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Bioinformatics and Genomic Medicine (Yang Lab)

News

2022

May: Li have contributed an article in Annu Rev Cell Dev Biol. Well done!

April: Li has been selected as the 2021 Highly Cited Chinese Researchers (released by Elsevier). Congratulations to Li!

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March: Bao-Qing, Ying, Jia and Li have contributed an article in Nat Commun. Well done!

This study developed spegRNA by introducing same-sense mutations to increase PE’s base-editing efficiency and developed apegRNA by altering the pegRNA secondary structure to increase PE’s indelediting efficiency.

March: Zhi-Can, Ying, Jia and Li have contributed an article in The CRISPR Journal. Congratulations!

This study demonstrates that CRISPR-based PE tools induced no observable genome- or transcriptome-wide pegRNA-independent OT effects in human cells, suggesting a high editing specificity of its RTase moiety.

February: Yang Lab has moved to Institutes of Biomedical Sciences, Fudan University, Shanghai.

January: Guo-Wei has obtained President Award (Special Prize) at the 4th Graduate Research Appreciation Day (GRAD), Shanghai Institute of Nutrition and Health (SINH). Congratulations to Guo-Wei.

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January: Xu-Kai, Guo-Wei,Ying, Jia and Li have contributed an article in Genome Biology. Congratulations!

This study provided an efficient method to deplete circRNAs by editing their back-splicing sites for functional study.

January: Fang and Li have contributed an article in Mol Cell. Well done!

This study sought a method to synthesize immunogenicity-free, short dsRNA-containing RNA circles as PKR inhibitors, and raise a possibility that extra nucleotides in IVT circRNA is the key to triger cellular immune responses.

2021

November: Fang has passed the dissertation defense! Congratulations!

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August: Yun-Ni, Wei, Fang, Jia and Li have contributed an article in Sci China Life Sci. Well done!

This study reports that many circular intronic RNAs (ciRNAs) contain high GC% and tend to form DNA:RNA hybrids (R-loops) for RNase H1 cleavage, a process that appears to promote Pol II transcriptional elongation at ciRNA-producing loci.

August: Guo-Wei, Fang, Guo-Hua and Li have contributed an article in Genome Biology. Congratulations to Guo-Wei, Fang, Guo-Hua and Li!

This study developed a method to identify, evaluate, and quantify cleavage and polyadenylation sites(PASs) from 3′ tag-based scRNA-seq.

July: Fang and Li have contributed an article in Science. Well done! Congratulations to Fang and Li! Looking forward to the next masterpiece!

This study report that the sno-lncRNA SLERT is an RNA regulator that controls the biophysical properties of FC/DFCs by DDX21 and thus ribosomal RNA production.

May: Wei has passed the dissertation defense! Congratulations!

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May: Congratulations to Wei, Jia, Yun-Ni and Li for their contribution to a work published in Nat Cell Biol. Well done!

This study constructs a transformer BE (tBE) system that induces efficient editing with only background levels of genome-wide and transcriptome-wide OT mutations.

May: Guo-Wei and Li have contributed an article in Cell Reports. Congratulations to Guo-Wei and Li!

April: Li has been selected as the 2020 Highly Cited Chinese Researchers (released by Elsevier). Congratulations to Li!

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February: Congratulations to Xu-Kai, Wei and Li for their contribution to a method paper published in Methods. Well done!

This review provides a step-by-step protocol to annotate and quantify circRNAs from RNA-seq datasets, by using a series of CIRCexplorer pipelines.

February: Fang and Li have contributed an article in Methods. Congratulations to Fang and Li!

This method paper describes the experimental protocol and computational pipeline unique for circular RNA secondary structural assembly in living cells.

January: Congratulations to Wei, Xu-Kai and Li for their contribution to a review article published in Sci. China Life Sci. Well done!

This review highlights current understanding of back splicing regulation during nascent RNA synthesis by taking advantage of metabolic tagging nascent RNA sequencing. The faster Pol II transcription, the more back-splicing for circRNA biogenesis.

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2020

December: Congratulations to Wei, Yun-Ni, Jia and Li for their contribution to a work published in Nat Methods. Well done!

This study establishs CRISPR–RfxCas13d as a useful tool for the discovery and functional study of circRNAs at both individual and large-scale levels.

December: Xu-Kai has been selected into the "Super Postdoctoral Fellow" program of Shanghai. Congratulations to Xu-Kai.

November: Ying has passed the dissertation defense! Congratulations!

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November: Meng-Ran has passed the dissertation defense! Congratulations!

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November: Xu-Kai and Li have contributed an article in Chemistry of Life. Congratulations to Xu-Kai and Li .

This paper introduces the study that nonconserved RNA processing of conserved lncRNAs contribute to their functional evolution.

June: Xu-Kai has passed the dissertation defense! Congratulations!

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June: Jia-Lin has passed the dissertation defense! Congratulations!

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June: Ying, Yi-Chun, Jia and Li has contributed an article in Cell Rep. Congratulations to Ying, Yi-Chun, Jia and Li!

