Bjoern Peters is a Professor in the Infectious Disease and Vaccine Center. 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.
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
T cells take the lead in controlling SARS-CoV-2 and reducing COVID-19 disease severityFinding may help explain why people 65 and above face a higher risk of falling critically ill with COVID-19
LJI Scientists Awarded New Funding to Combat COVID-19To aid vaccine design, researchers will investigate how a diverse population fights off viral attack
La Jolla Institute for Immunology to host coronavirus immunotherapy clearinghouseLed by LJI scientist Erica Ollmann Saphire, the global effort will streamline and accelerate the development of effective treatments for COVID-19.
LJI scientists identify potential targets for immune responses to novel coronavirusTheir analysis provides essential information for vaccine design and the evaluation of diagnostics and vaccine candidates
Antigen-specific adaptive immunity to SARS-CoV-2 in acute COVID-19 and associations with age and disease severity
Supplementary Materials for: Antigen-specific adaptive immunity to SARS-CoV-2 in acute COVID-19 and associations with age and disease severity
A sequence homology and bioinformatics approach can predict candidate tagets for immune responses in SARS-CoV-2
T cell epitope predictions
Identification of plasmodium falciparum circumsporozoite protein-specific CD8+ T cell epitopes in a malaria exposed population
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook
Major histocompatibility complex binding, eluted ligands, and immunogenicity: benchmark testing and predictions
Epitope-specific airway-resident CD4+ T cell dynamics during experimental huyman RSV infection
Epitope-specific airway-resident CD4+ T cell dynamics during experimental human RSV infection
The human immunopeptidone project: A roadmap to predict and treat immune diseases
The human immunopeptidone project: A roadmap to predict and treat immune diseases
A structured model for immune exposures
Molecular signatures of Dengue virus-specific IL-10/FN-g co-producing CD4 T clls and their association with Dengue disease
A modified injector and sample acquisition protocol can improve data quality and reduce inter-instrument variability of the helios mass cytometer
A survey of known immune epitopes in the enteroviruses strains associated with acute flaccid myelitis
MOGSA: integrative single sample gene-set analysis of multiple omics data
Restricted myeloperoxidase epitopes drive the adaptive immune response in MPO-ANCA vasculitis
Characterization of magnitude and antigen specificity of HLA-DP, DQ and DRB3/4/5 restricted DENV-specific CD4+T cell responses
Analysis of allergen-specific T cell and IgE reactivity to different preparations of cow’s milk-containing food extracts
IEDB-AR: immune epitope database – analysis resource in 2019
Widespread Tau-specific CD4 T cell reactivity in the general population
MOGSA: integrative single sample gene-set analysis of multiple omics data
Circulating T cell-monocyte complexes are markers of immune perturbations
Circulating T cell-monocyte complexes are markers of immune perturbations
Reporting and connecting cell type names and gating definitions through ontologies
Characterization and epitope identification of the T cell response in non-allergic individuals exposed to mouse allergen
Dengue-specific CD8+ T cell subsets display specialized transcriptomic and TCR profiles
Variability in german cockroach extract composition greatly impacts T cell potency in cockroach-allergic donors
Antibody specific B-cell epitope predictions: leveraging information from antibody-antigen protein complexes
Most viral peptides displayed by class I MHC on infected cells are immunogenic
Host transcriptomics as a tool to identify diagnostic and mechanistic immune signatures of tuberculosis
The immune epitope database (IEDB): 2018 update
Cutting edge: transcriptional profiling reveals multifunctional and cytotoxic antiviral responses of zika virus-specific CD8+ T cells
GOnet: a tool for interactive gene ontology analysis
A review on T cell epitopes identified using prediction and cell-mediated immune models for mycobacterium tuberculosis and bordetella pertussis
Impact of genetic polymorphisms on human immune cell gene expression
Epitope specific antibodies and T cell receptors in the immune epitope database
Footprints of antigen processing boost MHC class II natural ligand predictions
ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference protein
Investigation of outbreak-specific nonsynonymous mutations on ebolavirus GP in the context of known immune reactivity
Putting benchmarks in their rightful place: The heart of computational biology
Development of a novel clustering tool for linear peptide sequences
Mrp1 is involved in lipid presentation and iNKT cell activation by Streptococcus pneumoniae
