S. Stephen Yi
Picture
S. Stephen Yi
Associate Professor
Positions
- Associate Professor
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Neurosurgery
Baylor College of Medicine
- Director of Bioinformatics
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School of Medicine - Temple
Baylor College of Medicine
- Associate Professor
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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
- Souto EP, Gong P, Landua JD, Rajaram Srinivasan R, Ganesan A, Dobrolecki LE, Purdy SC, Pan X, Zeosky M, Chung A, Yi SS, Ford HL, Lewis MT. "Lineage Tracing and Single-Cell RNA Sequencing Reveal a Common Transcriptional State in Breast Cancer Tumor-Initiating Cells Characterized by IFN/STAT1 Activity.." Cancer Res.. 2025; Pubmed PMID: 40230213
- Datar GK, Khabusheva E, Anand A, Beale J, Sadek M, et al., 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. "Nuclear Phase Separation Drives NPM1-mutant Acute Myeloid Leukemia.." Cell. 2025; Pubmed PMID: 40501735
- Pan X, Yun J, Coban Akdemir ZH, Jiang X, Wu E, Huang JH, Sahni N, Yi SS. "Pan X, Yun J, Coban Akdemir ZH, Jiang X, Wu E, Huang JH, Sahni N, Yi SS.AI-DrugNet: A network-based deep learning model for drug repurposing and combination therapy in neurological disorders.." Comput Struct Biotechnol J.. 2023; Pubmed PMID: 36879885
- 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
- 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
- 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
- McGrail DJ, Li Y, Smith RS, Feng B, Dai H, Hu L, Dennehey B, Awasthi S, Mendillo ML, Sood AK, Mills GB, Lin SY, Yi SS, Sahni N. "Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA-binding proteins.." Cell Rep Med.. 2023; Pubmed PMID: 37909041
- 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
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