Research Team Publications Join Us
University of Chicago · Section of Genetic Medicine

Deciphering the Genetic Basis of Human Disease

We use computational approaches and genomics to study gene regulation, RNA splicing, and how to modulate it using drugs.

Explore Our Research Join Our Team
Research

Understanding Gene Regulation
at Scale

Our lab integrates computational biology, statistical genetics, and experimental genomics to understand how genetic variation shapes gene regulation and contributes to human disease.

Mechanisms of Gene Regulation

We study how genetic information flows through the regulatory cascade from chromatin to protein, using large-scale genomic data to identify the molecular mechanisms controlling gene expression in diverse cellular contexts.

RNA Splicing in Disease

We seek to understand functional links between genetic variants and complex traits -- from Alzheimer's disease to autoimmune conditions -- with a particular emphasis on RNA splicing as a key mechanism mediating disease risk.

Drugging RNA Splicing

We study how splice-switching molecules impact RNA splicing and explore their potential as therapeutic drugs, aiming to develop new approaches for modulating gene expression in disease-relevant tissues and cell types.

Our Team

Meet the People Behind
the Science

Our lab is dedicated to training the next generation of computational biologists and geneticists. We foster a collaborative, inclusive environment where curiosity drives discovery.

Yang I Li
Yang I Li, DPhil
Associate Professor · PI
Section of Genetic Medicine, Department of Medicine
Ben Fair
Ben Fair, PhD
Staff Scientist
Drugging unproductive splicing
Carlos Buen Abad
Carlos Buen Abad, PhD
Postdoctoral Fellow
Computational approaches to gene regulation
Jimmy Elias
Jimmy Elias, PhD
Postdoctoral Fellow
Kinetics of RNA splicing
Connor Kenny
Connor Kenny, PhD
Postdoctoral Fellow
Mechanistic models of RNA splicing
Dylan Stermer
Dylan Stermer, B.Sc.
PhD Student · GGSB
Genetics, Genomics & Systems Biology
Quinn Hauck
Quinn Hauck, B.Sc.
PhD Student · Human Genetics
Department of Human Genetics
Hao Yu
Hao Yu, B.S.
PhD Student · GGSB
Genetics, Genomics & Systems Biology
Sara Fritz
Sara Fritz, B.S.
Research Lab Technician
Laboratory operations and experimental support
Fabio Morgante, PhD — Postdoc (2018–2020) • Now faculty at Clemson University
Phoenix (Zepeng) Mu, B.S. — PhD Student (2019–2024) • Now postdoc at Harvard
Ankeeta Shah, B.A. — PhD Student (2018–2023) • Now at Piper Sandler
Chao Dai, B.S. — PhD Student (2021–2025)
Gabriela Mossian, B.A. — Lab Technician (2021–2023)
Eric Chen, B.S. — Research Assistant (2021–2023) • Now PhD student at Harvard
Yi Zeng, PhD — Postdoc (2021–2022) • Now postdoc at Stanford
Austin Reilley — Lab Technician (2020–2021)
Stephanie Lozano, B.S. — Lab Technician (2018–2020) • Now at UC Davis Neuroscience
Tony Zeng, B.S. — Undergrad (2018–2021) • Now PhD student at Stanford Genetics
Shane Warland — Undergrad (2018–2021) • Now PhD student at Cornell
Henry Bloom — Undergrad (2022–2024)
Alex Williams — Undergrad (2023–2024)
Publications

Selected Publications

A selection of recent work from the lab. Visit our Google Scholar page for a complete list of publications.

