Center for Biomolecular and Tissue Engineering Center for Biomolecular and Tissue Engineering
Pratt School of Engineering
Duke University

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Thomas B. Kepler, Professor of Biostatistics and Bioinformatics and Center for Biomolecular and Tissue Engineering and Chief, Computational Biology

Thomas B. Kepler

Please note: Thomas has left the "Center for Biomolecular and Tissue Engineering" group at Duke University; some info here might not be up to date.

Contact Info:
Office Location:  101A North Building
Email Address: send me a message
Web Page:


Ph.D.Brandeis University1989
B.A.University of Massachusetts at Amherst1985

Representative Publications   (More Publications)

  1. Markert, ML; Devlin, BH; Alexieff, MJ; Li, J; McCarthy, EA; Gupton, SE; Chinn, IK; Hale, LP; Kepler, TB; He, M; Sarzotti, M; Skinner, MA; Rice, HE; Hoehner, JC, Review of 54 patients with complete DiGeorge anomaly enrolled in protocols for thymus transplantation: outcome of 44 consecutive transplants., Blood, vol. 109 no. 10 (May, 2007), pp. 4539-4547, ISSN 0006-4971 [17284531], [doi]  [abs]
  2. Kepler, TB; Chan, C, Spatiotemporal programming of a simple inflammatory process., Immunological Reviews, vol. 216 (April, 2007), pp. 153-163, ISSN 0105-2896 [17367341], [doi]  [abs]
  3. Chan, C; Kepler, TB, Computational immunology--from bench to virtual reality., Annals of the Academy of Medicine, Singapore, vol. 36 no. 2 (February, 2007), pp. 123-127, ISSN 0304-4602 [17364079]  [abs]
  4. Culton, DA; Nicholas, MW; Bunch, DO; Zhen, QL; Kepler, TB; Dooley, MA; Mohan, C; Nachman, PH; Clarke, SH, Similar CD19 dysregulation in two autoantibody-associated autoimmune diseases suggests a shared mechanism of B-cell tolerance loss., Journal of Clinical Immunology, vol. 27 no. 1 (January, 2007), pp. 53-68, ISSN 0271-9142 [17195045], [doi]  [abs]
  5. Ray, S; Kepler, TB, Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding., Immunome Research, vol. 3 (October, 2007), pp. 9, ISSN 1745-7580 [17967170], [doi]  [abs]
  6. Bauer, DC; Hunter, DJ; Abramson, SB; Attur, M; Corr, M; Felson, D; Heinegård, D; Jordan, JM; Kepler, TB; Lane, NE; Saxne, T; Tyree, B; Kraus, VB; Osteoarthritis Biomarkers Network, , Classification of osteoarthritis biomarkers: a proposed approach., Osteoarthritis and Cartilage, vol. 14 no. 8 (August, 2006), pp. 723-727, ISSN 1063-4584 [16733093], [doi]  [abs]
  7. Liu, C; He, M; Rooney, B; Kepler, TB; Chao, NJ, Longitudinal analysis of T-cell receptor variable beta chain repertoire in patients with acute graft-versus-host disease after allogeneic stem cell transplantation., Biology of Blood and Marrow Transplantation, vol. 12 no. 3 (March, 2006), pp. 335-345, ISSN 1083-8791 [16503503], [doi]  [abs]
  8. Fadel, SA; Cowell, LG; Cao, S; Ozaki, DA; Kepler, TB; Steeber, DA; Sarzotti, M, Neonate-primed CD8+ memory cells rival adult-primed memory cells in antigen-driven expansion and anti-viral protection., International Immunology, vol. 18 no. 2 (February, 2006), pp. 249-257, ISSN 0953-8178 [16418189], [doi]  [abs]
  9. Volpe, JM; Cowell, LG; Kepler, TB, SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations., Bioinformatics, vol. 22 no. 4 (February, 2006), pp. 438-444, ISSN 1367-4803 [16357034], [doi]  [abs]
  10. He, M; Tomfohr, JK; Devlin, BH; Sarzotti, M; Markert, ML; Kepler, TB, SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization., Bioinformatics, vol. 21 no. 18 (September, 2005), pp. 3697-3699, ISSN 1367-4803 [16051675], [doi]  [abs]
  11. Kepler, TB; He, M; Tomfohr, JK; Devlin, BH; Sarzotti, M; Markert, ML, Statistical analysis of antigen receptor spectratype data., Bioinformatics, vol. 21 no. 16 (August, 2005), pp. 3394-3400, ISSN 1367-4803 [15955781], [doi]  [abs]
