Thomas Kepler | Profiles RNS

Thomas Kepler, PhD

Emeritus Professor

Boston University Chobanian & Avedisian School of Medicine

Virology, Immunology & Microbiology

PhD, Brandeis University
BA, University of Massachusetts Boston

Websites

	Microbiology Faculty
	Immunology Training Program Faculty
	National Emerging Infectious Diseases Laboratories Faculty

ORCID : 0000-0002-1383-6865

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.

Faculty
Boston University
National Emerging Infectious Disease Lab

BU Research
NIH RePORTER Research

Research Training in Immunology
08/24/2020 - 07/31/2025 (PI of Sub-Project / SP)
PI: Suryaram Gummuluru, PhD
NIH/National Institute of Allergy & Infectious Diseases
5T32AI007309-35

Providence/Boston Center for AIDS Research (CFAR): Core Support (Cores A, B, E, G, K, SWG)
07/01/2018 - 06/30/2024 (PI of Sub-Project / SP)
The Miriam Hospital NIH NIAID
5P30AI042853-24

Structure-function analysis of infection- and vaccine-induced B-cell repertoires
08/01/2017 - 07/31/2023 (Subcontract PI)
The Children's Hospital Corporation NIH NIAID
5P01AI089618-10

HIV-1 vaccine-elicited antibodies target envelope glycans
06/01/2016 - 05/31/2023 (Subcontract PI)
Duke University NIH NIAID
5R01AI20801-03

The B cell repertoire as a window into the nature and impact of the lung virome
05/01/2019 - 04/30/2023 (Multi-PI)
PI: Thomas Kepler, PhD
NIH/National Heart, Lung, and Blood Institute
5R33HL137081-05

Immune Mechanisms of Protection against Mycobacterium Tuberculosis Center (IMPAc-TB)
09/30/2019 - 06/30/2022 (Subcontract PI)
President and Fellows of Harvard College dba Harvard T.H. Chan School of Public Health NIH NIAID

Modeling Affinity Maturation at Molecular Resolution
04/15/2015 - 03/31/2022 (Multi-PI)
PI: Thomas Kepler, PhD
NIH/National Institute of Allergy & Infectious Diseases
5U19AI117892-05

Neisserial Porins and Antigen Presenting Cells
09/01/2016 - 08/31/2021 (Subcontract PI)
Boston Medical Center Corporation NIH NIAID
5R01AI040944-22

Structure Based Design of Antibodies and Vaccines
05/01/2019 - 04/30/2021 (Subcontract PI)
Vanderbilt University Medical Center NIH NIAID
5U19AI117905-05

HIV-1 vaccine-elicited antibodies target envelope glycans
06/01/2018 - 05/31/2020 (Subcontract PI)
Duke University NIH NIAID
5R01AI120801-05

Showing 10 of 25 results. Show All Results

Title

Yr	Title	Project-Sub Proj	Pubs
2022	Research Training in Immunology	5T32AI007309-33
2021	The B cell repertoire as a window into the nature and impact of the lung virome	5R33HL137081-05
2021	Computational Core	5P01AI089618-10-5809	24
2021	Research Training in Immunology	5T32AI007309-32	73
2020	The B cell repertoire as a window into the nature and impact of the lung virome	5R33HL137081-04
2020	Computational Core	5P01AI089618-09-5809	24
2020	Research Training in Immunology	2T32AI007309-31A1	73
2019	The B cell repertoire as a window into the nature and impact of the lung virome	4R33HL137081-03
2019	Modeling affinity maturation at molecular resolution	5U19AI117892-05	17
2019	Model Development, Data Analysis, and Simulation for Affinity Maturation	5U19AI117892-05-8837	17

Showing 10 of 68 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.

iCite Analysis Copy PMIDs To Clipboard

Feng F, Yuen R, Wang Y, Hua A, Kepler TB, Wetzler LM. Characterizing adjuvants' effects at murine immunoglobulin repertoire level. iScience. 2024 Jan 19; 27(1):108749.View Related Profiles.

Wetzler, Lee
Kepler, Thomas

PMID: 38269092; PMCID: PMC10805652; DOI: 10.1016/j.isci.2023.108749;

Aihara F, Wang Y, Belkina AC, Fearns R, Mizgerd JP, Feng F, Kepler TB. Diversity of B Cell Populations and Ig Repertoire in Human Lungs. J Immunol. 2023 Aug 01; 211(3):486-496.View Related Profiles.

Belkina, Anna
Aihara, Fumiaki
Mizgerd, Joseph
Fearns, Rachel
Kepler, Thomas

PMID: 37314411; PMCID: PMC10352589; DOI: 10.4049/jimmunol.2200340;

Kepler T, Flanagan S, Hoegerl C. Urgency in the Treatment of Sudden Sensorineural Hearing Loss. Cureus. 2023 Jun; 15(6):e40409. PMID: 37456426; PMCID: PMC10348034; DOI: 10.7759/cureus.40409;

Caradonna TM, Ronsard L, Yousif AS, Windsor IW, Hecht R, Bracamonte-Moreno T, Roffler AA, Maron MJ, Maurer DP, Feldman J, Marchiori E, Barnes RM, Rohrer D, Lonberg N, Oguin TH, Sempowski GD, Kepler TB, Kuraoka M, Lingwood D, Schmidt AG. An epitope-enriched immunogen expands responses to a conserved viral site. Cell Rep. 2022 Nov 08; 41(6):111628. PMID: 36351401; PMCID: PMC9883670; DOI: 10.1016/j.celrep.2022.111628;

Gao N, Gai Y, Meng L, Wang C, Wang W, Li X, Gu T, Louder MK, Doria-Rose NA, Wiehe K, Nazzari AF, Olia AS, Gorman J, Rawi R, Wu W, Smith C, Khant H, de Val N, Yu B, Luo J, Niu H, Tsybovsky Y, Liao H, Kepler TB, Kwong PD, Mascola JR, Qin C, Zhou T, Yu X, Gao F. Development of Neutralization Breadth against Diverse HIV-1 by Increasing Ab-Ag Interface on V2. Adv Sci (Weinh). 2022 May; 9(15):e2200063. PMID: 35319830; PMCID: PMC9130890; DOI: 10.1002/advs.202200063;

Roark RS, Li H, Williams WB, Chug H, Mason RD, Gorman J, Wang S, Lee FH, Rando J, Bonsignori M, Hwang KK, Saunders KO, Wiehe K, Moody MA, Hraber PT, Wagh K, Giorgi EE, Russell RM, Bibollet-Ruche F, Liu W, Connell J, Smith AG, DeVoto J, Murphy AI, Smith J, Ding W, Zhao C, Chohan N, Okumura M, Rosario C, Ding Y, Lindemuth E, Bauer AM, Bar KJ, Ambrozak D, Chao CW, Chuang GY, Geng H, Lin BC, Louder MK, Nguyen R, Zhang B, Lewis MG, Raymond DD, Doria-Rose NA, Schramm CA, Douek DC, Roederer M, Kepler TB, Kelsoe G, Mascola JR, Kwong PD, Korber BT, Harrison SC, Haynes BF, Hahn BH, Shaw GM. Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth. Science. 2021 01 08; 371(6525). PMID: 33214287; PMCID: PMC8040783; DOI: 10.1126/science.abd2638;

Pavlovich SS, Darling T, Hume AJ, Davey RA, Feng F, Mühlberger E, Kepler TB. Egyptian Rousette IFN-? Subtypes Elicit Distinct Antiviral Effects and Transcriptional Responses in Conspecific Cells. Front Immunol. 2020; 11:435.View Related Profiles.

Hume, Adam
Muhlberger, Elke
Feng, Feng
Davey, Robert
Kepler, Thomas

PMID: 32231668; PMCID: PMC7083018; DOI: 10.3389/fimmu.2020.00435;

Easterhoff D, Pollara J, Luo K, Tolbert WD, Young B, Mielke D, Jha S, O'Connell RJ, Vasan S, Kim J, Michael NL, Excler JL, Robb ML, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Nitayaphan S, Sinangil F, Tartaglia J, Phogat S, Kepler TB, Alam SM, Wiehe K, Saunders KO, Montefiori DC, Tomaras GD, Moody MA, Pazgier M, Haynes BF, Ferrari G. Boosting with AIDSVAX B/E Enhances Env Constant Region 1 and 2 Antibody-Dependent Cellular Cytotoxicity Breadth and Potency. J Virol. 2020 01 31; 94(4). PMID: 31776278; PMCID: PMC6997759; DOI: 10.1128/JVI.01120-19;

Feng F, Ataca ST, Ran M, Wang Y, Breen M, Kepler TB. Gain-Scanning for Protein Microarray Assays. J Proteome Res. 2020 07 02; 19(7):2664-2675.View Related Profiles.

