Stephen B. Montgomery

Stephen Montgomery is an Endowed Professor of Pathology, Genetics, Biomedical Data Science and, by courtesy, Computer Science at Stanford University. He has trained in multiple countries including Canada, Germany, England, and Switzerland. He is best known for his work mapping the effects of genetic variation to gene expression and authored the first publications that compared whole genomes and transcriptome data within a human population and pioneered the use of molecular outliers to identify impactful rare variants (Montgomery et al, 2010, Montgomery et al, 2011).

Montgomery and his lab lead major genomics initiatives to understand the molecular mechanisms that underlie disease-associated variation. In 2017, they published analyses from the Genotype-Tissue-Expression (GTEx) Consortium which analyzed the impact of genetic variation on gene expression across tissues of the human body (GTEx Consortium, 2017). In 2024, his lab led major analyses in the NIH Common Fund MoTrPAC study identifying the molecular effects of exercise training across rat tissues (MoTrPAC, 2024). He is a Principal Investigator within multiple major NIH consortia including the GREGoR, MoTrPAC, TOPMed and Functional ADSP consortia and an Investigator in the Developmental GTEx, IGVF, SMaHT, AllOfUs, Undiagnosed Disease Network and ENCODE4 consortia demonstrating his labs ongoing impacts in multiple major genomics projects.

The Montgomery lab has a specific focus on mapping the molecular effects of rare and environment-responsive genetic variants. Work in his laboratory focuses on developing approaches for studying rare variants (such as Li et al, 2017; Ferraro et al, 2020) and seeing these approaches applied to understanding novel disease biology and providing diagnoses of individuals with genetic diseases (Fresard et al., 2017). As a PI of the GREGoR Stanford Site, his lab develops and applies these strategies to diagnose individuals with undiagnosed, rare diseases. The GREGoR Stanford site is currently recruiting 500 families with unsolved diagnoses in California to apply novel multi-omics and computational strategies to acheive diagnoses. His laboratory further has a specific focus on understanding the molecular consequences of structural variants and chromosomal copy number changes (Marderstein et al, 2024).

The Montgomery lab is also focused on advancing our understanding of common genetic variants and understudied RNAs. Examples of this work, his lab has demonstrated that multiple genetic variants contribute to genetic disease associations (Abell et al, 2022) and his lab has developed approaches to identify impactful long non-coding RNAs that contribute to complex disease (de Goede et al, 2021). Ongoing effort in his lab has focused on neurodegenerative and neurodevelopmental traits.

Montgomery is an active member of both the Stanford and broader research community. Among his contributions, he serves as a co-director of an NHGRI PhD T32 Training Grant, member of the Pathology DEI committee, Faculty Director of Graduate Admissions for the Biomedical Data Science program and served for 4 years as a Stanford University Faculty Senator. He has/or is currently on the programming committee for major conferences such as ASHG, AGBT and WTSI Genomics of Rare Diseases. He is the incoming chair for the ASHG Awards committee. He is also a standing member of the NIH GHD Study Section.

In 2019, Montgomery was awarded the annual American Society of Human Genetics Early Career Award for his multi-faceted impacts on human genetics and genomics. In 2023, he was awarded the annual Stanford Prize in Population Genetics and Society. In 2024, he was awarded the Stanford Pathology Research Mentor Award.