Yang Li
Li Yang, Ph.D.
1994.09-1998.07: Bachelor of Biochemistry, Lanzhou University, China
1998.09-2004.03: Ph.D. of Biochemistry and Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), China
2004.07-2006.12: Postdoctoral Associate, Yale University, lab of Sidney Altman (Nobel laureate of 1989)
2007.01-2010.10: Postdoctoral Fellow, University of Connecticut Health Center, lab of Brenton R. Graveley
2010.10-2011.07: Director, Department of Scientific Research Management, Shanghai Institutes for Biological Sciences (SIBS), CAS, China
2011.07-2022.01: Principal Investigator, Group leader, CAS-MPG Partner Institute of Computational Biology, Shanghai Institute of Nutrition and Health, SIBS, CAS, China
2022.02-date: Distinguished Principal Investigator, Group leader, Institutes of Biomedical Sciences, Fudan University and affiliated to Children’s Hospital, Fudan University, China
Address: Institutes of Biomedical Sciences, Fudan University, Shanghai 200032
Email: liyang_fudan@fudan.edu.cn
Lab homepage: http://yang-laboratory.com https://yanglab.github.io
Bioinformatics and computational biology
Systems RNA biology and RNomics
Genome editing and base editing technologies
Machine learning and deep learning
The completion of the human genome project (HGP) in the beginning of this century and the application of affordable high-throughput sequencing technologies in the past decade have led life science researches to the post-genome era. The resulting wealth of deep-sequencing datasets at genome (including epi-genome) and transcriptome (including epi-transcriptome) levels challenges us to fully understand how functional genomic elements are transcribed and regulated, which is related with human health and disease. Importantly, the advent of novel genome editing technologies provides us powerful methods to change genetic information at desired target sites at single nucleotide resolution, which benefits not only basic research aiming to decipher how different genotypes result in distinct phenotypes but also pre-clinical study potential to cure human diseases caused by genetic mutations.
In the last decade, my lab has developed and applied novel computational strategies, together with the-state-of-the-art deep-sequencing technologies and diverse biochemical methods, to dissect complex expression, novel function and potential application of long noncoding RNAs (lncRNAs), especially structured ones such as covalently-closed circular RNAs (circRNAs) from back-splicing. In addition, my lab has also been focusing on the invention of novel base editing technologies, along with distinct mechanisms of their unintended off-target effects for further improvement. These research findings shed new light on the functional potential of previously-underappreciated circRNAs, and provide powerful genome editing systems to achieve precise genetic changes in the application of biomedical research, biotechnology and therapeutics.
1. Yang L*, Wilusz JE* and Chen LL*. Biogenesis and regulatory roles of circular RNAs. Annu Rev Cell Dev Biol, 2022, doi: 10.1146/annurev-cellbio-120420-125117 (Review)
2. Li X#,*, Zhou L#, Gao BQ#, Li G#, Wang X#, Wang Y, Wei J, Han W, Wang Z, Li J, Gao R, Zhu J, Xu W, Wu J, Yang B, Sun X*, Yang L* and Chen J*. Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure. Nat Commun, 2022, 13: 1669
3. Gao R#, Fu ZC#, Li X#, Wang Y#, Wei J, Li G, Wang L, Wu J, Huang X*, Yang L* and Chen J*. Genomic and Transcriptomic Analyses of Prime Editing Guide RNA-Independent Off-Target Effects by Prime Editors. CRISPR J, 2022, 5: 276-293
4. Gao X#, Ma XK#, Li X, Li GW, Liu CX, Zhang J, Wang Y, Wei J, Chen J, Chen LL, Yang L*. Knockout of circRNAs by base editing back-splice sites of circularized exons. Genome Biol, 2022, 23:16
5. Wang L#, Xue W#, Zhang H#, Gao R#, Qiu H#, Wei J, Zhou L, Lei YN, Wu X, Li X, Liu C, Wu J, Chen Q, Ma H, Huang X, Cai C, Zhang Y, Yang B*, Yin H*, Yang L*, Chen J*. Eliminating genome-wide and transcriptome-wide off-target mutations by base editor. Nat Cell Biol, 2021, 23: 552-563