2026
Impact of disease-associated chromatin accessibility QTLs across immune cell types and contexts
Mu Z, Randolph HE, Aguirre-Gamboa R, Ketter E, Dumaine A, Locher V, et al.
Cell Genomics
2026
Protein–protein interactions shape trans-regulatory impact of genetic variation on protein expression and complex traits
Li J, Li YI, Liu X
Nature Genetics
2025
Integrative multi-omics QTL colocalization maps regulatory architecture in aging human brain
Cao X, Sun H, Feng R, Mazumder R, Buen Abad Najar CF, Li YI, et al.
medRxiv (preprint)
2025
Genetic and functional analysis of unproductive splicing using LeafCutter2
Buen Abad Najar CF, Feng R, Dai C, Fair B, Hauck Q, Li J, Cao X, Dey KK, et al.
bioRxiv (preprint)
2024
Global impact of unproductive splicing on human gene expression levels
Fair BJ, Buen Abad Najar CF, Zhao J, Lozano S, Reilly A, Mossian G, Staley JP, Wang J, Li YI
Nature Genetics
2024
Genetic and molecular architecture of complex traits
Lappalainen T, Li YI, Ramachandran S, Gusev A
Cell
2024
Epigenetic variation impacts individual differences in the transcriptional response to influenza infection
Aracena K et al.
Nature Genetics
2023
Genetics of sexually dimorphic adipose distribution in humans
Hansen GT et al.
Nature Genetics
2023
Molecular quantitative trait loci
Aguet F, Alasoo K, Li YI, Battle A, Im HK, Montgomery SB, Lappalainen T
Nature Reviews Methods Primers
2022
Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing
Zeng Y, Fair BJ, Zeng H, Krishnamohan A, Hou Y, Hall JM, Ruthenburg AJ, Li YI*, Staley JP*
Molecular Cell
2022
RNA editing underlies genetic risk of common inflammatory diseases
Li Q et al.
Nature
2022
Predicting RNA splicing from DNA sequence using Pangolin
Zeng T, Li YI
Genome Biology
2021
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Ebert et al.
Science
2021
Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation
Shah A, Mittleman B, Gilad Y, Li YI
Genome Biology
2021
Impact of cell-type and context-dependent regulatory variants on human immune traits
Mu Z, Wei W, Fair B, Miao J, Zhu P*, Li YI*
Genome Biology
2021
Alignment of single-cell RNA-seq samples without over-correction using kernel density matching
Chen M, Zhan Q, Mu Z, Wang L, Zheng Z, Miao J, Zhu P*, Li YI*
Genome Research
2020
Alternative polyadenylation mediates genetic regulation of gene expression
Mittleman B, Pott S, Warland S, Zeng T, Mu Z, Kaur M, Gilad Y, Li YI
eLife
2019
Trans effects on gene expression can drive omnigenic inheritance
Liu X*, Li YI*, Pritchard JK*
Cell
2019
Prioritizing Parkinson's Disease genes using population-scale transcriptomic data
Li YI*, Wong G*, et al.
Nature Communications
2018
Annotation-free quantification of RNA splicing using LeafCutter
Li YI*, Knowles DA*, Humphrey J, Barbeira AN, Dickinson SP, Im HK, Pritchard JK
Nature Genetics
2017
An expanded view of complex traits: from polygenic to omnigenic
Boyle EA*, Li YI*, Pritchard JK*
Cell
2016
RNA splicing is a primary link between genetic variation and disease
Li YI, van de Geijn B, Raj A, Knowles DA, Petti A, Golan D, Gilad Y, Pritchard JK
Science
View All on Google Scholar
Opportunities

Join Our Team

We are always looking for talented and motivated individuals to join our team. If you are passionate about computational genomics and gene regulation, we would love to hear from you.

Postdoctoral Fellows

We are seeking postdocs with a strong background in computational biology, statistical genetics, or related fields. Experience with genomic data analysis, machine learning, or molecular biology is highly valued. We provide a collaborative environment with access to world-class resources at the University of Chicago.

PhD Students

Prospective PhD students can join through the Genetics, Genomics & Systems Biology (GGSB), Human Genetics, or Computational Biology programs at the University of Chicago. We welcome students with backgrounds in biology, computer science, statistics, or related quantitative disciplines.

What to Expect from the PI

  • Identification and creation of career-advancing opportunities
  • Weekly meetings to discuss research and exchange ideas
  • Support designing focused projects for timely publication
  • Assistance interpreting results and prioritizing next steps
  • Editing and feedback on grants and written materials
  • Annual career development plan reviews
  • Attendance at 1–2 conferences per year

What is Expected from Lab Members

  • Conduct yourself with the utmost scientific integrity
  • Maintain sustainable, reproducible code for data analysis
  • Read approximately 5 papers weekly
  • Attend lab meetings (with advance notice if absent)
  • Actively pursue external funding and grant applications
  • Be present in lab minimum 4 days/week, 10am–5pm
  • Identify and apply for all relevant external funding opportunities

Interested? Reach out with your CV and a brief description of your research interests.

yangili1@uchicago.edu