Peters Lab

Peters Lab

"The challenge in bioinformatics for immunology is not to develop faster algorithms, but to accurately translate immunological questions into a computable form." — Bjoern Peters, Ph.D. // Associate Professor
Center for Infectious Disease

Overview

Research in the Peters lab is focused in three areas, all relating to the development of computational tools to address fundamental questions in immunology.

Starting as a PhD student in 2000, Dr. Peters has worked on the development and validation of tools to analyze and predict which parts of a pathogen, allergen or cancer cell are targeted by immune responses. Identifying these specific molecular targets of immune responses, called epitopes, recognized by diseased individuals opens a path towards the development of diagnostics, vaccines and therapeutics for that particular disease. The tools the Peters lab develops aim to reduce the experimental effort required to identify these targets; computer-based predictions allow researchers to focus on the components most likely to be recognized rather than screening thousands of molecules.

The second research area of the lab is the identification of differences between immune cells in individuals with opposite disease outcomes. Powerful experimental tools have been developed to detect differences in how cells utilize the diverse parts of the genome. The Peters lab is using these tools to characterize how immune cells from diseased individuals differ from healthy individuals. These cells are isolated using disease-specific epitopes (or reagents based on them), so our epitope-identifying algorithms directly aid our disease-focused work. This research helps us understand how the disease develops and identifies potential targets in the genome for interventions to treat or prevent the disease.

Finally, the Peters lab is deeply involved in the development of community standards for knowledge representation to promote interoperability and re-use of data. The Peters and Sette lab maintain the Immune Epitope Database (www.iedb.org), which catalogs all published experiments on immune epitope recognition. This requires transforming free text information from journal publications into a structured format, and to make the information optimally useful, connecting it with information stored elsewhere. Doing this efficiently requires a community consensus on knowledge representation. Dr. Peters’ team is contributing to such consensus building and standardization efforts through active work on scientific community initiatives such as the Ontology of Biomedical Investigations (OBI, http://obi-ontology.org/).

From The Lab

Apr 8, 2016

Mapping T cells

Dec 17, 2015

La Jolla Institute for Allergy and Immunology team receives $18 million consortium grant

Jan 25, 2013 // San Diego Union Tribune

Anxiety about vaccines: how to neutralize concerns- La Jolla Institute's Alex Sette, Ph.D. and Bjoern Peters, Ph.D.

Peters Lab

Publications

Immunology

Reproducibility and conflicts in immune epitope data

2016-03
Vita R, Vasilevsky N, Bandrowski A, Haendel M, Sette A, Peters B
Clin Exp Allergy

Distinct modulation of allergic T cell responses by subcutaneous vs. sublingual allergen-specific immunotherapy

2016-03
J Virol

Immunodominant dengue virus specific CD8+ T cells responses are associated with a memory PD-1+ phenotype

2016-02
de Alwis R, Bangs DJ, Angelo MA, Cerpas C, Fernando A, Sidney J, Peters B, Gresh L, Balmaseda A, De Silva AD, Harris E,…
J Virol

Linear epitopes in A27 are targets of protective antibodies induced by vaccination against smallpox

2016-02
Kaever T, Matho MH, Meng Z, Crickard L, Schlossman A, Xiang Y, Crotty S, Peters B, Zajonc DM
J Immunol

The length distribution of class I-restricted T cell epitopes is determined by both peptide supply and MHC allele-specific binding preference

2016-02
Trolle T, McMurtrey CP, Sidney J, Bardet W, Osborn SC, Kaever T, Sette A, Hildebrand WH, Nielsen M, Peters B
Immunology

Epitope specific T-cell responses against influenza A in a healthy population

2016-02
Savic M, Dembinski JL, Kim Y, Tunheim G, Cox RJ, Oftung F, Peters B, Mjaaland S
J Allergy Clin Immunol

T-cell epitope conservation across allergen species is a major determinant of immunogenicity

2016-02
Westernberg L, Schulten V, Greenbaum JA, Natali S, Tripple V, McKinney DM, Frazier A, Hofer H, Wallner M, Sallusto F,…
Malar J

Measurement of ex vivo ELISpot interferon-gamma recall responses to plasmodium falciparum AMA1 and CSP in Ghanaian adults with natural exposure to malaria

2016-02
Ganeshan H, Kusi KA, Anum D, Hollingdale MR, Peters B, Kim Y, Tetteh JK, Ofori MF, Gyan BA, Koram KA, Huang J, Belmonte…
eLIFE

Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove

2016-01
McMurtrey C, Trolle T, Sansom T, Remesh SG, Kaever T, Bardet W, Jackson K, McLeod R, Sette A, Nielsen M, Zajonc DM,…
Immunology

T cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome

2016-01
Bresciani A, Paul S, Schommer N, Dillon MB, Bancroft T, Greenbaum J, Sette A, Nielsen M, Peters B
J Biomed Semantics

An ontology for major histocompatibility restriction

2016-01
Vita R, Overton JA, Seymour E, Sidney J, Kaufman J, Tallmadge RL, Ellis S, Hammond J, Butcher GW, Sette A, Peters B
Clin Exp Allergy

Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with allergen-specific modulation of immune reactivity

2015-12
Hinz D, Seumois G, Gholami AM, Greenbaum JA, Lane J, White B, Broide DH, Schulten V, Sidney J, Bakhru P, Oseroff C,…
Clinical and Experimental Allergy

Different Bla-g T cell antigens dominate responses in asthma versus rhinitis subjects

2015-12
Dillon MB, Schulten V, Oseroff C, Paul S, Dullanty LM, Frazier A, Belles X, Piulachs MD, Visness C, Bacharier L,…
Nature Communications

