Publications – Peñagaricano Lab

Publications

L Cavani, LC Novo, BM Nascimento, et al. (2024)
Associations between body temperature and feed efficiency traits in lactating Holstein cows.
JDS Communications (forthcoming)

G Martinez Boggio, P Lutz, M Harrison, KA Weigel, and F Peñagaricano (2024)
greenfeedr: an R-package for processing and reporting GreenFeed data.
JDS Communications (forthcoming)

L Cavani, KL Parker Gaddis, RL Baldwin, JEP Santos, JE Koltes, RJ Tempelman, MJ VandeHaar, HM White, F Peñagaricano, and KA Weigel (2024)
Genetic characterization of feeding patterns in lactating Holstein cows and their association with feed efficiency traits.
Journal of Animal Breeding and Genetics (in press)

G Martinez Boggio, HF Monteiro, FS Lima, et al. (2024)
Revealing host genome-microbiome networks underlying feed efficiency in dairy cows.
Scientific Reports 14: 26060.

FL Guinan, RH Fourdraine, F Peñagaricano, and KA Weigel (2024)
Genetic analysis of daily milk weights in U.S. Holsteins using pen-based contemporary groups.
JDS Communications (forthcoming)

AM Gonella-Diaza, M Sponchiado, MR França, L Liu, G Pugliesi, EG Lo Turco, F Peñagaricano, and M Binelli (2024)
The metabolomic composition of the oviductal fluid is controlled by the periovulatory hormonal context in Bos indicus cows.
Biology of Reproduction (in press)

LT Casarotto, HN Jones, P Chavatte-Palmer, J Laporta, F Peñagaricano, V Ouellet, JJ Bromfield, and GE Dahl (2024)
Late gestation heat stress alters placental structure and function in multiparous dairy cows.
Journal of Dairy Science (forthcoming)

HO Toledo-Alvarado, RJ Tempelman, M Lopez-Cruz, MJ VandeHaar, JEP Santos, F Peñagaricano, P Khanal, and G de los Campos (2024)
Selection indices for residual feed intake derived from milk spectra.
Journal of Dairy Science (in press)

G Martinez Boggio, HF Monteiro, FS Lima, et al. (2024)
Investigating relationships between the genome, rumen microbiome, and feed efficiency using mediation analysis with structural equation modeling.
Journal of Dairy Science 107: 8193-8204.

A Yilmaz Adkinson, M Abouhawwash, KL Parker Gaddis, et al. (2024)
Assessing different cross-validation schemes for predicting novel traits using sensor data: an application to DMI and RFI using milk spectral data.
Journal of Dairy Science 107: 8084-8099.

BM Nascimento, L Cavani, MJ Caputo, M Nehme Marinho, MR Borchers, RL Wallace, JEP Santos, HM White, F Peñagaricano, and KA Weigel (2024)
Genetic relationships between behavioral traits and feed efficiency traits in lactating Holstein cows.
Journal of Dairy Science 107: 8141-8149.

HA Pacheco, A Rossoni, A Cecchinato, and F Peñagaricano (2024)
Genomic prediction of male fertility in Brown Swiss cattle.
JDS Communications 5: 568-571.

S Toghiani, PM VanRaden, MJ VandeHaar, 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: 7009-7021.

KA Weigel, A Chasco, HA Pacheco, A Sigdel, FL Guinan, MR Lauber, PM Fricke, and F Peñagaricano (2024)
Genomic selection in dairy cattle: impact and contribution to the improvement of bovine fertility.
Clinical Theriogenology (in press)

G Madureira, B Mion, B Van Winters, F Peñagaricano, J Li, and ES Ribeiro (2024)
Endometrial responsiveness to interferon-tau and its association with subsequent reproductive performance in dairy heifers.
Journal of Dairy Science 107: 7371-7391.

AR Guadagnin, F Peñagaricano, GE Dahl, and J Laporta (2024)
Programming effects of intrauterine hyperthermia on adrenal gland development.
Journal of Dairy Science 107: 6308-6321.