  12. Lu, J; Tomfohr, JK; Kepler, TB, Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach., BMC Bioinformatics, vol. 6 (June, 2005), pp. 165, ISSN 1471-2105 [15987513], [doi]  [abs]
  13. Tomfohr, J; Lu, J; Kepler, TB, Pathway level analysis of gene expression using singular value decomposition., BMC Bioinformatics, vol. 6 (September, 2005), pp. 225, ISSN 1471-2105 [16156896], [doi]  [abs]
  14. Smith, JT; Tomfohr, JK; Wells, MC; Beebe, TP; Kepler, TB; Reichert, WM, Measurement of cell migration on surface-bound fibronectin gradients., Langmuir, vol. 20 no. 19 (September, 2004), pp. 8279-8286, ISSN 0743-7463 [15350103], [doi]  [abs]
  15. Zhang, S-M; Adema, CM; Kepler, TB; Loker, ES, Diversification of Ig superfamily genes in an invertebrate., Science, vol. 305 no. 5681 (July, 2004), pp. 251-254, ISSN 1095-9203 [15247481], [doi]  [abs]
  16. Loker, ES; Adema, CM; Zhang, S-M; Kepler, TB, Invertebrate immune systems--not homogeneous, not simple, not well understood., Immunological Reviews, vol. 198 (April, 2004), pp. 10-24, ISSN 0105-2896 [15199951]  [abs]
  17. Gao, F; Chen, Y; Levy, DN; Conway, JA; Kepler, TB; Hui, H, Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious., Journal of virology, vol. 78 no. 5 (March, 2004), pp. 2426-2433, ISSN 0022-538X [14963138]  [abs]
  18. Bartl, S; Miracle, AL; Rumfelt, LL; Kepler, TB; Mochon, E; Litman, GW; Flajnik, MF, Terminal deoxynucleotidyl transferases from elasmobranchs reveal structural conservation within vertebrates., Immunogenetics, vol. 55 no. 9 (December, 2003), pp. 594-604, ISSN 0093-7711 [14579105], [doi]  [abs]
  19. Trachtenberg, E; Korber, B; Sollars, C; Kepler, TB; Hraber, PT; Hayes, E; Funkhouser, R; Fugate, M; Theiler, J; Hsu, YS; Kunstman, K; Wu, S; Phair, J; Erlich, H; Wolinsky, S, Advantage of rare HLA supertype in HIV disease progression., Nature Medicine, vol. 9 no. 7 (July, 2003), pp. 928-935, ISSN 1078-8956 [12819779], [doi]  [abs]
  20. Cowell, LG; Davila, M; Yang, K; Kepler, TB; Kelsoe, G, Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling., The Journal of Experimental Medicine, vol. 197 no. 2 (January, 2003), pp. 207-220, ISSN 0022-1007 [12538660]  [abs]
  21. Kepler, TB; Crosby, L; Morgan, KT, Normalization and analysis of DNA microarray data by self-consistency and local regression., Genome Biology, vol. 3 no. 7 (June, 2002), pp. RESEARCH0037, ISSN 1465-6914 [12184811]  [abs]
  22. Cowell, LG; Davila, M; Kepler, TB; Kelsoe, G, Identification and utilization of arbitrary correlations in models of recombination signal sequences., Genome Biology, vol. 3 no. 12 (2002), pp. RESEARCH0072, ISSN 1465-6914 [12537561]  [abs]
  23. Zavolan, M; Kepler, TB, Statistical inference of sequence-dependent mutation rates., Current Opinion in Genetics & Development, vol. 11 no. 6 (December, 2001), pp. 612-615, ISSN 0959-437X [11682302]  [abs]
  24. Kepler, TB; Elston, TC, Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations., Biophysical Journal, vol. 81 no. 6 (December, 2001), pp. 3116-3136, ISSN 0006-3495 [11720979], [doi]  [abs]
  25. Buchman, TG; Cobb, JP; Lapedes, AS; Kepler, TB, Complex systems analysis: a tool for shock research., Shock, vol. 16 no. 4 (October, 2001), pp. 248-251, ISSN 1073-2322 [11580104]  [abs]
  26. Radmacher, MD; Kepler, TB, Waiting times to appearance and dominance of advantageous mutants: estimation based on the likelihood., Mathematical Biosciences, vol. 170 no. 1 (March, 2001), pp. 59-77, ISSN 0025-5564 [11259803]  [abs]
  27. Kepler, TB; Oprea, M, Improved inference of mutation rates: I. An integral representation for the Luria-Delbrück distribution., Theoretical Population Biology, vol. 59 no. 1 (February, 2001), pp. 41-48, ISSN 0040-5809 [11243927], [doi]  [abs]
