Associated Departments

Veterinary Science

Scholars@UK

Running a genetic stop sign accelerates oxygen metabolism and energy production in horses

Castiglione, G. M., Chen, X., Xu, Z., Dbouk, N. H., Bose, A. A., Carmona-Berrio, D., Chi, E. E., Zhou, L., Boronina, T. N., Cole, R. N., Wu, S., Liu, A. D., Liu, T. D., Lu, H., Kalbfleisch, T., Rinker, D., Rokas, A., Ortved, K. & Duh, E. J., Mar 28 2025, In: Science. 387, 6741, p. eadr8589

Research output: Contribution to journal › Article › peer-review

Annotation of cis-regulatory-associated histone modifications in the genomes of two Thoroughbred stallions

Barber, A. M., Kingsley, N. B., Peng, S., Giulotto, E., Bellone, R. R., Finno, C. J., Kalbfleisch, T. & Petersen, J. L., 2025, In: Frontiers in Genetics. 16, 1534461.

Research output: Contribution to journal › Article › peer-review

A comprehensive allele specific expression resource for the equine transcriptome

Heath, H. D., Peng, S., Szmatola, T., Ryan, S., Bellone, R. R., Kalbfleisch, T., Petersen, J. L. & Finno, C. J., Dec 2025, In: BMC Genomics. 26, 1, 88.

Research output: Contribution to journal › Article › peer-review

Data reuse in agricultural genomics research: Challenges and recommendations

Hafner, A., Deleo, V., Deng, C. H., Elsik, C. G., S Fleming, D., Harrison, P. W., Kalbfleisch, T. S., Petry, B., Pucker, B., Quezada-Rodríguez, E. H., Tuggle, C. K. & Koltes, J. E., 2025, In: GigaScience. 14, giae106.

Research output: Contribution to journal › Review article › peer-review

Three decades of rat genomics: approaching the finish(ed) line

Kalbfleisch, T. S., Smith, M. L., Ciosek, J. L., Li, K. & Doris, P. A., Dec 2024, In: Physiological Genomics. 56, 12, p. 807-818 12 p.

Research output: Contribution to journal › Review article › peer-review

Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding

Li, K., Smith, M. L., Blazier, J. C., Kochan, K. J., Wood, J. M. D., Howe, K., Kwitek, A. E., Dwinell, M. R., Chen, H., Ciosek, J. L., Masterson, P., Murphy, T. D., Kalbfleisch, T. S. & Doris, P. A., Nov 2024, In: Genome Research. 34, 11, p. 2081-2093 13 p.

Research output: Contribution to journal › Article › peer-review

Analyses of whole-genome sequences from 185 North American Thoroughbred horses, spanning 5 generations

Bailey, E., Finno, C. J., Cullen, J. N., Kalbfleisch, T. & Petersen, J. L., Dec 2024, In: Scientific Reports. 14, 1, 22930.

Research output: Contribution to journal › Article › peer-review

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

de Jong, T. V., Pan, Y., Rastas, P., Munro, D., Tutaj, M., Akil, H., Benner, C., Chen, D., Chitre, A. S., Chow, W., Colonna, V., Dalgard, C. L., Demos, W. M., Doris, P. A., Garrison, E., Geurts, A. M., Gunturkun, H. M., Guryev, V., Hourlier, T. & Howe, K. & 31 others, Huang, J., Kalbfleisch, T., Kim, P., Li, L., Mahaffey, S., Martin, F. J., Mohammadi, P., Ozel, A. B., Polesskaya, O., Pravenec, M., Prins, P., Sebat, J., Smith, J. R., Solberg Woods, L. C., Tabakoff, B., Tracey, A., Uliano-Silva, M., Villani, F., Wang, H., Sharp, B. M., Telese, F., Jiang, Z., Saba, L., Wang, X., Murphy, T. D., Palmer, A. A., Kwitek, A. E., Dwinell, M. R., Williams, R. W., Li, J. Z. & Chen, H., Apr 10 2024, In: Cell Genomics. 4, 4, 100527.