LC Novo, KL Parker Gaddis, XL Wu, TM McWhorter, J Burchard, HD Norman, J Dürr, RH Fourdraine, and F Peñagaricano (2024)
Genetic parameters and genetic trends for Johne’s disease in U.S. Holsteins: an updated study.
Journal of Dairy Science 107: 4804-4821.

HF Monteiro, CC Figueiredo, B Mion, et al. (2024)
An artificial intelligence approach depicts the rumen microbiome contribution to feed and milk production efficiency in dairy cows.
Animal Microbiome 6:5.

U Arshad, F Peñagaricano, and HM White (2024)
Effects of feeding rumen-protected lysine during the postpartum period on performance and amino acids profile in dairy cows: A meta-analysis.
Journal of Dairy Science 107: 4537-4557.

G Martinez Boggio, HF Monteiro, FS Lima, CC Figueiredo, RS Bisinotto, JEP Santos, B Mion, FS Schenkel, ES Ribeiro, KA Weigel, and F Peñagaricano (2024)
Host and rumen microbiome contributions to feed efficiency traits in Holstein cows.
Journal of Dairy Science 107: 3090-3103.

FL Guinan, RH Fourdraine, F Peñagaricano, and KA Weigel (2024)
Genetic analysis of lactation consistency in U.S. Holsteins using temporal variation in daily milk weights.
Journal of Dairy Science 107: 2194-2206.

N van Staaveren, HR Oliveira, K Houlahan 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: 1510-1522.

K Houlahan, FS Schenkel, F Miglior et al. (2024)
Estimation of genetic parameters for feed efficiency traits using random regression models in dairy cattle.
Journal of Dairy Science 107: 1523-1534.

L Cavani, KL Parker Gaddis, RL Baldwin, JEP Santos, JE Koltes, RJ Tempelman, MJ VandeHaar, HM White, F Peñagaricano, and KA Weigel (2024)
Consistency of dry matter intake in Holstein cows: heritability estimates and associations with feed efficiency.
Journal of Dairy Science 107: 1054-1067.

F Peñagaricano (2024)
Genomics and dairy bull fertility.
Veterinary Clinics of North America: Food Animal Practice 40: 185-190.

LC Novo, MB Poindexter, FM Rezende, JEP Santos, CD Nelson, LL Hernandez, BW Kirkpatrick, and F Peñagaricano (2023)
Identification of genetic variants and individual genes associated with postpartum hypocalcemia in Holstein cows.
Scientific Reports 13: 21900.

RB Stephansen, P Martin, CIV Manzanilla-Pech, et al. (2023)
Novel genetic parameters for 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: 9078-9094.

HA Pacheco, A Rossoni, A Cecchinato, and F Peñagaricano (2023)
Identification of runs of homozygosity associated with male fertility in Italian Brown Swiss cattle.
Frontiers in Genetics 14: 1227310.

FACC Silva, T Martins, M Sponchiado, CC Rocha, N Ashrafi, SF Graham, KG Pohler, F Peñagaricano, AM Gonella-Diaza, and M Binelli (2023)
Pre-estrus progesterone does not affect post-estrus luminal metabolome in cross-bred beef cows.
Reproduction 166: 99-116.

JA de los Santos, JPN Andrade, LR Cangiano, A Iriarte, F Peñagaricano, and JJ Parrish (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: 946–954.

FACC Silva, T Martins, M Sponchiado, CC Rocha, KG Pohler, F Peñagaricano, and M Binelli (2023)
Hormonal profile prior to luteolysis modulates the uterine luminal transcriptome in the subsequent cycle in beef cross-bred cows.
Biology of Reproduction 108: 922-935.

B Hatew, F Peñagaricano, M Gebremikael, CS Jones, GE Dahl, and AT Adesogan (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.

R Amorín, L Liu, P Moriel, N DiLorenzo, PA Lancaster, and F Peñagaricano (2023)
Maternal diet induces persistent DNA methylation changes in the muscle of beef calves.
Scientific Reports 13: 1587.

BM Nascimento, CW Wolfe, KA Weigel, and F Peñagaricano (2023)
Effects of type traits, inbreeding, and production on survival in US Jersey cattle.
Journal of Dairy Science 106: 4825-4835.

