Thomas Kepler, PhD
Professor
Boston University School of Medicine
Dept of Microbiology

PhD, Brandeis University



The Kepler laboratory develops computational tools and applies them in the context of systems-level experimentation to address outstanding questions in immunology and vaccine development. Much of their work is centered on antibodies and the cells (B cells) that produce them.

Antibodies are genetically extraordinary: their genes are encoded only as fragments in the genome. The B cell’s genome must be cut, rearranged and re-ligated in several places to make the genes required for antibody production. Furthermore, after a B cell has encountered a molecule that binds its antibody (whether on a pathogen, an infected cell, a cancerous tumor, or, in the case of autoimmune disease, normal tissue) the B cell directs mutations into its rearranged antibody genes, and is then subject to competitive selection for improved ability to bind the eliciting molecule. In this Darwinian process, known as affinity maturation, the antibody response is rapidly improved and prepared as the memory response that confers long-term immunity and serves as the basis for vaccination.

The Kepler group works with multiple collaborating laboratories to generate and integrate data from many different assays, each of which provides one perspective on the workings of affinity maturation. By using computational means to coordinate the integration of these diverse data, a comprehensive picture of the process at a systems level emerges.

Professor Kepler, in partnership with colleagues at Duke and Harvard Universities, has developed a new approach to vaccination that uses computational methods to select combinations of immunogens to use in vaccines that drive affinity maturation in specific directions. These methods are being used to develop vaccines against HIV, influenza, and anthrax.

Graduate Faculty (Primary Mentor of Grad Students)
Boston University School of Medicine, Division of Graduate Medical Sciences


Member
Boston University
Bioinformatics Graduate Program




Research Training in Immunology
09/01/2014 - 08/31/2018 (PI)
NIH/National Institute of Allergy & Infe
5T32AI007309-28

Lifespan/Tufts/brown Center for AIDS Research (CFAR): Core A, Core B, Core G and SWG1
07/01/2016 - 06/30/2018 (PI of Sub-Project / SP)
PI: C. Robert Horsburgh Jr, MD
The Miriam Hospital NIH NIAID
4P30AI042853-19

CHAVI-SRSC J Computational Biology
07/15/2012 - 06/30/2018 (PI)
Duke University NIH NIAID
5UM1AI100645-05

HIV-1 vaccine-elicited antibodies target envelope glycans
06/01/2016 - 05/31/2018 (PI)
Duke University NIH NIAID
5R01AI20801-02

The B cell repertoire as a window into the nature and impact of the lung virome
05/01/2017 - 04/30/2018 (PI)
NIH/National Heart, Lung, and Blood Inst
1R61HL137081-01

Modeling Affinity Maturation at Molecular Resolution
04/15/2015 - 03/31/2018 (PI)
NIH/National Institute of Allergy & Infe
5U19AI117892-03

Neisserial Porins and Antigen Presenting Cells
09/01/2016 - 08/31/2017 (PI)
Boston Medical Center Corporation NIH NIAID
2R01AI040944-19A1

T and B Cell Mechanisms of HIV Control: Implications for Vaccine Design
09/01/2016 - 08/31/2017 (PI)
Massachusetts General Hospital Bill & Melinda Gates


Structure-function Analysis of Infection and Vaccine-induced B-cell Repertoires (Core D)
01/01/2012 - 06/30/2017 (PI)
The Children's Hospital Corporation NIH NIAID
5P01AI089618-05

Statistical analysis of anti-tau and anti-influenza antibodies
09/01/2016 - 12/31/2016 (PI)
Janssen Vaccines & Prevention B.V.


