Bioinformatics Department

Overview

The Bioinformatics Department, as part of BRI's Systems Immunology Division, specializes in helping scientists make sense of complex multi-dimensional data. We work with researchers throughout BRI and beyond to optimize the biological insights they can gain from their data. We strive to be involved throughout the research process, from project planning and experimental design, through data collection and quality assessment, to analysis and interpretation. By collaborating with researchers, we combine our knowledge bases, generate creative solutions, and leverage institutional knowledge to ensure best practices. In short, we work together to get the best results.

BRI has an institutional focus on basic and translational research related to immune-mediated diseases. Given this focus, we frequently work with data related to immunology, immune cell activity, and their effects on disease. There is a particular research emphasis on interrogating cellular phenotypes using flow cytometry and cellular activity using gene expression as measured by RNA sequencing (RNA-seq). Much of our work has a translational component, using data from laboratory experiments and patient samples to identify biomarkers or targets for clinical therapy.

The Bioinformatics Department operates at the intersection of data collection, storage, and analysis. We work with PI research labs and BRI Core Facilities to integrate these processes and ensure that our valuable data remain secure, accessible, interconnected, and interpretable. As the volume and diversity of data grows, we use a combination of local resources, high-performance cloud computing, and web-based user applications to meet these needs.

Our role

Data analysis and visualization

We provide flexible analysis and visualization solutions to support a wide range of research projects. One of our primary objectives is to interrogate data from BRI’s unique patient samples to develop new biologic insights and identify biomarkers and therapeutic targets. We work with a range of data types, including RNA-seq, flow cytometry and mass cytometry (CyTOF), DNA sequence variants, and high-throughput PCR. As processes become more routinized, we build tools to empower researchers to perform their own analyses and produce visualizations.

We have a particular expertise in single-cell RNA-seq of rare cell populations implicated in immune-mediated diseases. In collaboration with BRI researchers, we have developed and are constantly optimizing methods to isolate these cells and extract data from them in order to understand their role in disease.

Genomic data collection

The Bioinformatics Department works closely with BRI’s Genomics Core, which specializes in collecting genomic data from biological samples. Our relationship with this core lab allows us to bridge the experimental design, data collection, and analytical plans to gain maximum insight from experiments and samples. We develop and maintain software pipelines for processing sequencing data, using high-performance cluster computing. We also use informatics to improve lab processes by connecting data quality to the laboratory techniques that generated those data.

Data storage and access

We work with the Data Management & Software Development Core to optimize data storage and accessibility throughout BRI. We aim to capture data as close to the source as possible, store that data in robust and access-controlled locations, connect experiments and data types using flexible databases, and develop tools that allow researchers to interact directly with their data in a user-friendly environment.

Grants And Publications

Our involvement in the research process extends well beyond conducting analyses. We actively participate in the grant proposal process, collaborating on project development and/or providing input on appropriate experimental methods, sample sizes, and statistical plans. We are also extensively involved in manuscript preparation, whether taking the lead on analysis-driven manuscripts, or contributing figures, analysis, and interpretation to more general publications. Finally, we help to ensure compliance with data accessibility and reporting requirements mandated by journals and funding agencies.

Training And Education

Bioinformatics is a new and rapidly evolving field, with a need for people capable of manipulating data and understanding it from the source through biological insights. We have a proven record of training bioinformaticians in biology, and training biologists in informatics. This provides a dual understanding of the data and the science behind it, enabling highly productive collaborations with researchers of diverse analytical backgrounds.

We further increase our impact by educating BRI staff on general and specific statistical methods. We conduct formal seminars and informal training sessions to help researchers understand bioinformatics analysis approaches, and enable them to do their own analysis when possible. Increasing the analytical and statistical literacy throughout the institute leverages our knowledge and facilitates communication between analysts and researchers.