MR Lauber, F Peñagaricano, RH Fourdraine, JS Clay, and PM Fricke (2023)
Characterization of semen type prevalence and allocation in Holstein and Jersey females in the United States.
Journal of Dairy Science 106: 3748-3760.

L Cavani, KL Parker Gaddis, RL Baldwin, JEP Santos, JE Koltes, RJ Tempelman, MJ VandeHaar, MJM Caputo, HM White, F Peñagaricano, and KA Weigel (2023)
Impact of parity differences on residual feed intake estimation in Holstein cows.
JDS Communications 4: 201-204.

A Mirzaei, VR Merenda, LF Ferraretto, RD Shaver, F Peñagaricano, and RC Chebel (2023)
Individual animal variability in rumination, activity, and lying behavior during the periparturient period of dairy cattle.
JDS Communications 4: 205-209.

M Binelli, FACC Silva, CC Rocha, T Martins, M Sponchiado, V Van Hoeck, A Cordeiro, M Campbell, JLMR Leroy, F Peñagaricano, and G Pugliesi (2022)
Endometrial receptivity in cattle: the mutual reprogramming paradigm.
Animal Reproduction 19: e20220097.

Z Liang, D Prakapenka, KL Parker Gaddis, MJ VandeHaar, KA Weigel, RJ Tempelman, JE Koltes, JEP Santos, HM White, F Peñagaricano, RL Baldwin, and Y Da (2022)
Impact of epistasis effects on the accuracy of predicting phenotypic values of residual feed intake in U.S. Holstein cows.
Frontiers in Genetics 13: 1017490.

WE Brown, MJ Caputo, C Siberski, JE Koltes, F Peñagaricano, KA Weigel, and HM White (2022)
Predicting dry matter intake in mid-lactation Holstein cows using point-in-time data streams available on dairy farms.
Journal of Dairy Science 105: 9666-9681.

A Sigdel, RS Bisinotto, and F Peñagaricano (2022)
Genetic analysis of fetal loss in Holstein cattle.
Journal of Dairy Science 105: 9012-9020.

HA Pacheco, A Rossoni, A Cecchinato, and F Peñagaricano (2022)
Deciphering the genetic basis of male fertility in Italian Brown Swiss dairy cattle.
Scientific Reports 12: 10575.

WE Brown, L Cavani, F Peñagaricano, KA Weigel, and HM White (2022)
Feeding behavior parameters and temporal patterns in mid-lactation Holstein cows across a range of residual feed intake values.
Journal of Dairy Science 105: 8130-8142.

L Cavani, WE Brown, KL Parker Gaddis, RJ Tempelman, MJ VandeHaar, HM White, F Peñagaricano, and KA Weigel (2022)
Estimates of genetic parameters for feeding behavior traits and their associations with feed efficiency in Holstein cows.
Journal of Dairy Science 105: 7564-7574.

E Jara, F Peñagaricano, E Armstrong, C Menezes, L Tardiz, G Rodons, and A Iriarte (2022)
Identification of long noncoding RNAs involved in eyelid pigmentation of Hereford cattle.
Frontiers in Genetics 13: 864567.

E Jara, F Peñagaricano, E Armstrong, G Ciappesoni, A Iriarte, and EA Navajas (2022)
Revealing the genetic basis of eyelid pigmentation in Hereford cattle.
Journal of Animal Science 100: skac110.

A Sigdel, XL Wu, KL Parker Gaddis, HD Norman, JA Carrillo, JF Burchard, F Peñagaricano, and JW Dürr (2022)
Genetic evaluations of stillbirth for five US dairy breeds: a data-resource feasibility study.
Frontiers in Genetics 13: 819678.

P Khanal, KL Parker Gaddis, MJ Vandehaar, KA Weigel, HM White, F Peñagaricano, JE Koltes, JEP Santos, RL Baldwin, JF Burchard, JW Dürr, and RJ Tempelman (2022)
Multiple trait random regression modeling of feed efficiency in US Holsteins.
Journal of Dairy Science 105: 5954-5971.

CM Sheftel, L Liu, SL Field, SR Weaver, CM Vezina, F Peñagaricano, and LL Hernandez (2022)
Impact of fluoxetine treatment and folic acid supplementation on the mammary gland transcriptome during peak lactation.
Frontiers in Pharmacology 13: 828735.