Showing 10 of 16 results. Show All Results



Yr Title Project-Sub Proj Pubs
2017 The B cell repertoire as a window into the nature and impact of the lung virome 1R61HL137081-01
2017 Modeling affinity maturation at molecular resolution 5U19AI117892-03 2
2017 Computational Core 2P01AI089618-06-5809 4
2017 Research Training in Immunology 5T32AI007309-29 46
2017 Administrative Core 5U19AI117892-03-8835 2
2017 Model Development, Data Analysis, and Simulation for Affinity Maturation 5U19AI117892-03-8837 2
2016 Modeling affinity maturation at molecular resolution 5U19AI117892-02 2
2016 Research Training in Immunology 5T32AI007309-28 46
2016 Administrative Core 5U19AI117892-02-8835 2
2016 Model Development, Data Analysis, and Simulation for Affinity Maturation 5U19AI117892-02-8837 2
Showing 10 of 47 results. Show All Results
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

  1. Han Q, Williams WB, Saunders KO, Seaton KE, Wiehe KJ, Vandergrift N, Von Holle TA, Trama AM, Parks RJ, Luo K, Gurley TC, Kepler TB, Marshall DJ, Montefiori DC, Sutherland LL, Alam MS, Whitesides JF, Bowman CM, Permar SR, Graham BS, Mascola JR, Seed PC, Van Rompay KKA, Tomaras GD, Moody MA, Haynes BF. HIV DNA-Adenovirus Multiclade Envelope Vaccine Induces gp41 Antibody Immunodominance in Rhesus Macaques. J Virol. 2017 Nov 01; 91(21). PMID: 28794027.
  2. Hwang JK, Wang C, Du Z, Meyers RM, Kepler TB, Neuberg D, Kwong PD, Mascola JR, Joyce MG, Bonsignori M, Haynes BF, Yeap LS, Alt FW. Sequence intrinsic somatic mutation mechanisms contribute to affinity maturation of VRC01-class HIV-1 broadly neutralizing antibodies. Proc Natl Acad Sci U S A. 2017 Aug 08; 114(32):8614-8619. PMID: 28747530.
  3. Kepler TB. Unconventional Interrogation Yields HIV''s Escape Plan. Cell Host Microbe. 2017 Jun 14; 21(6):659-660. PMID: 28618264.
  4. Bradley T, Pollara J, Santra S, Vandergrift N, Pittala S, Bailey-Kellogg C, Shen X, Parks R, Goodman D, Eaton A, Balachandran H, Mach LV, Saunders KO, Weiner JA, Scearce R, Sutherland LL, Phogat S, Tartaglia J, Reed SG, Hu SL, Theis JF, Pinter A, Montefiori DC, Kepler TB, Peachman KK, Rao M, Michael NL, Suscovich TJ, Alter G, Ackerman ME, Moody MA, Liao HX, Tomaras G, Ferrari G, Korber BT, Haynes BF. Pentavalent HIV-1 vaccine protects against simian-human immunodeficiency virus challenge. Nat Commun. 2017 Jun 08; 8:15711. PMID: 28593989.
  5. Cale EM, Gorman J, Radakovich NA, Crooks ET, Osawa K, Tong T, Li J, Nagarajan R, Ozorowski G, Ambrozak DR, Asokan M, Bailer RT, Bennici AK, Chen X, Doria-Rose NA, Druz A, Feng Y, Joyce MG, Louder MK, O''Dell S, Oliver C, Pancera M, Connors M, Hope TJ, Kepler TB, Wyatt RT, Ward AB, Georgiev IS, Kwong PD, Mascola JR, Binley JM. Virus-like Particles Identify an HIV V1V2 Apex-Binding Neutralizing Antibody that Lacks a Protruding Loop. Immunity. 2017 May 16; 46(5):777-791.e10. PMID: 28514685.
  6. Bonsignori M, Kreider EF, Fera D, Meyerhoff RR, Bradley T, Wiehe K, Alam SM, Aussedat B, Walkowicz WE, Hwang KK, Saunders KO, Zhang R, Gladden MA, Monroe A, Kumar A, Xia SM, Cooper M, Louder MK, McKee K, Bailer RT, Pier BW, Jette CA, Kelsoe G, Williams WB, Morris L, Kappes J, Wagh K, Kamanga G, Cohen MS, Hraber PT, Montefiori DC, Trama A, Liao HX, Kepler TB, Moody MA, Gao F, Danishefsky SJ, Mascola JR, Shaw GM, Hahn BH, Harrison SC, Korber BT, Haynes BF. Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies. Sci Transl Med. 2017 Mar 15; 9(381). PMID: 28298420; DOI: 10.1126/scitranslmed.aai7514;.
