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:  http://faculty.duhs.duke.edu/faculty/info?pid=6764

Education:

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 and 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. 4539-4547, ISSN 0006-4971 [17284531], [doi]  [abs]
  2. TB Kepler and C Chan, Spatiotemporal programming of a simple inflammatory process., Immunol Rev, vol. 216 (April, 2007), pp. 153-163, ISSN 0105-2896 [17367341], [doi]  [abs]
  3. C Chan and TB Kepler, Computational immunology--from bench to virtual reality., Ann Acad Med Singapore, vol. 36 no. 2 (February, 2007), pp. 123-127, ISSN 0304-4602 [17364079]  [abs]
  4. DA Culton, MW Nicholas, DO Bunch, QL Zhen, TB Kepler, MA Dooley, C Mohan, PH Nachman and SH Clarke, Similar CD19 dysregulation in two autoantibody-associated autoimmune diseases suggests a shared mechanism of B-cell tolerance loss., J Clin Immunol, vol. 27 no. 1 (January, 2007), pp. 53-68, ISSN 0271-9142 [17195045], [doi]  [abs]
  5. S Ray and TB Kepler, Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding., Immunome Res, vol. 3 (2007), pp. 9, ISSN 1745-7580 [17967170], [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 and Osteoarthritis Biomarkers Network, Classification of osteoarthritis biomarkers: a proposed approach., Osteoarthritis Cartilage, vol. 14 no. 8 (August, 2006), pp. 723-727, ISSN 1063-4584 [16733093], [doi]  [abs]
  7. C Liu, M He, B Rooney, TB Kepler and 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., Biol Blood Marrow Transplant, vol. 12 no. 3 (March, 2006), pp. 335-345, ISSN 1083-8791 [16503503], [doi]  [abs]
  8. SA Fadel, LG Cowell, S Cao, DA Ozaki, TB Kepler, DA Steeber and M Sarzotti, Neonate-primed CD8+ memory cells rival adult-primed memory cells in antigen-driven expansion and anti-viral protection., Int Immunol, vol. 18 no. 2 (February, 2006), pp. 249-257, ISSN 0953-8178 [16418189], [doi]  [abs]
  9. JM Volpe, LG Cowell and TB Kepler, 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. M He, JK Tomfohr, BH Devlin, M Sarzotti, ML Markert and TB Kepler, 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. TB Kepler, M He, JK Tomfohr, BH Devlin, M Sarzotti and ML Markert, Statistical analysis of antigen receptor spectratype data., Bioinformatics, vol. 21 no. 16 (August, 2005), pp. 3394-3400, ISSN 1367-4803 [15955781], [doi]  [abs]
  12. J Lu, JK Tomfohr and 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 [15987513], [doi]  [abs]
  13. J Tomfohr, J Lu and TB Kepler, Pathway level analysis of gene expression using singular value decomposition., BMC Bioinformatics, vol. 6 (2005), pp. 225, ISSN 1471-2105 [16156896], [doi]  [abs]
  14. JT Smith, JK Tomfohr, MC Wells, TP Beebe, TB Kepler and WM Reichert, 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. SM Zhang, CM Adema, TB Kepler and ES Loker, 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. ES Loker, CM Adema, SM Zhang and TB Kepler, Invertebrate immune systems--not homogeneous, not simple, not well understood., Immunol Rev, vol. 198 (April, 2004), pp. 10-24, ISSN 0105-2896 [15199951]  [abs]
  17. F Gao, Y Chen, DN Levy, JA Conway, TB Kepler and H Hui, Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious., J Virol, vol. 78 no. 5 (March, 2004), pp. 2426-2433, ISSN 0022-538X [14963138]  [abs]
  18. S Bartl, AL Miracle, LL Rumfelt, TB Kepler, E Mochon, GW Litman and 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 [14579105], [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 and S Wolinsky, Advantage of rare HLA supertype in HIV disease progression., Nat Med, vol. 9 no. 7 (July, 2003), pp. 928-935, ISSN 1078-8956 [12819779], [doi]  [abs]
  20. LG Cowell, M Davila, K Yang, TB Kepler and G Kelsoe, Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling., J Exp Med, vol. 197 no. 2 (January, 2003), pp. 207-220, ISSN 0022-1007 [12538660]  [abs]
