Todd P. Knutson, PhD
RI Bioinformatics LM&P Group Lead
Expertise
- Clinical genomics pipeline development (CLIA-compliant)
- Somatic and germline variant calling (SNP/indel, structural variants, copy number)
- Single-cell RNA sequencing (scRNA-seq) and CITE-seq analysis
- Bulk RNA-seq: differential gene expression and pathway analysis
- Long-read whole genome sequencing (Oxford Nanopore Technologies)
- Cell-free DNA (cfDNA) sequencing and circulating tumor DNA (ctDNA) detection
- Metagenomics for viral detection, assembly, and phylogenetics
- Prognostic gene signatures and biomarker analysis
- Reproducible research and workflow automation (HPC, AWS)
Education & Training
- MS, Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota
- Postdoc, Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, Minnesota
- Postdoc, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- PhD, Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota, Minneapolis, Minnesota
- BS, Genetics, Cell Biology, and Development & Neuroscience, University of Minnesota, Minneapolis, Minnesota
Bio
Todd leads a team of bioinformatics analysts in the Research Informatics (Bioinformatics) division of MSI, supporting research projects for the Department of Laboratory Medicine and Pathology (LMP) and custom clinical genomics pipelines for Fairview's Molecular Diagnostics Laboratory (MDL). He is also a member of the Molecular Pathology & Genomics division. His current research collaborations span cancer biology and immunology, with projects involving single-cell RNA sequencing to characterize immune cell compartments and DNA sequencing to characterize genetic mechanisms of cancer. He also develops and validates clinical-grade sequencing pipelines for whole genome, whole exome, and targeted panel sequencing, supporting both germline and somatic variant detection.
Prior to his current role, Todd completed a postdoctoral fellowship in the UMN Veterinary Diagnostic Laboratory, where he developed pipelines for analyzing metagenomic shotgun sequencing data for the discovery of novel viral and bacterial pathogens. His doctoral training at the University of Minnesota focused on the genetic mechanisms of breast cancer, where he investigated how activated growth factor signaling pathways regulate post-translational modifications of the progesterone receptor, causing altered gene expression programming and tumor progression.