Feng, Feng
Ataca, Sila
Kepler, Thomas

PMID: 31928020; PMCID: PMC7783788; DOI: 10.1021/acs.jproteome.9b00892;

LaBranche CC, Henderson R, Hsu A, Behrens S, Chen X, Zhou T, Wiehe K, Saunders KO, Alam SM, Bonsignori M, Borgnia MJ, Sattentau QJ, Eaton A, Greene K, Gao H, Liao HX, Williams WB, Peacock J, Tang H, Perez LG, Edwards RJ, Kepler TB, Korber BT, Kwong PD, Mascola JR, Acharya P, Haynes BF, Montefiori DC. Correction: Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies. PLoS Pathog. 2019 Dec; 15(12):e1008200. PMID: 31790514; PMCID: PMC6886749; DOI: 10.1371/journal.ppat.1008200;

Showing 10 of 182 results. Show More

Gorman J, Mason RD, Nettey L, Cavett N, Chuang GY, Peng D, Tsybovsky Y, Verardi R, Nguyen R, Ambrozak D, Biris K, LaBranche CC, Ramesh A, Schramm CA, Zhou J, Bailer RT, Kepler TB, Montefiori DC, Shapiro L, Douek DC, Mascola JR, Roederer M, Kwong PD. Isolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan Shields. Immunity. 2019 10 15; 51(4):724-734.e4.View Related Profiles.

Ramesh, Akshaya
Kepler, Thomas

PMID: 31586542

LaBranche CC, Henderson R, Hsu A, Behrens S, Chen X, Zhou T, Wiehe K, Saunders KO, Alam SM, Bonsignori M, Borgnia MJ, Sattentau QJ, Eaton A, Greene K, Gao H, Liao HX, Williams WB, Peacock J, Tang H, Perez LG, Edwards RJ, Kepler TB, Korber BT, Kwong PD, Mascola JR, Acharya P, Haynes BF, Montefiori DC. Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies. PLoS Pathog. 2019 09; 15(9):e1008026. PMID: 31527908; PMCID: PMC6764681; DOI: 10.1371/journal.ppat.1008026;

Watanabe A, McCarthy KR, Kuraoka M, Schmidt AG, Adachi Y, Onodera T, Tonouchi K, Caradonna TM, Bajic G, Song S, McGee CE, Sempowski GD, Feng F, Urick P, Kepler TB, Takahashi Y, Harrison SC, Kelsoe G. Antibodies to a Conserved Influenza Head Interface Epitope Protect by an IgG Subtype-Dependent Mechanism. Cell. 2019 05 16; 177(5):1124-1135.e16.View Related Profiles.

Feng, Feng
Kepler, Thomas

PMID: 31100267; PMCID: PMC6825805; DOI: 10.1016/j.cell.2019.03.048;

Bonsignori M, Scott E, Wiehe K, Easterhoff D, Alam SM, Hwang KK, Cooper M, Xia SM, Zhang R, Montefiori DC, Henderson R, Nie X, Kelsoe G, Moody MA, Chen X, Joyce MG, Kwong PD, Connors M, Mascola JR, McGuire AT, Stamatatos L, Medina-Ramírez M, Sanders RW, Saunders KO, Kepler TB, Haynes BF. Inference of the HIV-1 VRC01 Antibody Lineage Unmutated Common Ancestor Reveals Alternative Pathways to Overcome a Key Glycan Barrier. Immunity. 2018 12 18; 49(6):1162-1174.e8. PMID: 30552024; PMCID: PMC6303191; DOI: 10.1016/j.immuni.2018.10.015;

Ferdman J, Palladino G, Liao HX, Moody MA, Kepler TB, Del Giudice G, Dormitzer PR, Harrison SC, Settembre EC, Suphaphiphat P. Intra-seasonal antibody repertoire analysis of a subject immunized with an MF59®-adjuvanted pandemic 2009 H1N1 vaccine. Vaccine. 2018 08 23; 36(35):5325-5332. PMID: 30055967; PMCID: PMC6521956; DOI: 10.1016/j.vaccine.2018.06.054;

Wiehe K, Bradley T, Meyerhoff RR, Hart C, Williams WB, Easterhoff D, Faison WJ, Kepler TB, Saunders KO, Alam SM, Bonsignori M, Haynes BF. Functional Relevance of Improbable Antibody Mutations for HIV Broadly Neutralizing Antibody Development. Cell Host Microbe. 2018 06 13; 23(6):759-765.e6. PMID: 29861171; PMCID: PMC6002614; DOI: 10.1016/j.chom.2018.04.018;

Pavlovich SS, Lovett SP, Koroleva G, Guito JC, Arnold CE, Nagle ER, Kulcsar K, Lee A, Thibaud-Nissen F, Hume AJ, Mühlberger E, Uebelhoer LS, Towner JS, Rabadan R, Sanchez-Lockhart M, Kepler TB, Palacios G. The Egyptian Rousette Genome Reveals Unexpected Features of Bat Antiviral Immunity. Cell. 2018 05 17; 173(5):1098-1110.e18.View Related Profiles.

Hume, Adam
Muhlberger, Elke
Kepler, Thomas

PMID: 29706541; PMCID: PMC7112298; DOI: 10.1016/j.cell.2018.03.070;

McCarthy KR, Watanabe A, Kuraoka M, Do KT, McGee CE, Sempowski GD, Kepler TB, Schmidt AG, Kelsoe G, Harrison SC. Memory B Cells that Cross-React with Group 1 and Group 2 Influenza A Viruses Are Abundant in Adult Human Repertoires. Immunity. 2018 01 16; 48(1):174-184.e9. PMID: 29343437; PMCID: PMC5810956; DOI: 10.1016/j.immuni.2017.12.009;

Williams WB, Zhang J, Jiang C, Nicely NI, Fera D, Luo K, Moody MA, Liao HX, Alam SM, Kepler TB, Ramesh A, Wiehe K, Holland JA, Bradley T, Vandergrift N, Saunders KO, Parks R, Foulger A, Xia SM, Bonsignori M, Montefiori DC, Louder M, Eaton A, Santra S, Scearce R, Sutherland L, Newman A, Bouton-Verville H, Bowman C, Bomze H, Gao F, Marshall DJ, Whitesides JF, Nie X, Kelsoe G, Reed SG, Fox CB, Clary K, Koutsoukos M, Franco D, Mascola JR, Harrison SC, Haynes BF, Verkoczy L. Initiation of HIV neutralizing B cell lineages with sequential envelope immunizations. Nat Commun. 2017 11 23; 8(1):1732.View Related Profiles.

Ramesh, Akshaya
Kepler, Thomas

PMID: 29170366; PMCID: PMC5701043; DOI: 10.1038/s41467-017-01336-3;

Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol. 2017; 8:1418. PMID: 29163494; PMCID: PMC5671925; DOI: 10.3389/fimmu.2017.01418;

Ramesh A, Darko S, Hua A, Overman G, Ransier A, Francica JR, Trama A, Tomaras GD, Haynes BF, Douek DC, Kepler TB. Structure and Diversity of the Rhesus Macaque Immunoglobulin Loci through Multiple De Novo Genome Assemblies. Front Immunol. 2017; 8:1407.View Related Profiles.

Ramesh, Akshaya
Kepler, Thomas

PMID: 29163486; PMCID: PMC5663730; DOI: 10.3389/fimmu.2017.01407;

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; PMCID: PMC5640856; DOI: 10.1128/JVI.00923-17;

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 08 08; 114(32):8614-8619. PMID: 28747530; PMCID: PMC5559054; DOI: 10.1073/pnas.1709203114;

Kepler TB. Unconventional Interrogation Yields HIV's Escape Plan. Cell Host Microbe. 2017 Jun 14; 21(6):659-660. PMID: 28618264

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 06 08; 8:15711. PMID: 28593989; PMCID: PMC5472724; DOI: 10.1038/ncomms15711;

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; PMCID: PMC5512451; DOI: 10.1016/j.immuni.2017.04.011;

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; PMCID: PMC5562351; DOI: 10.1126/scitranslmed.aai7521;

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; PMCID: PMC5562350; DOI: 10.1126/scitranslmed.aai7514;

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; PMCID: PMC5408352; DOI: 10.1016/j.celrep.2017.02.003;

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; PMCID: PMC5342261; DOI: 10.1371/journal.ppat.1006182;

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; PMCID: PMC5905719; DOI: 10.1126/sciimmunol.aal2200;

Kepler TB, Wiehe K. Genetic and structural analyses of affinity maturation in the humoral response to HIV-1. Immunol Rev. 2017 Jan; 275(1):129-144. PMID: 28133793; PMCID: PMC5362126; DOI: 10.1111/imr.12513;