  21. TB Kepler, L Crosby and KT Morgan, Normalization and analysis of DNA microarray data by self-consistency and local regression., Genome Biol, vol. 3 no. 7 (June, 2002), pp. RESEARCH0037, ISSN 1465-6914 [12184811]  [abs]
  22. LG Cowell, M Davila, TB Kepler and G Kelsoe, Identification and utilization of arbitrary correlations in models of recombination signal sequences., Genome Biol, vol. 3 no. 12 (2002), pp. RESEARCH0072, ISSN 1465-6914 [12537561]  [abs]
  23. M Zavolan and TB Kepler, Statistical inference of sequence-dependent mutation rates., Curr Opin Genet Dev, vol. 11 no. 6 (December, 2001), pp. 612-615, ISSN 0959-437X [11682302]  [abs]
  24. TB Kepler and TC Elston, Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations., Biophys J, vol. 81 no. 6 (December, 2001), pp. 3116-3136, ISSN 0006-3495 [11720979], [doi]  [abs]
  25. TG Buchman, JP Cobb, AS Lapedes and TB Kepler, Complex systems analysis: a tool for shock research., Shock, vol. 16 no. 4 (October, 2001), pp. 248-251, ISSN 1073-2322 [11580104]  [abs]
  26. MD Radmacher and TB Kepler, Waiting times to appearance and dominance of advantageous mutants: estimation based on the likelihood., Math Biosci, vol. 170 no. 1 (March, 2001), pp. 59-77, ISSN 0025-5564 [11259803]  [abs]
  27. TB Kepler and M Oprea, Improved inference of mutation rates: I. An integral representation for the Luria-Delbrück distribution., Theor Popul Biol, vol. 59 no. 1 (February, 2001), pp. 41-48, ISSN 0040-5809 [11243927], [doi]  [abs]
  28. M Oprea and TB Kepler, Improved inference of mutation rates: II. Generalization of the Luria-Delbrück distribution for realistic cell-cycle time distributions., Theor Popul Biol, vol. 59 no. 1 (February, 2001), pp. 49-59, ISSN 0040-5809 [11243928], [doi]  [abs]
  29. M Oprea, LG Cowell and TB Kepler, The targeting of somatic hypermutation closely resembles that of meiotic mutation., J Immunol, vol. 166 no. 2 (January, 2001), pp. 892-899, ISSN 0022-1767 [11145665]  [abs]
  30. LM Crosby, KS Hyder, AB DeAngelo, TB Kepler, B Gaskill, GR Benavides, L Yoon and KT Morgan, Morphologic analysis correlates with gene expression changes in cultured F344 rat mesothelial cells., Toxicol Appl Pharmacol, vol. 169 no. 3 (December, 2000), pp. 205-221, ISSN 0041-008X [11133343], [doi]  [abs]
  31. DA Keys, DG Wallace, TB Kepler and RB Conolly, Quantitative evaluation of alternative mechanisms of blood disposition of di(n-butyl) phthalate and mono(n-butyl) phthalate in rats., Toxicol Sci, vol. 53 no. 2 (February, 2000), pp. 173-184, ISSN 1096-6080 [10696765]  [abs]
  32. LG Cowell and TB Kepler, The nucleotide-replacement spectrum under somatic hypermutation exhibits microsequence dependence that is strand-symmetric and distinct from that under germline mutation., J Immunol, vol. 164 no. 4 (February, 2000), pp. 1971-1976, ISSN 0022-1767 [10657647]  [abs]
  33. M Oprea and TB Kepler, Genetic plasticity of V genes under somatic hypermutation: statistical analyses using a new resampling-based methodology., Genome Res, vol. 9 no. 12 (December, 1999), pp. 1294-1304, ISSN 1088-9051 [10613852]  [abs]
  34. MR Betts, JF Krowka, TB Kepler, M Davidian, C Christopherson, S Kwok, L Louie, J Eron, H Sheppard and 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 Res Hum Retroviruses, vol. 15 no. 13 (September, 1999), pp. 1219-1228, ISSN 0889-2229 [10480635], [doi]  [abs]
  35. LG Cowell, HJ Kim, T Humaljoki, C Berek and TB Kepler, Enhanced evolvability in immunoglobulin V genes under somatic hypermutation., J Mol Evol, vol. 49 no. 1 (July, 1999), pp. 23-26, ISSN 0022-2844 [10368430]  [abs]
  36. DA Keys, DG Wallace, TB Kepler and RB Conolly, Quantitative evaluation of alternative mechanisms of blood and testes disposition of di(2-ethylhexyl) phthalate and mono(2-ethylhexyl) phthalate in rats., Toxicol Sci, vol. 49 no. 2 (June, 1999), pp. 172-185, ISSN 1096-6080 [10416263]  [abs]