JR Vinyard, F Peñagaricano, and AP Faciola (2022)
The effects of course format, sex, semester, and institution on student performance in an undergraduate animal science course.
Translational Animal Science 6: txac004.

LC Novo, L Cavani, P Pinedo, P Melendez, and F Peñagaricano (2022)
Genomic analysis of visceral fat accumulation in Holstein cows.
Frontiers in Genetics 12: 803216.

T Martins, M Sponchiado, FACC Silva, E Estrada-Cortés, PJ Hansen, F Peñagaricano, and M Binelli (2022)
Progesterone-dependent and -independent modulation of luminal epithelial transcription to support pregnancy in cattle.
Physiological Genomics 54: 71–85.

L Cavani, MB Poindexter, CD Nelson, JEP Santos, and F Peñagaricano (2022)
Gene mapping, gene-set analysis, and genomic prediction of postpartum blood calcium in Holstein cows.
Journal of Dairy Science 105: 525-534.

L Liu, R Amorín, P Moriel, N DiLorenzo, PA Lancaster, and F Peñagaricano (2021)
Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle.
BMC Genomics 22: 780.

LFM Mota, S Pegolo, T Baba, G Morota, F Peñagaricano, G Bittante, and A Cecchinato (2021)
Comparison of single-breed and multi-breed training populations for infrared predictions of novel phenotypes in Holstein cows.
Animals 11: 1993.

MA Mezera, W Li, L Liu, R Meidan, F Peñagaricano, and MC Wiltbank (2021)
Effect of natural pre-luteolytic prostaglandin F2α pulses on the bovine luteal transcriptome during spontaneous luteal regression.
Biology of Reproduction 105: 1016-1029.

HA Pacheco, M Battagin, A Rossoni, A Cecchinato, and F Peñagaricano (2021)
Evaluation of bull fertility in Italian Brown Swiss dairy cattle using cow field data.
Journal of Dairy Science 104: 10896-10904.

EA Palmer, F Peñagaricano, M Vedovatto, RA Oliveira, SL Field, J Laporta, and P Moriel (2021)
Effects of maternal gestational diet on muscle transcriptome of beef calves following a vaccine-induced immunological challenge.
PLoS ONE 16: e0253810.

A Sigdel, RS Bisinotto, and F Peñagaricano (2021)
Genes and pathways associated with pregnancy loss in dairy cattle.
Scientific Reports 11: 13329.

R Abdollahi-Arpanahi, HA Pacheco, and F Peñagaricano (2021)
Targeted sequencing reveals candidate causal variants for dairy bull subfertility.
Animal Genetics 52: 509-513.

SL Field, MG Marrero, L Liu, F Peñagaricano, and J Laporta (2021)
Histological and transcriptomic analysis of adipose and muscle of dairy calves supplemented with 5-hydroxytryptophan.
Scientific Reports 11: 9665.

LFM Mota, S Pegolo, T Baba, F Peñagaricano, G Morota, G Bittante, and A Cecchinato (2021)
Evaluating the performance of [different] methods for predicting difficult-to-measure traits in Holstein dairy cattle using milk infrared spectral data.
Journal of Dairy Science 104: 8107-8121.

T Baba, S Pegolo, LFM Mota, F Peñagaricano, G Bittante, A Cecchinato, and G Morota (2021)
Integrating genomic and infrared spectral data improves the prediction of milk protein composition in dairy cattle.
Genetics Selection Evolution 53: 29.

P Fan, CD Nelson, D Driver, MA Elzo, F Peñagaricano, KC Jeong (2021)
Host genetics exerts lifelong effects upon hindgut microbiota and its association with bovine growth and immunity.
The ISME Journal 15: 2306–2321.

LF Brito, N Bedere, F Douhard, HR Oliveira, M Arnal, F Peñagaricano, AP Schinckel, CF Baes, and F Miglior (2021)
Genetic selection of high-yielding dairy cattle towards sustainable farming systems in a rapidly-changing world.
Animal 15: 100292.