Bradley T, Yang G, Ilkayeva O, Holl TM, Zhang R, Zhang J, Santra S, Fox CB, Reed SG, Parks R, Bowman CM, Bouton-Verville H, Sutherland LL, Scearce RM, Vandergrift N, Kepler TB, Moody MA, Liao HX, Alam SM, McLendon R, Everitt JI, Newgard CB, Verkoczy L, Kelsoe G, Haynes BF. HIV-1 Envelope Mimicry of Host Enzyme Kynureninase Does Not Disrupt Tryptophan Metabolism. J Immunol. 2016 Dec 15; 197(12):4663-4673. PMID: 27849170; PMCID: PMC5136304; DOI: 10.4049/jimmunol.1601484;

Raymond DD, Stewart SM, Lee J, Ferdman J, Bajic G, Do KT, Ernandes MJ, Suphaphiphat P, Settembre EC, Dormitzer PR, Del Giudice G, Finco O, Kang TH, Ippolito GC, Georgiou G, Kepler TB, Haynes BF, Moody MA, Liao HX, Schmidt AG, Harrison SC. Influenza immunization elicits antibodies specific for an egg-adapted vaccine strain. Nat Med. 2016 Dec; 22(12):1465-1469. PMID: 27820604; PMCID: PMC5485662; DOI: 10.1038/nm.4223;

Bradley T, Trama A, Tumba N, Gray E, Lu X, Madani N, Jahanbakhsh F, Eaton A, Xia SM, Parks R, Lloyd KE, Sutherland LL, Scearce RM, Bowman CM, Barnett S, Abdool-Karim SS, Boyd SD, Melillo B, Smith AB, Sodroski J, Kepler TB, Alam SM, Gao F, Bonsignori M, Liao HX, Moody MA, Montefiori D, Santra S, Morris L, Haynes BF. Amino Acid Changes in the HIV-1 gp41 Membrane Proximal Region Control Virus Neutralization Sensitivity. EBioMedicine. 2016 Oct; 12:196-207. PMID: 27612593; PMCID: PMC5078591; DOI: 10.1016/j.ebiom.2016.08.045;

Nelson CS, Pollara J, Kunz EL, Jeffries TL, Duffy R, Beck C, Stamper L, Wang M, Shen X, Pickup DJ, Staats HF, Hudgens MG, Kepler TB, Montefiori DC, Moody MA, Tomaras GD, Liao HX, Haynes BF, Ferrari G, Fouda GG, Permar SR. Combined HIV-1 Envelope Systemic and Mucosal Immunization of Lactating Rhesus Monkeys Induces a Robust Immunoglobulin A Isotype B Cell Response in Breast Milk. J Virol. 2016 May 15; 90(10):4951-65. PMID: 26937027; PMCID: PMC4859715; DOI: 10.1128/JVI.00335-16;

Zhang R, Verkoczy L, Wiehe K, Munir Alam S, Nicely NI, Santra S, Bradley T, Pemble CW, Zhang J, Gao F, Montefiori DC, Bouton-Verville H, Kelsoe G, Larimore K, Greenberg PD, Parks R, Foulger A, Peel JN, Luo K, Lu X, Trama AM, Vandergrift N, Tomaras GD, Kepler TB, Moody MA, Liao HX, Haynes BF. Initiation of immune tolerance-controlled HIV gp41 neutralizing B cell lineages. Sci Transl Med. 2016 Apr 27; 8(336):336ra62. PMID: 27122615; PMCID: PMC5006673; DOI: 10.1126/scitranslmed.aaf0618;

Bonsignori M, Zhou T, Sheng Z, Chen L, Gao F, Joyce MG, Ozorowski G, Chuang GY, Schramm CA, Wiehe K, Alam SM, Bradley T, Gladden MA, Hwang KK, Iyengar S, Kumar A, Lu X, Luo K, Mangiapani MC, Parks RJ, Song H, Acharya P, Bailer RT, Cao A, Druz A, Georgiev IS, Kwon YD, Louder MK, Zhang B, Zheng A, Hill BJ, Kong R, Soto C, Mullikin JC, Douek DC, Montefiori DC, Moody MA, Shaw GM, Hahn BH, Kelsoe G, Hraber PT, Korber BT, Boyd SD, Fire AZ, Kepler TB, Shapiro L, Ward AB, Mascola JR, Liao HX, Kwong PD, Haynes BF. Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody. Cell. 2016 Apr 7; 165(2):449-63. PMID: 26949186; PMCID: PMC4826291; DOI: 10.1016/j.cell.2016.02.022;

Kuraoka M, Schmidt AG, Nojima T, Feng F, Watanabe A, Kitamura D, Harrison SC, Kepler TB, Kelsoe G. Complex Antigens Drive Permissive Clonal Selection in Germinal Centers. Immunity. 2016 Mar 15; 44(3):542-52.View Related Profiles.

Feng, Feng
Kepler, Thomas

PMID: 26948373; PMCID: PMC4794380; DOI: 10.1016/j.immuni.2016.02.010;

Bradley T, Fera D, Bhiman J, Eslamizar L, Lu X, Anasti K, Zhang R, Sutherland LL, Scearce RM, Bowman CM, Stolarchuk C, Lloyd KE, Parks R, Eaton A, Foulger A, Nie X, Karim SS, Barnett S, Kelsoe G, Kepler TB, Alam SM, Montefiori DC, Moody MA, Liao HX, Morris L, Santra S, Harrison SC, Haynes BF. Structural Constraints of Vaccine-Induced Tier-2 Autologous HIV Neutralizing Antibodies Targeting the Receptor-Binding Site. Cell Rep. 2016 Jan 5; 14(1):43-54. PMID: 26725118; PMCID: PMC4706810; DOI: 10.1016/j.celrep.2015.12.017;

Schmidt AG, Do KT, McCarthy KR, Kepler TB, Liao HX, Moody MA, Haynes BF, Harrison SC. Immunogenic Stimulus for Germline Precursors of Antibodies that Engage the Influenza Hemagglutinin Receptor-Binding Site. Cell Rep. 2015 Dec 29; 13(12):2842-50. PMID: 26711348; PMCID: PMC4698027; DOI: 10.1016/j.celrep.2015.11.063;

Ip B, Cilfone NA, Belkina AC, DeFuria J, Jagannathan-Bogdan M, Zhu M, Kuchibhatla R, McDonnell ME, Xiao Q, Kepler TB, Apovian CM, Lauffenburger DA, Nikolajczyk BS. Th17 cytokines differentiate obesity from obesity-associated type 2 diabetes and promote TNFa production. Obesity (Silver Spring). 2016 Jan; 24(1):102-12.View Related Profiles.

Belkina, Anna
Nikolajczyk, Barbara
Apovian, Caroline
Defuria, Jason
Kepler, Thomas

PMID: 26576827; PMCID: PMC4688084; DOI: 10.1002/oby.21243;

Yeap LS, Hwang JK, Du Z, Meyers RM, Meng FL, Jakubauskaite A, Liu M, Mani V, Neuberg D, Kepler TB, Wang JH, Alt FW. Sequence-Intrinsic Mechanisms that Target AID Mutational Outcomes on Antibody Genes. Cell. 2015 Nov 19; 163(5):1124-37. PMID: 26582132; PMCID: PMC4751889; DOI: 10.1016/j.cell.2015.10.042;

Williams WB, Liao HX, Moody MA, Kepler TB, Alam SM, Gao F, Wiehe K, Trama AM, Jones K, Zhang R, Song H, Marshall DJ, Whitesides JF, Sawatzki K, Hua A, Liu P, Tay MZ, Seaton KE, Shen X, Foulger A, Lloyd KE, Parks R, Pollara J, Ferrari G, Yu JS, Vandergrift N, Montefiori DC, Sobieszczyk ME, Hammer S, Karuna S, Gilbert P, Grove D, Grunenberg N, McElrath MJ, Mascola JR, Koup RA, Corey L, Nabel GJ, Morgan C, Churchyard G, Maenza J, Keefer M, Graham BS, Baden LR, Tomaras GD, Haynes BF. HIV-1 VACCINES. Diversion of HIV-1 vaccine-induced immunity by gp41-microbiota cross-reactive antibodies. Science. 2015 Aug 14; 349(6249):aab1253.View Related Profiles.

Sawatzki, Kaitlin
Kepler, Thomas

PMID: 26229114; PMCID: PMC4562404; DOI: 10.1126/science.aab1253;

Feng F, Kepler TB. Bayesian Estimation of the Active Concentration and Affinity Constants Using Surface Plasmon Resonance Technology. PLoS One. 2015; 10(6):e0130812.View Related Profiles.

