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Yang Li

TitleAssociate Professor
InstitutionUniversity of Chicago
DepartmentMedicine-Genetic Medicine
AddressChicago IL 60637
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    Research in the Li lab lies at interface of genetics, gene regulation, and disease. A large part of our work aims to dissect the role of genetic variation on gene regulation at multiple levels. In particular, we develop computational approaches to study genetic effects on gene regulatory mechanisms that have so far been under-appreciated. These include RNA splicing, co-transcriptional dynamics, and post-transcriptional processes. We study how dysregulation of these processes play roles in complex disease. A second focus of the lab is the use of state-of-the-art genomics tools such as single-cell RNA-sequencing to understand cellular composition and function in disease progression.
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    Collapse Biography 
    Collapse education and training
    University of Oxford, OxfordDPhil2014Evolutionary Genomics
    Collapse awards and honors
    2010 - 2014Nuffield Prize Scholarship, University of Oxford

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    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Zeng T, Li YI. Predicting RNA splicing from DNA sequence using Pangolin. Genome Biol. 2022 04 21; 23(1):103. PMID: 35449021; PMCID: PMC9022248.
      Citations: 21     Fields:    Translation:AnimalsCells
    2. Shah A, Mittleman BE, Gilad Y, Li YI. Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. Genome Biol. 2021 10 14; 22(1):291. PMID: 34649612; PMCID: PMC8518154.
      Citations: 14     Fields:    Translation:HumansCells
    3. Mu Z, Wei W, Fair B, Miao J, Zhu P, Li YI. The impact of cell type and context-dependent regulatory variants on human immune traits. Genome Biol. 2021 04 29; 22(1):122. PMID: 33926512; PMCID: PMC8082814.
      Citations: 23     Fields:    Translation:HumansCells
    4. Chen M, Zhan Q, Mu Z, Wang L, Zheng Z, Miao J, Zhu P, Li YI. Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching. Genome Res. 2021 04; 31(4):698-712. PMID: 33741686; PMCID: PMC8015859.
      Citations: 3     Fields:    Translation:Humans
    5. Shah A, Li YI. Identification and Quantification of Splicing Quantitative Trait Loci. Methods Mol Biol. 2020; 2082:51-62. PMID: 31849007.
      Citations:    Fields:    Translation:HumansCells
    6. Xu H, Dzhashiashvili Y, Shah A, Kunjamma RB, Weng YL, Elbaz B, Fei Q, Jones JS, Li YI, Zhuang X, Ming GL, He C, Popko B. m6A mRNA Methylation Is Essential for Oligodendrocyte Maturation and CNS Myelination. Neuron. 2020 01 22; 105(2):293-309.e5. PMID: 31901304; PMCID: PMC7137581.
      Citations: 66     Fields:    Translation:AnimalsCells
    7. Liu X, Li YI, Pritchard JK. Trans Effects on Gene Expression Can Drive Omnigenic Inheritance. Cell. 2019 05 02; 177(4):1022-1034.e6. PMID: 31051098; PMCID: PMC6553491.
      Citations: 192     Fields:    Translation:Humans
    8. Sarkar AK, Tung PY, Blischak JD, Burnett JE, Li YI, Stephens M, Gilad Y. Discovery and characterization of variance QTLs in human induced pluripotent stem cells. PLoS Genet. 2019 04; 15(4):e1008045. PMID: 31002671; PMCID: PMC6474585.
      Citations: 33     Fields:    Translation:HumansCells
    9. Li YI, Wong G, Humphrey J, Raj T. Prioritizing Parkinson's disease genes using population-scale transcriptomic data. Nat Commun. 2019 03 01; 10(1):994. PMID: 30824768; PMCID: PMC6397174.
      Citations: 73     Fields:    Translation:HumansCells
    10. Li YI, Knowles DA, Humphrey J, Barbeira AN, Dickinson SP, Im HK, Pritchard JK. Annotation-free quantification of RNA splicing using LeafCutter. Nat Genet. 2018 01; 50(1):151-158. PMID: 29229983; PMCID: PMC5742080.