  28. Oprea, M; Kepler, TB, Improved inference of mutation rates: II. Generalization of the Luria-Delbrück distribution for realistic cell-cycle time distributions., Theoretical Population Biology, vol. 59 no. 1 (February, 2001), pp. 49-59, ISSN 0040-5809 [11243928], [doi]  [abs]
  29. Oprea, M; Cowell, LG; Kepler, TB, The targeting of somatic hypermutation closely resembles that of meiotic mutation., Journal of immunology (Baltimore, Md. : 1950), vol. 166 no. 2 (January, 2001), pp. 892-899, ISSN 0022-1767 [11145665]  [abs]
  30. Crosby, LM; Hyder, KS; DeAngelo, AB; Kepler, TB; Gaskill, B; Benavides, GR; Yoon, L; Morgan, KT, Morphologic analysis correlates with gene expression changes in cultured F344 rat mesothelial cells., Toxicology and Applied Pharmacology, vol. 169 no. 3 (December, 2000), pp. 205-221, ISSN 0041-008X [11133343], [doi]  [abs]
  31. Keys, DA; Wallace, DG; Kepler, TB; Conolly, RB, Quantitative evaluation of alternative mechanisms of blood disposition of di(n-butyl) phthalate and mono(n-butyl) phthalate in rats., Toxicological Sciences (Elsevier), vol. 53 no. 2 (February, 2000), pp. 173-184, ISSN 1096-6080 [10696765]  [abs]
  32. Cowell, LG; Kepler, TB, The nucleotide-replacement spectrum under somatic hypermutation exhibits microsequence dependence that is strand-symmetric and distinct from that under germline mutation., Journal of immunology (Baltimore, Md. : 1950), vol. 164 no. 4 (February, 2000), pp. 1971-1976, ISSN 0022-1767 [10657647]  [abs]
  33. Oprea, M; Kepler, TB, Genetic plasticity of V genes under somatic hypermutation: statistical analyses using a new resampling-based methodology., Genome research, vol. 9 no. 12 (December, 1999), pp. 1294-1304, ISSN 1088-9051 [10613852]  [abs]
  34. Betts, MR; Krowka, JF; Kepler, TB; Davidian, M; Christopherson, C; Kwok, S; Louie, L; Eron, J; Sheppard, H; Frelinger, JA, Human immunodeficiency virus type 1-specific cytotoxic T lymphocyte activity is inversely correlated with HIV type 1 viral load in HIV type 1-infected long-term survivors., AIDS Research and Human Retroviruses, vol. 15 no. 13 (September, 1999), pp. 1219-1228, ISSN 0889-2229 [10480635], [doi]  [abs]
  35. Cowell, LG; Kim, HJ; Humaljoki, T; Berek, C; Kepler, TB, Enhanced evolvability in immunoglobulin V genes under somatic hypermutation., Journal of Molecular Evolution, vol. 49 no. 1 (July, 1999), pp. 23-26, ISSN 0022-2844 [10368430]  [abs]
  36. Keys, DA; Wallace, DG; Kepler, TB; Conolly, RB, Quantitative evaluation of alternative mechanisms of blood and testes disposition of di(2-ethylhexyl) phthalate and mono(2-ethylhexyl) phthalate in rats., Toxicological Sciences (Elsevier), vol. 49 no. 2 (June, 1999), pp. 172-185, ISSN 1096-6080 [10416263]  [abs]
  37. Gangi-Peterson, L; Sorscher, DH; Reynolds, JW; Kepler, TB; Mitchell, BS, Nucleotide pool imbalance and adenosine deaminase deficiency induce alterations of N-region insertions during V(D)J recombination., Journal of Clinical Investigation, vol. 103 no. 6 (March, 1999), pp. 833-841, ISSN 0021-9738 [10079104], [doi]  [abs]
  38. Kepler, TB; Perelson, AS, Drug concentration heterogeneity facilitates the evolution of drug resistance., Proceedings of the National Academy of Sciences of USA, vol. 95 no. 20 (September, 1998), pp. 11514-11519, ISSN 0027-8424 [9751697]  [abs]
  39. Radmacher, MD; Kelsoe, G; Kepler, TB, Predicted and inferred waiting times for key mutations in the germinal centre reaction: evidence for stochasticity in selection., Immunology and cell biology, vol. 76 no. 4 (August, 1998), pp. 373-381, ISSN 0818-9641 [9723780], [doi]  [abs]
  40. Cowell, LG; Kepler, TB; Janitz, M; Lauster, R; Mitchison, NA, The distribution of variation in regulatory gene segments, as present in MHC class II promoters., Genome research, vol. 8 no. 2 (February, 1998), pp. 124-134, ISSN 1088-9051 [9477340]  [abs]