Research output: Contribution to journal › Article › peer-review

The Ruminant Telomere-to-Telomere (RT2T) Consortium

Kalbfleisch, T. S., McKay, S. D., Murdoch, B. M., Adelson, D. L., Almansa-Villa, D., Becker, G., Beckett, L. M., Benítez-Galeano, M. J., Biase, F., Casey, T., Chuong, E., Clark, E., Clarke, S., Cockett, N., Couldrey, C., Davis, B. W., Elsik, C. G., Faraut, T., Gao, Y. & Genet, C. & 58 others, Grady, P., Green, J., Green, R., Guan, D., Hagen, D., Hartley, G. A., Heaton, M., Hoyt, S. J., Huang, W., Jarvis, E., Kalleberg, J., Khatib, H., Koepfi, K. P., Koltes, J., Koren, S., Kuehn, C., Leeb, T., Leonard, A., Liu, G. E., Low, W. Y., McConnell, H., McRae, K., Miga, K., Mousel, M., Neibergs, H., Olagunju, T., Pennell, M., Petry, B., Pewsner, M., Phillippy, A. M., Pickett, B. D., Pineda, P., Potapova, T., Rachagani, S., Rhie, A., Rijnkels, M., Robic, A., Rodriguez Osorio, N., Safonova, Y., Schettini, G., Schnabel, R. D., Sirpu Natesh, N., Stegemiller, M., Storer, J., Stothard, P., Stull, C., Tosser-Klopp, G., Traglia, G. M., Tuggle, C. K., Van Tassell, C. P., Watson, C., Weikard, R., Wimmers, K., Xie, S., Yang, L., Smith, T. P. L., O’Neill, R. J. & Rosen, B. D., Aug 2024, In: Nature Genetics. 56, 8, p. 1566-1573 8 p.

Research output: Contribution to journal › Article › peer-review

Association of ARRDC3 and NFIA variants with bovine congestive heart failure in feedlot cattle

Heaton, M. P., Harhay, G. P., Bassett, A. S., Clark, H. J., Carlson, J. M., Jobman, E. E., Sadd, H. R., Pelster, M. C., Workman, A. M., Kuehn, L. A., Kalbfleisch, T. S., Piscatelli, H., Carrie, M., Krafsur, G. M., Grotelueschen, D. M. & Vander Ley, B. L., 2022, In: F1000Research. 11, p. 385 1 p.

Research output: Contribution to journal › Article › peer-review

The localization of centromere protein A is conserved among tissues

Cappelletti, E., Piras, F. M., Sola, L., Santagostino, M., Petersen, J. L., Bellone, R. R., Finno, C. J., Peng, S., Kalbfleisch, T. S., Bailey, E., Nergadze, S. G. & Giulotto, E., Dec 2023, In: Communications Biology. 6, 1, 963.

Research output: Contribution to journal › Article › peer-review

Imputed genomes of historical horses provide insights into modern breeding

Todd, E. T., Fromentier, A., Sutcliffe, R., Running Horse Collin, Y., Perdereau, A., Aury, J. M., Èche, C., Bouchez, O., Donnadieu, C., Wincker, P., Kalbfleisch, T., Petersen, J. L. & Orlando, L., Jul 21 2023, In: iScience. 26, 7, 107104.

Research output: Contribution to journal › Article › peer-review

First gene-edited calf with reduced susceptibility to a major viral pathogen

Workman, A. M., Heaton, M. P., Vander Ley, B. L., Webster, D. A., Sherry, L., Bostrom, J. R., Larson, S., Kalbfleisch, T. S., Harhay, G. P., Jobman, E. E., Carlson, D. F. & Sonstegard, T. S., May 1 2023, In: PNAS Nexus. 2, 5, pgad125.

Research output: Contribution to journal › Article › peer-review

Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features

Jevit, M. J., Castaneda, C., Paria, N., Das, P. J., Miller, D., Antczak, D. F., Kalbfleisch, T. S., Davis, B. W. & Raudsepp, T., Dec 2023, In: Scientific Reports. 13, 1, 20180.

Research output: Contribution to journal › Article › peer-review

Functional annotation of the animal genomes: An integrated annotation resource for the horse

Peng, S., Dahlgren, A. R., Donnelly, C. G., Hales, E. N., Petersen, J. L., Bellone, R. R., Kalbfleisch, T. & Finno, C. J., Mar 1 2023, In: PLoS Genetics. 19, 3, p. e1010468

Research output: Contribution to journal › Review article › peer-review

Using whole genome sequence to compare variant callers and breed differences of US sheep

Stegemiller, M. R., Redden, R. R., Notter, D. R., Taylor, T., Taylor, J. B., Cockett, N. E., Heaton, M. P., Kalbfleisch, T. S. & Murdoch, B. M., Jan 4 2023, In: Frontiers in Genetics. 13, 1060882.