RSV-specific airway resident memory CD8+ T cells and differential disease severity after experimental human infection

2015-12
Jozwik A, Habibi MS, Paras A, Zhu J, Guvenel A, Dhariwal J, Almond M, Wong EH, Sykes A, Maybeno M, Del Rosario J,…
Human Immunology

Development and validation of a sample sparing strategy for HLA typing utilizing next generation sequencing

2015-12
McKinney DM, Fu Z, Le L, Greenbaum JA, Peters B, Sette A
Journal of Infectious Disease

Human CD8+ T-cell responses against the 4 dengue virus serotypes are associated with distinct patterns of protein targets

2015-12
Weiskopf D, Cerpas C, Angelo MA, Bangs DJ, Sidney J, Paul S, Peters B, Sanches FP, Silvera CG, Costa PR, Kallas EG,…
PLoS One

Immune responses in accute and convalescent patients with mild, moderate and severe disease during the 2009 influenza pandemic in Norway

2015-11
Mohn KG, Cox RJ, Tunheim G, Berdal JE, Hauge AG, Jul-Larsen A, Norwegian Pandemic Group, Peters B, Oftung F, Jonassen…
Journal of Investigative Dertamology Symposium Proceedings

The use of the immune epitope database to study autoimmune epitope data related to alopecia areata

2015-11
Sette A, Paul S, Vaughan K, Peters B
Clinical and Experimental Allergy

Definition of a pool of epitopes that recapitulates the T cell reactivity against major house dust mite allergens

2015-10
Hinz D, Oseroff C, Pham J, Sidney J, Peters B, Sette A
Journal of Virology

Cytomeglaovirus-specific CD4 T cells are cytolytic and mediate vaccine protection

2015-10
Verma S, Weiskopf D, Gupta A, McDonald B, Peters B, Sette A, Benedict CA
Immunogenetics

The common equine class I molecule Eqca-1*00101 (ELA-A3.1) is characterized by narrow peptide binding and T cell epitope repertoires

2015-09
Bergmann T, Moore C, Sidney J, Miller D, Tallmadge R, Harman RM, Oseroff C, Wriston A, Shabanowitz J, Hunt DF,…
PLoS Pathogens

Structural and functional characterization of anti-A33 antibodies reveal a potent cross-species orthopoxviruses neutralizer

2015-09
Matho MH, Schlossman A, Meng X, Benhnia MR, Kaever T, Buller M, Doronin K, Parker S, Peters B, Crotty S, Xiang Y,…
Proceedings of the National Academy of Sciences of the United States of America

Dengue virus infection elicits highly polarized CX3CR1+ cytotoxic CD4+ T cells associated with portective immunity

2015-08
Weiskopf D, Bangs DJ, Sidney J, Kolla RV, De Silva AD, de Silva AM, Crotty S, Peters B, Sette A
Journal of Immunological Methods

Development and validation of a broad scheme for predition of HLA class II restricted T cell epitopes

2015-07
Paul S, Lindestam Arlenhamn CS, Scriba TJ, Dillon MB, Oseroff C, Hinz D, McKinney DM, Pro SC, Sidney J, Peters B, Sette…
Bioinformatics

Automated benchmarking of peptide-MHC class I binding predictions

2015-07
Trolle T, Metushi IG, Greenbaum JA, Kim Y, Sidney J, Lund O, Sette A, Peters B, Nielsen M
Journal of Immunology

A population response analysis approach to assign class II HLA-epitope restrictions

2015-06
Paul S, Dillon MB, Lindestam Arlehamn CS, Huang H, Davis MM, McKinney DM, Scriba TJ, Sidney J, Peters B, Sette A
Nature Communications

IL-10-producing intestinal macrophages prevent excessive antibacterial innate immunity by limiting IL-23 synthesis

2015-05
Krause P, Morris V, Greenbaum JA, Park Y, Bjoerheden U, Mikulski Z, Muffley T, Shui JW, Kim G, Cheroutre H, Liu YC,…
PLoS One

Acyclovir has low but detectable infleunce on HLA-B*57:01 specificity without inducing hypersensitivity

2015-05
Metushi IG, Wriston A, Banerjee P, Gohlke BO, English AM, Lucas A, Moore C, Sidney J, Buus S, Ostrov DA, Mallal S,…
Journal of Virology

Dengue viral evolution under a hose-targeted antiviral

2015-05
Plummer E, Buck MD, Sanchez M, Greenbaum JA, Turner J, Frewal R, Klose B, Sampath A, Warfield KL, Peters B, Ramstedt U,…
PLoS One

Analysis of human RSV immunity at the molecular level: learning from the past and present

2015-05
Vaughan K, Ponomarenko J, Peters B, Sette A
Bioinformatics

PEASE: predicting B-cell epitopes utilizing antibody sequence

2015-04
Sela-Culang I, Ashkenazi S, Peters B, Ofran Y
Current Opinion in Virology

Antibody specific epitope prediction-emergence of a new paradigm

2015-03
Sela-Culang I, Ofran Y, Peters B
Journal of Allergy and Clinical Immunology

Immunoproteomic analysis of German cockroach (Blattella germanica) reveals antigens differentially recognized as a function of disease severity

2015-02
Dillon MB, Schulten VM, Hinz D, Oseroff C, Dullanty L, Tripple V, Pham J, Paul S, Frazier A, Sidney J, Peters B, Sette A
PLoS One

Abacavir-reactive memory T cells are present in drug naïve individuals

2015-02
Lucas A, Lucas M, Strhyn A, Keane NM, McKinnon E, Pavlos R, Moran EM, Meyer-Pannwitt V, Gaudieri S, D'Orsogna L, Kalams…
Journal of Allergy and Clinical Immunology

