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Yi, Stephen

Yi, Stephen

Assistant Professor of Oncology, Director of Bioinformatics
Department of Oncology, Biomedical Engineering



stephen.yi@austin.utexas.edu

Phone: 512-495-5245

Office Location
HDB 6.230

Dr. Stephen Yi is a recognized expert in cancer systems biology and functional variomics/proteomics. Dr. Yi is faculty of Oncology and Director of Bioinformatics, Developmental Therapeutics Lab, at Dell Medical School and Livestrong Cancer Institutes. He is faculty at the Interdisciplinary Life Sciences Graduate Programs (ILSGP), and the Oden Institute for Computational Engineering and Sciences (ICES). Dr. Yi was conferred with a Komen Scholar award, an NIH Outstanding Investigator Award, an NIH Early Career Development Award, and Dean’s Distinguished Dissertation Award, for his work on signal transduction, network biology and evolution in human disease and translational therapeutics. Prior to coming to UT Austin, Dr. Yi was a faculty member at MD Anderson Cancer Center. He has authored over 40 high-impact publications, including Cell and Nature Reviews Genetics. Dr. Yi has successfully mentored many students and postdocs, who are now successful in the next stage of their career.

         Dr. Yi received his doctoral degree with distinction from University of Iowa, and completed a postdoctoral fellowship at Harvard Medical School and Dana-Farber Cancer Institute.

 

Positions available at The Stephen Yi Laboratory

We are always interested in motivated graduate students and postdoc candidates, and we welcome you to join our group!  Candidates with background and interest in cancer biology, molecular genetics, bioinformatics or relevant fields are encouraged to apply. Prior experience in next-generation sequencing analysis, cell culture, and high-throughput functional screens is a plus. For further information, please contact Dr. Yi at  Stephen.yi(AT)austin.utexas.edu, with your CV, research interest, and the contact info of three references.

Our lab research is at the interface of human disease biology and informatics in the modern era of personalized precision medicine. The lab combines computational and experimental expertise (the two arms of the lab) to build a quantitative understanding of genetic/epigenetic variation and signaling network perturbation in disease. Currently, our research interests include network reprograming/engineering, tumor immunology and metabolism, synthetic lethality and drug resistance, next-gen sequencing analysis and multi-omics network biology. We have a long-term interest in addressing fundamental questions in human disease underlying genotype-phenotype relationships. We are also dedicated in constantly developing new technologies to address these questions.

 

Selected Publications

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 and Yi S#. (2020) Integrated genomic characterization of human immunome in cancer. Cancer Research. 80, 4854-4867. (#corresponding author)

Li Y, Burgman B, Khatri IS, Pentaparthi SR, McGrail DJ, Li Y, Wu E, Eckhardt SG, Sahni N and Yi S#. (2020) e-MutPath: Computational modelling reveals the functional landscape of genetic mutations rewiring interactome networks. Nucleic Acids Research. In press. (#corresponding author)

Li Y, McGrail DJ, Xu J, Mills GB, Sahni N and Yi S#. (2018) Gene regulatory network perturbation by genetic and epigenetic variation. Trends in Biochemical Sciences 43, 576-592. (#corresponding author)

Ng PK, Li J, Jeong KJ, Shao S, Chen H, Tsang S, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi D, Moreno D, Dogruluk T, Lu H, Zeng J, Ip CK, Ju Z, Wester M, Yu S, Li Y, Vellano C, Gao J, Schultz N, Karchin R, Ding L, Lu Y, Cheung LW, Chen K, Scott KL, Yi S#, Sahni N#, Liang H# and Mills GB. (2018) Systematic functional annotation of somatic mutations in cancer. Cancer Cell 33, 450-462. (#co-corresponding author)

McGrail DJ, Federico L, Li Y, Dai H, Lu Y, Mills GB, Yi S#, Lin SY# and Sahni N#. (2018) Multi-omics analysis reveals neoantigen-independent immune cell infiltration in copy-number driven cancers. Nature Commun. 9, 1317. (#co-corresponding author)

Li Y, Li L, Wang Z, Pan T, Sahni N, Jin X, Wang G, Li J, Zheng X, Zhang Y, Xu J#, Yi S#, Li X#. (2018) LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations. Nucleic Acids Res. 46, 1113-23. (#co-corresponding author)

Li Y, Sahni N, Pancsa R, McGrail DJ, Xu J, Hua X, Coulombe-Huntington J, Ryan M, Tychhon B, Sudhakar D, Hu L, Tyers M, Jiang X, Lin SY, Babu MM, and Yi S#. (2017) Revealing the determinants of widespread alternative splicing perturbation in cancer. Cell Rep. 21, 798-812. (#corresponding author)

Yi S#, Lin S, Li Y, Zhao W, Mills GB and Sahni N. (2017) Functional variomics and network perturbation: Connecting genotype to phenotype in cancer. Nature Rev. Genet. 18, 395-410. (journal cover) (#corresponding author)

Karras GI, Yi S, Sahni N, Fischer M, Xie J, Vidal M, D’Andrea AD, Whitesell L and Lindquist S. (2017) HSP90 shapes the consequences of human genetic variation. Cell 168, 856-866.

Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordân R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML. (2016) Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science 351,1450-1454.

Sahni N, Yi S*, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, et al. (2015) Widespread macromolecular interaction perturbations in human genetic disorders. Cell 161, 647-660. (*co-first author)

Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, Yi S, Hill DE, Vidal M and Walhout AJ. (2015) Human gene-centered transcription factor networks for enhancers and disease variants. Cell 161, 661-673.

Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S*, Lemmens I, Fontanillo C, Mosca R, et al. (2014) A proteome-scale map of the human interactome network. Cell 159, 1212-1226. (*co-first author)

Yi S, Sahni N, Daniels KJ, Lu KL, Srikantha T, Huang G, Garnaas AM and Soll DR. (2011) Alternative mating type configurations (a/alpha versus a/a or alpha/alpha) of Candida albicans result in alternative biofilms regulated by different pathways. PLoS Biol. 9, e1001117. ● Highlighted in a Research Highlight: Microbiology: Biofilm for yeast sex. Nature. 476, 129, Aug 2011

Wessels D, Srikantha T, Yi S, Kuhl S, Aravind L and Soll DR. (2006) The Shwachman-Bodian-Diamond syndrome gene encodes an RNA-binding protein that localizes to the pseudopod of Dictyostelium amoebae during chemotaxis. J. Cell Sci. 119, 370-379. ● Highlighted in a “Research Highlights” section in the journal Nature, 26 Jan 2006, 439, 372-373.

Positions available at The Stephen Yi Laboratory

We are always interested in motivated graduate students and postdoc candidates, and we welcome you to join our group!  Candidates with background and interest in cancer biology, molecular genetics, bioinformatics or relevant fields are encouraged to apply. Prior experience in next-generation sequencing analysis, cell culture, and high-throughput functional screens is a plus. For further information, please contact Dr. Yi at  Stephen.yi(AT)austin.utexas.edu, with your CV, research interest, and the contact info of three references.