Peanut-specific T cell responses in patients with different clinical reactivity
Th1/Th17 polarization persists following whole-cell pertussis vaccination dspite repeated acellular boosters
Predicting T cell recognition of MHC class I restricted neoepitopes
Determination of a predictive cleavage motif for eluted MHC class II ligands
Improved methods for predicting peptide binding affinity to MHC class II molecules
Predicting HLA CD4 immunogenicity in human populations
DAFi: a directed recursive data filtering and clustering approach for improving and integrating data clustering identification of cell populations from polychromatic flow cytometry data
Minimal information about an immune-peptidomics experiment (MIAIPE)
Microbiota epitope similarity either damperns or enhances the immunogenicity of disease-associated antigenic eptiopes
Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes
An automated benchmarking platform for MHC class II binding prediction methods
Discovering transcriptional signatures of disease for diagnosis versus mechanism
Characterization of murine antibody responses to vaccinia virus envelope protein A14 reveals an immunodominant antigen lacking of effective neutralization targets
Transcriptomic analysis of CD4+ T cells reveals novel immune signatures of latent tuberculosis
Urinary peptides as a novel source of T cell allergen epitopes
Allergen and epitope targets of mouse-specific T cell responses in allergy and asthma
Allergen-specific immunotherapy modulates the balance of circulating Tfh and Tfr cells
Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis
Structure-function characterization of three human antibodies targeting the vaccinia virus adhesion molecule D8
The SysteMHC Atlas project
Development of a strategy and computational application to select candidate protein analogues with reduced HLA binding and immunogenicity
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability
Identification of errors in the IEDB using ontologies
Adaptive immune receptor repertoire community recommendations for sharing immune-repertoire sequencing data
Unique phenotypes and clonal expansions of human CD4 effector memory T cell re-expressing CD45RA
NetMHCpan-4.0: improved peptide-MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data
Reproducibility and reuse of adaptive immune receptor repertoire data
Global assessment of dengue virus-specific CD4+ T cell responses in dengue-endemic areas
Prior dengue virus exposure shapes T cell immunity to zika virus in humans
Differential recognition of mycobacterium tuberculosis-specific epitopes as a function of tuberculosis disease history
Deciphering the MHC-associated peptidome: a review of naturally processed ligand data
Shared peptide binding of HLA class I and II alleles associate with cutaneous nevirapine hypersensitivity and identify novel risk alleles
T cells from patients with Parkinson's disease recognize α-synuclein peptides
Experimental validation of the RATE tool for inferring HLA restrictions of T cell epitopes
Machine learning reveals a non-canonical mode of peptide binding to MHC class II molecules
Citrullination only infrequently impacts peptide binding to HLA class II MHC
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes
Immunoproteomic analysis of house dust mite antigens reveals distinct classes of dominant T cell antigens according to function and serological reactivity
Unconventional peptide presentation by major histocompatibility complex (MHC) class I allele HLA-A*02:01: breaking confinement
Patterns of cellular immunity associated with experimental infection with rDEN2∆30 (Tonga/74) support its suitability as a human dengue virus challenge strain
The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design
An integrated workflow to assess technical and biological variability of cell population frequencies in human peripheral blood by flow cytometry
Human CD4+ T cell responses to an attenuated tetravalent dengue vaccine parallel those induced by natural infection, in magnitude, HLA restriction and antigen specificity
Human CD4+ T cell responses to an attenuated tetravalent dengue vaccine parallel those induced by natural infection in magnitude, HLA restriction, and antigen specificity
Better living through ontologies at the Immune Epitope Database
The immune epitope database: how data are entered and retrieved
Vaccine strain-specificity of protective HLA-restricted class 1 P. falciparum epitopes
HLA-DRB1 alleles are associated with different magnitudes of engue virus-specific CD4+ T-cell responses
TepiTool: a pipeline for computational prediction T cell epitope candidates
Transcriptional profiling of Th2 cells identifies pathogenic features associated with asthma
A quantitative analysis of complexity of human pathogen-specific CD4 T cell responses in healthy M. tuberculosis infected south africans
Sequence conservation predicts T cell reactivity against ragweed allergens
