Watson Lab

About 

We are part of the Biochemistry and Molecular Genetics Department at the University of Louisville School of Medicine (Louisville, KY). Our research projects, using both human and animal model systems, span the fields of molecular, population, evolutionary, and disease genomics. The primary projects in the lab are focused on characterizing and cataloguing genetic diversity in immune receptor genes across human populations and several animal model species. Our aim is to understand how genetic and epigenetic variation influence immune receptor function and the dynamics of the immune response, and how this information can be leveraged to inform our understanding of disease susceptibility and clinical health outcomes.

Key Research Areas

• Immunogenomics
• Antibody and T cell receptor function
• Immunobiology
• Gene regulation
• Disease genetics (infectious disease, autoimmunity, cancer) 

Current Projects

• Population genotyping of the germline immunoglobulin repertoire in AIDS-designated rhesus macaque breeding colonies, NIAID, 2R24AI162317
• A genomic reference resource for the human heavy and light chain immunoglobulin loci, NIAID, R24AI138963
• Investigating the drivers of interspecific variation in antibody immunity using comparative genomic and phylogenetic approaches, NSF, 2536096
• Antibody gene signatures in rheumatic heart disease: uncovering pathways toward improved patient outcomes, American Heart Association, 24TPA1301777
• Collaborative Team Science to Delineate the Mechanisms Underlying Primary Resistance or Response to Tumor-infiltrating Lymphocyte Therapy in Cancer Patients, NIH/NIGMS, 3P20GM135004-05S1
• iAKC: Integrated AIRR Knowledge Commons, NIAID, U24 AI170505
• Towards a predictive understanding of influenza immunity through experimental data integration, iterative model development, and rigorous assessment of model quality, NIAID 

Team 

• Kaitlyn Shields – Lab Coordinator
• Zach Vanwinkle – Research Assistant III\
• Brandon Croslin – Research Technician I
• Connor Murray – Data Analyst III
• Uddalok Jana – PhD Candidate
• Chandrima Bharadwaj – PhD Candidate