Characterization of the T cell response targeting Timothy grass antigens in allergic, healthy and specific immunotherapy-treated patients

2015-02
Schulten VM, Tripple V, Frazier A, Alam R, Broide D, Sette A, Peters B
Journal of Allergy and Clinical Immunology

A systematic analysis of pollen transcriptomes from plant allergens reveals conserved targets of immune responses

2015-02
Sternberg L, Greenbaum J, Schulten VM, Tripple V, Baker D, Frazier A, Hofer H, Wallner M, Sette A, Peters B
Molecular Biology of the Cell

Visual and functional demonstration of growing bax-induced pores in mitochondrial outer membranes

2015-01
Gillies LA, Du H, Peters B, Knudson CM, Newmeyer DD, Kuwana T
Proceedings of the National Academy of Sciences of the United States of America

Immunological consequences of intragenus conservation of mycobacterium tuberculosis T-cell epitopes

2015-01
Lindestam Arlehamn CS, Paul S, Mele F, Huang C, Greenbaum JA, Vita R, Sidney J, Peters B, Sallusto F, Sette A
Annual Review of Medicine

T cell-mediated hypersensitivity reactions to drugs

2015-01
Pavlos R, Mallal S, Osterov D, Buus S, Metushi I, Peters B, Phillips E
Nucleic Acids Research

The immune epitope database (IEDB) 3.0

2015-01
Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, Wheeler DK, Gabbard JL, Hix D, Sette A, Peters B
Journal of Virology

The human CD8+ T cell responses induced by a live attenuated tetravalent dengue vaccine are directed against highly conserved epitopes

2015-01
Weiskopf D, Angelo MA, Bangs DJ, Sidney J, Paul S, Peters B, de Silva AD, Lindow JC, Diehl SA, Whitehead S, Durbin A,…
Molecular & Cellular Proteomics

The development and application of a quantitative peptide microarray based approach to protein interaction domain specificity space

2014-12
Engelmann BW, Kim Y, Wang M, Peters B, Rock RS, Nash PD
Journal of Immunology

CD4 T cells specific for a latency-associated γ-herpesvirus epitope are polyfunctional and cytotoxic

2014-12
Freeman ML, Burkum CE, Cookenham T, Roberts AD, Lanzer KG, Huston GE, Jensen MK, Sidney J, Peters B, Kohlmeier JE,…
PLoS Pathogens

Murine anti-vaccinia virus D8 antibodies target different epitopes and differ in their ability to block D8 binding to CS-E

2014-12
Matho MH, de Val N, Miller GM, Brown J, Schlossman A, Meng X, Crotty S, Peters B, Xiang Y, Hsieh-Wilson LC, Ward AB,…
International Archives of Allergy and Immunology

New strategies for allergen T cell epitope identification: going beyond IgE

2014-11
Schulten V, Peters B, Sette A
Journal of Allergy and Clinical Immunology

Association between specific timothy grass antigens and changes in TH1- and TH2-cell responses following specific immunotherapy

2014-11
Schulten V, Tripple V, Sidney J, Greenbaum J, Frazier A, Alam R, Broide D, Peters B, Sette A
World Allergy Organization Journal

Allergy-associated T cell epitope repertoiries are surprisingly diverse and include non-IgE reactive antigens

2014-10
Frazier A, Schulten V, Hinz D, Oseroff C, Sidney J, Peters B, Sette A
Journal of Virology

Potent neutralization of vaccinia virus by divergent murine antibodies targeting a common site of vulnerability in L1 protien

2014-10
Kaever T, Meng X, Matho MH, Schlossman A, Li S, Sela-Culang I, Ofran Y, Buller M, Crump RW, Parker S, Fraizer A, Crotty…
Journal of Virology

Immunodominance changes as a function of the infecting dengue virus serotype and primary versus secondard infection

2014-10
Weiskopf D, Angelo MA, Sidney J, Peters B, Shresta S, Sette A
Journal of Immunology

Transcriptional profile of tuberculosis antigen-specific T cells reveals novel multifunctional features

2014-09
Arlehamn CL, Seumois G, Gerasimova A, Huang C, Fu Z, Yue X, Sette A, Vijayanand P, Peters B
PLoS One

Sterile immunity to malaria after DNA prime/adenovirus boost immunization is associated with effector memory CD8+T cells targeting AMA1 class I epitopes

2014-09
Sedegah M, Hollingdale MR, Farooq F, Ganeshan H, Belmonte M, Kim Y, Peters B, Sette A, Huang J, McGrath S, Abot E,…
Immunity

In vivo RNA interference screens identify regulators of antiviral CD4(+) and CD8(+) T cell differentiation

2014-08
Chen R, Bélanger S, Frederick MA, Li B, Johnston RJ, Xiao N, Liu YC, Sharma S, Peters B, Rao A, Crotty S, Pipkin ME
Nature Immunology

Epigenomic analysis of primart human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility

2014-08
Seumois G, Chavez L, Gerasimova A, Leinhard M, Omran N, Kalinke L, Vedanayagam M, Ganesan AP, Chawla A, Djukanovic R,…
BMC Bioinformatics

Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions

2014-07
Kim Y, Sidney J, Buus S, Sette A, Nielsen M, Peters B
Journal of Autoimmunity

CD8 T-cell reactivity to islet antigens is unique to type 1 while CD4 T-cell reactivity exists in both type 1 and type 2 diabetes

2014-05
Sarikonda G, Pettus J, Phatak S, Sachithanantham S, Miller JF, Wesley JD, Cadag E, Chae J, Ganesan L, Mallios R,…
Human Immunology

Substantial gaps in knowledge of bordetella pertussis antibody and T cell epitopes relevant for natural immunity and vaccine efficacy