M Nehme Marinho, R Zimpel, F Peñagaricano, and JEP Santos (2021)
Assessing feed efficiency in early and mid-lactation and its associations with performance and health in Holstein.
Journal of Dairy Science 104: 5493-5507.

L Liu, R Amorín, P Moriel, N DiLorenzo, PA Lancaster, and F Peñagaricano (2020)
Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition.
BMC Genomics 21: 684.

E Jara, F Peñagaricano, C Menezes, L Tardiz, G Rodons, A Iriarte, and E Armstrong (2020)
Transcriptomic analysis of eyelid pigmentation in Hereford cattle.
Animal Genetics 51: 935-939.

JD Leal Gutierrez, FM Rezende, JM Reecy, LM Kramer, F Peñagaricano, and RG Mateescu (2020)
Whole genome sequence data provides novel insights into the genetic architecture of meat quality traits in beef.
Frontiers in Genetics 11: 538640.

FM Rezende, M Haile-Mariam, JE Pryce, and F Peñagaricano (2020)
Across-country genomic prediction of bull fertility in Jersey dairy cattle.
Journal of Dairy Science 103: 11618-11627.

JP Nani and F Peñagaricano (2020)
Whole-genome homozygosity mapping reveals candidate regions affecting bull fertility in US Holstein cattle.
BMC Genomics 21: 338.

A Sigdel, L Liu, R Abdollahi-Arpanahi, I Aguilar, and F Peñagaricano (2020)
Genetic dissection of reproductive performance of dairy cows under heat stress.
Animal Genetics 51: 511–520.

N Gross, F Peñagaricano, and H Khatib (2020)
Integration of whole-genome DNA methylation data with RNA sequencing data to identify markers for bull fertility.
Animal Genetics 51: 502-510.

R Abdollahi-Arpanahi, D Gianola, and F Peñagaricano (2020)
Deep learning versus parametric and ensemble methods for genomic prediction of complex phenotypes.
Genetics Selection Evolution 52: 12.

H Louvandini, PS Corrêa, R Amorín, L Liu, EH Ieda, CR Jimenez, SM Tsai, CM McManus, and F Peñagaricano (2020)
Gestational and lactational exposure to gossypol alters the testis transcriptome.
BMC Genomics 21: 59.

FS Lima, FT Silvestre, F Peñagaricano, and WW Thatcher (2020)
Early genomic prediction of daughter pregnancy rate is associated with improved reproductive performance in Holstein dairy cows.
Journal of Dairy Science 103: 3312-3324.

HA Pacheco, FM Rezende, and F Peñagaricano (2020)
Gene mapping and genomic prediction of bull fertility using sex chromosome markers.
Journal of Dairy Science 103: 3304-3311.

MR Carvalho, C Aboujaoude, F Peñagaricano, JEP Santos, TJ DeVries, BW McBride, and ES Ribeiro (2020)
Associations between maternal characteristics and health, survival, and performance of dairy heifers from birth through to first lactation.
Journal of Dairy Science 103: 823-839.

N Gross, MG Strillacci, F Peñagaricano, and H Khatib (2019)
Characterization and functional roles of paternal RNAs in 2–4 cell bovine embryos.
Scientific Reports 9: 20347.

JE Koltes and F Peñagaricano (2019)
Linking genotype to phenotype: functional annotation as a tool to advance dairy cattle breeding.
In: Advances in Breeding of Dairy Cattle. Chapter 16. Burleigh Dodds Science.

A Sigdel, R Abdollahi-Arpanahi, I Aguilar, and F Peñagaricano (2019)
Whole genome mapping reveals novel genes and pathways involved in milk production under heat stress in US Holstein cows.
Frontiers in Genetics 10: 928.

MR Carvalho, F Peñagaricano, JEP Santos, TJ DeVries, B McBride, and ES Ribeiro (2019)
Long-term impact of postpartum clinical disease on milk production, reproduction, and culling of dairy cows.
Journal of Dairy Science 102: 11701-11717.

R Abdollahi-Arpanahi, MR Carvalho, ES Ribeiro, and F Peñagaricano (2019)
Association of lipid-related genes implicated in conceptus elongation with female fertility traits in dairy cattle.
Journal of Dairy Science 102: 10020–10029.

