
Martinez-Boggio, G., Monteiro, H. F., Lima, F. S., Figueiredo, C. C., Bisinotto, R. S., et al. (2024). Revealing host genome–microbiome networks underlying feed efficiency in dairy cows. Scientific Reports, 14(1), 26060.
Martinez-Boggio, G., Monteiro, H. F., Lima, F. S., Figueiredo, C. C., Bisinotto, R. S., et al. (2024). Investigating relationships between the host genome, rumen microbiome, and dairy cow feed efficiency using mediation analysis with structural equation modeling. Journal of Dairy Science, 107(10), 8193–8204.
Adkinson, A. Y., Abouhawwash, M., VandeHaar, M. J., Gaddis, K. L. P., Burchard, J., et al. (2024). Assessing different cross-validation schemes for predicting novel traits using sensor data: An application to dry matter intake and residual feed intake using milk spectral data. Journal of Dairy Science, 107(10), 8084–8099.
Nascimento, B. M., Cavani, L., Caputo, M. J., Marinho, M. N., Borchers, M. R., et al. (2024). Genetic relationships between behavioral traits and feed efficiency traits in lactating Holstein cows. Journal of Dairy Science, 107(10), 8141–8149.
Guinan, F. L., Fourdraine, R., Peñagaricano, F., & Weigel, K. (2024). Genetic parameters for daily milk weights in US Holsteins using pen-based contemporary groups. Interbull Bulletin, 1–7.
Toghiani, S., VanRaden, P. M., VandeHaar, M. J., Baldwin, R. L., Weigel, K. A., et al. (2024). Dry matter intake in US Holstein cows: Exploring the genomic and phenotypic impact of milk components and body weight composite. Journal of Dairy Science, 107(9), 7009–7021.
Madureira, G., Mion, B., Van Winters, B., Peñagaricano, F., Li, J., & Ribeiro, E. S. (2024). Endometrial responsiveness to interferon-tau and its association with subsequent reproductive performance in dairy heifers. Journal of Dairy Science, 107(9), 7371–7391.
Guadagnin, A. R., Peñagaricano, F., Dahl, G. E., & Laporta, J. (2024). Programming effects of intrauterine hyperthermia on adrenal gland development. Journal of Dairy Science, 107(8), 6308–6321.
Novo, L. C., Gaddis, K. L. P., Wu, X. L., McWhorter, T. M., Burchard, J., Norman, H. D., et al. (2024). Genetic parameters and trends for Johne's disease in US Holsteins: An updated study. Journal of Dairy Science, 107(7), 4804–4821.
Arshad, U., Peñagaricano, F., & White, H. M. (2024). Effects of feeding rumen-protected lysine during the postpartum period on performance and amino acid profile in dairy cows: A meta-analysis. Journal of Dairy Science, 107(7), 4537–4557.
Martinez-Boggio, G., Monteiro, H. F., Lima, F. S., Figueiredo, C. C., Bisinotto, R. S., et al. (2024). Host and rumen microbiome contributions to feed efficiency traits in Holstein cows. Journal of Dairy Science, 107(5), 3090–3103.
Guinan, F. L., Fourdraine, R. H., Peñagaricano, F., & Weigel, K. A. (2024). Genetic analysis of lactation consistency in US Holsteins using temporal variation in daily milk weights. Journal of Dairy Science, 107(4), 2194–2206.
Weigel, K., Chasco, A., Pacheco, H., Sigdel, A., Guinan, F., Lauber, M., Fricke, P., et al. (2024). Genomic selection in dairy cattle: impact and contribution to the improvement of bovine fertility. Clinical Theriogenology, 16.
Houlahan, K., Schenkel, F. S., Miglior, F., Jamrozik, J., Stephansen, R. B., et al. (2024). Estimation of genetic parameters for feed efficiency traits using random regression models in dairy cattle. Journal of Dairy Science, 107(3), 1523–1534.
van Staaveren, N., de Oliveira, H. R., Houlahan, K., Chud, T. C. S., Oliveira Jr, G. A., et al. (2024). The Resilient Dairy Genome Project—A general overview of methods and objectives related to feed efficiency and methane emissions. Journal of Dairy Science, 107(3), 1510–1522.
Monteiro, H. F., Figueiredo, C. C., Mion, B., Santos, J. E. P., Bisinotto, R. S., et al. (2024). An artificial intelligence approach of feature engineering and ensemble methods depicts the rumen microbiome contribution to feed efficiency in dairy cows. Animal Microbiome, 6(1), 5.
Cavani, L., Gaddis, K. L. P., Baldwin, R. L., Santos, J. E. P., Koltes, J. E., et al. (2024). Consistency of dry matter intake in Holstein cows: heritability estimates and associations with feed efficiency. Journal of Dairy Science, 107(2), 1054–1067.
Novo, L. C., Poindexter, M. B., Rezende, F. M., Santos, J. E. P., Nelson, C. D., et al. (2024). Identification of genetic variants and individual genes associated with postpartum hypocalcemia in Holstein cows. Scientific Reports, 13(1), 21900.

