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

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. ML Markert, BH Devlin, MJ Alexieff, J Li, EA McCarthy, SE Gupton, IK Chinn, LP Hale, TB Kepler, M He, M Sarzotti, MA Skinner, HE Rice, JC Hoehner, 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. 4539-47, ISSN 0006-4971 [doi]  [abs]
  2. TB Kepler, C Chan, Spatiotemporal programming of a simple inflammatory process., Immunological reviews, vol. 216 (April, 2007), pp. 153-63, ISSN 0105-2896 [doi]  [abs]
  3. C Chan, TB Kepler, Computational immunology--from bench to virtual reality., Annals of the Academy of Medicine, Singapore, vol. 36 no. 2 (February, 2007), pp. 123-7, ISSN 0304-4602  [abs]
  4. DA Culton, MW Nicholas, DO Bunch, QL Zhen, TB Kepler, MA Dooley, C Mohan, PH Nachman, SH Clarke, 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 [doi]  [abs]
  5. S Ray, TB Kepler, Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding., Immunome research, vol. 3 (2007), pp. 9, ISSN 1745-7580 [doi]  [abs]
  6. DC Bauer, DJ Hunter, SB Abramson, M Attur, M Corr, D Felson, D Heinegård, JM Jordan, TB Kepler, NE Lane, T Saxne, B Tyree, VB Kraus, Osteoarthritis Biomarkers Network, Classification of osteoarthritis biomarkers: a proposed approach., Osteoarthritis and cartilage / OARS, Osteoarthritis Research Society, vol. 14 no. 8 (August, 2006), pp. 723-7, ISSN 1063-4584 [doi]  [abs]
  7. C Liu, M He, B Rooney, TB Kepler, NJ Chao, 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 : journal of the American Society for Blood and Marrow Transplantation, vol. 12 no. 3 (March, 2006), pp. 335-45, ISSN 1083-8791 [doi]  [abs]
  8. SA Fadel, LG Cowell, S Cao, DA Ozaki, TB Kepler, DA Steeber, M Sarzotti, 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. 249-57, ISSN 0953-8178 [doi]  [abs]
  9. JM Volpe, LG Cowell, TB Kepler, SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations., Bioinformatics (Oxford, England), vol. 22 no. 4 (February, 2006), pp. 438-44, ISSN 1367-4803 [doi]  [abs]
  10. M He, JK Tomfohr, BH Devlin, M Sarzotti, ML Markert, TB Kepler, SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization., Bioinformatics (Oxford, England), vol. 21 no. 18 (September, 2005), pp. 3697-9, ISSN 1367-4803 [doi]  [abs]
  11. TB Kepler, M He, JK Tomfohr, BH Devlin, M Sarzotti, ML Markert, Statistical analysis of antigen receptor spectratype data., Bioinformatics (Oxford, England), vol. 21 no. 16 (August, 2005), pp. 3394-400, ISSN 1367-4803 [doi]  [abs]
  12. J Lu, JK Tomfohr, TB Kepler, Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach., BMC bioinformatics, vol. 6 (2005), pp. 165, ISSN 1471-2105 [doi]  [abs]
  13. J Tomfohr, J Lu, TB Kepler, Pathway level analysis of gene expression using singular value decomposition., BMC bioinformatics, vol. 6 (2005), pp. 225, ISSN 1471-2105 [doi]  [abs]
  14. JT Smith, JK Tomfohr, MC Wells, TP Beebe Jr, TB Kepler, WM Reichert, Measurement of cell migration on surface-bound fibronectin gradients., Langmuir : the ACS journal of surfaces and colloids, vol. 20 no. 19 (September, 2004), pp. 8279-86, ISSN 0743-7463 [doi]  [abs]
  15. SM Zhang, CM Adema, TB Kepler, ES Loker, Diversification of Ig superfamily genes in an invertebrate., Science (New York, N.Y.), vol. 305 no. 5681 (July, 2004), pp. 251-4, ISSN 1095-9203 [doi]  [abs]
  16. ES Loker, CM Adema, SM Zhang, TB Kepler, Invertebrate immune systems--not homogeneous, not simple, not well understood., Immunological reviews, vol. 198 (April, 2004), pp. 10-24, ISSN 0105-2896  [abs]
  17. F Gao, Y Chen, DN Levy, JA Conway, TB Kepler, H Hui, 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. 2426-33, ISSN 0022-538X  [abs]
