Faculty |
Yinqing Li, Ph.D.

Yinqing Li, Ph.D. is a tenured Associate Professor in the School of Pharmaceutical Sciences at Tsinghua University. With training that spans microelectronics (B.S. Fudan University, 2008), systems engineering (S.M./Ph.D. Massachusetts Institute of Technology EECS, 2012/2016), and neuroscience (post-doctoral fellowship, the Broad Institute of Harvard and MIT and the Stanley Center for Psychiatric Research, 2016-2018), he leverages quantitative principles to drive cross-disciplinary advances in experimental genomics and neurobiology. Working with Feng Zhang, Aviv Regev and Guoping Feng, he co-invented single-nucleus multi-omics and helped engineer first-generation CRISPR tools for neuroscience. His lab now builds technologies that both read and rewrite gene regulation to tackle fundamental questions in ageing, degeneration, development and regeneration.


Current Research Interest

Cells encode their long-term “self” in chromatin marks that are, paradoxically, erased and rewritten reversibly. Our central question is therefore not “what marks exist?” but “how do reversible reactions maintain a stable equilibrium and what pushes the system over the ridge into disease?”

To dissect these processes, we combine wet-lab innovation with computational modelling, and we focus on two complementary systems: (1) Neuronal transcription and epigenetic homeostasis: How do neurons maintain activity-dependent gene programs for years? What breaks first in Alzheimer’s disease or addiction? (2) T-cell fate decisions: How does a T cell decide a balance between proliferating, killing, or exhaustion? Can we return the set-point to boost cancer therapy or curb autoimmunity?

We develop technologies to tackle these questions, including: single-cell temporal and spatial multi-omics, genome and epigenomic editing, and integrated computational analyses.


Scientific Contributions

1. Transcriptional condensates in expression control and stability (Cell 2024)

2. Attention network and cortical-thalamic circuity regulation (Nature 2020)

3. Single nucleus omics for neuron and neural stem cell (Science 2016)

4. Genome and epigenetic editing systems

5. Systems biology and gene circuit


Honors and awards

2019       MIT Technology Review, 35 under 35, China

2016       Extraordinary Potential Prize of 2016 Chinese Government Award for Students Abroad

2016       Wenner-Gren Fellowship

2013       McGovern Institute Fellowship


Selected Publications

1.He J*, Huo X*, Pei G*, Jia Z*, Yan Y, Yu J, Qu H, Xie Y, Yuan J, Zheng Y, Hu Y, Shi M, You K, Li T, Ma T, Zha ng MQ, Ding S, Li P#, Li Y#. Dual-role transcription factors stabilize intermediate expression levels. Cell. 2024 Apr 10:S0092-8674(24)00314-3.


2.Li Y, Lopez-Huerta VG, Adiconis X, Levandowski K, Choi S, Simmons SK, Arias-Garcia MA, Guo B, Yao AY, Blosser TR, Wimmer RD, Aida T, Atamian A, Naik T, Sun X, Bi D, Malhotra D, Hession CC, Shema R, Gomes M, Li T, Hwang E, Krol A, Kowalczyk M, Peça J, Pan G, Halassa MM, Levin JZ#, Fu Z#, Feng G#. Distinct subnetworks of the thalamic reticular nucleus. Nature. 2020, 583(7818):819-824.


3.Habib N*, Li Y*, Heidenreich M, Swiech L, Avraham-Davidi I, Trombetta JJ, Hession C, Zhang F#, Regev A#. Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. SCIENCE. 2016, 353(6302):925-8.


Personal Webpage: http://web.mit.edu/yinqingl/www/