Recent Publications

• Lindeman, I., Officer, A., Dahal-Koirala, S., Risnes, L. F., Hjort, R., Lundin, K. E. A., Ness-Jensen, E., Watson, C. T., & Sollid, L. M. 2026. A predisposing effect of HLA class II genes in celiac disease by skewing the naïve CD4+ T-cell receptor repertoire. PNAS. 123(26):e2520636123
• Nguyen, Y. T. K., Chen, F., Giang, E., Saha, S., Ueno, L. A., Chen, C., Watson, C. T., Tzarum, N., Wilson, I. A., Law, M., Stanfield, R. 2026. Structural and genetic signatures of two classes of HCV E2 neutralizing face antibodies from non-human primates immunized with a recombinant E1E2. NPJ Vaccines. doi: 10.1038/s41541-026-01449-1
• Officer, A., Watson, C. T., Engelbrecht, E., Dahal-Koirala, S., Risnes, L. F., Lundin, K. E. A., Ness-Jensen, E., Lindeman, I., & Sollid, L. M. 2026. Immunoglobulin gene polymorphisms shape the naïve B-cell receptor repertoire; relevance to celiac disease. Genes Immun. 27(2):210-222.
• Rasche, K. M., Tieri, D., Morrissey, S. M., Li, H., Zhang, F., Gibson, W. S., Ford, E. E., Jana, U., Smith, M. L., Yan, J., & Watson, C. T.* 2026. B cell phenotypes and antibody signatures associate with interpatient variation in the lung adenocarcinoma tumor microenvironment. Front Immunol. 16:1739637. 
• Peres, A., Upadhyay, A. A., Klein, V., Saha, S., Rodriguez, O. L., Vanwinkle, Z. M., Karunakaran, K., Metz, A., Lauer, W., Lin, M. C., Melton, T., Granholm, L., Polak, P., Peterson, S. M., Peterson, E. J., Raju, N., Shields, K., Schultze, S., Ton, T., Ericsen, A., Lapp, S. A., Villinger, F., Ohlin, M., Cottrell, C. A., Amara, R. R., Derdeyn, C. A., Crotty, S., Schief, W. R., Karlsson Hedestam, G. B., Smith, L. L., Lees, W., Watson, C. T.*, Yaari, G.*, Bosinger, S. E.* 2026. Population-level genomic analysis of immunoglobulin loci variation in rhesus macaques reveals extensive germline diversity. Immunity. 
• Jana, U., Rodriguez, O. L., Lees, W. D., Engelbrecht, E., Vanwinkle, Z. M., Peres, A., Gibson, W. S., Shields, K., Schultze, S., Dorgham, A., Emery, M., Deikus, G., Sebra, R., Eichler, E. E., Yaari, G., Smith, L. M.*, Watson, C. T.* 2026. The human immunoglobulin heavy chain constant gene locus is enriched for large complex structural variants and coding polymorphisms that vary in frequency among human populations. Cell Genomics. 101058. 
• Engelbrecht, E., Rodriguez, O. L., Lees, W. D., Vanwinkle, Z. M., Shields, K., Schultze, S., Gibson, W. S., Smith, D. R., Jana, U., Saha, S., Peres, A., Yaari, G., Smith, L. M., Watson, C. T.* 2026. Germline polymorphisms in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire. Nature Communications. 
• Safonova, Y., Collins, A. M., Murdoch, B. M., Rosen, B. D., Smith, T. P. L., Watson, C. T. 2025. Immunogenomics Approaches to Studying Antibody Repertoires and Vaccine Responses in Ruminants. Annu Rev Anim Biosci. 
• Lees, W. D.*, Peres, A., Klein, V., Amos, N., Jana, U., Engelbrecht, E., Vanwinkle, Z. M., Malach, Y., Konstantinovsky, T., Polak, P., Watson, C. T.*, Yaari, G*. 2025. The current landscape of adaptive immune receptor genomic and repertoire data: OGRDB and VDJbase. Nucleic Acids Res. 6:gkaf1094. 
• Cowell, L. G., Christley, S., Breden, F., Burns, K. A., Corrie, B. D., Lees, W. D., Overton, J. A., Peters, B., Richardson, E., Roskin, K. M., Scheffer, L., Vita, R., Watson, C. T., Yaari, G. 2025. The Adaptive Immune Receptor Repertoire Knowledge Commons: An invitation to the community. Cell Syst. 16(9):101401. 
• Collins, A. M., Watson, C. T., Van den Ham, H. J., Teyton, L., Rosati, E., Safonova, Y. 2025. Challenges for the immunoglobulin and T cell receptor gene nomenclatures in the modern genomics era. Immunoinformatics. 100053 
• Watson, C. T.*, Collins, A. M., Ohlin, M., Heather, J. M., Peres, A., Lees, W. D., Yaari, G*. 2025. Building immunoglobulin and T cell receptor gene databases for the future. Immunoinformatics. 100059
• Pospelova, M., Voss, K., Zamyatin, A., Watson, C. T., Koepfli, K. P., Bankevich, A., Pennell, M., Safonova, Y. 2025. Comparative analysis of mammalian adaptive immune loci revealed spectacular divergence and common genetic patterns. Mol Biol Evol. 42(7):msaf152
• Gornitzka, M. B., Røsjø, E., Jana, U., Ford, E. E., Tourancheau, A., Lees, W. D., Vanwinkle, Z. M., Smith, L. M., Watson, C. T.*, Lossius, A.* 2025. Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus. Genome Res. 1;35(10):2240-2251. 
• Kos, J. T., Safonova, Y., Shields, K. M., Silver, C. A., Lees, W. D., Collins, A. M., Watson, C. T*. 2025. Characterization of Extensive Diversity In Immunoglobulin Light Chain Variable Germline Genes Across Biomedically Important Mouse Strains. ImmunoHorizons. 9(8):vlaf031. 
• Zhu, Y., Watson, C. T., Safonova, Y., Pennell, M., Bankevich, A. 2025. CloseRead: a tool for assessing assembly errors in immunoglobulin loci applied to vertebrate long-read genome assemblies. Genome Biol.26(1):131. 