  18. S Bartl, AL Miracle, LL Rumfelt, TB Kepler, E Mochon, GW Litman, MF Flajnik, Terminal deoxynucleotidyl transferases from elasmobranchs reveal structural conservation within vertebrates., Immunogenetics, vol. 55 no. 9 (December, 2003), pp. 594-604, ISSN 0093-7711 [doi]  [abs]
  19. E Trachtenberg, B Korber, C Sollars, TB Kepler, PT Hraber, E Hayes, R Funkhouser, M Fugate, J Theiler, YS Hsu, K Kunstman, S Wu, J Phair, H Erlich, S Wolinsky, Advantage of rare HLA supertype in HIV disease progression., Nature medicine, vol. 9 no. 7 (July, 2003), pp. 928-35, ISSN 1078-8956 [doi]  [abs]
  20. LG Cowell, M Davila, K Yang, TB Kepler, G Kelsoe, 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. 207-20, ISSN 0022-1007  [abs]
  21. TB Kepler, L Crosby, KT Morgan, 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  [abs]
  22. LG Cowell, M Davila, TB Kepler, G Kelsoe, Identification and utilization of arbitrary correlations in models of recombination signal sequences., Genome biology, vol. 3 no. 12 (2002), pp. RESEARCH0072, ISSN 1465-6914  [abs]
  23. M Zavolan, TB Kepler, Statistical inference of sequence-dependent mutation rates., Current opinion in genetics & development, vol. 11 no. 6 (December, 2001), pp. 612-5, ISSN 0959-437X  [abs]
  24. TB Kepler, TC Elston, Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations., Biophysical journal, vol. 81 no. 6 (December, 2001), pp. 3116-36, ISSN 0006-3495 [doi]  [abs]
  25. TG Buchman, JP Cobb, AS Lapedes, TB Kepler, Complex systems analysis: a tool for shock research., Shock (Augusta, Ga.), vol. 16 no. 4 (October, 2001), pp. 248-51, ISSN 1073-2322  [abs]
  26. MD Radmacher, TB Kepler, 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  [abs]
  27. TB Kepler, M Oprea, Improved inference of mutation rates: I. An integral representation for the Luria-Delbrück distribution., Theoretical population biology, vol. 59 no. 1 (February, 2001), pp. 41-8, ISSN 0040-5809 [doi]  [abs]
  28. M Oprea, TB Kepler, 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 [doi]  [abs]
  29. M Oprea, LG Cowell, TB Kepler, The targeting of somatic hypermutation closely resembles that of meiotic mutation., Journal of immunology (Baltimore, Md. : 1950), vol. 166 no. 2 (January, 2001), pp. 892-9, ISSN 0022-1767  [abs]
  30. LM Crosby, KS Hyder, AB DeAngelo, TB Kepler, B Gaskill, GR Benavides, L Yoon, KT Morgan, Morphologic analysis correlates with gene expression changes in cultured F344 rat mesothelial cells., Toxicology and applied pharmacology, vol. 169 no. 3 (December, 2000), pp. 205-21, ISSN 0041-008X [doi]  [abs]
  31. DA Keys, DG Wallace, TB Kepler, RB Conolly, Quantitative evaluation of alternative mechanisms of blood disposition of di(n-butyl) phthalate and mono(n-butyl) phthalate in rats., Toxicological sciences : an official journal of the Society of Toxicology, vol. 53 no. 2 (February, 2000), pp. 173-84, ISSN 1096-6080  [abs]
  32. LG Cowell, TB Kepler, 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. 1971-6, ISSN 0022-1767  [abs]
  33. M Oprea, TB Kepler, 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. 1294-304, ISSN 1088-9051  [abs]
  34. MR Betts, JF Krowka, TB Kepler, M Davidian, C Christopherson, S Kwok, L Louie, J Eron, H Sheppard, JA Frelinger, 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. 1219-28, ISSN 0889-2229 [doi]  [abs]
  35. LG Cowell, HJ Kim, T Humaljoki, C Berek, TB Kepler, Enhanced evolvability in immunoglobulin V genes under somatic hypermutation., Journal of molecular evolution, vol. 49 no. 1 (July, 1999), pp. 23-6, ISSN 0022-2844  [abs]
  36. DA Keys, DG Wallace, TB Kepler, RB Conolly, Quantitative evaluation of alternative mechanisms of blood and testes disposition of di(2-ethylhexyl) phthalate and mono(2-ethylhexyl) phthalate in rats., Toxicological sciences : an official journal of the Society of Toxicology, vol. 49 no. 2 (June, 1999), pp. 172-85, ISSN 1096-6080  [abs]