Feng, Feng
Kepler, Thomas

PMID: 26098764; PMCID: PMC4476803; DOI: 10.1371/journal.pone.0130812;

Nicely NI, Wiehe K, Kepler TB, Jaeger FH, Dennison SM, Rerks-Ngarm S, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Robb ML, O'Connell RJ, Michael NL, Kim JH, Liao HX, Munir Alam S, Hwang KK, Bonsignori M, Haynes BF. Structural analysis of the unmutated ancestor of the HIV-1 envelope V2 region antibody CH58 isolated from an RV144 vaccine efficacy trial vaccinee. EBioMedicine. 2015 Jul; 2(7):713-22. PMID: 26288844; PMCID: PMC4534707; DOI: 10.1016/j.ebiom.2015.06.016;

Schmidt AG, Therkelsen MD, Stewart S, Kepler TB, Liao HX, Moody MA, Haynes BF, Harrison SC. Viral receptor-binding site antibodies with diverse germline origins. Cell. 2015 May 21; 161(5):1026-34. PMID: 25959776; PMCID: PMC4441819; DOI: 10.1016/j.cell.2015.04.028;

Francica JR, Sheng Z, Zhang Z, Nishimura Y, Shingai M, Ramesh A, Keele BF, Schmidt SD, Flynn BJ, Darko S, Lynch RM, Yamamoto T, Matus-Nicodemos R, Wolinsky D, Nason M, Valiante NM, Malyala P, De Gregorio E, Barnett SW, Singh M, O'Hagan DT, Koup RA, Mascola JR, Martin MA, Kepler TB, Douek DC, Shapiro L, Seder RA. Analysis of immunoglobulin transcripts and hypermutation following SHIV(AD8) infection and protein-plus-adjuvant immunization. Nat Commun. 2015; 6:6565.View Related Profiles.

Ramesh, Akshaya
Kepler, Thomas

PMID: 25858157; PMCID: PMC4403371; DOI: 10.1038/ncomms7565;

Xu H, Schmidt AG, O'Donnell T, Therkelsen MD, Kepler TB, Moody MA, Haynes BF, Liao HX, Harrison SC, Shaw DE. Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage. Proteins. 2015 Apr; 83(4):771-80. PMID: 25524709; PMCID: PMC4368477; DOI: 10.1002/prot.24745;

Wiehe K, Easterhoff D, Luo K, Nicely NI, Bradley T, Jaeger FH, Dennison SM, Zhang R, Lloyd KE, Stolarchuk C, Parks R, Sutherland LL, Scearce RM, Morris L, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Sinangil F, Phogat S, Michael NL, Kim JH, Kelsoe G, Montefiori DC, Tomaras GD, Bonsignori M, Santra S, Kepler TB, Alam SM, Moody MA, Liao HX, Haynes BF. Antibody light-chain-restricted recognition of the site of immune pressure in the RV144 HIV-1 vaccine trial is phylogenetically conserved. Immunity. 2014 Dec 18; 41(6):909-18. PMID: 25526306; PMCID: PMC4324565; DOI: 10.1016/j.immuni.2014.11.014;

Moody MA, Easterhoff D, Gurley TC, Whitesides JF, Marshall DJ, Foulger A, Lloyd KE, Parks R, Pollara J, Duffy R, Shen S, Kim JH, Michael NL, Robb ML, O'Connell RJ, Vasan S, Excler JL, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Nitayaphan S, Sinangil F, Francis D, Lee C, Kepler TB, Alam SM, Ferrari G, Montefiori DC, Liao HX, Tomaras GD, Haynes BF. Induction of Antibodies with Long Variable Heavy Third Complementarity Determining Regions by Repetitive Boosting with AIDSVAX® B/E in RV144 Vaccinees. AIDS Res Hum Retroviruses. 2014 Oct; 30 Suppl 1:A36. PMID: 25357837; DOI: 10.1089/aid.2014.5057a.abstract;

Liao LH, Trama AM, Williams WB, Moody MA, Vandergrift N, Tomaras GD, Marshall DJ, Gurley T, Whitesides J, Eudailey J, Foulger A, Parks R, Stolarchuk C, Lloyd KE, Soderberg K, Mascola JR, Koup R, Corey L, Nabel GB, Gilber P, Morgan C, Maenza J, Keefer M, Hammer S, Churchyard G, Montefior DC, Graham BS, Baden LR, Kepler TB, Haynes BF. Role of Intestinal Microbiota in Shaping the B Cell Repertoire in HIV Infection and Env Vaccination. AIDS Res Hum Retroviruses. 2014 Oct; 30 Suppl 1:A19. PMID: 25357530; DOI: 10.1089/aid.2014.5023a.abstract;

Francica J, Sheng Z, Nishimura Y, Zhang Z, Singh M, O'Hagan DT, Douek D, Kepler T, Martin M, Shapiro L, Seder R. Genetic Assessment of B-cell Responses Following Immunization with HIV Env Protein and Adjuvants or SHIV (AD8) Infection in Nonhuman Primates. AIDS Res Hum Retroviruses. 2014 Oct; 30 Suppl 1:A45. PMID: 25357858; DOI: 10.1089/aid.2014.5076.abstract;

Kepler TB, Liao HX, Alam SM, Bhaskarabhatla R, Zhang R, Yandava C, Stewart S, Anasti K, Kelsoe G, Parks R, Lloyd KE, Stolarchuk C, Pritchett J, Solomon E, Friberg E, Morris L, Karim SS, Cohen MS, Walter E, Moody MA, Wu X, Altae-Tran HR, Georgiev IS, Kwong PD, Boyd SD, Fire AZ, Mascola JR, Haynes BF. Immunoglobulin gene insertions and deletions in the affinity maturation of HIV-1 broadly reactive neutralizing antibodies. Cell Host Microbe. 2014 Sep 10; 16(3):304-13. PMID: 25211073; PMCID: PMC4163498; DOI: 10.1016/j.chom.2014.08.006;

Trama AM, Moody MA, Alam SM, Jaeger FH, Lockwood B, Parks R, Lloyd KE, Stolarchuk C, Scearce R, Foulger A, Marshall DJ, Whitesides JF, Jeffries TL, Wiehe K, Morris L, Lambson B, Soderberg K, Hwang KK, Tomaras GD, Vandergrift N, Jackson KJ, Roskin KM, Boyd SD, Kepler TB, Liao HX, Haynes BF. HIV-1 envelope gp41 antibodies can originate from terminal ileum B cells that share cross-reactivity with commensal bacteria. Cell Host Microbe. 2014 Aug 13; 16(2):215-26. PMID: 25121750; PMCID: PMC4294419; DOI: 10.1016/j.chom.2014.07.003;

Sacha CR, Vandergrift N, Jeffries TL, McGuire E, Fouda GG, Liebl B, Marshall DJ, Gurley TC, Stiegel L, Whitesides JF, Friedman J, Badiabo A, Foulger A, Yates NL, Tomaras GD, Kepler TB, Liao HX, Haynes BF, Moody MA, Permar SR. Restricted isotype, distinct variable gene usage, and high rate of gp120 specificity of HIV-1 envelope-specific B cells in colostrum compared with those in blood of HIV-1-infected, lactating African women. Mucosal Immunol. 2015 Mar; 8(2):316-26. PMID: 25100291; PMCID: PMC4320043; DOI: 10.1038/mi.2014.69;

Gao F, Bonsignori M, Liao HX, Kumar A, Xia SM, Lu X, Cai F, Hwang KK, Song H, Zhou T, Lynch RM, Alam SM, Moody MA, Ferrari G, Berrong M, Kelsoe G, Shaw GM, Hahn BH, Montefiori DC, Kamanga G, Cohen MS, Hraber P, Kwong PD, Korber BT, Mascola JR, Kepler TB, Haynes BF. Cooperation of B cell lineages in induction of HIV-1-broadly neutralizing antibodies. Cell. 2014 Jul 31; 158(3):481-91. PMID: 25065977; PMCID: PMC4150607; DOI: 10.1016/j.cell.2014.06.022;

Fera D, Schmidt AG, Haynes BF, Gao F, Liao HX, Kepler TB, Harrison SC. Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domains. Proc Natl Acad Sci U S A. 2014 Jul 15; 111(28):10275-80. PMID: 24982157; PMCID: PMC4104889; DOI: 10.1073/pnas.1409954111;

Nair SK, Tomaras GD, Sales AP, Boczkowski D, Chan C, Plonk K, Cai Y, Dannull J, Kepler TB, Pruitt SK, Weinhold KJ. High-throughput identification and dendritic cell-based functional validation of MHC class I-restricted Mycobacterium tuberculosis epitopes. Sci Rep. 2014; 4:4632. PMID: 24755960; PMCID: PMC4894389; DOI: 10.1038/srep04632;