  37. L Gangi-Peterson, DH Sorscher, JW Reynolds, TB Kepler and BS Mitchell, Nucleotide pool imbalance and adenosine deaminase deficiency induce alterations of N-region insertions during V(D)J recombination., J Clin Invest, vol. 103 no. 6 (March, 1999), pp. 833-841, ISSN 0021-9738 [10079104], [doi]  [abs]
  38. TB Kepler and AS Perelson, Drug concentration heterogeneity facilitates the evolution of drug resistance., Proc Natl Acad Sci U S A, vol. 95 no. 20 (September, 1998), pp. 11514-11519, ISSN 0027-8424 [9751697]  [abs]
  39. MD Radmacher, G Kelsoe and TB Kepler, Predicted and inferred waiting times for key mutations in the germinal centre reaction: evidence for stochasticity in selection., Immunol Cell Biol, vol. 76 no. 4 (August, 1998), pp. 373-381, ISSN 0818-9641 [9723780], [doi]  [abs]
  40. LG Cowell, TB Kepler, M Janitz, R Lauster and NA Mitchison, The distribution of variation in regulatory gene segments, as present in MHC class II promoters., Genome Res, vol. 8 no. 2 (February, 1998), pp. 124-134, ISSN 1088-9051 [9477340]  [abs]
  41. LG Cowell, LB Crowder and TB Kepler, Density-dependent prenatal androgen exposure as an endogenous mechanism for the generation of cycles in small mammal populations, J Theor Biol, vol. 190 no. 1 (January, 1998), pp. 93-106, ISSN 1095-8541 [9473394], [doi]  [abs]
  42. TB Kepler and S Bartl, Plasticity under somatic mutation in antigen receptors., Curr Top Microbiol Immunol, vol. 229 (1998), pp. 149-162, ISSN 0070-217X [9479853]
  43. TB Kepler, Codon bias and plasticity in immunoglobulins., Mol Biol Evol, vol. 14 no. 6 (June, 1997), pp. 637-643, ISSN 0737-4038 [9190065]  [abs]
  44. TB Kepler, M Borrero, B Rugerio, SK McCray and SH Clarke, Interdependence of N nucleotide addition and recombination site choice in V(D)J rearrangement., J Immunol, vol. 157 no. 10 (November, 1996), pp. 4451-4457, ISSN 0022-1767 [8906821]  [abs]
  45. TB Kepler and AS Perelson, Modeling and optimization of populations subject to time-dependent mutation., Proc Natl Acad Sci U S A, vol. 92 no. 18 (August, 1995), pp. 8219-8223, ISSN 0027-8424 [7667271]  [abs]
  46. S Han, K Hathcock, B Zheng, TB Kepler, R Hodes and G Kelsoe, Cellular interaction in germinal centers. Roles of CD40 ligand and B7-2 in established germinal centers., J Immunol, vol. 155 no. 2 (July, 1995), pp. 556-567, ISSN 0022-1767 [7541819]  [abs]
  47. TB Kepler and AS Perelson, Somatic hypermutation in B cells: an optimal control treatment., J Theor Biol, vol. 164 no. 1 (September, 1993), pp. 37-64, ISSN 0022-5193 [8264243], [doi]  [abs]
  48. TB Kepler and AS Perelson, Cyclic re-entry of germinal center B cells and the efficiency of affinity maturation., Immunol Today, vol. 14 no. 8 (August, 1993), pp. 412-415, ISSN 0167-5699 [8397781], [doi]  [abs]
  49. TB Kepler and E Marder, Spike initiation and propagation on axons with slow inward currents., Biol Cybern, vol. 68 no. 3 (1993), pp. 209-214, ISSN 0340-1200 [8452888]  [abs]
  50. TB Kepler, LF Abbott and E Marder, Reduction of conductance-based neuron models., Biol Cybern, vol. 66 no. 5 (1992), pp. 381-387, ISSN 0340-1200 [1562643]  [abs]
  51. TB Kepler, ML Kagan and IR Epstein, Geometric phases in dissipative systems., Chaos, vol. 1 no. 4 (December, 1991), pp. 455-461, ISSN 1089-7682 [12779941], [doi]  [abs]
  52. ML Kagan, TB Kepler and IR Epstein, Geometric phase shifts in chemical oscillators., Nature, vol. 349 no. 6309 (February, 1991), pp. 506-508, ISSN 0028-0836 [1992353], [doi]  [abs]
  53. TB Kepler and ML Kagan, Geometric phase shifts under adiabatic parameter changes in classical dissipative systems., Phys Rev Lett, vol. 66 no. 7 (February, 1991), pp. 847-849, ISSN 1079-7114 [10043921], [doi]
  54. TB Kepler, E Marder and LF Abbott, 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. KT Morgan, H Ni, HR Brown, L Yoon, CW Qualls, 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 and 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., Toxicol Pathol, vol. 30 no. 4 (July, 2002), pp. 435-451, ISSN 0192-6233 [12187936]  [abs]

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