Thomas B Kepler, Professor of Biostatistics and Bioinformatics and Statistics and Statistical Science

Contact Info:

101A North Bldg.

919 681-0620

kepler@duke.edu

Education:

Ph.D., Brandeis University, 1989

Representative Publications

1. S Ray, TB Kepler. "Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding.." Immunome research, England 3 (2007): 9.  [abs]
2. 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, England 18.2 (February, 2006): 249-57.  [abs]
3. C Chan, TB Kepler. "Computational immunology--from bench to virtual reality.." Annals of the Academy of Medicine, Singapore, Singapore 36.2 (February, 2007): 123-7.  [abs]
4. JM Volpe, LG Cowell, TB Kepler. "SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations.." Bioinformatics (Oxford, England), England 22.4 (February, 2006): 438-44.  [abs]
5. 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, United States 109.10 (May, 2007): 4539-47.  [abs]
6. J Lu, JK Tomfohr, TB Kepler. "Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach.." BMC bioinformatics, England 6 (2005): 165.  [abs]
7. 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, United States 27.1 (January, 2007): 53-68.  [abs]
8. J Tomfohr, J Lu, TB Kepler. "Pathway level analysis of gene expression using singular value decomposition.." BMC bioinformatics, England 6 (2005): 225.  [abs]
9. TB Kepler, C Chan. "Spatiotemporal programming of a simple inflammatory process.." Immunological reviews, Denmark 216 (April, 2007): 153-63.  [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), England 21.18 (September, 2005): 3697-9.  [abs]
11. 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, England 14.8 (August, 2006): 723-7.  [abs]
12. TB Kepler, M He, JK Tomfohr, BH Devlin, M Sarzotti, ML Markert. "Statistical analysis of antigen receptor spectratype data.." Bioinformatics (Oxford, England), England 21.16 (August, 2005): 3394-400.  [abs]
13. 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, United States 12.3 (March, 2006): 335-45.  [abs]
14. SM Zhang, CM Adema, TB Kepler, ES Loker. "Diversification of Ig superfamily genes in an invertebrate.." Science (New York, N.Y.), United States 305.5681 (July, 2004): 251-4.  [abs]
15. ES Loker, CM Adema, SM Zhang, TB Kepler. "Invertebrate immune systems--not homogeneous, not simple, not well understood.." Immunological reviews, Denmark 198 (April, 2004): 10-24.  [abs]
16. JT Smith, JK Tomfohr, MC Wells, TP Beebe, TB Kepler, WM Reichert. "Measurement of cell migration on surface-bound fibronectin gradients.." Langmuir : the ACS journal of surfaces and colloids, United States 20.19 (September, 2004): 8279-86.  [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, United States 78.5 (March, 2004): 2426-33.  [abs]
18. 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, United States 9.7 (July, 2003): 928-35.  [abs]
19. 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, United States 197.2 (January, 2003): 207-20.  [abs]
20. 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, United States 55.9 (December, 2003): 594-604.  [abs]
21. LG Cowell, M Davila, TB Kepler, G Kelsoe. "Identification and utilization of arbitrary correlations in models of recombination signal sequences.." Genome biology, England 3.12 (2002): RESEARCH0072.  [abs]
22. TB Kepler, L Crosby, KT Morgan. "Normalization and analysis of DNA microarray data by self-consistency and local regression.." Genome biology, England 3.7 (June, 2002): RESEARCH0037.  [abs]
23. TG Buchman, JP Cobb, AS Lapedes, TB Kepler. "Complex systems analysis: a tool for shock research.." Shock (Augusta, Ga.), United States 16.4 (October, 2001): 248-51.  [abs]
24. TB Kepler, M Oprea. "Improved inference of mutation rates: I. An integral representation for the Luria-Delbrück distribution.." Theoretical population biology, United States 59.1 (February, 2001): 41-8.  [abs]
25. 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, United States 59.1 (February, 2001): 49-59.  [abs]
26. M Zavolan, TB Kepler. "Statistical inference of sequence-dependent mutation rates.." Current opinion in genetics & development, England 11.6 (December, 2001): 612-5.  [abs]