2014-05
Vaughan K, Seymour E, Peters B, Sette A
Journal of Immunology

Relapsing-remitting cenral vervous system autoimmunity ediate by GFAP-secific CD8 T cells

2014-04
Sasaki K, Bean A, Shah S, Schutten E, Huseby PG, Peters B, Shen ZT, Vanguri V, Liggitt D, Huseby ES
Structure

Using a combined computational-exterimental approach to predict antibody-specific B cell epitopes

2014-04
Sela-Culang I, Benhnia MR, Matho MH, Kaever T, Maybeno M, Scholossman A, Nimrod G, Li S, Ziang Y, Zajonc D, Crotty S,…
PLoS Pathogens

Broadly reactive human CD8 T cells that recognize an epitope conserved between VZV, HSZ and EBV

2014-03
Chiu C, McCausland M, Sidney J, Duh FM, Rouphael N, Mehta A, Mulligan M, Carrington M, Wieland A, Sullivan NL, Weinburg…
Journal of Neuroimmunology

A molecular view of multiple sclerosis and experimental autoimmune encephalitis: what can we learn from the epitope data?

2014-02
Vaughan K, Peters B, O'Connor KC, Martin R, Sette A
Proceedings of the National Academy of Sciences of the United States of America

Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells

2014-01
Huang Y, Chavez L, Chang X, Wang X, Pastor WA, Kang J, Zepeda-Martinez JA, Pape UJ, Jacobsen SE, Peters B, Rao A
Journal of Immunology

HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity

2013-12
Paul S, Weiskopf D, Angelo MA, Sidney J, Peters B, Sette A
PLoS One

Temporal intra-individual variation of immunological biomarkers in type 1 diabetes patients: implications for future use in cross-sectional assessment

2013-11
Sarikonda G, Pettus J, Sachithanantham S, Phatak S, Miller JF, Ganesan L, Chae J, Mallios R, Edelman S, Peters B, von…
PLoS Computational Biology

Properties of MHC class I presented peptides that enhance immunogenicity

2013-10
Calis JJ, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Keşmir C, Peters B
Malaria Journal

Ex vivo tetramer staining and cell surface phenotyping for early activation markers CD38 and HLA-DR to enumerate and characterize malaria antigen-specific CD8+ T-cells induced in human volunteers immunized with a plasmodium falciparum adenovirus-vectored malaria vaccine expressing AMA1

2013-10
Schwenk R, Banania G, Epstein J, Kim Y, Peters B, Belmonte M, Ganeshan H, Huang J, Reyes S, Stryhn A, Ockenhouse CF,…
Malaria Journal

Identification of minimal human MHC-restricted CD8+ T-cell epitopes within the plasmodium falciparum circumsporozoite protein (CSP)

2013-06
Sedegah M, Kim Y, Ganeshan H, Huang J, Belmonte M, Abot E, Banania JG, Farooq F, McGrath S, Peters B, Sette A, Soisson…
Immunogenetics

A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population

2013-05
McKinney DM, Southwood S, Hinz D, Oseroff C, Arlenhamn CS, Schulten V, Taplitz R, Broide D, Hanekom WA, Scriba TJ, Wood…
Proceedings of the National Academy of Sciences of the United States of America

Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells

2013-05
Weiskopf D, Angelo MA, de Azeredo EL, Sidney J, Greenbaum JA, Fernando AN, Broadwater A, Kolla RA, De Silva AD, de…
Journal of Immunology

Blc6 expressing follicular helper CD4 T cells are fate committed early and have the capacity to form memory

2013-04
Choi YS, Yang JA, Yusuf I, Johnston RJ, Greenbaum J, Peters B, Crotty S
Journal of Biomedical Semantics

Query enhancement through the practical application of ontology: the IEDB and OBI

2013-04
Vita R, Overton JA, Greenbaum JA, Sette A, OBI consortium, Peters B
Journal of Virology

Unusual features of vaccinia virus extracellular virion form neutralization resistance revealed in human antibody responses to the smallpox vaccine

2013-02
Behnnia MR, Maybeno M, Blum D, Agular-Sino R, Matho M, Meng X, Head S, Felgner PL, Zajonc DM, Koriazova L, Katho S,…
Proceedings of the National Academy of Sciences of the United States of America

Previously undescribed grass pollen antigens are the major inducers of T helper 2 cytokine-producing T cells in allergic individuals

2013-02
Schulten V, Greenbaum JA, Hauser M, McKinney DM, Sidney J, Kolla R, Lindestam Arlehamn CS, Oseroff C, Alam R, Broide…
PLoS Computational Biology

Positional bias of MHC class I restricted T-cell epitopes in viral antigens is likely due to a bias in conservation

2013-01
Kim Y, Yewdell JW, Sette A, Peters B
PLoS Pathogens

Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subset

2013-01
Lindestam Arlehamn CS, Gerasimova A, Mele F, Henderson R, Swann J, Greenbaum JA, Kim Y, Sidney J, James EA, Taplitz R,…
Annals of Allergy Asthma & Immunology

The identification of potentially pathogenic and therapeutic epitopes from common human allergens

2013-01
Schulten V, Oseroff C. Alam R, Broide D, Vijayanand P, Peters B, Sette A
Immunological Reveiws

The structural basis of HLA-associated drug hypersensitivity syndromes

2012-11
Pompeu YA, Stewart JD, Mallal S, Phillips E, Peters B, Ostrov DA
Immunology

The immune epitope database: a historical retrospective of the first decade

2012-10
Salimi N, Fleri W, Peters B, Sette A
Proceedings of the National Academy of Sciences of the United States of America

Selective inhibition of CD4+ T-cell cytokine production and autoimmunity by BET protein and c-Myc inhibitors

