Biography
Yinqing Li moved to Tsinghua in 2018, where he is now an associate professor in the School of Pharmaceutical Sciences and a principal investigator at the IDG/McGovern Institute for Brain Research at Tsinghua. He received his B.S. in microelectronics from Fudan University in 2008 and his S.M. and PhD in electrical engineering and computer science from Massachusetts Institute of Technology in 2012 and 2016, where he worked with Dr. Feng Zhang and Dr. Aviv Regev. He then performed postdoctoral research with Dr. Guoping Feng and Dr. Zhanyan Fu in the Broad Institute of Harvard and MIT and Stanley Center for Psychiatric Research. During the course of his doctoral and postdoctoral research, Yinqing pioneered several advances in engineering and characterization of cell and gene editing tools with TALE and CRISPR, co-invented single-nucleus transcriptome profiling technologies, and broadened these tools to systematically interrogate cortical-thalamic circuity function and in disease models.
He held an affiliate position the McGovern Institute for Brain Research at Massachusetts Institute of Technology, and visiting position in the Karolinska Institutet.
Yinqing has received prestigious fellowships and awards for his work, including MIT TR 35 under 35, China (2018), the Thousand Talents Plan for Young Professionals (2017), Extraordinary Potential Prize of 2016 Chinese Government Award for Outstanding Self-financed Students Abroad, 10 Awardees Globally (2016), Wenner-Gren Fellowship (2016), and McGovern Institute Fellowship (2013).
People
Advisees and Students
Research
Dr. Yinqing Li's research focuses on the molecular and cellular changes that drive the onset and progression of complex diseases. The crucial aspect of his approach is to discern which molecules and cells undergo pivotal changes at specific time points during disease development, and to determine how these changes affect cellular functionality and interactions. This understanding is critical for developing effective diagnostic and therapeutic strategies, including targeting and modifying these essential molecules and cells to manage diseases.
His main research efforts are categorized into three primary areas:
Single-cell Characterization Technologies: Developing single-cell multi-omics techniques to capture dynamic changes in the epigenome, transcriptome, and signaling pathways. These methods allow for analysis at very rapid temporal and precise spatial scales, providing a detailed view of molecular and cellular interactions.
Gene Editing Technologies: Exploring novel gene editing systems for accurate gene replacement and epigenetic control, enabling holistic regulation of cellular states at the genetic level.
Bioinformatics: Advancing and applying statistical inference and machine learning algorithms to analyze high-throughput data in depth, discovering new genomic phenomena and modalities.
Scientific Contributions
- Transcriptional condensates in precise expression control and stability (Cell 2024)
- Graded neuronal heterogeneity in cortical-thalamic circuity regulation (Nature 2020)
- Single nucleus omics in tracing adult neural stem cell (Science 2016)
- Genome editing and chromatin modulation systems
- Systems biology and gene circuit
Publications
- 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, Zhang MQ, Ding S, Li P, Li Y. Dual-role transcription factors stabilize intermediate expression levels. CELL. 2024 Apr 10:S0092-8674(24)00314-3.
- Meng Q, Wei L, Ma K, Shi M, Lin X, Ho JWK, Li Y, Zhang X. scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq. BRIEF BIOINFORM. 2024 Jan 22;25(2):bbae011.
- Lyu H, Yuan G, Liu X, Wang X, Geng S, Xia T, Zhou X, Li Y, Hu X, Shi Y. Sustained store-operated calcium entry utilizing activated chromatin state leads to instability in iTregs. ELIFE. 2023 Dec 6;12:RP88874.
- Zhu Z, Li D, Jia Z, Zhang W, Chen Y, Zhao R, Zhang YP, Zhang WH, Deng H, Li Y, Li W, Guang S, Ou G. Global histone H2B degradation regulates insulin/IGF signaling-mediated nutrient stress. THE EMBO JOURNAL. 2023 Oct 4;42(19):e113328.
- Xu Z, Ma D, Su H, Jia X, Li Y, Lu Y, Xie Z. Explore the dominant factor in prime editing via a view of DNA processing. SYNTHETIC AND SYSTEMS BIOTECHNOLOGY. 2023 Jun 3;8(3):371-377.
- Hu Y, Yang Y, Tan P, Zhang Y, Han M, Yu J, Zhang X, Jia Z, Wang D, Li Y, Ma T, Liu K, Ding S. Induction of mouse totipotent stem cells by a defined chemical cocktail. NATURE. 2022 Jun 21.