  7. Alam SM, Aussedat B, Vohra Y, Meyerhoff RR, Cale EM, Walkowicz WE, Radakovich NA, Anasti K, Armand L, Parks R, Sutherland L, Scearce R, Joyce MG, Pancera M, Druz A, Georgiev IS, Von Holle T, Eaton A, Fox C, Reed SG, Louder M, Bailer RT, Morris L, Abdool-Karim SS, Cohen M, Liao HX, Montefiori DC, Park PK, Fernández-Tejada A, Wiehe K, Santra S, Kepler TB, Saunders KO, Sodroski J, Kwong PD, Mascola JR, Bonsignori M, Moody MA, Danishefsky S, Haynes BF. Mimicry of an HIV broadly neutralizing antibody epitope with a synthetic glycopeptide. Sci Transl Med. 2017 03 15; 9(381). PMID: 28298421; DOI: 10.1126/scitranslmed.aai7521;.
  8. Saunders KO, Nicely NI, Wiehe K, Bonsignori M, Meyerhoff RR, Parks R, Walkowicz WE, Aussedat B, Wu NR, Cai F, Vohra Y, Park PK, Eaton A, Go EP, Sutherland LL, Scearce RM, Barouch DH, Zhang R, Von Holle T, Overman RG, Anasti K, Sanders RW, Moody MA, Kepler TB, Korber B, Desaire H, Santra S, Letvin NL, Nabel GJ, Montefiori DC, Tomaras GD, Liao HX, Alam SM, Danishefsky SJ, Haynes BF. Vaccine Elicitation of High Mannose-Dependent Neutralizing Antibodies against the V3-Glycan Broadly Neutralizing Epitope in Nonhuman Primates. Cell Rep. 2017 Feb 28; 18(9):2175-2188. PMID: 28249163; DOI: 10.1016/j.celrep.2017.02.003;.
  9. Easterhoff D, Moody MA, Fera D, Cheng H, Ackerman M, Wiehe K, Saunders KO, Pollara J, Vandergrift N, Parks R, Kim J, Michael NL, O''Connell RJ, Excler JL, Robb ML, Vasan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Nitayaphan S, Sinangil F, Tartaglia J, Phogat S, Kepler TB, Alam SM, Liao HX, Ferrari G, Seaman MS, Montefiori DC, Tomaras GD, Harrison SC, Haynes BF. Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV-1 vaccine trial. PLoS Pathog. 2017 Feb; 13(2):e1006182. PMID: 28235027; DOI: 10.1371/journal.ppat.1006182;.
  10. Williams LD, Ofek G, Schätzle S, McDaniel JR, Lu X, Nicely NI, Wu L, Lougheed CS, Bradley T, Louder MK, McKee K, Bailer RT, O''Dell S, Georgiev IS, Seaman MS, Parks RJ, Marshall DJ, Anasti K, Yang G, Nie X, Tumba NL, Wiehe K, Wagh K, Korber B, Kepler TB, Munir Alam S, Morris L, Kamanga G, Cohen MS, Bonsignori M, Xia SM, Montefiori DC, Kelsoe G, Gao F, Mascola JR, Moody MA, Saunders KO, Liao HX, Tomaras GD, Georgiou G, Haynes BF. Potent and broad HIV-neutralizing antibodies in memory B cells and plasma. Sci Immunol. 2017 Jan 27; 2(7). PMID: 28783671.
Showing 10 of 158 results. Show More

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 158 publications over 29 distinct years, with a maximum of 11 publications in 2010 and 2017

YearPublications
19881
19892
19906
19915
19923
19934
19954
19961
19972
19985
19995
20003
20018
20025
20033
20044
20056
20064
20074
20089
20095
201011
20118
20124
20139
20149
201510
20167
201711
In addition to these self-described keywords below, a list of MeSH based concepts is available here.

affinity maturation
antibody
B cell
bats
computational biology
mathematical modeling
systems biology
vaccine
wildlife immunology

Available to Mentor as: (Review Mentor Role Definitions):
  • Advisor
  • Research / Scholarly Mentor
Contact for Mentoring:


72 E. Concord St Instructional (L)
Boston MA 02118
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