Systems Immunology Division

Systems ImmunologyWith the explosion of data from genome studies and molecular profiling technologies, huge amounts of biological information are now available. Scientists in the Systems Immunology Division use complex systems theory and high throughput techniques as well as mathematical and computational tools to understand the functioning of the immune system in health and disease. The Systems Immunology Division is developing ways to use simple blood tests to measure immune system profiles that predict individual's responses to immunotherapy for autoimmune disease or cancer. With these profiles, treatment for these diseases may be specifically tailored to each person.

Leadership - Co-Directors

Peter LinsleyPeter S. Linsley, PhD
Scientific/Intellectual Oversight
Director of Systems Immunology, Associate Member

Tom SkillmanTom Skillman
Reseach Data Systems and Administration
Director of Research Technology                              

Bioinformatics Department

The BRI Bioinformatics Department consists of PhD computational biologists and biostatisticians, with access to a high-performance computing infrastructure and specialized software to support processing, analyzing and visualizing data from heterogeneous sources, including BRI and Virginia Mason laboratories.

Research Data Management

Our data management and software development team has created an extensive data infrastructure to provide our scientists with flexible acquisition and query-based access to research data. Our system is designed to link with advanced bioinformatics analysis, where the co-location of data and scalable computational power is essential.

Included in our system are a collection of secure web-based applications:

  • Participant Disease Registries
  • Sample Repository
  • Study Modifications and Gatekeeper
  • Genomics LIMS
  • Flow Cytometry Core data capture and annotation
  • Mobile participant survey capture
  • Automated data exchange with clinical laboratories
  • Genomic Sequence cloud-based analysis pipeline

We are committed to free distribution of our datasets, and code. Upon publication, we deposit supporting data files into public repositories like FlowRepository and GEO. In many cases we share our application and analysis code via GitHub.

Core Laboratories

Data Management & Software Development Core
Offers knowledge and data management services and general informatics services to different immunology research centers including BRI.

Genomics Core
Provides resources to BRI and external investigators for gene expression analysis, from sample processing through data generation. Currently available technologies include RNA-sequencing and high throughput real-time PCR.

Research Laboratories

Linsley Laboratory
Advancing immunotherapy with big data

Presenell Laboratory
Advancing the understanding of childhood allergies

Staff Members

Matt AltmanMatt Altman, PhD
Visiting Scientist

Brenda NorrisBrenda Norris
Administrative Assistant
Tee BahnsonTee Bahnson, PhD
Principle Biostatistician
Kimberly ObrienKimberly O'Brien
Research Technician
Anna BjorkAnna Bjork
UI Front End Designer
Scott PresnellScott Presnell, PhD
Research Associate Member
Hannah DebergHannah DeBerg, PhD
Bioinformatics Project Lead
Charlie QuinnCharlie Quinn
Software Development Director
Matt DufortMatt Dufort, PhD
Bioinformatics Project Lead
Mario RosascoMario Rosasco
Vivian GersukVivian Gersuk, PhD
Genomics Core Manager
Sam SkinnerSam Skinner
Bertrand HaasBertrand Haas
Marty TimourMarty Timour
Research Technician
Adarsh ManjunathAdarsh Manjunath
Software Engineer
Alex WalkerAlex Walker
Software Engineer
Virginia MuirVirginia Muir
Post Doctoral Research Associate
Elizabeth WhalenElizabeth Whalen
Quynh-Anh NguyenQuynh-Anh Nguyen
Research Technician
Fari WhitmanFari Whitman
Staff Scientist