2012-09
Bandukwala HS, Gagnon J, Togher S, Greenbaum JA, Lamperti ED, Parr NK, Molesworth AM, Smithers N, Lee K, Witherington…
Journal of Virology

Structural and biochemical characterization of the vaccinia virus envelope protein D8 and its recognition by the antibody LA5

2012-08
Matho MH, Maybeno M, Benhnia MR, Becker D, Meng X, Xiang Y, Crotty S, Peters B, Zajonc DM
Journal of Immunology

T cell responses to known allergen proteins are differently polarized and account for a variable fraction of total response to allergen extracts

2012-08
Oseroff C, Sidney J, Tripple V, McKinney DM, Southwood S, Brodie TM, Sallusto F, Grey H, Alam R, Broide D, Greenbaum…
Journal of Immunology

Analysis of T cell responses to the major allergens from german cockroack: epitope specificity and relationship to IgE production

2012-07
Oseroff C, Sidney J, Tripple V, Grey H, Wood R, Broide DH, Greenbaum J, Kolla R, Peters B, Pomés A, Sette A
Nucleic Acids Research

Immune epitope database analysis resource

2012-07
Kim Y, Ponomarenko J, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B
Proceedings of the National Academy of Sciences of the United States of America

Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire

2012-06
Ostrov DA, Grant BJ, Pompeu YA, Sidney J, Harndahi M, Southwood S, Oseroff C, Lu S, Jakoncic J, de Oliveira CA, Yang L,…
Journal of Immunology

Dissecting mechanisms of immunodominance to the common tuberculosis antigens ESAT-6, CFP1-, Rv2031c (hspX), Rv2654c (TB7.7), and Rv1038c (EsxJ)

2012-05
Arkegan CS, Sidney J, Henderson R, Greenbaum JA, James EA, Moutaftsi M, Coler R, McKinney DM, Park D, Taplitz R, Kwok…
PLoS Computational Biology

Structural consensus among antibodies defines the antigen binding site

2012-02
Kunik V, Peters B, Ofran Y
BMC Bioinformatics

Cost sensitive hierarchial document classification to triage Pubmed abstracts for manual curation

2011-12
Seymour E, Damale R, Sette A, Peters B
Journal of Immunological Methods

Applications for T-cell epitope queries and tools in the Immune Epitope Database and Anaylsis Resource

2011-11
Kim Y, Sette A, Peters B
Journal of Virology

Human CD8+ and CD4+ T cell memort to LCMV infection

2011-11
Kotturi M, Swann JA, Peters B, Arlehamn CL, Sidney J, Kolla RV, James EA, Akondy RS, Ahmen R, Kwok WW, Buchmeier MJ,…
Immunome Research

A computational pipeline to generate MHC binding motifs

2011-11
Wang P, Sidney J, Sette A, Peters B
Journal of Immunology

Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design

2011-10
Weiskopf D, Yauch LE, Angelo MA, John DV, Greenbaum JA, Sidney J, Kolla RV, De Silva AD, de Silva AM, Grey H, Peters B,…
Immunogenetics

Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes

2011-06
Greenbaum J, Sidney J, Chung J, Brander C, Peters B, Sette A
Immunogenetics

Functional analysis of frequently expressed Chinese rhesus macaque MHC class I molecules Mamu-A1*02601 and Mamu-B*08301 reveals HLA-A2 and HLA-A3 supertypic specificities

2011-05
Southwood S, Solomon C, Hoof I, Rudersdorf R, Sidney J, Peters B, Wahl A, Hawkins O, Hildebrand W, Mothé BR, Sette A
Journal of Immunology

Defining the herpes simplex virus-specific CD8+ T cell repertoire in C57BL/6 mice

2011-04
St Leger AJ, Peters B, Sidney J, Sette A, Hendricks RL
Immunome Research

A model for collaborative curation, the IEDB and CHEBI curation of non-peptidic epitopes

2011-04
Vita R, Peters B, Josephs Z, de Matos P, Ennis M, Turner S, Steinbeck C, Seymour E, Zarbski L, Sette A
PLoS One

Identification of CD4+ T cell epitopes in C. burnetii antigens targeted by antibody responses

2011-03
Chen C, Dow C, Wang P, Sidney J, Read A, Harmsen A, Samuel JE, Peters B
Journal of Allergy

Towards defining molecular determinants recognized by adaptive immunity in allergic disease: an inventory of the available data

2011-02
Vaughan K, Greenbaum J, Kim Y, Vita R, Chung J, Peters B, Broide D, Goodman R, Grey H, Sette A
Nucleic Acids Research

IEDB-3D: structural data within the immune epitope database

2011-01
Ponomarenko J, Papangelopoulos N, Zajonc DM, Peters B, Sette A, Bourne PE
Journal of Immunology Research

Automatic generation of validated specific epitope sets

2005-07
Carrasco Pro S, Sidney J, Paul S, Lindestam Arlehamn C, Weiskopf D, Peters B, Sette A
Sci Rep

Pro-apoptotic bax molecules densely populate the edges of membrane pores

2016-06
Kuwana T, Olson NH, Kiosses WB, Peters B, Newmeyer DD
Cell Immunol

Th1 versus Th2 T cell polarization by whole-cell and acellular childhood pertussis vaccines persists upon re-immunication in adolescence and adulthood

2016-06
Bancroft T, Dillon MB, de Silva Antunes R, Paul S, Peters B, Crotty S, Lindestam Arlehamn CS, Sette A
Immunology

T cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome

2016-05
Bresciani A, Paul S, Schommer N, Dillon MB, Bancroft T, Greenbaum J, Sette A, Nielsen M, Peters B
Clin Exp Allergy

Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with allergen-specific modulation of immune reactivity