      Citations: 265     Fields:    Translation:AnimalsCells
    11. Banovich NE, Li YI, Raj A, Ward MC, Greenside P, Calderon D, Tung PY, Burnett JE, Myrthil M, Thomas SM, Burrows CK, Romero IG, Pavlovic BJ, Kundaje A, Pritchard JK, Gilad Y. Impact of regulatory variation across human iPSCs and differentiated cells. Genome Res. 2018 01; 28(1):122-131. PMID: 29208628; PMCID: PMC5749177.
      Citations: 68     Fields:    Translation:HumansCells
    12. Boyle EA, Li YI, Pritchard JK. An Expanded View of Complex Traits: From Polygenic to Omnigenic. Cell. 2017 Jun 15; 169(7):1177-1186. PMID: 28622505; PMCID: PMC5536862.
      Citations: 1106     Fields:    Translation:HumansAnimals
    13. Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. Elife. 2016 05 27; 5. PMID: 27232982; PMCID: PMC4940163.
      Citations: 70     Fields:    Translation:HumansCells
    14. Li YI, van de Geijn B, Raj A, Knowles DA, Petti AA, Golan D, Gilad Y, Pritchard JK. RNA splicing is a primary link between genetic variation and disease. Science. 2016 Apr 29; 352(6285):600-4. PMID: 27126046; PMCID: PMC5182069.
      Citations: 292     Fields:    Translation:HumansCells
    15. Jore MM, Johnson S, Sheppard D, Barber NM, Li YI, Nunn MA, Elmlund H, Lea SM. Structural basis for therapeutic inhibition of complement C5. Nat Struct Mol Biol. 2016 05; 23(5):378-86. PMID: 27018802; PMCID: PMC5771465.
      Citations: 53     Fields:    Translation:HumansAnimalsCells
    16. Macaulay IC, Haerty W, Kumar P, Li YI, Hu TX, Teng MJ, Goolam M, Saurat N, Coupland P, Shirley LM, Smith M, Van der Aa N, Banerjee R, Ellis PD, Quail MA, Swerdlow HP, Zernicka-Goetz M, Livesey FJ, Ponting CP, Voet T. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat Methods. 2015 Jun; 12(6):519-22. PMID: 25915121.
      Citations: 332     Fields:    Translation:HumansAnimalsCells
    17. Keane M, Semeiks J, Webb AE, Li YI, Craig T, Madsen LB, van Dam S, Brawand D, Michalak P, Kang L, Bhak J, Yim HS, Grishin NV, Nielsen NH, Oziolor EM, Matson CW, Church GM, Stuart GW, Patton JC, George JC, Suydam R, Larsen K, O'Connell MJ, Bickham JW, Thomsen B, Quesada V, Marques PI, Heide-Jørgensen MP, López-Otín C, de Magalhães JP. Insights into the evolution of longevity from the bowhead whale genome. Cell Rep. 2015 Jan 06; 10(1):112-22. PMID: 25565328; PMCID: PMC4536333.
      Citations: 143     Fields:    Translation:HumansAnimals
    18. Li YI, Sanchez-Pulido L, Haerty W, Ponting CP. RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts. Genome Res. 2015 Jan; 25(1):1-13. PMID: 25524026; PMCID: PMC4317164.
      Citations: 79     Fields:    Translation:HumansAnimalsCells
    19. Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Amemiya C, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Gante HF, Gnerre S, Greuter L, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Penman DJ, Przybylski D, Renn SCP, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F, Alföldi J, Azzouzi N, Baroiller JF, Barloy-Hubler F, Galibert F, Guyon R, Ozouf-Costaz C, Rakotomanga M. The genomic substrate for adaptive radiation in African cichlid fish. Nature. 2014 Sep 18; 513(7518):375-381. PMID: 25186727; PMCID: PMC4353498.
      Citations: 347     Fields:    Translation:AnimalsCells
    20. Li YI, Kong L, Ponting CP, Haerty W. Rapid evolution of Beta-keratin genes contribute to phenotypic differences that distinguish turtles and birds from other reptiles. Genome Biol Evol. 2013; 5(5):923-33. PMID: 23576313; PMCID: PMC3673632.
      Citations: 16     Fields:    Translation:AnimalsCells
    21. Li YI, Copley RR. Scaffolding low quality genomes using orthologous protein sequences. Bioinformatics. 2013 Jan 15; 29(2):160-5. PMID: 23162087; PMCID: PMC3546802.
      Citations: 8     Fields:    Translation:HumansAnimals
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