2023 12

Stephansen, R. B., Martin, P., Manzanilla-Pech, C. I. V., Gredler-Grandl, B., et al. (2023). Novel genetic parameters for genetic residual feed intake in dairy cattle using time series data from multiple parities and countries in North America and Europe. Journal of Dairy Science, 106(12), 9078–9094.
Peñagaricano, F. (2023). Genomics and dairy bull fertility. The Veterinary Clinics of North America. Food Animal Practice, S0749-0720.
Silva, F. A. C. C., Martins, T., Sponchiado, M., Rocha, C. C., Ashrafi, N., Graham, S. F., et al. (2023). Pre-estrus progesterone does not affect post-estrus luminal metabolome in cross-bred beef cows. Reproduction, 166(2), 99–116.
Pacheco, H. A., Rossoni, A., Cecchinato, A., & Peñagaricano, F. (2023). Identification of runs of homozygosity associated with male fertility in Italian Brown Swiss cattle. Frontiers in Genetics, 14, 1227310.
Nascimento, B. M., Wolfe, C. W., Weigel, K. A., & Peñagaricano, F. (2023). Effects of type traits, inbreeding, and production on survival in US Jersey cattle. Journal of Dairy Science, 106(7), 4825–4835.
De los Santos, J. A., Andrade, J. P. N., Cangiano, L. R., Iriarte, A., Peñagaricano, F., et al. (2023). Transcriptomic analysis reveals gene expression changes in peripheral white blood cells of cows after embryo transfer: Implications for pregnancy tolerance. Reproduction in Domestic Animals, 58(7), 946–954.
Silva, F. A. C. C., Martins, T., Sponchiado, M., Rocha, C. C., Pohler, K. G., et al. (2023). Hormonal profile prior to luteolysis modulates the uterine luminal transcriptome in the subsequent cycle in beef cross-bred cows. Biology of Reproduction, 108(6), 922–935.
Lauber, M. R., Peñagaricano, F., Fourdraine, R. H., Clay, J. S., & Fricke, P. M. (2023). Characterization of semen type prevalence and allocation in Holstein and Jersey females in the United States. Journal of Dairy Science, 106(5), 3748–3760.
Mirzaei, A., Merenda, V. R., Ferraretto, L. F., Shaver, R. D., Peñagaricano, F., et al. (2023). Individual animal variability in rumination, activity, and lying behavior during the periparturient period of dairy cattle. JDS Communications, 4(3), 205–209.
Cavani, L., Gaddis, K. L. P., Baldwin, R. L., Santos, J. E. P., Koltes, J. E., et al. (2023). Impact of parity differences on residual feed intake estimation in Holstein cows. JDS Communications, 4(3), 201–204.
Hatew, B., Peñagaricano, F., Balehegn, M., Jones, C. S., Dahl, G. E., et al. (2023). Synergies of feed, management trainings, and genetics on milk production of dairy cows in the tropics: The case of Ethiopian smallholder farmers. Frontiers in Animal Science, 4, 1119786.
Amorín, R., Liu, L., Moriel, P., DiLorenzo, N., Lancaster, P. A., & Peñagaricano, F. (2023). Maternal diet induces persistent DNA methylation changes in the muscle of beef calves. Scientific Reports, 13(1), 1587.

For publications prior to 2023, please see Google Scholar.