Th1 versus Th2 T cell polarization by whole-cell and acellular childhood pertussis vaccines persists upon re-immunication in adolescence and adulthood
Pro-apoptotic bax molecules densely populate the edges of membrane pores
T-cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome
The ontology for biomedical investigations
Linear epitopes in vaccinia virus A27 are targets of protective antibodies induced by vaccination against smallpox
Immunodominant dengue virus specific CD8+ T cells responses are associated with a memory PD-1+ phenotype
Distinct modulation of allergic T cell responses by subcutaneous vs. sublingual allergen-specific immunotherapy
Reproducibility and conflicts in immune epitope data
Linear epitopes in A27 are targets of protective antibodies induced by vaccination against smallpox
The length distribution of class I-restricted T cell epitopes is determined by both peptide supply and MHC allele-specific binding preference
Epitope specific T-cell responses against influenza A in a healthy population
T-cell epitope conservation across allergen species is a major determinant of immunogenicity
Measurement of ex vivo ELISpot interferon-gamma recall responses to plasmodium falciparum AMA1 and CSP in Ghanaian adults with natural exposure to malaria
Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove
T cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome
An ontology for major histocompatibility restriction
Different Bla-g T cell antigens dominate responses in asthma versus rhinitis subjects
RSV-specific airway resident memory CD8+ T cells and differential disease severity after experimental human infection
Development and validation of a sample sparing strategy for HLA typing utilizing next generation sequencing
Human CD8+ T-cell responses against the 4 dengue virus serotypes are associated with distinct patterns of protein targets
Immune responses in accute and convalescent patients with mild, moderate and severe disease during the 2009 influenza pandemic in Norway
The use of the immune epitope database to study autoimmune epitope data related to alopecia areata
Definition of a pool of epitopes that recapitulates the T cell reactivity against major house dust mite allergens
Cytomeglaovirus-specific CD4 T cells are cytolytic and mediate vaccine protection
The common equine class I molecule Eqca-1*00101 (ELA-A3.1) is characterized by narrow peptide binding and T cell epitope repertoires
Structural and functional characterization of anti-A33 antibodies reveal a potent cross-species orthopoxviruses neutralizer
Dengue virus infection elicits highly polarized CX3CR1+ cytotoxic CD4+ T cells associated with portective immunity
Automatic generation of validated specific epitope sets
Development and validation of a broad scheme for predition of HLA class II restricted T cell epitopes
Automated benchmarking of peptide-MHC class I binding predictions
A population response analysis approach to assign class II HLA-epitope restrictions
Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with allergen-specific modulation of immune reactivity
IL-10-producing intestinal macrophages prevent excessive antibacterial innate immunity by limiting IL-23 synthesis
Acyclovir has low but detectable influence on HLA-B*57:01 specificity without inducing hypersensitivity
Dengue viral evolution under a hose-targeted antiviral
Analysis of human RSV immunity at the molecular level: learning from the past and present
PEASE: predicting B-cell epitopes utilizing antibody sequence
Antibody specific epitope prediction-emergence of a new paradigm
Immunoproteomic analysis of German cockroach (Blattella germanica) reveals antigens differentially recognized as a function of disease severity
Abacavir-reactive memory T cells are present in drug naïve individuals
Characterization of the T cell response targeting Timothy grass antigens in allergic, healthy and specific immunotherapy-treated patients
A systematic analysis of pollen transcriptomes from plant allergens reveals conserved targets of immune responses
Visual and functional demonstration of growing bax-induced pores in mitochondrial outer membranes
Immunological consequences of intragenus conservation of mycobacterium tuberculosis T-cell epitopes
T cell-mediated hypersensitivity reactions to drugs
The immune epitope database (IEDB) 3.0
The human CD8+ T cell responses induced by a live attenuated tetravalent dengue vaccine are directed against highly conserved epitopes
The development and application of a quantitative peptide microarray based approach to protein interaction domain specificity space
CD4 T cells specific for a latency-associated γ-herpesvirus epitope are polyfunctional and cytotoxic
Murine anti-vaccinia virus D8 antibodies target different epitopes and differ in their ability to block D8 binding to CS-E
New strategies for allergen T cell epitope identification: going beyond IgE