  37. L Gangi-Peterson, DH Sorscher, JW Reynolds, TB Kepler, BS Mitchell, Nucleotide pool imbalance and adenosine deaminase deficiency induce alterations of N-region insertions during V(D)J recombination., The Journal of clinical investigation, vol. 103 no. 6 (March, 1999), pp. 833-41, ISSN 0021-9738 [doi]  [abs]
  38. TB Kepler, AS Perelson, Drug concentration heterogeneity facilitates the evolution of drug resistance., Proceedings of the National Academy of Sciences of the United States of America, vol. 95 no. 20 (September, 1998), pp. 11514-9, ISSN 0027-8424  [abs]
  39. MD Radmacher, G Kelsoe, TB Kepler, 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. 373-81, ISSN 0818-9641 [doi]  [abs]
  40. LG Cowell, TB Kepler, M Janitz, R Lauster, NA Mitchison, The distribution of variation in regulatory gene segments, as present in MHC class II promoters., Genome research, vol. 8 no. 2 (February, 1998), pp. 124-34, ISSN 1088-9051  [abs]
  41. LG Cowell, LB Crowder, TB Kepler, 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 [doi]  [abs]
  42. TB Kepler, S Bartl, Plasticity under somatic mutation in antigen receptors., Current topics in microbiology and immunology, vol. 229 (1998), pp. 149-62, ISSN 0070-217X
  43. TB Kepler, Codon bias and plasticity in immunoglobulins., Molecular biology and evolution, vol. 14 no. 6 (June, 1997), pp. 637-43, ISSN 0737-4038  [abs]
  44. TB Kepler, M Borrero, B Rugerio, SK McCray, SH Clarke, 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. 4451-7, ISSN 0022-1767  [abs]
  45. TB Kepler, AS Perelson, Modeling and optimization of populations subject to time-dependent mutation., Proceedings of the National Academy of Sciences of the United States of America, vol. 92 no. 18 (August, 1995), pp. 8219-23, ISSN 0027-8424  [abs]
  46. S Han, K Hathcock, B Zheng, TB Kepler, R Hodes, G Kelsoe, 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. 556-67, ISSN 0022-1767  [abs]
  47. TB Kepler, AS Perelson, 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 [doi]  [abs]
  48. TB Kepler, AS Perelson, Cyclic re-entry of germinal center B cells and the efficiency of affinity maturation., Immunology today, vol. 14 no. 8 (August, 1993), pp. 412-5, ISSN 0167-5699 [doi]  [abs]
  49. TB Kepler, E Marder, Spike initiation and propagation on axons with slow inward currents., Biological cybernetics, vol. 68 no. 3 (1993), pp. 209-14, ISSN 0340-1200  [abs]
  50. TB Kepler, LF Abbott, E Marder, Reduction of conductance-based neuron models., Biological cybernetics, vol. 66 no. 5 (1992), pp. 381-7, ISSN 0340-1200  [abs]
  51. TB Kepler, ML Kagan, IR Epstein, Geometric phases in dissipative systems., Chaos (Woodbury, N.Y.), vol. 1 no. 4 (December, 1991), pp. 455-461, ISSN 1089-7682 [doi]  [abs]
  52. ML Kagan, TB Kepler, IR Epstein, Geometric phase shifts in chemical oscillators., Nature, vol. 349 no. 6309 (February, 1991), pp. 506-8, ISSN 0028-0836 [doi]  [abs]
  53. TB Kepler, ML Kagan, 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
  54. TB Kepler, E Marder, LF Abbott, The effect of electrical coupling on the frequency of model neuronal oscillators., Science (New York, N.Y.), vol. 248 no. 4951 (April, 1990), pp. 83-5, ISSN 0036-8075  [abs]
  55. KT Morgan, H Ni, HR Brown, L Yoon, CW Qualls Jr, LM Crosby, R Reynolds, B Gaskill, SP Anderson, TB Kepler, T Brainard, N Liv, M Easton, C Merrill, D Creech, D Sprenger, G Conner, PR Johnson, T Fox, M Sartor, E Richard, S Kuruvilla, W Casey, G Benavides, 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, vol. 30 no. 4 (March, 2003), pp. 435-51, ISSN 0192-6233  [abs]

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