  41. Cowell, LG; Crowder, LB; Kepler, TB, Density-dependent prenatal androgen exposure as an endogenous mechanism for the generation of cycles in small mammal populations , Journal of Theoretical Biology, vol. 190 no. 1 (January, 1998), pp. 93-106, ISSN 1095-8541 [9473394], [doi]  [abs]
  42. Kepler, TB; Bartl, S, Plasticity under somatic mutation in antigen receptors., Current topics in microbiology and immunology, vol. 229 (1998), pp. 149-162, ISSN 0070-217X [9479853]
  43. Kepler, TB, Codon bias and plasticity in immunoglobulins., Molecular Biology and Evolution, vol. 14 no. 6 (June, 1997), pp. 637-643, ISSN 0737-4038 [9190065], [doi]  [abs]
  44. Kepler, TB; Borrero, M; Rugerio, B; McCray, SK; Clarke, SH, Interdependence of N nucleotide addition and recombination site choice in V(D)J rearrangement., Journal of immunology (Baltimore, Md. : 1950), vol. 157 no. 10 (November, 1996), pp. 4451-4457, ISSN 0022-1767 [8906821]  [abs]
  45. Kepler, TB; Perelson, AS, Modeling and optimization of populations subject to time-dependent mutation., Proceedings of the National Academy of Sciences of USA, vol. 92 no. 18 (August, 1995), pp. 8219-8223, ISSN 0027-8424 [7667271]  [abs]
  46. Han, S; Hathcock, K; Zheng, B; Kepler, TB; Hodes, R; Kelsoe, G, Cellular interaction in germinal centers. Roles of CD40 ligand and B7-2 in established germinal centers., Journal of immunology (Baltimore, Md. : 1950), vol. 155 no. 2 (July, 1995), pp. 556-567, ISSN 0022-1767 [7541819]  [abs]
  47. Kepler, TB; Perelson, AS, Somatic hypermutation in B cells: an optimal control treatment., Journal of Theoretical Biology, vol. 164 no. 1 (September, 1993), pp. 37-64, ISSN 0022-5193 [8264243], [doi]  [abs]
  48. Kepler, TB; Perelson, AS, Cyclic re-entry of germinal center B cells and the efficiency of affinity maturation., Immunology Today, vol. 14 no. 8 (August, 1993), pp. 412-415, ISSN 0167-5699 [8397781], [doi]  [abs]
  49. Kepler, TB; Marder, E, Spike initiation and propagation on axons with slow inward currents., Biological Cybernetics, vol. 68 no. 3 (1993), pp. 209-214, ISSN 0340-1200 [8452888]  [abs]
  50. Kepler, TB; Abbott, LF; Marder, E, Reduction of conductance-based neuron models., Biological Cybernetics, vol. 66 no. 5 (1992), pp. 381-387, ISSN 0340-1200 [1562643]  [abs]
  51. Kepler, TB; Kagan, ML; Epstein, IR, Geometric phases in dissipative systems., Chaos, vol. 1 no. 4 (December, 1991), pp. 455-461, ISSN 1089-7682 [12779941], [doi]  [abs]
  52. Kagan, ML; Kepler, TB; Epstein, IR, Geometric phase shifts in chemical oscillators., Nature, vol. 349 no. 6309 (February, 1991), pp. 506-508, ISSN 0028-0836 [1992353], [doi]  [abs]
  53. Kepler, TB; Kagan, ML, Geometric phase shifts under adiabatic parameter changes in classical dissipative systems., Physical Review Letters, vol. 66 no. 7 (February, 1991), pp. 847-849, ISSN 1079-7114 [10043921], [doi]
  54. Kepler, TB; Marder, E; Abbott, LF, The effect of electrical coupling on the frequency of model neuronal oscillators., Science, vol. 248 no. 4951 (April, 1990), pp. 83-85, ISSN 0036-8075 [2321028]  [abs]
  55. Morgan, KT; Ni, H; Brown, HR; Yoon, L; Qualls, CW; Crosby, LM; Reynolds, R; Gaskill, B; Anderson, SP; Kepler, TB; Brainard, T; Liv, N; Easton, M; Merrill, C; Creech, D; Sprenger, D; Conner, G; Johnson, PR; Fox, T; Sartor, M; Richard, E; Kuruvilla, S; Casey, W; Benavides, G, Application of cDNA microarray technology to in vitro toxicology and the selection of genes for a real-time RT-PCR-based screen for oxidative stress in Hep-G2 cells., Toxicologic Pathology (Sage), vol. 30 no. 4 (July, 2002), pp. 435-451, ISSN 0192-6233 [12187936], [doi]  [abs]

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