Kepler TB, Munshaw S, Wiehe K, Zhang R, Yu JS, Woods CW, Denny TN, Tomaras GD, Alam SM, Moody MA, Kelsoe G, Liao HX, Haynes BF. Reconstructing a B-Cell Clonal Lineage. II. Mutation, Selection, and Affinity Maturation. Front Immunol. 2014; 5:170. PMID: 24795717; PMCID: PMC4001017; DOI: 10.3389/fimmu.2014.00170;

Bonsignori M, Wiehe K, Grimm SK, Lynch R, Yang G, Kozink DM, Perrin F, Cooper AJ, Hwang KK, Chen X, Liu M, McKee K, Parks RJ, Eudailey J, Wang M, Clowse M, Criscione-Schreiber LG, Moody MA, Ackerman ME, Boyd SD, Gao F, Kelsoe G, Verkoczy L, Tomaras GD, Liao HX, Kepler TB, Montefiori DC, Mascola JR, Haynes BF. An autoreactive antibody from an SLE/HIV-1 individual broadly neutralizes HIV-1. J Clin Invest. 2014 Apr 1; 124(4):1835-43. PMID: 24614107; PMCID: PMC3973118; DOI: 10.1172/JCI73441;

Lynch HE, Stewart SM, Kepler TB, Sempowski GD, Alam SM. Surface plasmon resonance measurements of plasma antibody avidity during primary and secondary responses to anthrax protective antigen. J Immunol Methods. 2014 Feb; 404:1-12. PMID: 24316020; PMCID: PMC4104170; DOI: 10.1016/j.jim.2013.11.026;

Alam SM, Dennison SM, Aussedat B, Vohra Y, Park PK, Fernández-Tejada A, Stewart S, Jaeger FH, Anasti K, Blinn JH, Kepler TB, Bonsignori M, Liao HX, Sodroski JG, Danishefsky SJ, Haynes BF. Recognition of synthetic glycopeptides by HIV-1 broadly neutralizing antibodies and their unmutated ancestors. Proc Natl Acad Sci U S A. 2013 Nov 5; 110(45):18214-9. PMID: 24145434; PMCID: PMC3831483; DOI: 10.1073/pnas.1317855110;

Wesemann DR, Portuguese AJ, Meyers RM, Gallagher MP, Cluff-Jones K, Magee JM, Panchakshari RA, Rodig SJ, Kepler TB, Alt FW. Microbial colonization influences early B-lineage development in the gut lamina propria. Nature. 2013 Sep 5; 501(7465):112-5. PMID: 23965619; PMCID: PMC3807868; DOI: 10.1038/nature12496;

Ciupe SM, Devlin BH, Markert ML, Kepler TB. Quantification of total T-cell receptor diversity by flow cytometry and spectratyping. BMC Immunol. 2013; 14:35. PMID: 23914737; PMCID: PMC3750526; DOI: 10.1186/1471-2172-14-35;

Kepler TB. Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors. F1000Res. 2013; 2:103. PMID: 24555054; PMCID: PMC3901458; DOI: 10.12688/f1000research.2-103.v1;

Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD, Fire AZ, Roskin KM, Schramm CA, Zhang Z, Zhu J, Shapiro L, Mullikin JC, Gnanakaran S, Hraber P, Wiehe K, Kelsoe G, Yang G, Xia SM, Montefiori DC, Parks R, Lloyd KE, Scearce RM, Soderberg KA, Cohen M, Kamanga G, Louder MK, Tran LM, Chen Y, Cai F, Chen S, Moquin S, Du X, Joyce MG, Srivatsan S, Zhang B, Zheng A, Shaw GM, Hahn BH, Kepler TB, Korber BT, Kwong PD, Mascola JR, Haynes BF. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature. 2013 Apr 25; 496(7446):469-76. PMID: 23552890; PMCID: PMC3637846; DOI: 10.1038/nature12053;

Yang G, Holl TM, Liu Y, Li Y, Lu X, Nicely NI, Kepler TB, Alam SM, Liao HX, Cain DW, Spicer L, VandeBerg JL, Haynes BF, Kelsoe G. Identification of autoantigens recognized by the 2F5 and 4E10 broadly neutralizing HIV-1 antibodies. J Exp Med. 2013 Feb 11; 210(2):241-56. PMID: 23359068; PMCID: PMC3570098; DOI: 10.1084/jem.20121977;

Liao HX, Bonsignori M, Alam SM, McLellan JS, Tomaras GD, Moody MA, Kozink DM, Hwang KK, Chen X, Tsao CY, Liu P, Lu X, Parks RJ, Montefiori DC, Ferrari G, Pollara J, Rao M, Peachman KK, Santra S, Letvin NL, Karasavvas N, Yang ZY, Dai K, Pancera M, Gorman J, Wiehe K, Nicely NI, Rerks-Ngarm S, Nitayaphan S, Kaewkungwal J, Pitisuttithum P, Tartaglia J, Sinangil F, Kim JH, Michael NL, Kepler TB, Kwong PD, Mascola JR, Nabel GJ, Pinter A, Zolla-Pazner S, Haynes BF. Vaccine induction of antibodies against a structurally heterogeneous site of immune pressure within HIV-1 envelope protein variable regions 1 and 2. Immunity. 2013 Jan 24; 38(1):176-86. PMID: 23313589; PMCID: PMC3569735; DOI: 10.1016/j.immuni.2012.11.011;

Chan C, Billard M, Ramirez SA, Schmidl H, Monson E, Kepler TB. A model for migratory B cell oscillations from receptor down-regulation induced by external chemokine fields. Bull Math Biol. 2013 Jan; 75(1):185-205. PMID: 23296998; PMCID: PMC3547247; DOI: 10.1007/s11538-012-9799-9;

Schmidt AG, Xu H, Khan AR, O'Donnell T, Khurana S, King LR, Manischewitz J, Golding H, Suphaphiphat P, Carfi A, Settembre EC, Dormitzer PR, Kepler TB, Zhang R, Moody MA, Haynes BF, Liao HX, Shaw DE, Harrison SC. Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody. Proc Natl Acad Sci U S A. 2013 Jan 2; 110(1):264-9. PMID: 23175789; PMCID: PMC3538208; DOI: 10.1073/pnas.1218256109;

Manolopoulou I, Kepler TB, Merl DM. Mixtures of Gaussian Wells: Theory, Computation, and Application. Comput Stat Data Anal. 2012 Dec 01; 56(12):3809-3820. PMID: 22754052; PMCID: PMC3384503; DOI: 10.1016/j.csda.2012.03.027;

Haynes BF, Kelsoe G, Harrison SC, Kepler TB. B-cell-lineage immunogen design in vaccine development with HIV-1 as a case study. Nat Biotechnol. 2012 May; 30(5):423-33. PMID: 22565972; PMCID: PMC3512202; DOI: 10.1038/nbt.2197;

Bonsignori M, Montefiori DC, Wu X, Chen X, Hwang KK, Tsao CY, Kozink DM, Parks RJ, Tomaras GD, Crump JA, Kapiga SH, Sam NE, Kwong PD, Kepler TB, Liao HX, Mascola JR, Haynes BF. Two distinct broadly neutralizing antibody specificities of different clonal lineages in a single HIV-1-infected donor: implications for vaccine design. J Virol. 2012 Apr; 86(8):4688-92. PMID: 22301150; PMCID: PMC3318651; DOI: 10.1128/JVI.07163-11;

Moody MA, Zhang R, Walter EB, Woods CW, Ginsburg GS, McClain MT, Denny TN, Chen X, Munshaw S, Marshall DJ, Whitesides JF, Drinker MS, Amos JD, Gurley TC, Eudailey JA, Foulger A, DeRosa KR, Parks R, Meyerhoff RR, Yu JS, Kozink DM, Barefoot BE, Ramsburg EA, Khurana S, Golding H, Vandergrift NA, Alam SM, Tomaras GD, Kepler TB, Kelsoe G, Liao HX, Haynes BF. H3N2 influenza infection elicits more cross-reactive and less clonally expanded anti-hemagglutinin antibodies than influenza vaccination. PLoS One. 2011; 6(10):e25797. PMID: 22039424; PMCID: PMC3198447; DOI: 10.1371/journal.pone.0025797;

Liao HX, Chen X, Munshaw S, Zhang R, Marshall DJ, Vandergrift N, Whitesides JF, Lu X, Yu JS, Hwang KK, Gao F, Markowitz M, Heath SL, Bar KJ, Goepfert PA, Montefiori DC, Shaw GC, Alam SM, Margolis DM, Denny TN, Boyd SD, Marshal E, Egholm M, Simen BB, Hanczaruk B, Fire AZ, Voss G, Kelsoe G, Tomaras GD, Moody MA, Kepler TB, Haynes BF. Initial antibodies binding to HIV-1 gp41 in acutely infected subjects are polyreactive and highly mutated. J Exp Med. 2011 Oct 24; 208(11):2237-49. PMID: 21987658; PMCID: PMC3201211; DOI: 10.1084/jem.20110363;

