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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
- B.A., University of Massachusetts at Amherst, 1985
- Representative Publications
(More Publications)
- 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 109.10 (May, 2007): 4539-4547. [17284531], [doi] [abs]
- Kepler, TB; Chan, C. "Spatiotemporal programming of a simple inflammatory process.." Immunological Reviews 216 (April, 2007): 153-163. [17367341], [doi] [abs]
- Chan, C; Kepler, TB. "Computational immunology--from bench to virtual reality.." Annals of the Academy of Medicine, Singapore 36.2 (February, 2007): 123-127. [17364079] [abs]
- 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 27.1 (January, 2007): 53-68. [17195045], [doi] [abs]
- Ray, S; Kepler, TB. "Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding.." Immunome Research 3 (October, 2007): 9. [17967170], [doi] [abs]
- 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 14.8 (August, 2006): 723-727. [16733093], [doi] [abs]
- 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 12.3 (March, 2006): 335-345. [16503503], [doi] [abs]
- 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 18.2 (February, 2006): 249-257. [16418189], [doi] [abs]
- Volpe, JM; Cowell, LG; Kepler, TB. "SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations.." Bioinformatics 22.4 (February, 2006): 438-444. [16357034], [doi] [abs]
- He, M; Tomfohr, JK; Devlin, BH; Sarzotti, M; Markert, ML; Kepler, TB. "SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization.." Bioinformatics 21.18 (September, 2005): 3697-3699. [16051675], [doi] [abs]
- Kepler, TB; He, M; Tomfohr, JK; Devlin, BH; Sarzotti, M; Markert, ML. "Statistical analysis of antigen receptor spectratype data.." Bioinformatics 21.16 (August, 2005): 3394-3400. [15955781], [doi] [abs]
- Lu, J; Tomfohr, JK; Kepler, TB. "Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach.." BMC Bioinformatics 6 (June, 2005): 165. [15987513], [doi] [abs]
- Tomfohr, J; Lu, J; Kepler, TB. "Pathway level analysis of gene expression using singular value decomposition.." BMC Bioinformatics 6 (September, 2005): 225. [16156896], [doi] [abs]
- Smith, JT; Tomfohr, JK; Wells, MC; Beebe, TP; Kepler, TB; Reichert, WM. "Measurement of cell migration on surface-bound fibronectin gradients.." Langmuir 20.19 (September, 2004): 8279-8286. [15350103], [doi] [abs]
- Zhang, S-M; Adema, CM; Kepler, TB; Loker, ES. "Diversification of Ig superfamily genes in an invertebrate.." Science 305.5681 (July, 2004): 251-254. [15247481], [doi] [abs]
- Loker, ES; Adema, CM; Zhang, S-M; Kepler, TB. "Invertebrate immune systems--not homogeneous, not simple, not well understood.." Immunological Reviews 198 (April, 2004): 10-24. [15199951] [abs]
- 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 78.5 (March, 2004): 2426-2433. [14963138] [abs]
- 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 55.9 (December, 2003): 594-604. [14579105], [doi] [abs]
- 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 9.7 (July, 2003): 928-935. [12819779], [doi] [abs]
- 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 197.2 (January, 2003): 207-220. [12538660] [abs]
- Kepler, TB; Crosby, L; Morgan, KT. "Normalization and analysis of DNA microarray data by self-consistency and local regression.." Genome Biology 3.7 (June, 2002): RESEARCH0037. [12184811] [abs]
- Cowell, LG; Davila, M; Kepler, TB; Kelsoe, G. "Identification and utilization of arbitrary correlations in models of recombination signal sequences.." Genome Biology 3.12 (2002): RESEARCH0072. [12537561] [abs]
- Zavolan, M; Kepler, TB. "Statistical inference of sequence-dependent mutation rates.." Current Opinion in Genetics & Development 11.6 (December, 2001): 612-615. [11682302] [abs]
- Kepler, TB; Elston, TC. "Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.." Biophysical Journal 81.6 (December, 2001): 3116-3136. [11720979], [doi] [abs]
- Buchman, TG; Cobb, JP; Lapedes, AS; Kepler, TB. "Complex systems analysis: a tool for shock research.." Shock 16.4 (October, 2001): 248-251. [11580104] [abs]
- Radmacher, MD; Kepler, TB. "Waiting times to appearance and dominance of advantageous mutants: estimation based on the likelihood.." Mathematical Biosciences 170.1 (March, 2001): 59-77. [11259803] [abs]