Association between specific timothy grass antigens and changes in TH1- and TH2-cell responses following specific immunotherapy
Allergy-associated T cell epitope repertoiries are surprisingly diverse and include non-IgE reactive antigens
Potent neutralization of vaccinia virus by divergent murine antibodies targeting a common site of vulnerability in L1 protien
Immunodominance changes as a function of the infecting dengue virus serotype and primary versus secondard infection
Sterile immunity to malaria after DNA prime/adenovirus boost immunization is associated with effector memory CD8+T cells targeting AMA1 class I epitopes
In vivo RNA interference screens identify regulators of antiviral CD4(+) and CD8(+) T cell differentiation
Epigenomic analysis of primart human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions
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
Substantial gaps in knowledge of bordetella pertussis antibody and T cell epitopes relevant for natural immunity and vaccine efficacy
Relapsing-remitting cenral vervous system autoimmunity ediate by GFAP-secific CD8 T cells
Using a combined computational-exterimental approach to predict antibody-specific B cell epitopes
Broadly reactive human CD8 T cells that recognize an epitope conserved between VZV, HSZ and EBV
A molecular view of multiple sclerosis and experimental autoimmune encephalitis: what can we learn from the epitope data?
Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells
HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity
Temporal intra-individual variation of immunological biomarkers in type 1 diabetes patients: implications for future use in cross-sectional assessment
Evaluating the immunogenicity of protein drugs by applyinng in vitro MHC binding data and the immune epitope database and analysis resource
Properties of MHC class I presented peptides that enhance immunogenicity
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
Identification of minimal human MHC-restricted CD8+ T-cell epitopes within the plasmodium falciparum circumsporozoite protein (CSP)
A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population
Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells
Blc6 expressing follicular helper CD4 T cells are fate committed early and have the capacity to form memory
Query enhancement through the practical application of ontology: the IEDB and OBI
Unusual features of vaccinia virus extracellular virion form neutralization resistance revealed in human antibody responses to the smallpox vaccine
Previously undescribed grass pollen antigens are the major inducers of T helper 2 cytokine-producing T cells in allergic individuals
Positional bias of MHC class I restricted T-cell epitopes in viral antigens is likely due to a bias in conservation
Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subset
The identification of potentially pathogenic and therapeutic epitopes from common human allergens
Strategies to query and display allergy-derived epitope data from the immune epitope database
The structural basis of HLA-associated drug hypersensitivity syndromes
The immune epitope database: a historical retrospective of the first decade
Polyfunctional CD4(+) T cell responses to immunodominant epitopes correlate with disease activity of virulent salmonella
Structural and biochemical characterization of the vaccinia virus envelope protein D8 and its recognition by the antibody LA5
T cell responses to known allergen proteins are differently polarized and account for a variable fraction of total response to allergen extracts
Analysis of T cell responses to the major allergens from german cockroack: epitope specificity and relationship to IgE production
Immune epitope database analysis resource
Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire
A meta-analysis of the existing knowledge of immunoreactivity against hepatitis C virus (HCV)
Dissecting mechanisms of immunodominance to the common tuberculosis antigens ESAT-6, CFP1-, Rv2031c (hspX), Rv2654c (TB7.7), and Rv1038c (EsxJ)
Structural consensus among antibodies defines the antigen binding site
Cost sensitive hierarchial document classification to triage Pubmed abstracts for manual curation
Applications for T-cell epitope queries and tools in the Immune Epitope Database and Anaylsis Resource
Human CD8+ and CD4+ T cell memort to LCMV infection
A computational pipeline to generate MHC binding motifs
Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design
Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes
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
Defining the herpes simplex virus-specific CD8+ T cell repertoire in C57BL/6 mice
A model for collaborative curation, the IEDB and CHEBI curation of non-peptidic epitopes
Identification of CD4+ T cell epitopes in C. burnetii antigens targeted by antibody responses
Towards defining molecular determinants recognized by adaptive immunity in allergic disease: an inventory of the available data