Research output: Contribution to journal › Article › peer-review

Genetic diversity and connectivity of moose (Alces americanus americanus) in eastern North America

Rosenblatt, E., Gieder, K., Donovan, T., Murdoch, J., Smith, T. P. L., Heaton, M. P., Kalbfleisch, T. S., Murdoch, B. M., Bhattarai, S., Pacht, E., Verbist, E., Basnayake, V. & McKay, S., Apr 2023, In: Conservation Genetics. 24, 2, p. 235-248 14 p.

Research output: Contribution to journal › Article › peer-review

The Assembled Genome of the Stroke-Prone Spontaneously Hypertensive Rat

Kalbfleisch, T. S., Hussien Abouel Ela, N. A., Li, K., Brashear, W. A., Kochan, K. J., Hillhouse, A. E., Zhu, Y., Dhande, I. S., Kline, E. J., Hudson, E. A., Murphy, T. D., Thibaud-Nissen, F., Smith, M. L. & Doris, P. A., Jan 1 2023, In: Hypertension. 80, 1, p. 138-146 9 p.

Research output: Contribution to journal › Article › peer-review

Evidence for origin of lavender foal syndrome among Egyptian Arabian horses in Egypt

AbouEl Ela, N. H., El Araby, I. E., Saleh, A. A., Abd El-fattah, A. H., Hagag, N. M., Brooks, S. A., Radwan, M. A. & Kalbfleisch, T., May 2023, In: Equine Veterinary Journal. 55, 3, p. 487-493 7 p.

Research output: Contribution to journal › Article › peer-review

mRatBN7.2: familiar and unfamiliar features of a new rat genome reference assembly

de Jong, T. V., Chen, H., Brashear, W. A., Kochan, K. J., Hillhouse, A. E., Zhu, Y., Dhande, I. S., Hudson, E. A., Sumlut, M. H., Smith, M. L., Kalbfleisch, T. S. & Doris, P. A., Jul 2022, In: Physiological Genomics. 54, 7, p. 251-260 10 p.

Research output: Contribution to journal › Article › peer-review

Animal Breeding-RCN: Farm Animal Genomics Collaborative

Kalbfleisch, T. (PI)

Utah State University

7/1/24 → 6/30/29

Project: Research project

Use of mRNA Expression and Serum Biomarkers as Tools to Monitor Musculoskeletal Adaptation in Thoroughbred Horses Returning to Race Training

Page, A. (PI), Adam, E. (CoI) & Kalbfleisch, T. (CoI)

Hong Kong Jockey Club Equine Welfare Research Foundation Limited

7/1/24 → 12/31/26

Project: Research project

Functionally Annotated Equine Pangenome with Infrastructure for an Accessible, Integrative, Community Genomics Resource

Kalbfleisch, T. (PI)

National Institute of Food and Agriculture

7/1/24 → 6/30/27

Project: Research project

Reference Free Query of High Throughput Genetic Data in a Distributed Environment

Kalbfleisch, T. (PI)

University of Arizona

8/25/23 → 12/31/23

Project: Research project

NIFA AG2PI Collaborative: Seeding the Future of Agricultural Genome to Phenome Research for Crops and Livestock (A Genetic Database to Enable Discovery of Deleterious Genetic Variants in Farmed Animals)

Kalbfleisch, T. (PI)

Iowa State University

6/1/22 → 8/31/23

Project: Research project

Long-Read Assembly and Annotation of Rat Genomes that are Important Models of Complex Genetic Disease

Kalbfleisch, T. (PI)

University of Texas Health Science Center at Houston

7/12/21 → 4/30/26

Project: Research project

Late onset hereditary cataract in the Boston Terrier: A whole genome sequencing approach

Graves, K. (PI) & Kalbfleisch, T. (CoI)

AKC Canine Health Foundation

8/1/21 → 7/31/22

Project: Research project

Identification of Novel mRNA Targets in Catastrophically Injured Thoroughbred Racehorses Using RNA Sequencing

Page, A. (PI), Adam, E. (CoI), Horohov, D. (CoI), Kalbfleisch, T. (CoI) & MacLeod, J. (CoI)

KY Horse Racing Commission

7/1/20 → 6/30/22

Project: Research project

Annotation of Functional Regulatory Regions in the Horse

Kalbfleisch, T. (PI)

University of Nebraska

4/1/19 → 2/28/22

Project: Research project