2016-05
Hinz D, Seumois G, Gholami AM, Greenbaum JA, Lane J, White B, Broide DH, Schulten V, Sidney J, Bakhru P, Oseroff C,…
Malar J

Measurement of ex vivo ELISpot interferon-gamma recall responses to plasmodium falciparum AMA1 and CSP in Ghanaian adults with natural exposure to malaria

2016-02
Ganeshan H, Kusi KA, Anum D, Hollingdale MR, Peters B, Kim Y, Tetteh JK, Ofori MF, Gyan BA, Koram KA, Huang J, Belmonte…
PLoS One

Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data

2016-08
Gerasimova A, Chavez L, Li B, Seumois G, Greenbaum JA, Rao A, Vijayanand P, Peters B
Clinical & Developmental Immunology

Evaluating the immunogenicity of protein drugs by applyinng in vitro MHC binding data and the immune epitope database and analysis resource

2016-08
Paul S, Kolla RV, Sidney J, Weiskopf D, Fleri W, Kim Y, Peters B, Sette A
International Archives of Allergy and Immunology

Strategies to query and display allergy-derived epitope data from the immune epitope database

2016-08
Vaughan K, Peters B, Larche M, Pomes A, Broide D, Sette A
PLoS One

Polyfunctional CD4(+) T cell responses to immunodominant epitopes correlate with disease activity of virulent salmonella

2016-08
Maybeno M, Redeker A, Welten SP, Peters B, Loughhead SM, Schoenberger SP, Sette A, Arens R
PLoS One

A meta-analysis of the existing knowledge of immunoreactivity against hepatitis C virus (HCV)

2016-08
Kim Y, Vaughan K, Greenbaum J, Peters B, Law M, Sette A
PLoS One

The ontology for biomedical investigations

2016-04
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan…
J Virol

Immunodominant dengue virus specific CD8+ T cells responses are associated with a memory PD-1+ phenotype

2016-04
de Alwis R, Bangs DJ, Angelo MA, Cerpas C, Fernando A, Sidney J, Peters B, Gresh L, Balmaseda A, de Silva AD, Harris E,…
J Virol

Linear epitopes in vaccinia virus A27 are targets of protective antibodies induced by vaccination against smallpox

2016-04
Kaever T, Matho MH, Meng Z, Crickard L, Schlossman A, Xiang Y, Crotty S, Peters B, Zajonc DM
PLoS Pathog

A quantitative analysis of complexity of human pathogen-specific CD4 T cell responses in healthy M. tuberculosis infected south africans

2016-07
Lindestam Arlehamn CS, McKinney DM, Carpenter C, Paul S, Rozot V, Makgotlho E, Gregg Y, van Rooyen M, ernst JD,…
Clin Exp Allergy

Sequence conservation predicts T cell reactivity against ragweed allergens

2016-06
Pham J, Oseroff C, Hinz D, Sidney J, Paul S, Greenbaum J, Vita R, Philips E, Mallal S, Peters B, Sette A
J Immunol

Transcriptional profiling of Th2 cells identifies pathogenic features associated with asthma

2016-07
Seumois G, Zapardiel-Gonzalo J, White B, Singh D, Shulten V, Dillon M, Hinz D, Broide DH, Sette A, Peters B, Vijayanand…

Principal Investigator

peters

Bjoern Peters, Ph.D.

Associate Professor

Bjoern Peters is an Associate Professor in the Vaccine Discovery Division. Dr. Peters’ research focuses on the analysis of immunological information using statistical and computational methods, with a particular interest in modeling the recognition of immune epitopes. In 2000, Dr. Peters received his Diploma degree in Physics at the University of Hamburg with a thesis on quantum noise-driven laser oscillations. In 2003, he earned his PhD in Theoretical Biophysics (summa cum laude), writing his thesis on modeling the MHC class I antigen processing and presentation pathway. In 2004, Dr. Peters came to LIAI for postdoctoral training in Dr. Alessandro Sette’s lab, focusing on the initiation and development of the Immune Epitope Database project (http://www.iedb.org). In contrast to his original plans, he has been trapped in San Diego ever since. There are worse places to be trapped. He was appointed Assistant Professor at LIAI in 2008, and promoted to Associate Professor with tenure in 2014.

Lab Members

Mariana Babor, Ph.D.

Postdoctoral Fellow

JulieBurel

Julie Burel, Ph.D.

Postdoctoral Research Fellow

Biosketch:
I obtained a master of sciences degree in 2010 from the biotechnology engineering school ESIL (Ecole Superieure d’Ingenieurs de Luminy, University of Aix-Marseille) in Marseille, France. I then pursued my studies in Australia and graduated from the University of Queensland/QIMR Berghofer Medical Research Institute in 2015 with a PhD in Immunology. I began working as a postdoctoral research fellow within the Peters laboratory at La Jolla Institute in January 2016.

Research Focus:
My research interests have been focusing so far on applying systems immunology approaches to decipher the molecular basis of protective immune responses to infection/vaccination in humans. More specifically, my research project at LJI is aiming at characterizing and comparing T-cell immune signatures in individuals with active tuberculosis, latent tuberculosis or in healthy controls following BCG vaccination.

Career goals:
I plan to pursue a career in academic research in the field of systems immunology to study human disease, with a specific focus on bridging the gap between immunology and computational biology.

Hsiuyi Chen

Visiting Scientist

SundeepKumarDanda

Sandeep Kumar Dhanda, Ph.D.

Postdoctoral Fellow

Biography:
Graduation in basic science from Government College, Hisar, Haryana, India. Post-graduation in Medical Biotechnology, Maharshi Dayanand University, Rothak , Haryana, India. Doctorate in Bioinformatics from Joint PhD program of CSIR-Institute of Microbial Technology and Jawaharlal Nehru University, under the supervision of Dr. G.P.S. Raghava Currently working as Bioinformatics Postdoc for developing new tools at IEDB.