IEDB-3D: structural data within the immune epitope database
Peptide binding predictions for HLA DR, DP and DQ molecules
CD4+ T Cells Are Not Required for the Induction of Dengue Virus-Specific CD8+ T Cell or Antibody Responses but Contribute to Protection after Vaccination
Divergent motifs but overlapping binding repertoires of six HLA-DQ molecules frequently expressed in the worldwide human population
Identification and localization of minimal MHC-restricted CD8+ T cell epitopes within the Plasmodium falciparum AMA1 protein
Molecular determinants of T cell epitope recognition of the common Timothy grass allergen
The most common Chinese rhesus macaque MHC class I molecule shares peptide binding repertoire with the HLA-B7 supertype
Coverage of related pathogenic species by multivalent and cross-protective vaccine design: arenaviruses as a model system
Meta-analysis of all immune epitope data in the Flavivirus genus: inventory of current immune epitope data status in the context of virus immunity and immunopathology
TiArA: a virtual appliance for the analysis of Tiling Array data
Design and utilization of epitope-based databases and predictive tools
Two kinetic patterns of epitope-specific CD8 T cell responses following murine gammaherpesvirus 68 infection
Polyfunctional CD4+ T cell responses to a set of pathogenic arenaviruses provide broad population coverage
Five HLA-DP molecules frequently expressed in the worldwide human population share a common HLA supertypic binding specificity
Limitations of Ab initio predictions of peptide binding to MHC class II molecules
Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens
IMMUNOCAT – A data management system for epitope mapping studies
The Immune Epitope Database 2.0
Cecilia Lindestam Arlehamn, Ph.D.
Research Assistant Professor
I graduated from University of Kalmar, Sweden in 2005 with a M.S. degree in Biomedicine. I then obtained my Ph.D. in Immunology and Microbiology from the University of Glasgow, Scotland, UK in 2009. I began working as a postdoc in the Sette laboratory at the La Jolla Institute for Immunology in January 2010 and was promoted to the Instructor position in January 2014.
My research projects are focused on defining the T cell responses against Mycobacterium tuberculosis, the causative agent of tuberculosis disease. I am interested in understanding the specific T cell responses mounted against MTB during latent or active infection and following vaccination, as well as the role of environmental exposure to other Mycobacterium species.
Jason Bennett is an undergraduate in the bioinformatics program at UCSD. He has been with the Peters lab since July 2018 and his research primarily focuses on developing quality control metrics to analyze clustering success and exploring novel clustering approaches. One aim of the project is to develop biologically meaningful gene modules that can aid in the identification of different disease states.
Julie Burel, Ph.D.
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.
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.
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.
Ferran Soldevila Casals, Ph.D.
Postdoc Fellow (0 year)
Research Technician I
Angela Frentzen graduated from UCSD in 2017 with a B.S. in Bioinformatics. During her time at UCSD she worked in the Imam Lab analyzing RNA-sequencing data via differential expression analysis. In November of 2017 she began working in the Peters lab at the La Jolla Institute for Immunology. She runs cancer patient data through a Neoantigen Identification pipeline that predicts possible personalized treatments for cancer patients. She also works to develop computational tools that automate and optimize TCR single cell sequencing data analysis. These contributions aim to make patient care more scalable, optimized and error-free.
Research Tech I
Bioinformatics Postdoctoral Fellow
I studied at the University of Tuebingen, Germany, where I received my Bachelor’s and Master’s degrees in Bioinformatics in 2009 and 2012. Subsequently, I pursued my PhD in the field of cancer immunotherapy at the National Center for Tumor Diseases in Heidelberg, Germany. After finishing my PhD in 2016, I moved to LJI for postdoctoral training in Dr. Bjoern Peters lab.
During my PhD I developed computational pipelines to effectively analyze large patient cohorts and retrieve comprehensive data about the mutational and neoepitope load, the type and densities of tumor-infiltrating immune cells, the expression of immunological markers, and the expression of specific cytokines. These pipelines were then used to characterize patient cohorts of various cancers and to identify patients who would most likely benefit from immunotherapy. Currently at LJI, we are specifically working on the development of optimized neoantigen prediction methods and are analyzing large cohorts of cancer patients.