- Kepler, TB; Oprea, M. "Improved inference of mutation rates: I. An integral representation for the Luria-Delbrück distribution.." Theoretical Population Biology 59.1 (February, 2001): 41-48. [11243927], [doi] [abs]
- 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 59.1 (February, 2001): 49-59. [11243928], [doi] [abs]
- Oprea, M; Cowell, LG; Kepler, TB. "The targeting of somatic hypermutation closely resembles that of meiotic mutation.." Journal of immunology (Baltimore, Md. : 1950) 166.2 (January, 2001): 892-899. [11145665] [abs]
- 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 169.3 (December, 2000): 205-221. [11133343], [doi] [abs]
- 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) 53.2 (February, 2000): 173-184. [10696765] [abs]
- 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) 164.4 (February, 2000): 1971-1976. [10657647] [abs]
- Oprea, M; Kepler, TB. "Genetic plasticity of V genes under somatic hypermutation: statistical analyses using a new resampling-based methodology.." Genome research 9.12 (December, 1999): 1294-1304. [10613852] [abs]
- 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 15.13 (September, 1999): 1219-1228. [10480635], [doi] [abs]
- Cowell, LG; Kim, HJ; Humaljoki, T; Berek, C; Kepler, TB. "Enhanced evolvability in immunoglobulin V genes under somatic hypermutation.." Journal of Molecular Evolution 49.1 (July, 1999): 23-26. [10368430] [abs]
- 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) 49.2 (June, 1999): 172-185. [10416263] [abs]
- 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 103.6 (March, 1999): 833-841. [10079104], [doi] [abs]
- Kepler, TB; Perelson, AS. "Drug concentration heterogeneity facilitates the evolution of drug resistance.." Proceedings of the National Academy of Sciences of USA 95.20 (September, 1998): 11514-11519. [9751697] [abs]
- 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 76.4 (August, 1998): 373-381. [9723780], [doi] [abs]
- 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 8.2 (February, 1998): 124-134. [9477340] [abs]
- 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 190.1 (January, 1998): 93-106. [9473394], [doi] [abs]
- Kepler, TB; Bartl, S. "Plasticity under somatic mutation in antigen receptors.." Current topics in microbiology and immunology 229 (1998): 149-162. [9479853]
- Kepler, TB. "Codon bias and plasticity in immunoglobulins.." Molecular Biology and Evolution 14.6 (June, 1997): 637-643. [9190065], [doi] [abs]
- 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) 157.10 (November, 1996): 4451-4457. [8906821] [abs]
- Kepler, TB; Perelson, AS. "Modeling and optimization of populations subject to time-dependent mutation.." Proceedings of the National Academy of Sciences of USA 92.18 (August, 1995): 8219-8223. [7667271] [abs]
- 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) 155.2 (July, 1995): 556-567. [7541819] [abs]
- Kepler, TB; Perelson, AS. "Somatic hypermutation in B cells: an optimal control treatment.." Journal of Theoretical Biology 164.1 (September, 1993): 37-64. [8264243], [doi] [abs]
- Kepler, TB; Perelson, AS. "Cyclic re-entry of germinal center B cells and the efficiency of affinity maturation.." Immunology Today 14.8 (August, 1993): 412-415. [8397781], [doi] [abs]
- Kepler, TB; Marder, E. "Spike initiation and propagation on axons with slow inward currents.." Biological Cybernetics 68.3 (1993): 209-214. [8452888] [abs]
- Kepler, TB; Abbott, LF; Marder, E. "Reduction of conductance-based neuron models.." Biological Cybernetics 66.5 (1992): 381-387. [1562643] [abs]
- Kepler, TB; Kagan, ML; Epstein, IR. "Geometric phases in dissipative systems.." Chaos 1.4 (December, 1991): 455-461. [12779941], [doi] [abs]
- Kagan, ML; Kepler, TB; Epstein, IR. "Geometric phase shifts in chemical oscillators.." Nature 349.6309 (February, 1991): 506-508. [1992353], [doi] [abs]
- Kepler, TB; Kagan, ML. "Geometric phase shifts under adiabatic parameter changes in classical dissipative systems.." Physical Review Letters 66.7 (February, 1991): 847-849. [10043921], [doi]
- Kepler, TB; Marder, E; Abbott, LF. "The effect of electrical coupling on the frequency of model neuronal oscillators.." Science 248.4951 (April, 1990): 83-85. [2321028] [abs]
- 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) 30.4 (July, 2002): 435-451. [12187936], [doi] [abs]