Email

song.yi@bcm.edu

Positions

Associate Professor

Neurosurgery
Baylor College of Medicine

Director of Bioinformatics

School of Medicine - Temple
Baylor College of Medicine

Associate Professor

Dan L Duncan Comprehensive Cancer Center
Baylor College of Medicine
Houston, Texas United States

Education

PhD from University of Iowa

Iowa City, Iowa United States

Postdoctoral Fellowship at Harvard Medical School

Boston, Massachusetts United States

Professional Interests

• AI & Machine/Deep Learning
• Computational and Systems Biology
• Single Cell and Multi-omics
• Drug Discovery and Immunotherapy

Professional Statement

Dr. Stephen Yi is Director of Bioinformatics at Baylor Research Institute, Baylor College of Medicine. Dr. Yi is co-chair of the Disease Focus Group and Flagship Writing Group at the NIH IGVF consortium. He is also an active member of the GREGoR and the Cancer Systems Biology consortium. His lab seeks to understand genetic/genomic variation and signaling perturbation in health and disease, by integrating AI, deep learning, systems/network biology and single cell multi-omics approaches. Dr. Yi started his lab as an Assistant Professor at the University of Texas, Austin. He has received numerous honors/awards in his career, including NIH Outstanding Investigator, NCI IMAT, Komen Foundation Award, Scialog Fellow, NIH Career Development Award.
Our long-term goal is to contribute toward a systems-level understanding of causal and mechanistic links between cellular activities and physiological function in biological networks that can be used for developing improved diagnostic biomarkers and therapeutic targets in human disease. We have extensive experience and expertise in developing integrated technologies to identify and validate novel target genes and pathways to improve mechanistic understanding. Our laboratory has made many seminal discoveries to reveal complex gene regulatory networks in the cell and how perturbation of these signaling networks leads to human disease.

Websites

Selected Publications

• Li Y, Burgman B, Khatri IS, Pentaparthi SR, Su Z, McGrail DJ, Li Y, Wu E, Eckhardt SG, Sahni N, Yi SS. "e-MutPath: computational modeling reveals the functional landscape of genetic mutations rewiring interactome networks.." Nucleic Acids Res.. 2021; Pubmed PMID: 33211847
• Kleist AB, Szpakowska M, Talbot LJ, Slodkowicz G, Malinverni D, Thomas MA, Crawford KS, McGrail DJ, Dishman AF, Wedemeyer MJ, Sluter M, Yi SS, Sahni N, Peterson FC, Chevigné A, Volkman BF, Babu MM. "Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network.." Cell. 2025; Pubmed PMID: 40273912
• Li Y, Burgman B, McGrail DJ, Sun M, Qi D, Shukla SA, Wu E, Capasso A, Lin SY, Wu CJ, Eckhardt SG, Mills GB, Li B, Sahni N, Yi SS. "Integrated Genomic Characterization of the Human Immunome in Cancer.." Cancer Res.. 2020; Pubmed PMID: 32855206
• Hua X, Li Y, Pentaparthi SR, McGrail DJ, Zou R, Guo L, Shrawat A, Cirillo KM, Li Q, Bhat A, Xu M, Qi D, Singh A, McGrath F, Andrews S, Aung KL, Das J, Zhou Y, Lodi A, Mills GB, Eckhardt SG, Mendillo ML, Tiziani S, Wu E, Huang JH, Sahni N, Yi SS. "Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer." Cancer Res.. 2023; Pubmed PMID: 36265133