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Yi, Song

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

Postal Address
1601 TRINITY ST BLDG B
AUSTIN, TX 78712

Research interests

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.

 

Biography

 

Dr. Song (Stephen) Yi is a recognized expert in cancer systems biology and functional variomics/proteomics. He is a recipient of the NIH/NCI K22 award, and the Principal Investigator on grants involving molecular signaling networks and translational therapeutics of human disease. He is affiliated with Institute for Cellular and Molecular Biology, and also affiliated with the Department of Biomedical Engineering. Prior to coming to UT Austin, Dr. Yi was a faculty member at MD Anderson Cancer Center. He has authored over 30 high-impact publications, including Cell and Nature Reviews Genetics. In the past five years, Dr. Yi’s work has been cited 2,000 times, and he has been invited to present platform talks and posters in numerous academic institutions and conferences. Dr. Yi has already successfully mentored many graduate students and postdocs, who are now successful in the next stage of their career.

         Dr. Yi received his bachelor’s degree from Peking University, and doctoral degree from University of Iowa. He was conferred with Dean’s Distinguished Dissertation Award for his work on signal transduction and evolution in human disease. Dr. Yi 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.

Selected Publications

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)

Li Y, McGrail DJ, Xu J, Li J, Liu NN, Sun M, Lin R, Pancsa R, Zhang J, Lee JS, Wang H, Mills GB, Li X, Yi S# and Sahni N#. (2018) MERIT: Systematic analysis and characterization of Mutational Effect on RNA Interactome Topology. Hepatology doi: 10.1002/hep.30242.

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)

Yi S#, Liu NN, Hu L, Wang H and Sahni N. (2017) Base-resolution stratification of cancer mutations using functional variomics. Nature Protoc 12, 2323-41. (#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.