27. TB Kepler, TC Elston. "Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.." Biophysical journal, United States 81.6 (December, 2001): 3116-36.  [abs]
28. M Oprea, LG Cowell, TB Kepler. "The targeting of somatic hypermutation closely resembles that of meiotic mutation.." Journal of immunology (Baltimore, Md. : 1950), UNITED STATES 166.2 (January, 2001): 892-9.  [abs]
29. MD Radmacher, TB Kepler. "Waiting times to appearance and dominance of advantageous mutants: estimation based on the likelihood.." Mathematical biosciences, United States 170.1 (March, 2001): 59-77.  [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, UNITED STATES 169.3 (December, 2000): 205-21.  [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, UNITED STATES 53.2 (February, 2000): 173-84.  [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), UNITED STATES 164.4 (February, 2000): 1971-6.  [abs]
33. LG Cowell, HJ Kim, T Humaljoki, C Berek, TB Kepler. "Enhanced evolvability in immunoglobulin V genes under somatic hypermutation.." Journal of molecular evolution, UNITED STATES 49.1 (July, 1999): 23-6.  [abs]
34. M Oprea, TB Kepler. "Genetic plasticity of V genes under somatic hypermutation: statistical analyses using a new resampling-based methodology.." Genome research, UNITED STATES 9.12 (December, 1999): 1294-304.  [abs]
35. 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, UNITED STATES 15.13 (September, 1999): 1219-28.  [abs]
36. 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, UNITED STATES 103.6 (March, 1999): 833-41.  [abs]
37. 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, UNITED STATES 49.2 (June, 1999): 172-85.  [abs]
38. LG Cowell, LB Crowder, TB Kepler. "Density-dependent prenatal androgen exposure as an endogenous mechanism for the generation of cycles in small mammal populations ." J Theor Biol 190.1 (January, 1998): 93-106.  [abs]
39. 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, UNITED STATES 95.20 (September, 1998): 11514-9.  [abs]
40. TB Kepler, S Bartl. "Plasticity under somatic mutation in antigen receptors.." Current topics in microbiology and immunology, GERMANY 229 (1998): 149-62.
41. 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, AUSTRALIA 76.4 (August, 1998): 373-81.  [abs]
42. 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, UNITED STATES 8.2 (February, 1998): 124-34.  [abs]
43. TB Kepler. "Codon bias and plasticity in immunoglobulins.." Molecular biology and evolution, UNITED STATES 14.6 (June, 1997): 637-43.  [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), UNITED STATES 157.10 (November, 1996): 4451-7.  [abs]
45. 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), UNITED STATES 155.2 (July, 1995): 556-67.  [abs]
46. 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, UNITED STATES 92.18 (August, 1995): 8219-23.  [abs]
47. TB Kepler, AS Perelson. "Cyclic re-entry of germinal center B cells and the efficiency of affinity maturation.." Immunology today, ENGLAND 14.8 (August, 1993): 412-5.  [abs]
48. TB Kepler, AS Perelson. "Somatic hypermutation in B cells: an optimal control treatment.." Journal of theoretical biology, ENGLAND 164.1 (September, 1993): 37-64.  [abs]
49. TB Kepler, E Marder. "Spike initiation and propagation on axons with slow inward currents.." Biological cybernetics, GERMANY 68.3 (1993): 209-14.  [abs]
50. TB Kepler, LF Abbott, E Marder. "Reduction of conductance-based neuron models.." Biological cybernetics, GERMANY 66.5 (1992): 381-7.  [abs]
51. ML Kagan, TB Kepler, IR Epstein. "Geometric phase shifts in chemical oscillators.." Nature, ENGLAND 349.6309 (February, 1991): 506-8.  [abs]
52. TB Kepler, ML Kagan. "Geometric phase shifts under adiabatic parameter changes in classical dissipative systems.." Phys Rev Lett 66.7 (February, 1991): 847-849.
53. TB Kepler, ML Kagan, IR Epstein. "Geometric phases in dissipative systems.." Chaos 1.4 (December, 1991): 455-461.  [abs]
54. TB Kepler, E Marder, LF Abbott. "The effect of electrical coupling on the frequency of model neuronal oscillators.." Science (New York, N.Y.), UNITED STATES 248.4951 (April, 1990): 83-5.  [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, 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, United States 30.4 (): 435-51.  [abs]