Yang I. Li, PhD

Associate Professor of Medicine
Associate Professor of Human Genetics
Committee on Genetics, Genomics and Systems Biology
Research and Scholarly Interests: Complex Traits, Gene Regulation, Genetics, Genomics, Population Genomics, RNA splicing, Single Cell Analysis
Websites: Li Lab, Research Network Profile
Contact: yangili1@uchicago.edu
Graduate Programs: Genetics, Genomics & Systems Biology, Human Genetics, UChicago Biosciences

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.

University of Oxford
Oxford
DPhil - Evolutionary Genomics
2014

Predicting RNA splicing from DNA sequence using Pangolin.
Predicting RNA splicing from DNA sequence using Pangolin. Genome Biol. 2022 04 21; 23(1):103.
PMID: 35449021

Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation.
Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. Genome Biol. 2021 10 14; 22(1):291.
PMID: 34649612

The impact of cell type and context-dependent regulatory variants on human immune traits.
The impact of cell type and context-dependent regulatory variants on human immune traits. Genome Biol. 2021 04 29; 22(1):122.
PMID: 33926512

Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching.
Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching. Genome Res. 2021 04; 31(4):698-712.
PMID: 33741686

Identification and Quantification of Splicing Quantitative Trait Loci.
Identification and Quantification of Splicing Quantitative Trait Loci. Methods Mol Biol. 2020; 2082:51-62.
PMID: 31849007

m6A mRNA Methylation Is Essential for Oligodendrocyte Maturation and CNS Myelination.
m6A mRNA Methylation Is Essential for Oligodendrocyte Maturation and CNS Myelination. Neuron. 2020 01 22; 105(2):293-309.e5.
PMID: 31901304

Trans Effects on Gene Expression Can Drive Omnigenic Inheritance.
Trans Effects on Gene Expression Can Drive Omnigenic Inheritance. Cell. 2019 05 02; 177(4):1022-1034.e6.
PMID: 31051098

Discovery and characterization of variance QTLs in human induced pluripotent stem cells.
Discovery and characterization of variance QTLs in human induced pluripotent stem cells. PLoS Genet. 2019 04; 15(4):e1008045.
PMID: 31002671

Prioritizing Parkinson's disease genes using population-scale transcriptomic data.
Prioritizing Parkinson's disease genes using population-scale transcriptomic data. Nat Commun. 2019 03 01; 10(1):994.
PMID: 30824768

Annotation-free quantification of RNA splicing using LeafCutter.
Annotation-free quantification of RNA splicing using LeafCutter. Nat Genet. 2018 01; 50(1):151-158.
PMID: 29229983

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Nuffield Prize Scholarship
University of Oxford
2010 - 2014