JP Nani, FM Rezende, and F Peñagaricano (2019)
Predicting male fertility in dairy cattle using markers with large effect and functional annotation data.
BMC Genomics 20: 258.

F Peñagaricano (2019)
Genetics and genomics of dairy cattle.
In: Animal Agriculture: Challenges, Innovations, and Sustainability. pp 101-119. Elsevier.

A Veronese, O Marques, F Peñagaricano, RS Bisinotto, KG Pohler, TR Bilby, and RC Chebel (2019)
Genomic merit for reproductive traits II: Physiological responses of Holstein heifers.
Journal of Dairy Science 102: 6639-6648.

A Veronese, O Marques, R Moreira, AL Belli, RS Bisinotto, TR Bilby, F Peñagaricano, and RC Chebel (2019)
Genomic merit for reproductive traits I: Estrous characteristics and fertility in Holstein heifers.
Journal of Dairy Science 102: 6624-6638.

FM Rezende, JP Nani, and F Peñagaricano (2019)
Genomic prediction of bull fertility in US Jersey dairy cattle.
Journal of Dairy Science 102: 3230–3240.

JD Leal Gutierrez, FM Rezende, MA Elzo, DD Johnson, F Peñagaricano, and RG Mateescu (2018)
Structural equation modeling and whole-genome scans uncover chromosome regions and enriched pathways for carcass and meat quality in beef.
Frontiers in Genetics 9: 532.

AL Skibiel, F Peñagaricano, R Amorín, BM Ahmed, GE Dahl, and J Laporta (2018)
In utero heat stress alters the offspring epigenome.
Scientific Reports 8: 14609.

HA Pacheco, S da Silva, A Sigdel, CK Mak, KN Galvão, RA Teixeira, LT Dias, and F Peñagaricano (2018)
Gene mapping and gene-set analysis for milk fever incidence in Holstein dairy cattle.
Frontiers in Genetics 9: 465.

B Dado-Senn, AL Skibiel, TF Fabris, Y Zhang, GE Dahl, F Peñagaricano, and J Laporta (2018)
RNA-Seq reveals novel genes and pathways involved in bovine mammary involution during the dry period and under environmental heat stress.
Scientific Reports 8: 11096.

E Armstrong, A Iriarte, P Nicolini, J De Los Santos, J Ithurralde, A Bielli, G Bianchi, and F Peñagaricano (2018)
Comparison of transcriptomic landscapes of different lamb muscles using RNA-Seq.
PLoS ONE 13: e0200732.

FM Rezende, GO Dietsch, and F Peñagaricano (2018)
Genetic dissection of bull fertility in U.S. Jersey dairy cattle.
Animal Genetics 49: 393–402.

RD López-Correa, F Peñagaricano, G Rovere, and JI Urioste (2018)
Genetic parameter estimation for long endurance trials in the Uruguayan Criollo horse.
Journal of Animal Breeding and Genetics 135: 186–193.

P Nicolini, R Amorín, Y Han, and F Peñagaricano (2018)
Whole-genome scan reveals significant non-additive effects for sire conception rate in Holstein cattle.
BMC Genetics 19: 14.

JC Ochoa, F Peñagaricano, GM Baez, LF Melo, JC Motta, A García-Guerra, R Meidan, JCP Ferreira, R Sartori, and MC Wiltbank (2018)
Mechanisms for rescue of CL during pregnancy: Gene expression in bovine CL following intrauterine pulses of Prostaglandins E1 and F2α.
Biology of Reproduction 98: 465–479.

H Namous, F Peñagaricano, E Capra, M Del Corvo, DL Thomas, A Stella, JL Williams, P Ajmone-Marsan, and H Khatib (2018)
Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy.
BMC Genomics 19: 123.

R Abdollahi-Arpanahi, G Morota, and F Peñagaricano (2017)
Predicting bull fertility using genomic data and biological information.
Journal of Dairy Science 100: 9656–9666.

F Peñagaricano, A De Vries, and DT Bennink (2017)
Genomic selection and reproductive technologies to optimize herd replacements.
In: Large Dairy Herd Management, 3rd ed. pp 379-388. ADSA® Foundation.

