S. Stephen Yi

Director of Bioinformatics and Associate Professor

Email

song.yi@bcm.edu

Positions

Director of Bioinformatics and Associate Professor: Department of Neurosurgery
School of Medicine-Temple
Baylor College of Medicine

Founding Director, Center for AI and Biomedical Discovery (AIBD): Neuroscience Institute
Baylor College of Medicine

Associate Professor and Research Member: Dan L Duncan Comprehensive Cancer Center
Baylor College of Medicine
Houston, Texas, United States

Associate Professor: Dan L Duncan Institute for Clinical and Translational Research
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.
Dr Yi's 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. He has extensive experience and expertise in developing integrated technologies to identify and validate novel target genes and pathways to improve mechanistic understanding. Dr. Yi's 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

Google Scholar

Stephen Yi Lab GitHub

Selected Publications

Pan X, Shrawat A, Raghavan S, Dong C, Yang Y, Li Z, Zheng WJ, Eckhardt SG, Wu E, Fuxman Bass JI, Jarosz DF, Chen S, McGrail DJ, Sheynkman GM, Huang JH, Sahni N, and Yi SS. " eSIG-Net: Accurate prediction of single-mutation induced perturbations on protein interactions using a language model. " Nature Methods. 2026 ; Accepted
Osorio D, Capasso A, Eckhardt SG, Giri U, Somma A, Pitts TM, Lieu CH, Messersmith WA, Bagby SM, Singh H, Das J, Sahni N, Yi SS, Kuijjer ML.. " Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data " Nat Comput Sci.. 2024 ;
Pubmed PMID: 38438786.
IGVF Consortium (Stephen Yi as co-chair of the Phenotypic Impact & Function Focus Group).. " Deciphering the impact of genomic variation on function " Nature. 2024 ;
Pubmed PMID: 39232149.
Datar GK, Khabusheva E, Anand A, et al., Liu G, De La Fuente J, Dollinger C, Guzman A, Martell A, Wohlan K, Maiti A, Short NJ, Yi SS, Andresen V, Gjertsen BT, Falini B, Rau RE, Brunetti L, Sahni N, Goodell MA, Riback JA.. " Disparate leukemia mutations converge on nuclear phase-separated condensates " Cell. 2025 ;
Pubmed PMID: 41192422.
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, 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.
Lacoste J, Haghighi M, Haider S, Reno C, Lin ZY, et al., Murray RR, Nyirakanani C, Hao T, McClain GG, Roth FP, Calderwood MA, Hill DE, Vidal M, Yi SS, Sahni N, Peng J, Gingras AC, Singh S, Carpenter AE, Taipale M.. " Pervasive mislocalization of pathogenic coding variants underlying human disorders " Cell. 2024 ;
Pubmed PMID: 39353438.
Ma Y, Guo W, Mou Q, Shao X, Lyu M, Garcia V, Kong L, Lewis W, Ward C, Yang Z, Pan X, Yi SS, Lu Y.. " Spatial imaging of glycoRNA in single cells with ARPLA " Nat Biotechnol.. 2024 ;
Pubmed PMID: 37217750.
GREGoR Consortium. " GREGoR: accelerating genomics for rare diseases " Nature. 2025 ;
Pubmed PMID: 41224980.
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.

Funding

Network-based Framework to Decode Novel Gain-of-Function Mutations and their Mechanistic Roles in General Human Diseases #2R35GM133658-06: (03/04/2026 - 02/28/2031); Grant funding from NIH/NIGMS