JoseMariaZapardiel

Jose Zapardiel Gonzalo

Research Technician II

Biosketch:
I studied Telecommunications Engineering at Carlos III University of Madrid. This degree combines studies from computer science and electrical engineering with additional courses about communication theory, which requires advance mathematical and statistical coursework. After moving to the United States I started working with Professor Matthias von Herrath´s laboratory at La Jolla Institute for Allergy and Immunology (LJI). This collaboration included statistical analysis support and development of scripts for histological image analysis. I also gave statistical support to other laboratories at LJI and I joined Professor Bjoern Peters’ laboratory in October of 2014. I have been working part time for both laboratories in a 20/80 basis since then.

Research Focus:
Under Prof. Peters supervision I work in the development of computational tools to address fundamental questions in immunology. Specifically, I analyze different types of data such as RNA-Seq, Chip-Seq or genotyping data from different diseases like Dengue, TB or common allergens. For this end I use a combination of tools and programming languages such as R-Bioconductor, Python or shell script.

My work in Prof. von Herrath’s laboratory includes the development of several scripts using a variety of tools (i.e. ImageJ, Matlab) to quantify diverse aspects of histology images such as pancreatic tissue infiltration, insulin area, number of alpha and beta cells and other indicators in the context of type 1 diabetes. In addition, I help with the statistical analysis of the results, giving advice about which tests should be used and performing, when needed, more advanced analysis using specialized software like R.

Career Goals:
My current interest is to apply knowledge and ideas from the engineering field to existing bioinformatics tools in order to develop new and improved methodologies that can advance biology research.

ThomasKaever

Thomas Kaever

Research Technician

About me:
Efficient, competent and enthusiastic Research Technician with 6+ years of practical lab experience in academia, predominantly in the fields of Molecular Biology and Immunology. I am naturally an entrepreneur, always eager to improve myself and the work I do. A strong work ethic is very important to me and I never hesitate to take on highly involved or intricate tasks. Besides displaying great expertise in working independently as well as in a team of highly motivated scientists, I have excellent communication skills, both verbal and written (fluent in English and German). Setting high goals for myself is what pushes and motivates me every day – I appreciate difficult tasks and new challenges in life and in my work environment.

Education / Research Experience:
I graduated from RWTH Aachen University, Germany, in 2011 with a B.S. degree in Biology while simultaneously working at the Fraunhofer IME. I then left Germany to study a semester abroad at San Diego State University in Fall 2011 and started working at LJI in February 2012 as an Intern in Dr. Peters lab. Over the course of the next 3 years I was promoted to my current position as Research Technician III. In fall 2015 I decided to take my education to the next level and started my part-time Master in Cell/Molecular Biology with emphasize in Immunology at San Diego State University.

Career Goals:
Research Associate / Project Manager / Clinical Research Associate. Haven’t quite decided yet.

Yohan Kim

Instructor

JeromeLane

Jerome Lane, Ph.D.

Bioinformatics Postdoctoral Fellow

Bio sketch:
I graduated in France from University of Rennes 1 with a fourth year university degree in biology (2004) and a Master’s degree in Bioinformatics research (2005) and from University of Angers 1 with a Master’s degree in complementary professional skills in computer science (2006). Then I obtained a PhD in Bioinformatics (2009) from University of Montpellier 2. From 2009 to 2014, I worked as a Bioinformatician postdoctorant in different places around the world acquiring and improving skills at IMGT (France), EPFL (Switzerland) and IUCPQ (Canada) and since January 2015, I am working in Peter’s laboratory in the Vaccine Discovery department at the La Jolla Institute for Allergy and Immunology.

Research Focus:
My research projects are mainly focused on human genetics, health and immune system. I developed IMGT/LIGMotif software to automate the annotation of antigen receptor genes in vertebrate genomic sequences. I studied genotypic data in order to reveal the genome-wide association of genetic variations that could be responsible for resistance to HIV infection in hemophiliacs. I also investigated the impact of statins on gene expression in human lung. Right now, I am characterizing T cell immune repertoire response to allergen or pathogen and building a computational model to predict reproducibility of the response.

Career goal:
I would like to contribute to personal medicine development notably in immunogenetics.

Manasa Lanka

Research Technician I

Swapnil

Swapnil Mahajan

Bioinformatics Postdoctoral Fellow

Biosketch:
I obtained a B.Sc. in biotechnology from the University of Pune in 2007, and a M.Sc. in bioinformatics from Bioinformatics center, University of Pune in 2009. After that, I joined Indian Institute of Science in Bangalore for one year as a junior research fellow. From there I moved to France, where I obtained my Ph.D. in bioinformatics from the La Reunion university in 2013. After Ph.D., I joined Dr. Yves-Henri Sanejouand’s lab in University of Nantes for two years. I joined Peters lab at the La Jolla Institute for Allergy and Immunology in June 2016.

Research Focus:
Since Ph.D., my research focus has been on algorithm development for protein structure analysis and prediction. In particular, I am interested in applying knowledge from three dimensional (3D) structural data, available in IEDB, to identify properties of epitopes that elicit the immune response.

Kristoffer Niss

Visiting Scientist

SinuPaul

Sinu Paul, Ph.D.

Postdoctoral Fellow

Biosketch:
I graduated from Kerala Agricultural University in India with a bachelor’s degree in Veterinary Medicine in 2004 and did an Advance Diploma program in Bioinformatics in 2005. I then obtained my Ph.D. in Biological Sciences from Kent State University, Ohio in 2012. I began working in the laboratory of Dr. Bjoern Peters at the La Jolla Institute for Allergy and Immunology in February 2012.