This work reported the development and application of a new base editor system, BEACON, which combines dCas12a with human APOBEC3A or its engineering version. BEACON induced efficient editing in cells and mouse embryos with basal levels of DNA damage response, RNA off-target mutations and unintended side-products. In the study, a new RNA-editing analysis-pipeline to decode all-twelve-types of RNA-editing, referred to as RADAR, was also constructed to decode any RNA editing, predominantly A-to-I, events in RNA-seq datasets, and to evaluate C-to-U off-target editing in the treatment with BEs.

June: Ying and Li has contributed an article in Nat Biotechnol. Congratulations to Ying and Li!

Ying and Li involved in this work to profile clinically-relevant variants in human, which can be potentially targeted by the reported dual adenine and cytosine base editor.

April: He-Na and Li has contributed an article in BMC Biology. Congratulations to He-Na and Li!

This work identifies ~ 1000 candidate m5C sites in the wider transcriptome, most in mRNAs, and further reveals a functional interdependence of cytosine methylation level with mRNA translation.

April: Xu-Kai and Li have contributed an article in Cell. Well done! Congratulations to Xu-Kai and Li! Looking forward to the next masterpiece!

This study suggests how conserved lncRNAs may achieve functional evolution through nonconserved RNA processing.

January: Xu-Kai, Meng-Ran and Li has contributed an article in Genomics Proteomics Bioinformatics. Congratulations to Xu-Kai, Meng-Ran and Li!

2019

December: Li has contributed a preview in Cell. Congratulations to Li.

October: Ying, Yi-Chun, Jia and Li has contributed an article in Genome Biol. Congratulations to Ying, Yi-Chun, Jia and Li!

September: Xu-Kai and Li have contributed an article in Theranostics. Congratulations to Xu-Kai and Li.

September: Ying and Li have contributed an article in Mol Cell. Congratulations to Ying and Li.

August: Congratulations to Li for winning The National Science Fund for Distinguished Young Scholars! Cheers!!!

June: Welcome new Research Associate Shi-Yi to join our group!

May: Yang lab and Chen lab had fun at Shanghai Disneyland on the 520 Day!

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April: Fang, Wei, Kai-Ge and Li have contributed an article in Cell. Well done! Congratulations to Fang, Wei, Kai-Ge and Li! Looking forward to the next masterpiece!

April: Li has contributed a review in CRISPR J. Congratulations to Li.

April: Li has contributed a news & views in Nat Biotechnol. Congratulations to Li.

March: Wei’s first child was born on 3/22! Congratulations on Wei's sweet angel!

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January: Rui, Xu-Kai and Li have contributed a chapter of Epitranscriptomics. Congratulations!

2018

December: Welcome new graduate students Yun-Ni and Pei-Hong to join our group!

November: Zheng has passed the dissertation defense! Congratulations to Zheng!

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September: Yang lab and Chen lab had a wonderful time together in the trampoline park.

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September: Meng-Ran and Li have contributed an article in Nat Cell Biol. Congratulations to Meng-Ran and Li.

September: Rui, Xu-Kai, Guo-Wei and Li have contributed a database article in Genomics Proteomics Bioinformatics. Congratulations to Rui, Xu-Kai, Guo-Wei and Li.

August: Ying, Jia and Li have contributed an article in Nat Biotechnol. Congratulations to Ying, Jia and Li.

August: Zheng and Li have contributed an article in PLoS Biol. Congratulations.

July: Li has contributed a review in Mol Cell. Congratulations to Li.

July: Welcome new Research Associate Yi-Chun to join our group!

May: Qin has passed the dissertation defense! Congratulations!

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March: Ying, Jia and Li have contributed an article in Nat Biotechnol. Congratulations to Ying, Jia and Li.

January: Jian-Feng, Qin and Li have contributed a short article in Mol Cell. Congratulations to Jian-Feng, Qin and Li.

2017

December: Wei, Jia and Li have contributed an article in Nat Struct Mol Biol. Congratulations to Wei, Jia and Li.

Novermber: Zheng and Li have contributed an article in Mol Cell. Congratulations to Zheng and Li.

Novermber: Li has contributed a perspectives in Science. Congratulations to Li.

October: Our lab participated in city hiking and won the second and forth prizes.

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August: Wei, Jia and Li have contributed a letter in Cell Res. Congratulations to Wei, Jia and Li.

June: Qin, Ying and Li have contributed a mini review in Quantitative Biology. Congratulations to Qin, Ying and Li.

July: Congratulations on our recent Mol Cell paper! Our paper has been selected as “Featured Article” of the issue. Moreover, the first authors of the paper were invited to take part in “Meet the Authors” section on the Mol Cell website to share their experience and the stories behind the paper. Congratulations to Wei again!

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June: Li has contributed a review in Trends Genet. Congratulations to Li.

June: Wei, Jia and Li have contributed an article in Mol Cell. Congratulations to Wei, Jia and Li!

May: Rui has passed the dissertation defense! He becomes the Ph.D graduate of our lab! Congratulations to Rui!