- Tan Y, Shen J, Si T, Ho CL, Li Y, Dai L. Engineered Live Biotherapeutics: Progress and Challenges. BIOTECHNOLOGY JOURNAL 2020 Oct;15(10):e2000155.
- Du J, Simmons S, Brunklaus A, Adiconis X, Hession CC, Fu Z, Li Y, Shema R, Møller RS, Barak B, Feng G, Meisler M, Sanders S, Lerche H, Campbell AJ, McCarroll S, Levin JZ, Lal D. Differential excitatory vs inhibitory SCN expression at single cell level regulates brain sodium channel function in neurodevelopmental disorders. EUROPEAN JOURNAL OF PAEDIATRIC NEUROLOGY 2020 Jan;24:129-133.
- 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 Jul;583(7818):819-824.
- Li Y, Weiss R., A Modular Approach to Building Complex Synthetic Circuits. Methods in Molecular Biology. 2017 pp. 231–248, DOI:10.1007/978-1-4939-7223-4_17.
- Yan WX, Mirzazadeh R, Garnerone S, Scott D, Schneider MW, Kallas T, Custodio J, Wernersson E, Li Y, Gao L, Federova Y, Zetsche B, Zhang F, Bienko M, Crosetto N., BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks. NATURE COMMUNICATIONS. 2017, 8:15058.
- 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.
- Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O. Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA. CELL. 2016, 165(4):949-62.
- Nishimasu H, Cong L, Yan W, Ran F, Bernd Z, Li Y, Kurabayashi A, Ishitani R, Zhang F, Nureki O. Crystal structure of Staphylococcus aureus Cas9. CELL. 2015, 162(5):1113-26.
- Davidsohn N, Beal J, Kiani S, Adler A, Yaman F, Li Y, Xie Z, Weiss R. Accurate predictions of genetic circuit behavior from part characterization and modular composition. ACS SYNTHETIC BIOLOGY. 2015, 4(6):673-81.
- Li Y*, Jiang Y*, Chen H*, Liao W, Li Z, Weiss R, Xie Z. Modular construction of mammalian gene circuits using TALE transcriptional repressors. NATURE CHEMICAL BIOLOGY. 2015, 11(3):207-13.
- Swiech L, Heidenreich M, Banerjee A, Habib N, Li Y, Trombetta J, Sur M, Zhang F. In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. NATURE BIOTECHNOLOGY. 2015, 33(1):102-6.
- Duportet X, Wroblewska L, Guye P, Li Y, Eyquem J, Rieders J, Rimchala T, Batt G, Weiss R. A platform for rapid prototyping of synthetic gene networks in mammalian cells. NUCLEIC ACIDS RESEARCH. 2014, 42(21):13440-51.
- Busskamp V, Lewis NE, Guye P, Ng AH, Shipman SL, Byrne SM, Sanjana NE, Murn J, Li Y, Li S, Stadler M, Weiss R, Church GM. Rapid neurogenesis through transcriptional activation in human stem cells. MOLECULAR SYSTEMS BIOLOGY. 2014, 10:760.
- Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN, Xie Z, Li Y, Weiss R. CRISPR transcriptional repression devices and layered circuits in mammalian cells. NATURE METHODS. 2014, 11(7):723-6.
- Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F. DNA targeting specificity of RNA-guided Cas9 nucleases. NATURE BIOTECHNOLOGY. 2013, 31(9):827-32.
- Guye P*, Li Y*, Wroblewska L, Duportet X, Weiss R. Rapid, modular and reliable construction of complex mammalian gene circuits. NUCLEIC ACIDS RESEARCH. 2013, 41(16):e156.
- Sakar MS, Neal D, Boudou T, Borochin MA, Li Y, Weiss R, Kamm RD, Chen CS, Asada HH. Formation and optogenetic control of engineered 3D skeletal muscle bioactuators. LAB ON A CHIP. 2012, 12(23):4976-85.
- Zhao P, Li Y, Zeng X, Zhou J, Huang Y, Liu R. EWOD using P(VDF-TrFE). IEEE Nano/Micro Engineered and Molecular Systems. 2009, 10.1109/NEMS.2009.5068559.
- Zhao P, Li Y, Zhou J, Huang Y, Xie H, Xu H. A novel EWOD digital microuidic device using P(VDF-TrFE). IEEE Solid-State and Integrated-Circuit Technology. 2008, 10.1109/ICSICT.2008.4735080.
Courses