Research Focus:
My work is mainly focused on development of computational algorithms and tools using machine learning techniques and statistical applications for application in immunology such as immune epitope prediction, identification of restricting alleles of epitopes etc. I also do computational prediction of immune epitope candidates as well as other computational and statistical analysis of the biological data generated in the labs.

Mikhail Pomaznoy

Bioinformatics Postdoctoral Fellow

Julia Ponomarenko

Scientific Associate

Max Qian, Ph.D.

Visiting Scientist

VeroniqueSchulten

Véronique Schulten, Ph.D.

Instructor

Biosketch:
I obtained a B.Sc. in biochemistry from the University of Edinburgh in 2006, and a M.Sc. from King’s College London in 2007. From there I moved to Austria, where I obtained my Ph.D. in Immunology from the Medical University of Vienna in 2011. I began working as a postdoc in the Sette laboratory at the La Jolla Institute for Allergy and Immunology in March 2011 and switched to the Peters lab in mid-2013, where I was promoted to the Instructor position in January 2015.

Research Focus:
Ever since my PhD studies, my research focus has been the allergenic T cell response in type I allergy. One of my major objectives is the identification and characterization of T cell epitopes in different allergies, such as respiratory allergies (plant pollen) or food allergies. Another important aspect of my research is focused on studying the mechanisms involved in immuno-modulation during allergen-specific immunotherapy.

LuiseSternberg

Luise Sternberg, Ph.D.

Scientific Associate

Biosketch:
I graduated from the University of California Los Angeles (UCLA) in 2005 with a
B.S. degree in Molecular, Cell and Developmental Biology. After two years of working as a Scientific Assistant for the Breast Care Center at UCSF, I obtained my Ph.D. in Immunology from the SCRIPPS Research Institute in La Jolla, California in 2013. I began working as a Scientific Associate in the Peters laboratory at the La Jolla Institute for Allergy and Immunology in June 2013 and was promoted to Lab Manager in November of 2015

Research Focus:
My research focuses on T-cell epitopes and how they impact the immune response in allergy and cancer.

Career Goals:
My goal is to manage clinical and translational research projects in cancer immunology, autoimmune diseases or allergy.

JianSun

Jian Sun

Sr. Bioinformatics Specialist

Biosketch:
I graduated from Hefei University of Technology in 1995 with a M.E. degree in Computer Application. After worked in Bank of China Anhui Branch for 4 years, I immigrated to Canada. I graduated from Concordia University in 2005 and obtained my second M.S. degree in Computer Science, major in Bioinformatics. In 2001, I started working in the Certre for Structural and Functional Genomics, Concordia University as a system administrator/bioinformatician for 4 years. From 2005 to 2007, I worked in the Virginia Bioinformatics Institute as a Bioinformatics Programmer. In 2007, I joined Dr. Peters’ group in the La Jolla Institute for Allergy and Immunology as a Bioinformatics Specialist and was promoted to the Sr. Bioinformatics Specialist in 2013.

Research Focus:
My major research tasks are to design and develop user-friendly bioinformatics databases and tools to help scientists to store, manage and analyze all kinds of biological and immunological information in their studies.

Career Goals:
My main career goal is to build a centralized, standardized bioinformatics data management platform to support different research activities from all of the projects in the Sette/Peters lab.

DorjeeTamang

Dorjee Tamang

Bioinformatics Specialist

Biosketch:
I graduated with a M.S. in Bioinformatics and Computational Biology from University of Leeds, UK. I began working as a Scientific Programmer in the Department of Biological Sciences, at University of California, San Diego (UCSD), where I initiated and developed Transporter Classification Database (TCDB), a comprehensive IUBMB approved classification system for membrane transport proteins. I joined LJI in 2010 as a Bioinformatics Specialist in Peter’s Laboratory, and since then have made significant contributions to the development, maintenance and improvement of IEDB Analysis Resources.

Research Focus:
My work includes development and maintenance of IEDB analysis tools, RESTful API development, develop standalone packages for all major web-based analysis tools, implementation of new tools, reverse engineering predated tools into Python, debugging and testing of both legacy and new software.

Career Goals:
I am passionate about the development of computational tools to address the basic questions in Biology. Leading and supervising projects related to computational biology is what I plan to pursue.

RandyVita

Randi Vita, M.D.

IEDB Data Quality Control

Biosketch:
I graduated from The University of Texas at Austin in 1991 with a degree in biology. I then worked in a rheumatology lab under Dr. Peter Lipsky at The University of Texas Southwestern Medical Center. I continued a research career in the allergy laboratory of Rafeul Alam throughout my training at The University of Texas Medical Branch, School of Medicine, graduating with an M.D. and special honors in immunology in 1988. After a clinical research fellowship at the Shriners Burns Institute, Surgery Department, Galveston, Texas, I came to The La Jolla Institute for Allergy and Immunology to complete a basic research fellowship in the laboratory of Amnon Altman. I have been working on the Immune Epitope Database and Analysis Project (IEDB) since 2005.

Research Focus:
My interests include data management, ontology development, and ontology integration into databases in order to allow interoperability and sophisticated reasoning. Additionally, I am interested in data accuracy and reproducibility, as well as transparency and free access to data and scholarly communications.

Career Goals:
I hope to facilitate the integration of formal ontologies into many public scientific resources, like the IEDB, to bring about more accurate data, interoperable data sets, and new scientific conclusions.

Lark Wang

Intern

Xiaojun Xu, Ph.D.

Postdoctoral Fellow

JoseMariaZapardiel

Jose Maria Zapardiel

Research Technician II

Peters Lab

Research Projects