Dr. Cowell received a M.S. in Biomathematics with a minor in Mathematics in 1995 from North Carolina State University. In 2000, she received a Ph.D. in Biomathematics with a minor in Immunology, also from North Carolina State University. She spent three years as a postdoctoral fellow in the Department of Immunology at Duke University Medical Center and then became an Assistant Professor in the Department of Biostatistics and Bioinformatics.  She was also on the graduate faculty at Duke for the Computational Biology and Bioinformatics Graduate Program. In September 2010, she joined the Biomedical Informatics Division in the Department of Clinical Sciences at UT Southwestern. Dr. Cowell is broadly interested in understanding the mechanisms of adaptive immunity and their role in infectious diseases, autoimmune diseases, cancer immunology, and vaccine responses. Her methodologic focus has centered on the development of probabilistic models and the use of formal logics for representing and computing with descriptive information. Dr. Cowell is also involved in the educational mission at UT Southwestern. She is a member of the Graduate Program in Immunology. She directs the Introduction to Statistics course for first year graduate students and is involved in training and mentoring graduate students and postdoctoral fellows.


Adaptive Immunity

Research in the Cowell group is directed toward advancing understanding of (1) the molecular mechanisms by which adaptive immune receptor genes are somatically generated and diversified, (2) the role of these mechanisms in disease, and (3) the dynamics of adaptive immune receptor repertoires in the context of various states of human health and disease. In addition to our basic science research, we have pursued clinical applications in the areas of autoimmune disease (e.g., multiple sclerosis), infectious disease (e.g., Staphylococcus aureus, HIV), and cancer immunology (e.g., HPV-related cancers, particularly cervical cancer, ovarian cancer, design of chimeric antigen receptors for cancer therapy).


Computable Representations of Descriptive Biological and Clinical Information 

Dr. Cowell’s research in this area has focused on using formal logics to represent and compute with biological and clinical information in the immunology and infectious diseases domains. She is interested in using logical representations to enhance the analysis of high-throughput biological data and its integration with electronic health record data.


University of North Carolina A (1992), Education
Graduate School
North Carolina State Universit (1995)
Graduate School
North Carolina State Universit (2000)

Research Interest

  • 1. Somatic diversification of antigen receptor encoding genes
  • 2. Antigen receptor repertoire dynamics
  • 3. Biomedical Ontologies and formal logic


Featured Publications LegendFeatured Publications

iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories.
Corrie BD, Marthandan N, Zimonja B, Jaglale J, Zhou Y, Barr E, Knoetze N, Breden FMW, Christley S, Scott JK, Cowell LG, Breden F Immunol. Rev. 2018 Jul 284 1 24-41
VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.
Christley S, Scarborough W, Salinas E, Rounds WH, Toby IT, Fonner JM, Levin MK, Kim M, Mock SA, Jordan C, Ostmeyer J, Buntzman A, Rubelt F, Davila ML, Monson NL, Scheuermann RH, Cowell LG Front Immunol 2018 9 976
Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data.
Rubelt F, Busse CE, Bukhari SAC, B├╝rckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, Scott JK, Breden F, Luning Prak ET, Kleinstein SH Nat. Immunol. 2017 Nov 18 12 1274-1278
VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.
Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG BMC Bioinformatics 2017 Oct 18 1 448
Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.
Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB Front Immunol 2017 8 1418
Peripheral VH4+ plasmablasts demonstrate autoreactive B cell expansion toward brain antigens in early multiple sclerosis patients.
Rivas JR, Ireland SJ, Chkheidze R, Rounds WH, Lim J, Johnson J, Ramirez DM, Ligocki AJ, Chen D, Guzman AA, Woodhall M, Wilson PC, Meffre E, White C, Greenberg BM, Waters P, Cowell LG, Stowe AM, Monson NL Acta Neuropathol. 2016 Oct
VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.
Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG BMC Bioinformatics 2016 Oct 17 Suppl 13 333
MSPrecise: A molecular diagnostic test for multiple sclerosis using next generation sequencing.
Rounds WH, Salinas EA, Wilks TB, Levin MK, Ligocki AJ, Ionete C, Pardo CA, Vernino S, Greenberg BM, Bigwood DW, Eastman EM, Cowell LG, Monson NL Gene 2015 Jul
owlcpp: a C++ library for working with OWL ontologies.
Levin MK, Cowell LG J Biomed Semantics 2015 6 35
A genome-wide association study of variants associated with acquisition of Staphylococcus aureus bacteremia in a healthcare setting.
Nelson CL, Pelak K, Podgoreanu MV, Ahn SH, Scott WK, Allen AS, Cowell LG, Rude TH, Zhang Y, Tong A, Ruffin F, Sharma-Kuinkel BK, Fowler VG BMC Infect. Dis. 2014 14 1 83