H Naya, F Peñagaricano, and JI Urioste (2017)
Modelling female fertility traits in beef cattle using linear and non-linear models.
Journal of Animal Breeding and Genetics 134: 202-212.

Y Han and F Peñagaricano (2016)
Unravelling the genomic architecture of bull fertility in Holstein cattle.
BMC Genetics 17: 143.

GJM Rosa, VPS Felipe, and F Peñagaricano (2016)
Applications of Graphical Models in Quantitative Genetics and Genomics.
In: Systems Biology in Animal Production and Health, Vol. 1. pp 95-116. Springer International Publishing.

G Morota, TM Beissinger, and F Peñagaricano F (2016)
MeSH-informed enrichment analysis and MeSH-guided semantic similarity among functional terms and gene products in chicken.
G3: Genes, Genomes, Genetics 6: 2447-2453.

EA Abdalla, F Peñagaricano, TM Byrem, KA Weigel, and GJM Rosa (2016)
Genome-wide association mapping and pathway analysis of leukosis incidence in a US Holstein cattle population.
Animal Genetics 47: 395–407.

AL Sanchez, JI Urioste, F Peñagaricano, K Neimaur, I Sienra, H Naya, and R Kremer (2016)
Genetic parameters of objectionable fibers and of their associations with fleece traits in Corriedale sheep.
Journal of Animal Science 94: 13-20.

J Laporta, F Peñagaricano, and LL Hernandez (2015)
Transcriptomic analysis of the mouse mammary gland reveals new insights for the role of serotonin in lactation.
PLoS ONE 10(10): e0140425.

F Peñagaricano, BD Valente, JP Steibel, RO Bates, CW Ernst, H Khatib, and GJM Rosa (2015)
Exploring causal networks underlying fat deposition and muscularity in pigs through the integration of phenotypic, genotypic and transcriptomic data.
BMC Systems Biology 9: 58.

F Peñagaricano, BD Valente, JP Steibel, RO Bates, CW Ernst, H Khatib, and GJM Rosa (2015)
Searching for causal networks involving latent variables in complex traits: application to growth, carcass, and meat quality traits in pigs.
Journal of Animal Science 93: 4617-4623.

J Laporta, SAE Moore, SR Weaver, CM Cronick, M Olsen, AP Prichard, BP Schnell, TD Crenshaw, F Peñagaricano, RM Bruckmaier, and LL Hernandez (2015)
Increasing serotonin concentrations alters calcium and energy metabolism in dairy cows.
Journal of Endocrinology 226: 43-55.

BD Valente, G Morota, F Peñagaricano, D Gianola, KA Weigel, and GJM Rosa (2015)
The causal meaning of genomic predictors and how it affects construction and comparison of genome-enabled selection models.
Genetics 200: 483-494.

G Morota, F Peñagaricano, JL Petersen, DC Ciobanu, K Tsuyuzaki, and I Nikaido (2015)
An application of MeSH enrichment analysis in livestock.
Animal Genetics 46: 381-387.

F Peñagaricano, X Wang, GJM Rosa, AE Radunz, and H Khatib (2014)
Maternal nutrition induces gene expression changes in fetal muscle and adipose tissues in sheep.
BMC Genomics 15:1034.

JI Urioste, F Peñagaricano, RD López-Correa, H Naya, and R Kremer (2014)
Incidence and relationships of black skin spots in the fleece area and pigmentation traits in commercial Corriedale flocks.
Small Ruminant Research 120: 64-70.

CN Hirsch, JM Foerster, JM Johnson, RS Sekhon, G Muttoni, B Vaillancourt, F Peñagaricano, et al. (2014)
Insights into the maize (Zea mays L.) pan-genome and pan-transcriptome.
The Plant Cell 26: 121-135.

J Kropp, F Peñagaricano, SM Salih, and H Khatib (2014)
Invited review: Genetic contributions underlying development of preimplantation bovine embryos.
Journal of Dairy Science 97: 1187-1201.

