Peters Lab

Bjoern Peters, Ph.D.

Professor

Center for Cancer Immunotherapy
Center for Vaccine Innovation

The challenge in bioinformatics for immunology is not to develop faster algorithms, but to accurately translate immunological questions into a computable form.

Overview

Research in the Peters lab is focused on three areas relating to developing 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 toward developing diagnostics, vaccines, and therapeutics. The tools the Peters lab develops aim to reduce the experimental effort required to identify these targets. Machine learning-based predictions allow researchers to focus their experiments on the molecules most likely to be recognized.

The second research area of the lab is the identification of differences between immune cells in individuals with divergent disease outcomes. Powerful experimental tools have been developed to characterize single cells in terms of their transcriptomic, proteomic and genomic state. The Peters lab uses 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 epitope-identifying algorithms developed in the lab directly aid in the disease-focused work. This research helps understand how the disease develops and identifies potential targets for interventions to treat or prevent the disease.

Finally, the Peters lab is deeply involved in developing community standards for knowledge representation to promote interoperability and re-use of data. The Peters and Sette lab have maintained the Immune Epitope Database (IEDB) since 2003, which catalogs all published experiments on immune epitope recognition. This requires transforming free text information from journal publications into a structured format and making it optimally useful, connecting it with information stored elsewhere. Doing this efficiently requires a community consensus on knowledge representation. The Peters lab contributes to such consensus-building and standardization efforts through active work on scientific community initiatives such as the Ontology of Biomedical Investigations (OBI) and the umbrella Open Biomedical Ontology (OBO) foundry project. These same standards are now utilized in projects such as ImmuneSpace that cover all experimental immunological data.

Featured Publications

Jason A Greenbaum, Maya F Kotturi, Yohan Kim, Carla Oseroff, Kerrie Vaughan, Nima Salimi, Randi Vita, Julia Ponomarenko, Richard H Scheuermann, Alessandro Sette, Bjoern Peters
Jan 08, 2019
Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR, Wheeler DK, Sette A, Peters B
Feb 11, 2020
Peters B, Nielsen M, Sette A
Jackson R, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, Courtot M, Diehl AD, Dooley DM, Duncan WD, Harris NL, Haendel MA, Lewis SE, Natale DA, Osumi-Sutherland D, Ruttenberg A, Schriml LM, Smith B, Stoeckert CJ Jr, Vasilevsky NA, Walls RL, Zheng J, Mungall CJ, Peters B.
Koşaloğlu-Yalçın Z, Blazeska N, Vita R, Carter H, Nielsen M, Schoenberger S, Sette A, Peters B
Lewis SA, Sutherland A, Soldevila F, Westernberg L, Aoki M, Frazier A, Maiche S, Erlewyn-Lajeunesse M, Arshad H, Leonard S, Laubach S, Dantzer JA, Wood RA, Sette A, Seumois G, Vijayanand P, Peters B

Lab Members

Ahmed Azhan

Data Coordinator

Hannah Battey, Masters

Graduate Student

Jason Bennett

Associate Bioinformatics Specialist I

Nina Blazeska

IEDB Project Manager

Julie Burel

Sr. Staff Scientist

Catherine Cheng

Research Tech II

Leila Chihab

UCSD Graduate Student

Marcus De Almeida Mendes, Ph.D.

Postdoctoral Fellow

Sebastian Duesing

Junior Ontologist

April Frazier, Ph.D.

Senior Project Manager

Angela Frentzen

Bioinformatics Specialist

Siddharth Gaywala

Associate Bioinformatics Specialist I

Mahita Jarjapu, Ph.D.

Postdoctoral Fellow

Ningxin Kang

UCSD Graduate Student

Kendall Kearns

UCSD Graduate Student

Mari Kojima, Masters

Project Manager

Zeynep Kosaloglu-Yalcin

Instructor

Daniel Marrama

Bioinformatics Specialist

Shelby Orfield

Project Coordinator

Sudhasini Panda, Ph.D.

Postdoctoral Fellow
Portrait photo of Bjoern Peters, Ph.D.

Bjoern Peters

Professor

Ziyuan Ren, Masters

Research Tech I

Eve Richardson, Ph.D.

Postdoctoral Fellow

Rhea Rupareliya

Student Volunteer

Lonneke Scheffer, Ph.D.

Postdoctoral Fellow

Pramod Shinde, Ph.D.

Postdoctoral Fellow

Jian Sun

Senior Bioinformatics Specialist

Nicola Thrupp, Ph.D.

Postdoctoral Fellow

Rashmi Tippalagama

Postdoctoral Fellow

Raphael Trevizani

Consulting Bioinform Postdoc Fellow

Randi Vita

Lead Ontology & Quality Manager

Kerstin Westendorf, Ph.D.

Data Submission Manager

Research Projects

COVIC-DB: To co-run the LJI-led CoVIC database in the effort to find ideal therapeutic combinations for the novel coronavirus, the assays that best predict efficacy, and the features that provide

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

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

From the Lab

Scientists find evidence that all cancer patients mount an immune response to their tumors, suggesting that many more patients could benefit from personalized immunotherapy
This year’s list features four scientists at La Jolla Institute for Immunology
LJI Professors Shane Crotty, Ph.D., Bjoern Peters, Ph.D., and Alessandro Sette, Dr. Biol. Sci., were named “Highly Cited Researchers” this week by Clarivate.
The IEDB gives biomedical researchers worldwide free access to a rapidly growing catalogue of epitopes—the specific, molecular structures that the immune system uses to tell friend from foe
National Cancer Institute support brings cancer researchers together to share key findings
The fellowship specifically supports interdisciplinary training to encourage understanding between immunology researchers and computational scientists
A record number of LJI researchers have been named to the 2022 list, including two early career scientists
NIAID support opens gateway to new research into human immune responses to viruses, the development of autoimmune diseases, and more
COVID-carrying skiers may help explain disease trends in Germany
LJI team finds that ‘doublet’ immune cells are much more common—and more important in disease—than previously thought
The bioinformatics tools Dr. Peters has developed are invaluable for immunologists worldwide.
The international recognition reflects how LJI research is valued by scientific peers
"This support allows LJI scientists to buy essential equipment and pursue fascinating early career research."
Vaccine researchers take on the challenge of predicting B. pertussis immunization outcomes

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