Morris L, Chen X, Alam M, Tomaras G, Zhang R, Marshall DJ, Chen B, Parks R, Foulger A, Jaeger F, Donathan M, Bilska M, Gray ES, Abdool Karim SS, Kepler TB, Whitesides J, Montefiori D, Moody MA, Liao HX, Haynes BF. Isolation of a human anti-HIV gp41 membrane proximal region neutralizing antibody by antigen-specific single B cell sorting. PLoS One. 2011; 6(9):e23532. PMID: 21980336; PMCID: PMC3184076; DOI: 10.1371/journal.pone.0023532;

Alam SM, Liao HX, Dennison SM, Jaeger F, Parks R, Anasti K, Foulger A, Donathan M, Lucas J, Verkoczy L, Nicely N, Tomaras GD, Kelsoe G, Chen B, Kepler TB, Haynes BF. Differential reactivity of germ line allelic variants of a broadly neutralizing HIV-1 antibody to a gp41 fusion intermediate conformation. J Virol. 2011 Nov; 85(22):11725-31. PMID: 21917975; PMCID: PMC3209283; DOI: 10.1128/JVI.05680-11;

Ma BJ, Alam SM, Go EP, Lu X, Desaire H, Tomaras GD, Bowman C, Sutherland LL, Scearce RM, Santra S, Letvin NL, Kepler TB, Liao HX, Haynes BF. Envelope deglycosylation enhances antigenicity of HIV-1 gp41 epitopes for both broad neutralizing antibodies and their unmutated ancestor antibodies. PLoS Pathog. 2011 Sep; 7(9):e1002200. PMID: 21909262; PMCID: PMC3164629; DOI: 10.1371/journal.ppat.1002200;

Whittle JR, Zhang R, Khurana S, King LR, Manischewitz J, Golding H, Dormitzer PR, Haynes BF, Walter EB, Moody MA, Kepler TB, Liao HX, Harrison SC. Broadly neutralizing human antibody that recognizes the receptor-binding pocket of influenza virus hemagglutinin. Proc Natl Acad Sci U S A. 2011 Aug 23; 108(34):14216-21. PMID: 21825125; PMCID: PMC3161572; DOI: 10.1073/pnas.1111497108;

Bonsignori M, Hwang KK, Chen X, Tsao CY, Morris L, Gray E, Marshall DJ, Crump JA, Kapiga SH, Sam NE, Sinangil F, Pancera M, Yongping Y, Zhang B, Zhu J, Kwong PD, O'Dell S, Mascola JR, Wu L, Nabel GJ, Phogat S, Seaman MS, Whitesides JF, Moody MA, Kelsoe G, Yang X, Sodroski J, Shaw GM, Montefiori DC, Kepler TB, Tomaras GD, Alam SM, Liao HX, Haynes BF. Analysis of a clonal lineage of HIV-1 envelope V2/V3 conformational epitope-specific broadly neutralizing antibodies and their inferred unmutated common ancestors. J Virol. 2011 Oct; 85(19):9998-10009. PMID: 21795340; PMCID: PMC3196428; DOI: 10.1128/JVI.05045-11;

Ciupe SM, De Leenheer P, Kepler TB. Paradoxical suppression of poly-specific broadly neutralizing antibodies in the presence of strain-specific neutralizing antibodies following HIV infection. J Theor Biol. 2011 May 21; 277(1):55-66. PMID: 21315731; DOI: 10.1016/j.jtbi.2011.01.050;

Feng F, Sales AP, Kepler TB. A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays. Bioinformatics. 2011 Mar 1; 27(5):707-12.View Related Profiles.

Feng, Feng
Kepler, Thomas

PMID: 21149344; PMCID: PMC3465100; DOI: 10.1093/bioinformatics/btq686;

Saunders KO, Ward-Caviness C, Schutte RJ, Freel SA, Overman RG, Thielman NM, Cunningham CK, Kepler TB, Tomaras GD. Secretion of MIP-1ß and MIP-1a by CD8(+) T-lymphocytes correlates with HIV-1 inhibition independent of coreceptor usage. Cell Immunol. 2011; 266(2):154-64. PMID: 21030011; PMCID: PMC3615706; DOI: 10.1016/j.cellimm.2010.09.011;

Bennett KM, Scarborough JE, Pappas TN, Kepler TB. Patient socioeconomic status is an independent predictor of operative mortality. Ann Surg. 2010 Sep; 252(3):552-7; discussion 557-8. PMID: 20739856; DOI: 10.1097/SLA.0b013e3181f2ac64;

Kepler TB, Sample C, Hudak K, Roach J, Haines A, Walsh A, Ramsburg EA. Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler. BMC Genomics. 2010; 11:444. PMID: 20663124; PMCID: PMC3091641; DOI: 10.1186/1471-2164-11-444;

Tang H, Cao W, Kasturi SP, Ravindran R, Nakaya HI, Kundu K, Murthy N, Kepler TB, Malissen B, Pulendran B. The T helper type 2 response to cysteine proteases requires dendritic cell-basophil cooperation via ROS-mediated signaling. Nat Immunol. 2010 Jul; 11(7):608-17. PMID: 20495560; PMCID: PMC3145206; DOI: 10.1038/ni.1883;

Sen D, Forrest L, Kepler TB, Parker I, Cahalan MD. Selective and site-specific mobilization of dermal dendritic cells and Langerhans cells by Th1- and Th2-polarizing adjuvants. Proc Natl Acad Sci U S A. 2010 May 4; 107(18):8334-9. PMID: 20404167; PMCID: PMC2889549; DOI: 10.1073/pnas.0912817107;

Koelle K, Khatri P, Kamradt M, Kepler TB. A two-tiered model for simulating the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to influenza. J R Soc Interface. 2010 Sep 6; 7(50):1257-74. PMID: 20335193; PMCID: PMC2894885; DOI: 10.1098/rsif.2010.0007;

Kraus VB, Kepler TB, Stabler T, Renner J, Jordan J. First qualification study of serum biomarkers as indicators of total body burden of osteoarthritis. PLoS One. 2010; 5(3):e9739. PMID: 20305824; PMCID: PMC2840035; DOI: 10.1371/journal.pone.0009739;

Vincent BG, Young EF, Buntzman AS, Stevens R, Kepler TB, Tisch RM, Frelinger JA, Hess PR. Toxin-coupled MHC class I tetramers can specifically ablate autoreactive CD8+ T cells and delay diabetes in nonobese diabetic mice. J Immunol. 2010 Apr 15; 184(8):4196-204. PMID: 20220085; PMCID: PMC2868268; DOI: 10.4049/jimmunol.0903931;

Kepler TB, Crossman C, Cook-Deegan R. Metastasizing patent claims on BRCA1. Genomics. 2010 May; 95(5):312-4. PMID: 20226239; PMCID: PMC2857658; DOI: 10.1016/j.ygeno.2010.03.003;

Munshaw S, Kepler TB. SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements. Bioinformatics. 2010 Apr 1; 26(7):867-72. PMID: 20147303; PMCID: PMC2844993; DOI: 10.1093/bioinformatics/btq056;

Ji C, Merl D, Kepler TB, West M. Spatial Mixture Modelling for Unobserved Point Processes: Examples in Immunofluorescence Histology. Bayesian Anal. 2009 Dec 04; 4(2):297-316. PMID: 21037943; PMCID: PMC2965046

Li L, He Q, Garland A, Yi Z, Aybar LT, Kepler TB, Frelinger JA, Wang B, Tisch R. beta cell-specific CD4+ T cell clonotypes in peripheral blood and the pancreatic islets are distinct. J Immunol. 2009 Dec 1; 183(11):7585-91. PMID: 19917704; DOI: 10.4049/jimmunol.0901587;

Ciupe SM, Devlin BH, Markert ML, Kepler TB. The dynamics of T-cell receptor repertoire diversity following thymus transplantation for DiGeorge anomaly. PLoS Comput Biol. 2009 Jun; 5(6):e1000396. PMID: 19521511; PMCID: PMC2690399; DOI: 10.1371/journal.pcbi.1000396;

Volpe JM, Kepler TB. Genetic correlates of autoreactivity and autoreactive potential in human Ig heavy chains. Immunome Res. 2009; 5:1. PMID: 19250530; PMCID: PMC2669064; DOI: 10.1186/1745-7580-5-1;

Liao HX, Levesque MC, Nagel A, Dixon A, Zhang R, Walter E, Parks R, Whitesides J, Marshall DJ, Hwang KK, Yang Y, Chen X, Gao F, Munshaw S, Kepler TB, Denny T, Moody MA, Haynes BF. High-throughput isolation of immunoglobulin genes from single human B cells and expression as monoclonal antibodies. J Virol Methods. 2009 Jun; 158(1-2):171-9. PMID: 19428587; PMCID: PMC2805188; DOI: 10.1016/j.jviromet.2009.02.014;

Barefoot B, Thornburg NJ, Barouch DH, Yu JS, Sample C, Johnston RE, Liao HX, Kepler TB, Haynes BF, Ramsburg E. Comparison of multiple vaccine vectors in a single heterologous prime-boost trial. Vaccine. 2008 Nov 11; 26(48):6108-18. PMID: 18809447; PMCID: PMC2646904; DOI: 10.1016/j.vaccine.2008.09.007;

Sales AP, Tomaras GD, Kepler TB. Improving peptide-MHC class I binding prediction for unbalanced datasets. BMC Bioinformatics. 2008; 9:385. PMID: 18803836; PMCID: PMC2586639; DOI: 10.1186/1471-2105-9-385;

Chan C, Feng F, Ottinger J, Foster D, West M, Kepler TB. Statistical mixture modeling for cell subtype identification in flow cytometry. Cytometry A. 2008 Aug; 73(8):693-701.View Related Profiles.