• Yoo, D. A., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G. A., Solar, S. J., Antipov, D., Pickett, B. D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J. M., Lin, J., Sequeira, A. N., Mangan, R. J., Hickey, G., Monfort Anez, G., Balachandran, P., Bankevich, A., Beck, C. R., Biddanda, A., Borchers, M., Bouffard, G. G., Brannan, E., Brooks, S. Y., Carbone, L., Carrel, L., Chan, A. P., Crawford, J., Diekhans, M., Engelbrecht, E., Feschotte, C., Formenti, G., Garcia, G. H., de Gennaro, L., Gilbert, D., Green, R. E., Guarracino, A., Gupta, I., Haddad, D., Han, J., Harris, R. S., Hartley, G. A., Harvey, W. T., Hiller, M., Hoekzema, K., Houck, M. L., Jeong, H., Kamali, K., Kellis, M., Kille, B., Lee, C., Lee, Y., Lees, W., Lewis, A. P., Li, Q., Loftus, M., Loh, Y. H. E., Loucks, H., Ma, J., Mao, Y., Martinez, J. F. I., Masterson, P., McCoy, R. C., McGrath, B., McKinney, S., Meyer, B. S., Miga, K. H., Mohanty, S. K., Munson, K. M., Pal, K., Pennell, M., Pevzner, P. A., Porubsky, D., Potapova, T., Ringeling, F. R., Rocha, J. L., Ryder, O. A., Sacco, S., Saha, S., Sasaki, T., Schatz, M. C., Schork, N. J., Shanks, C., Smeds, L., Son, D. R., Steiner, C., Sweeten, A. P., Tassia, M. G., Thibaud-Nissen, F., Torres-González, E., Trivedi, M., Wei, W., Wertz, J., Yang, M., Zhang, P., Zhang, S., Zhang, Y., Zhang, Z., Zhao, S. A., Zhu, Y., Jarvis, E. D., Gerton, J. L., Rivas-González, I., Paten, B., Szpiech, Z. A., Huber, C. D., Lenz, T. L., Konkel, M. K., Yi, S. V., Canzar, S., Watson, C. T., Sudmant, P. H., Molloy, E., Garrison, E., Lowe, C. B., Ventura, M., O’Neill, R. J., Koren, S., Makova, K. D., Phillippy, A. M., Eichler, E. E. 2025. Complete sequencing of ape genomes. Nature. 641(8062):401-418.
• Mikelov, A., Nefediev, G., Tashkeev, A., Rodriguez, O. L., Ortmans, D. A., Skatova, V., Izraelson, M., Davydov, A., Poslavsky, S., Rahmouni, S., Watson, C. T., Chudakov, D., Boyd, S. D., Bolotin, D. 2024. Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR. Genome Res. 34(12):2293-2303
• Kalbfleisch, T. S., McKay, S. D., Murdoch, B. M., Adelson, D. L., Almansa-Villa, D., Watson, C. T., Weikard, R., Wimmers, K., Xie, S., Yang, L., Smith, T. P. L., O’Neill, R. J., Rosen, B. D. 2024. The Ruminant Telomere-to-Telomere (RT2T) Consortium. Nature Genetics. 56(8):1566-1573
• Engelbrecht, E., Rodriguez, O. L., Watson, C. T.* 2024. Addressing technical pitfalls in pursuit of molecular factors that mediate immunoglobulin gene regulation. J Immunol. 213(5):651-662
• Engelbrecht, E., Rodriguez, O. L., Shields, K., Schultze, S., Tieri, D., Jana, U., Yaari, G., Lees, W. D., Smith, L. M., Watson, C. T.* 2024. Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry. Genes Immun. 25(4):297-306. 
• Schiffner, T., Phung, I., Ray, R., Irimia, A., Tian, M., Swanson, O., Lee, J. H., Lee, C. D., Marina-Zárate, E., Cho, S. Y., Huang, J., Ozorowski, G., Skog, P. D., Serra, A. M., Rantalainen, K., Allen, J. D., Baboo, S., Rodriguez, O. L., Himansu, S., Zhou, J., Hurtado, J., Flynn, C. T., McKenney, K., Havenar-Daughton, C., Saha, S., Shields, K., Schultze, S., Smith, L. M., Liang, C. H., Toy, L., Pecetta, S., Lin, Y. C., Willis, J. R., Sesterhenn, F., Kulp, D. W., Hu, X., Cottrell, C. A., Zhou, X., Ruiz, J., Wang, X., Nair, U., Kirsch, K. A., Cheng, H. J., Davis, J., Kalyuzhniy, O., Liguori, A., Diedrich, J. K., Ngo, J. T., Lewis, V., Phelps, N., Tingle, R. D., Spencer, S., Georgeson, E., Adachi, Y., Kubitz, M., Eskandarzadeh, S., Elsliger, M. A., Amara, R. R., Landais, E., Briney, B., Burton, D. R., Carnathan, D. G., Silvestri, G., Watson, C. T., Yates, J. R. 3rd, Paulson, J. C., Crispin, M., Grigoryan, G., Ward, A. B., Sok, D., Alt, F. W., Wilson, I. A., Batista, F. D., Crotty, S., Schief, W. R. 2024. Vaccination induces broadly neutralizing antibody precursors to HIV gp41. Nat Immunol. 25(6):1073-1082.
• Steichen, J. M., Phung, I., Salcedo, E., Ozorowski, G., Willis, J. R., Baboo, S., Liguori, A., Cottrell, C. A., Torres, J. L., Madden, P. J., Ma, K. M., Sutton, H. J., Lee, J. H., Kalyuzhniy, O., Allen, J. D., Rodriguez, O. L., Adachi, Y., Mullen, T. M., Georgeson, E., Kubitz, M., Burns, A., Barman, S., Mopuri, R., Metz, A., Altheide, T. K., Diedrich, J. K., Saha, S., Shields, K., Schultze, S. E., Smith, L. M., Schiffner, T., Burton, D. R., Watson, C. T., Bosinger, S. E., Crispin, M., Yates, J. R. 3rd, Paulson, J. C., Ward, A. B., Sok, D., Crotty, S., Schief, W. R. 2024. Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates. Science. 384(6697):eadj8321.
• Lees, W. D., Saha, S., Yaari, G., Watson, C. T. 2024. Digger: Directed annotation of immunoglobulin and T cell receptor V, D and J gene sequences and assemblies. Bioinformatics. 40(3):btae144.
• Collins, A. M., Ohlin, M., Corcoran, M. M., Heather, J. M., Ralph, D., Law, M., Martínez-Barnetche, J., Ye, J., Richardson, E., Gibson, W. S., Rodriguez, O. L., Peres, A., Yaari, G., Watson, C. T., Lees, W. D. 2024. AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes. Front Immunol. 4:1330153. 

A complete listing of publications can be found here.