F Peñagaricano, AH Souza, PD Carvalho, AM Driver, R Gambra, J Kropp, KS Hackbart, D Luchini, RD Shaver, MC Wiltbank, and H Khatib (2013)
Effect of maternal methionine supplementation on the transcriptome of bovine preimplantation embryos.
PLoS ONE 8(8): e72302.

AM Driver, W Huang, J Kropp, F Peñagaricano, and H Khatib (2013)
Knockdown of CDKN1C (p57kip2) and PHLDA2 results in developmental changes in bovine pre-implantation embryos.
PLoS ONE 8(7): e69490.

AI Trujillo, A Casal, F Peñagaricano, M Carriquiry, and P Chilibroste (2013)
Association of SNP of neuropeptide Y, leptin and IGF-1 genes with residual feed intake in confinement and under grazing condition in Angus cattle.
Journal of Animal Science 91: 4235-4244.

R Gambra, F Peñagaricano, J Kropp, K Khateeb, KA Weigel, J Lucey, and H Khatib (2013)
Genomic architecture of bovine kappa-casein and beta-lactoglobulin.
Journal of Dairy Science 96: 5324–5332.

XY Lan, EC Cretney, J Kropp, K Khateeb, M Berg, F Peñagaricano, R Magness, A Radunz, and H Khatib (2013)
Maternal diet during pregnancy induces gene expression and DNA methylation changes in fetal tissues in sheep.
Frontiers in Genetics 4: 49.

R Abdollahi-Arpanahi, F Peñagaricano, A Aliloo, H Ghiasi, and JI Urioste (2013)
Comparison of Poisson, probit and linear models for analysis of number of inseminations and success at first insemination in Iranian Holstein cows.
Livestock Science 153: 20–26.

XY Lan, F Peñagaricano, L DeJung, KA Weigel, and H Khatib (2013)
Short Communication: A missense mutation in the PROP1 gene affects male fertility and milk production traits in US Holstein population.
Journal of Dairy Science 96: 1255–1257.

F Peñagaricano, KA Weigel, GJM Rosa, and H Khatib (2013)
Inferring quantitative trait pathways associated with bull fertility from a genome-wide association study.
Frontiers in Genetics 3: 307.

G Li, F Peñagaricano, KA Weigel, Y Zhang, GJM Rosa, and H Khatib (2012)
Comparative genomics between fly, mouse, and cattle identifies genes associated with sire conception rate.
Journal of Dairy Science 95: 6122–6129.

F Peñagaricano, KA Weigel, and H Khatib (2012)
Genome-wide association study identifies candidate markers for bull fertility in Holstein dairy cattle.
Animal Genetics 43: 65–71.

X Wang, F Peñagaricano, R Tal-Stein, E Lipkin, and H Khatib (2012)
Short Communication: Association of an OLR1 polymorphism with milk production traits in the Israeli Holstein population.
Journal of Dairy Science 95: 1565–1567.

AM Driver, F Peñagaricano, W Huang, KR Ahmad, KS Hackbart, MC Wiltbank, and H Khatib (2012)
RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts.
BMC Genomics 13: 118.

AI Trujillo, F Peñagaricano, P Grignola, P Nicolini, A Casal, AC Espasandín, H Naya, M Carriquiry, and P Chilibroste (2012)
Using high resolution melting analysis to identify variation of NPY, LEP and IGF-1 genes in Angus cattle.
Livestock Science 146: 193–198.

B Zhang, F Peñagaricano, H Chen, and H Khatib (2012)
Novel transcripts and alternatively spliced genes are associated with early development in bovine embryos.
Animal 68: 1199–1205.

F Peñagaricano and H Khatib (2012)
Association of milk protein genes with fertilization rate and early embryonic development in Holstein dairy cattle.
Journal of Dairy Research 79: 47–52.

W Huang, F Peñagaricano, K Ahmad, J Lucey, KA Weigel, and H Khatib (2012)
Association between milk protein gene variants and protein composition traits in dairy cattle.
Journal of Dairy Science 95: 440–449.

F Peñagaricano, P Zorrilla, H Naya, C Robello, and JI Urioste (2012)
Gene expression analysis identifies new candidate genes associated with the development of black skin spots in Corriedale sheep.
Journal of Applied Genetics 53: 99–106.