Feng, Feng
Kepler, Thomas

PMID: 18496851; PMCID: PMC2840702; DOI: 10.1002/cyto.a.20583;

Frelinger J, Kepler TB, Chan C. Flow: Statistics, visualization and informatics for flow cytometry. Source Code Biol Med. 2008; 3:10. PMID: 18559108; PMCID: PMC2442075; DOI: 10.1186/1751-0473-3-10;

Riddle DS, Miller PJ, Vincent BG, Kepler TB, Maile R, Frelinger JA, Collins EJ. Rescue of cytotoxic function in the CD8alpha knockout mouse by removal of MHC class II. Eur J Immunol. 2008 Jun; 38(6):1511-21. PMID: 18465769; PMCID: PMC2957804; DOI: 10.1002/eji.200737710;

Mitha F, Lucas TA, Feng F, Kepler TB, Chan C. The Multiscale Systems Immunology project: software for cell-based immunological simulation. Source Code Biol Med. 2008; 3:6.View Related Profiles.

Feng, Feng
Kepler, Thomas

PMID: 18442405; PMCID: PMC2426691; DOI: 10.1186/1751-0473-3-6;

Buckley KM, Munshaw S, Kepler TB, Smith LC. The 185/333 gene family is a rapidly diversifying host-defense gene cluster in the purple sea urchin Strongylocentrotus purpuratus. J Mol Biol. 2008 Jun 13; 379(4):912-28. PMID: 18482736; DOI: 10.1016/j.jmb.2008.04.037;

Munshaw S, Kepler TB. An information-theoretic method for the treatment of plural ancestry in phylogenetics. Mol Biol Evol. 2008 Jun; 25(6):1199-208. PMID: 18359947; DOI: 10.1093/molbev/msn066;

Volpe JM, Kepler TB. Large-scale analysis of human heavy chain V(D)J recombination patterns. Immunome Res. 2008; 4:3. PMID: 18304322; PMCID: PMC2275228; DOI: 10.1186/1745-7580-4-3;

Ray S, Kepler TB. Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding. Immunome Res. 2007; 3:9. PMID: 17967170; PMCID: PMC2186325; DOI: 10.1186/1745-7580-3-9;

Kepler TB, Chan C. Spatiotemporal programming of a simple inflammatory process. Immunol Rev. 2007 Apr; 216:153-63. PMID: 17367341

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. 2007 May 15; 109(10):4539-47. PMID: 17284531; PMCID: PMC1885498; DOI: 10.1182/blood-2006-10-048652;

Chan C, Kepler TB. Computational immunology--from bench to virtual reality. Ann Acad Med Singapore. 2007 Feb; 36(2):123-7. PMID: 17364079

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. J Clin Immunol. 2007 Jan; 27(1):53-68. PMID: 17195045

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. Classification of osteoarthritis biomarkers: a proposed approach. Osteoarthritis Cartilage. 2006 Aug; 14(8):723-7.View Related Profiles.

Felson, David
Kepler, Thomas

PMID: 16733093

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. Biol Blood Marrow Transplant. 2006 Mar; 12(3):335-45. PMID: 16503503

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. Int Immunol. 2006 Feb; 18(2):249-57. PMID: 16418189

Volpe JM, Cowell LG, Kepler TB. SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations. Bioinformatics. 2006 Feb 15; 22(4):438-44. PMID: 16357034

Tomfohr J, Lu J, Kepler TB. Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics. 2005; 6:225. PMID: 16156896; PMCID: PMC1261155; DOI: 10.1186/1471-2105-6-225;

He M, Tomfohr JK, Devlin BH, Sarzotti M, Markert ML, Kepler TB. SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization. Bioinformatics. 2005 Sep 15; 21(18):3697-9. PMID: 16051675

Lu J, Tomfohr JK, Kepler TB. Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach. BMC Bioinformatics. 2005; 6:165. PMID: 15987513; PMCID: PMC1189357; DOI: 10.1186/1471-2105-6-165;

Kepler TB, He M, Tomfohr JK, Devlin BH, Sarzotti M, Markert ML. Statistical analysis of antigen receptor spectratype data. Bioinformatics. 2005 Aug 15; 21(16):3394-400. PMID: 15955781

Kepler TB. Microsimulation of Inducible Reorganization in Immunity. Complex Systems Science in BioMedicine (International Topics in Biomedical Engineering), eds. TS Deisboeck, YJ Kresh. Plenum. US. 2005.

Smith JT, Tomfohr JK, Wells MC, Beebe TP, Kepler TB, Reichert WM. Measurement of cell migration on surface-bound fibronectin gradients. Langmuir. 2004 Sep 14; 20(19):8279-86. PMID: 15350103

Zhang SM, Adema CM, Kepler TB, Loker ES. Diversification of Ig superfamily genes in an invertebrate. Science. 2004 Jul 9; 305(5681):251-4. PMID: 15247481

Loker ES, Adema CM, Zhang SM, Kepler TB. Invertebrate immune systems--not homogeneous, not simple, not well understood. Immunol Rev. 2004 Apr; 198:10-24. PMID: 15199951

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. J Virol. 2004 Mar; 78(5):2426-33. PMID: 14963138; PMCID: PMC369203

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. 2003 Dec; 55(9):594-604. PMID: 14579105

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. Nat Med. 2003 Jul; 9(7):928-35. PMID: 12819779

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. J Exp Med. 2003 Jan 20; 197(2):207-20. PMID: 12538660; PMCID: PMC2193808

Cowell LG, Davila M, Kepler TB, Kelsoe G. Identification and utilization of arbitrary correlations in models of recombination signal sequences. Genome Biol. 2002; 3(12):RESEARCH0072. PMID: 12537561; PMCID: PMC151174

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. Toxicol Pathol. 2002 Jul-Aug; 30(4):435-51. PMID: 12187936

Kepler TB, Crosby L, Morgan KT. Normalization and analysis of DNA microarray data by self-consistency and local regression. Genome Biol. 2002 Jun 28; 3(7):RESEARCH0037. PMID: 12184811; PMCID: PMC126242

McLain JET, Kepler TB, Ahmann D. (2002) Factors Influencing Methane Consumption in a Temperate Coniferous Forest Soil under Elevated Atmospheric CO2: A Field Study. Global Biogeochemical Cycles 10.1029/2001GB001439. Factors Influencing Methane Consumption in a Temperate Coniferous Forest Soil under Elevated Atmospheric CO2: A Field Study. Global Biogeochemical Cycles. 2002; (10.1029):10.1029/2001GB001439.
Sole RV, Pastor-Satorras R, Smith DE, Kepler TB. A Model of Large-Scale Proteome Evolution. Adv. Complex Sys. 2002; 5:43-54.

Kepler TB, Elston TC. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys J. 2001 Dec; 81(6):3116-36. PMID: 11720979; PMCID: PMC1301773

Zavolan M, Kepler TB. Statistical inference of sequence-dependent mutation rates. Curr Opin Genet Dev. 2001 Dec; 11(6):612-5. PMID: 11682302

Buchman TG, Cobb JP, Lapedes AS, Kepler TB. Complex systems analysis: a tool for shock research. Shock. 2001 Oct; 16(4):248-51. PMID: 11580104

Radmacher MD, Kepler TB. Waiting times to appearance and dominance of advantageous mutants: estimation based on the likelihood. Math Biosci. 2001 Mar; 170(1):59-77. PMID: 11259803

Kepler TB, Oprea M. Improved inference of mutation rates: I. An integral representation for the Luria-Delbrück distribution. Theor Popul Biol. 2001 Feb; 59(1):41-8. PMID: 11243927

Oprea M, Kepler TB. Improved inference of mutation rates: II. Generalization of the Luria-Delbrück distribution for realistic cell-cycle time distributions. Theor Popul Biol. 2001 Feb; 59(1):49-59. PMID: 11243928

Oprea M, Cowell LG, Kepler TB. The targeting of somatic hypermutation closely resembles that of meiotic mutation. J Immunol. 2001 Jan 15; 166(2):892-9. PMID: 11145665

Elston T, Kepler TB. A linear two-state model with complex dynamics. Phys. Lett. A. 2001; 280:204-208.