6. Li GW#, Nan F#, Yuan GH, Liu CX, Liu X, Chen LL, Tian B, Yang L*. SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3' tag-based RNA-seq of single cells. Genome Biol, 2021, 22: 221
7. Li SQ#, Li X#, Xue W#, Zhang L#, Cao SM, Lei YN, Yang LZ, Guo SK, Zhang JL, Gao X, Wei J, Li J*, Yang L*, and Chen LL*. Screening for functional circular RNAs using the CRISPR-Cas13 system. Nat Methods, 2021, 18: 51–59
·Highlighted by Nat Rev Genet, 2021, 22: 68
8. Yang L* and Chen J*. A tale of two moieties: rapidly-evolving CRISPR/Cas-based genome editing. Trends Biochem Sci, 2020, 45: 874-888 (Review)
9. Wang X#, Ding C#, Yu W#, Wang Y#, He S#, Yang B#, Xiong YC, Wei J, Li J, Liang J, Lu Z, Zhu W, Wu J, Zhou Z, Huang X, Liu Z*, Yang L* and Chen J*. Cas12a base editors induce efficient and specific editing with low DNA damage response. Cell Rep, 2020, 31: 107723
10. Ma XK, Wang MR, Liu CX, Dong R, Carmichael GG, Chen LL and Yang L*. CIRCexplorer3: A CLEAR pipeline for direct comparison of circular and linear RNA expression. Genomics Proteomics Bioinformatics, 2019, 17: 511–521
11. Wang Y#, Gao R#, Wu J#, Xiong YC, Wei J, Zhang S, Yang B, Chen J* and Yang L*. Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs. Genome Biol, 2019, 20: 218
12. Liu CX#, Li X#, Nan F#, Jiang S, Gao X, Guo SK, Xue W, Cui Y, Dong K, Ding H, Qu B, Shen N*, Yang L* and Chen LL*. Structure and degradation of circular RNAs regulate PKR activation in innate immunity. Cell, 2019, 177: 865-880 (Featured Article)
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·Highlighted by Cell, 2019, 177: 797-799
·Highlighted by Science, 2019, 364: 847
·Highlighted by Nat Rev Immunol, 2019, 19: 351
·Highlighted by Nat Rev Mol Cell Biol, 2019, 20: 387
·Highlighted by Cell Bio sci, 2019, 9: 43
·Highlighted by F1000 Prime, https://f1000.com/prime/735608202
·Highlighted by Science News Magazine, https://www.sciencenews.org/article/lack-circular-rna-may-trigger-lupus
13. Yang B*, Chen J* andYang L*. To BE or not to BE, that is the question. Nat Biotechnol, 2019, 37: 520-522 (News and Views)
14. WangX#, Li J#, Wang Y#, Yang B#, Wei J#, Wu J, Wang R, Huang X*, Chen J* and Yang L*. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion. Nat Biotechnol, 2018, 36: 946-949
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·Highlighted by Nat Methods, 2018, 15: 763
·Highlighted by Nature Index, 2018, https://www.natureindex.com/article/10.1038/nbt.4198
15. Li X#, Wang Y#, Liu Y#, Yang B#, Wang X, Wei J, Lu Z, Zhang Y, Wu J, Huang X*, Yang L* and Chen J*. Base editing with a Cpf1-cytidine deaminase fusion. Nat Biotechnol, 2018, 36: 324-327
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·Highlighted by Nat Methods, 2018, 15: 314
16. Xiang JF#, Yang Q#, Liu CX#, Wu M, Chen LL* and Yang L*. N6-methyladenosines modulate A-to-I RNA editing. Mol Cell, 2018, 69: 126-135
17. Zhang XO#, Dong R#, Zhang Y#, Zhang JL, Luo Z, Zhang J, Chen LL* and Yang L*. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res, 2016, 26: 1277-1287
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18. Dong R, Zhang XO, Zhang Y, Ma XK, Chen LL and Yang L*. CircRNA-derived pseudogenes. Cell Res,2016, 26:747-750
19. Zhang XO#, Wang HB#, Zhang Y, Lu X, Chen LL* and Yang L*. Complementary sequence-mediated exon circularization. Cell, 2014,159: 134-147
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·Highlighted by Cell, 2014, 159: 13-14
·Highlighted by Nat Rev Genet, 2014, 15: 707
·Highlighted by F1000 Prime, https://f1000.com/prime/718882519
20. Zhang Y#, Zhang XO#, Chen T, Xiang JF, Yin QF, Xing YH, Zhu S, Yang L* and Chen LL*. Circular intronic long noncoding RNAs. Mol Cell, 2013, 51: 792-806 (Issue Highlight)
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·Highlighted by Mol Cell, 2013, 51:705-706
·Highlighted by Nature China, 2013, Epub. on Oct. 2nd (doi:10.1038)
·Highlighted by Institute for Creation Res, 2013, Epub. on Oct. 9th
·Highlighted by Nature, 2013, 501:464