I plan to pursue a career in scientific research primarily focused on developing optimized computational methods to characterize cancer patients for immunotherapy.
Research Tech I
Research Tech I
Research Tech I
Senior Bioinformatics Specialist
Luise Sternberg, Ph.D.
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 Immunology in June 2013 and was promoted to Lab Manager in November of 2015
My research focuses on T-cell epitopes and how they impact the immune response in allergy and cancer.
My goal is to manage clinical and translational research projects in cancer immunology, autoimmune diseases or allergy.
Sr. Bioinformatics Specialist
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 Immunology as a Bioinformatics Specialist and was promoted to the Sr. Bioinformatics Specialist in 2013.
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.
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.
Visiting Graduate Student
Randi Vita, M.D.
Lead Ontology and Quality Manager
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 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.
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.
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.
Visiting Graduate Student
IMMUNE EPITOPE DATABASE AND ANALYSIS RESOURCE PROGRAM
A collaboration with LJI Professor Alessandro Sette, Dr. Biol. Sci, to maintain and further develop the Immune Epitope Database (IEDB) and associated analysis resource.
Previously awarded as HHSN26620040006C, and HHSN272201200010C.
Investigation of human immune signatures of latent MTB infection, active disease and BCG vaccination. (NIH/NIAID, U19 AI118626)
Proteome-wide characterization of T cell epitopes from Mycobacterium tuberculosis in vaccination and active infection. (NIH/NIAID, 75N93019C00067)
Goal: To define MTB-derived T cell epitopes associated with vaccination and active TB infection, and submit them to the IEDB.
Research to identify mechanisms and correlates of long-lasting vaccine-induced immunity to whooping cough. The lab aims to define transcriptional responses to vaccine boost from donors originally primed with aP vs. wP and identify cell types associated with differential responses, as well as characterize the differences in memory T cell responses in aP vs. wP donors and characterize the molecular mechanisms of differences in APC-priming of T cells in aP- vs. wP-vaccinated donors.
Pediatric Milk Allergy: To study the frequency and phenotype of milk allergen-specific T cells in cohorts with different disease manifestations and define molecular markers of disease status and progression to tolerance. This research will contribute to developing improved and new diagnostic tests.
Childhood Asthma: Research to investigate the epigenetic basis of childhood asthma.
NIH/NIAID (R01 AI121426)
HIPC Data Standards: A collaboration with various centers of the Human Immune Profiling Consortium (HIPC) to build upon the existing infrastructure of ImmPort, a publically-available data repository, which includes standardization of defined data elements such as immune exposures, including vaccinations, infectious diseases or environmental exposures, as well as the representation of common experimental data types such as transcriptomic data.
NIH/NIAID (U19 AI118610)
OBO Foundry Standards: To implement a set of services that allows different ontology producers to develop ontologies in a standardized fashion that will make it easier to use them together.
NIH/NHGRI (R24 HG010032)
Immunotherapies for head and neck cancer: To develop new cancer therapies by studying how the immune system, by way of neo-antigens, can recognize and eliminate tumor cells by targeting molecules only found on the surface of the tumor cells.
The research is part of the Immuno-Oncology Translational Network, which was established as part of the National Cancer Institute’s Cancer Moonshot program. A collaboration with the UC San Diego Moores Cancer Center and LJI Professor Stephen Schoenberger, Ph.D.
In a collaboration with Vanderbilt University researchers, the Peters lab is also comparing data from MHC ligand elution experiments, in silicon predictions, and experimental T cell recognition assays to determine what drives immune recognition in head and neck cancers
Pipeline tool to predict immunogenicity of cancer neo-epitopes: Research to provide in-depth characterization of the importance of several variables affecting cancer neo-epitope immunogenicity. These findings in turn will allow the development of bioinformatic tools, and a unified analysis pipeline, towards the identification of cancer neo-epitopes. Identification of such epitopes is expected to allow quick identification of cancer-associated, patient-specific, mutations potentially recognized as epitopes, with direct applicability to the development of efficacious therapeutics.