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. Toxicol Appl Pharmacol. 2000 Dec 15; 169(3):205-21. PMID: 11133343

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. J Immunol. 2000 Feb 15; 164(4):1971-6. PMID: 10657647

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. Toxicol Sci. 2000 Feb; 53(2):173-84. PMID: 10696765

Oprea M, Kepler TB. Genetic plasticity of V genes under somatic hypermutation: statistical analyses using a new resampling-based methodology. Genome Res. 1999 Dec; 9(12):1294-304. PMID: 10613852; PMCID: PMC310983

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 Res Hum Retroviruses. 1999 Sep 1; 15(13):1219-28. PMID: 10480635

Cowell LG, Kim HJ, Humaljoki T, Berek C, Kepler TB. Enhanced evolvability in immunoglobulin V genes under somatic hypermutation. J Mol Evol. 1999 Jul; 49(1):23-6. PMID: 10368430

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. Toxicol Sci. 1999 Jun; 49(2):172-85. PMID: 10416263

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. J Clin Invest. 1999 Mar; 103(6):833-41. PMID: 10079104; PMCID: PMC408138

Kepler TB, Perelson AS. Drug concentration heterogeneity facilitates the evolution of drug resistance. Proc Natl Acad Sci U S A. 1998 Sep 29; 95(20):11514-9. PMID: 9751697; PMCID: PMC21672

Radmacher MD, Kelsoe G, Kepler TB. Predicted and inferred waiting times for key mutations in the germinal centre reaction: evidence for stochasticity in selection. Immunol Cell Biol. 1998 Aug; 76(4):373-81. PMID: 9723780

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 Res. 1998 Feb; 8(2):124-34. PMID: 9477340

Cowell LG, Crowder LB, Kepler TB. Density-dependent prenatal androgen exposure as an endogenous mechanism for the generation of cycles in small mammal populations. J Theor Biol. 1998 Jan 07; 190(1):93-106. PMID: 9473394; DOI: 10.1006/jtbi.1997.0543;

Kepler TB, Bartl S. Plasticity under somatic mutation in antigen receptors. Curr Top Microbiol Immunol. 1998; 229:149-62. PMID: 9479853

Kepler TB. Codon bias and plasticity in immunoglobulins. Mol Biol Evol. 1997 Jun; 14(6):637-43. PMID: 9190065

Kepler TB. Oligomerization and PrPSc Stability in Prion Propagation: A Mathematical Analysis. Advances in Mathematical Population Dynamics: Molecules, Cells and Man, Eds. O. Arino, D. Axelrod and M. Kimmel. World Scientific. Singapore. 1997.

Kepler TB, Borrero M, Rugerio B, McCray SK, Clarke SH. Interdependence of N nucleotide addition and recombination site choice in V(D)J rearrangement. J Immunol. 1996 Nov 15; 157(10):4451-7. PMID: 8906821

Kepler TB, Perelson AS. Modeling and optimization of populations subject to time-dependent mutation. Proc Natl Acad Sci U S A. 1995 Aug 29; 92(18):8219-23. PMID: 7667271; PMCID: PMC41128

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. J Immunol. 1995 Jul 15; 155(2):556-67. PMID: 7541819

Perelson AS, Kepler TB. The immune system as a complex system: Adaptation by somatic mutation. Chaos & Complexity 93, J. Tran Tranh Van, P. Berge, R. Conte and M. Dubois, eds. Editiones Frontieres. Gif-sur-Yvette, France. 1995; pp 97-106.
Kelsoe G, Zeng B, Kepler TB. Do T-cells hypermutate?. Nature. 1995; 375:286 (Scientific Correspondence.

Kepler TB, Perelson AS. Somatic hypermutation in B cells: an optimal control treatment. J Theor Biol. 1993 Sep 7; 164(1):37-64. PMID: 8264243

Kepler TB, Perelson AS. Cyclic re-entry of germinal center B cells and the efficiency of affinity maturation. Immunol Today. 1993 Aug; 14(8):412-5. PMID: 8397781

Kepler TB, Marder E. Spike initiation and propagation on axons with slow inward currents. Biol Cybern. 1993; 68(3):209-14. PMID: 8452888

Marder E, Abbott LF, Buchholtz F, Epstein IR, Golowasch J, Hooper SL, Kepler TB. Physiological insights from cellular and network models of the stomatogastric nervous system of lobsters and crabs. Am. Zool. 1993; 33:29-39.
Marder E, Weimann JM, Kepler TB, Abbott LF. Computational implications of a serotonin-sensitive region of axonal membrane on a dual-function motor neuron. Analysis and Modeling of Neural Systems II, F Eeckman, ed. Kluwer Academic Press. Norwell. 1992; pp. 377-390.
Kepler TB (1992). Geometric phases in dissipative classical systems. Mod. Phys. Lett. 1992; 6:1613-1622.

Kepler TB, Abbott LF, Marder E. Reduction of conductance-based neuron models. Biol Cybern. 1992; 66(5):381-7. PMID: 1562643

Kepler TB, Kagan ML, Epstein IR. Geometric phases in dissipative systems. Chaos. 1991 Dec; 1(4):455-461. PMID: 12779941; DOI: 10.1063/1.165855;

Kepler TB, Kagan ML. Geometric phase shifts under adiabatic parameter changes in classical dissipative systems. Phys Rev Lett. 1991 Feb 18; 66(7):847-849. PMID: 10043921

Kagan ML, Kepler TB, Epstein IR. Geometric phase shifts in chemical oscillators. Nature. 1991 Feb 7; 349(6309):506-8. PMID: 1992353

Kepler TB, Abbott LF, Marder E. Order reduction for dynamical systems describing the behavior of complex neurons. Advances in Neural Information Processing Systems 3, RP Lippmann, JE Moody and DS Touretzky, eds. Morgan Kaufmann. San Mateo. 1991.
Alexander HR, Jensen JC, Doherty GM, Block MI, Buresh CM, Norton JA. Induction of manganous superoxide dismutase (MnSOD) gene expression by interleukin-1 (IL-1): possible molecular basis for IL-1 protection against experimental sepsis. Surg Forum. 1991; 42:98-100.

Kepler TB, Marder E, Abbott LF. The effect of electrical coupling on the frequency of model neuronal oscillators. Science. 1990 Apr 6; 248(4951):83-5. PMID: 2321028

Alexander HR, Langstein HN, Doherty GM, Jensen JC, Norton JA. Human recombinant tumor necrosis factor (hrTNF) protection against endotoxin induced shock and lethality in the rat. Surg Forum. 1990; 41:103-105.
Kepler TB (1990). Domains of attraction and the density of static metastable states in single-pattern iterated neural networks. J. Phys. A: Math. Gen. 1990; 24:1083-1092.
Abbott LF, Kepler TB. Model neurons: from Hodgkin-Huxley to Hopfield. Statistical Mechanics of Neural Networks, L Garrido, ed. Springer-Verlag. Berlin. 1990.
Marder E, Abbott LF, Kepler TB, Hooper S. Modification of oscillator function by electrically coupled neurons. Induced Rhythmicities in the Brain, T Bullock and E Basar, eds. Birkhauser. Boston. 1990.
Kepler TB, Datt S, Meyer RB, Abbott LF. Chaos in a neural network circuit. Physica D. 1990; 46:449-457.
Abbott LF, Kepler TB. Universality in the space of interactions for network models. J. Phys. A: Math. Gen. 1989; 22:2031-2038.
Abbott LF, Kepler TB. Optimal learning in neural network memories. J Phys A: Math. Gen. 1989; 22:L711-L717.
Kepler TB, Abbott LF. Domains of attraction in neural networks. J. Phys. France. 1988; 49:1657-1662.

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

Bar chart showing 182 publications over 34 distinct years, with a maximum of 14 publications in 2017

Bar chart showing 182 publications over 34 distinct years, with a maximum of 14 publications in 2017

Year	Publications
1988	1
1989	2
1990	6
1991	5
1992	3
1993	4
1995	4
1996	1
1997	2
1998	5
1999	5
2000	3
2001	8
2002	5
2003	3
2004	4
2005	6
2006	4
2007	4
2008	9
2009	5
2010	11
2011	8
2012	4
2013	9
2014	12
2015	10
2016	7
2017	14
2018	5
2019	4
2020	4
2022	2
2023	3