 Yang Li
| Title | Assistant Professor |
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| Institution | University of Chicago |
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| Department | Medicine-Genetic Medicine |
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| Address | Chicago IL 60637
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| vCard | Download vCard |
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 Overview 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.
Biography | University of Oxford, Oxford | DPhil | 2014 | Evolutionary Genomics |
| 2010 - 2014 | Nuffield Prize Scholarship, University of Oxford |
ORNG Applications Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
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Zeng T, Li YI. Predicting RNA splicing from DNA sequence using Pangolin. Genome Biol. 2022 04 21; 23(1):103. PMID: 35449021.
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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.
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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.
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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.
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Shah A, Li YI. Identification and Quantification of Splicing Quantitative Trait Loci. Methods Mol Biol. 2020; 2082:51-62. PMID: 31849007.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Keane M, Semeiks J, Webb AE, Li YI, Quesada V, Craig T, Madsen LB, van Dam S, Brawand D, Marques PI, Michalak P, Kang L, Bhak J, Yim HS, Grishin NV, Nielsen NH, Heide-Jørgensen MP, Oziolor EM, Matson CW, Church GM, Stuart GW, Patton JC, George JC, Suydam R, Larsen K, López-Otín C, O'Connell MJ, Bickham JW, Thomsen B, 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.
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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.
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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, Alföldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, 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, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, 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. The genomic substrate for adaptive radiation in African cichlid fish. Nature. 2014 Sep 18; 513(7518):375-381. PMID: 25186727.
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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.
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Li YI, Copley RR. Scaffolding low quality genomes using orthologous protein sequences. Bioinformatics. 2013 Jan 15; 29(2):160-5. PMID: 23162087.
This graph shows the total number of publications by year, by first, middle/unknown, or last author.
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| Year | Publications |
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| 2012 | 1 | | 2013 | 1 | | 2014 | 1 | | 2015 | 3 | | 2016 | 3 | | 2017 | 3 | | 2019 | 4 | | 2020 | 1 | | 2021 | 3 | | 2022 | 1 |
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