With Researcher Spotlights, the Microbial Systems Initiative aims to introduce you to the breadth and diversity of research interests and potential growth opportunities at the University of Illinois Urbana-Champaign campus. We hope that by highlighting both the researchers and their research, we can help you to learn more about and connect with your colleagues to enhance multidisciplinary research and education in microbial sciences here at Illinois.
Christopher J. Fields, PhD
Director HPCBio
Roy J. Carver Biotechnology
Christopher J. Fields is the Director of HPCBio, a high-performance biological computing facility that provides infrastructure, support, and training to address the computational needs of the biomedical research community at Illinois. His work focuses on the development of infrastructure for genomic analyses and encompasses high-throughput analysis workflows for whole genome data processing, implementation of self-contained pipelines like MAKER and Interproscan, and the development of customized solutions based on specific project needs. He coordinates closely with the IGB Computer Network Resource Group for server-side scalability and cluster job submissions. With a strong background as a BioPerl core developer and contributions to projects like the Generic Genome Browser and the Toil workflow system, Chris has over two decades of experience in computational biology, open-source bioinformatics development, and collaborative research across various bioinformatics platforms. His role extends to serving as the Secretary of the Board for the Open Bioinformatics Foundation, actively fostering advancements in bioinformatics.
Do you have a personal story to share or path that led to your interest in this area of study?
My road to becoming a computational biologist is a bit unique. I earned my Ph.D. in molecular microbiology at the University of North Texas in 2002, primarily in a wet-lab research environment. However, I have always had a strong interest in computational biology, and over the course of my graduate and postdoctoral appointments decided that I wanted to focus completely on computational biology, joining the Institute for Genomic Biology as an IGB Postdoctoral Fellow. I became one of the lead developers of the BioPerl open-source bioinformatics toolkit during my post-graduate research in 2007. My experience and background as an open-source developer has led to a number of diverse collaborations over the last several years, including work with Biopython, toil, Nextflow, and Bioconductor. My role as a BioPerl developer has also led to two consecutive mentoring opportunities in the Google Summer of Code for NESCent and three more with the Open Bioinformatics Foundation.
How will your work help to improve society or reach people?
I focus on efforts that are primarily open source and open science, which ensures that tools and data developed for biological research are freely available for use by others. With that in mind, our group’s work is also fully open for our research collaborators, including the code we develop and the data we generate for their specific projects.
Part of MSI’s mission is to support high quality education and professional development experiences for trainees. How do you support this mission through your teaching and mentorship?
Our group offers workshops on data analyses for genomics, including workshops focused on microbiome analyses. We additionally partner with other campus researchers and research teams to develop training materials for their specific needs, such as the yearly Mayo-Illinois Computational Genomics workshop or past efforts such as training opportunities for HBCU-affiliated students.
How does being part of the microbial systems community (MSI) impact your research?
One of the biggest challenges in this field is the need to identify and classify microbes in complex and diverse environments using current sequencing technologies. There are general tools and databases available to work with these data, but they may have inherent biases which impact studies (e.g., developed primarily for human studies, overrepresentation of clinically relevant organisms, lack of a representative host genome sequence). Because we work in a research environment that is extremely broad in scope, we have to adapt the approach we use for such studies based on a case-by-case basis, which is challenging.
Do you want to tell us about any projects or activities that you are particularly excited about right now?
We have a few projects that involve pangenome generation and analysis, which will be a fundamental change in computational biology in the coming years.