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May: Rui and Li have contributed an article in Cell. Congratulations to Rui and Li!

February: Li has contributed a review in Trends Cell Biol. Congratulations to Li!

January: Jian-Feng, Qin and Li have contributed an article in Cell Disc. Congratulations to Jian-Feng, Qin and Li!

2016

December: Rui, Xu-Kai and Li have contributed an article in RNA Biol. Congratulations to Rui, Xu-Kai and Li!

Novermber: Xu-Kai, Zheng and Li took part in the Cold Spring Harbor Asia conference on RNA Biology and Li delivered a presentation.

Novermber: Rui and Wei participated in Cell Symposia Functional RNAs and Rui presented his latest public researches in the poster presentations.

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November: Our lab participated in city hiking and won the third prize.

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October: Zheng, Jian-Feng and Li have contributed an article in Mol Cell. Congratulations to Zheng, Jian-Feng and Li!

The authors have employed a variety of techniques including RNA immunoprecipitation and deep sequencing to explore the repertoire of snoRNA related lncRNAs. These approaches allowed the authors to identify a type of polycistronic transcript derived lncRNAs that are 5' snoRNA capped and 3' polyadenylated (SPAs). SPA processing is associated with nascent mRNA 3’ processing and kinetic competition between XRN2 trimming and Pol II elongation. Following cleavage/polyadenylation of its upstream gene, the downstream uncapped pre-SPA is trimmed by XRN2 until this exonuclease reaches the co-transcriptionally assembled snoRNP. This snoRNP complex prevents further degradation, generates a novel 5' end and allows continuous Pol II elongation. The imprinted 15q11-q13 encodes two SPAs that are deleted in Prader-Willi syndrome (PWS) patients. These PWS region SPAs, together with previously identified sno-lncRNAs (Yin et al., Mol Cell, 2012) form a nuclear accumulation that is enriched in multiple RNA binding proteins (RBPs) including TDP43, RBFOX2 and hnRNP M. Generation of a human PWS cellular model by depleting these lncRNAs results in altered patterns of RBPs binding and alternative splicing. Prader-Willi Syndrome is a multiple-system human disorder including global developmental delay, mental retardation, morbid obesity, and etc. These findings thus implicated previously unannotated class of lncRNAs in PWS pathogenesis during early embryonic development and adulthood.

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October: Zheng, Qin and Li have contributed a preview in Mol Cell. Congratulations to Zheng, Qin and Li.

September: Rui has obtained National Scholarship for Outstanding Graduate Student, Ministry of Education of the People's Republic of China. Congratulations to Rui!

July: Rui took part in the second circular RNA Research Forum and delivered a presentation.

June: Rui and Wei participated in the 2016 joint annual meeting of the RNA Society and the RNA Society of Japan and presented their latest public researches in the poster presentations.

June: We have published a collaborative work with Chen Lab in Genome Res. Congratulations to Xiao-Ou, Rui, Jia-Lin, Zheng and Li.

May: Xiao-Ou has passed the dissertation defense! He becomes the first Ph.D graduate of our lab! Congratulations to Xiao-Ou!

April: Welcome new graduate student Meng-Ran to join our group!

April: Our lab has contributed an article in Cell Reports. Congratulations to Wei, Jia-Lin and Li.

March: Our lab has contributed a letter in Cell Res. Congratulations to Rui, Xiao-Ou, Xu-Kai and Li.

March: Xiao-Ou has obtained 2016 Shanghai outstanding graduates and 2016 Shanghai tri-merit student honor award. Congratulations to Xiao-Ou.

March: Welcome new graduate students Kai-Xuan and Ying to join our group!

January: Li has contributed a chapter of Long Non-Coding RNAs. Congratulations to Li!

January: Rui and Li have contributed an article in Cell Res. Congratulations to Rui and Li!

2015

December: We welcome new Research Associate Jia to join our group!

October: Li has contributed a review on lncRNA biogenesis in WIREs RNA. Congratulations to Li.

August: Li has contributed an article in Genome Res. Congratulations to Li!

August: Xiao-Ou has been selected as a recipient of the 2015 Ray Wu Prize for Excellent in Life Sciences. Congratulations to Xiao-Ou!

August: Li has contributed a review in Curr Opin Genet Dev. Congratulations to Li!

July: We have published a collaborative work on haploid embryonic stem cells with Yang Lab in Cell Stem Cell. Congratulations to Rui and Li.

June: Li and Ling-Ling have contributed a preview in Mol Cell.

April: Li and Ling-Ling have contributed a review on circRNA biogenesis in RNA Biology.

April: We welcome new graduate students Xu-Kai and Jia-Lin to join our group!

April: Our website has been updated with wholly new engine and templates. Cheer Up!

March: We have published a collaborative work with Chen Lab in Genes & Dev. Congratulations to Wei and Li.

2014

December: Zheng has passed his prelim! Congratulations to Zheng!

September: We have published a collaborative work on circular RNAs with Chen Lab in Cell. Congratulations to Xiao-Ou and Li.

May: We have published a collaborative work on sno-lncRNAs with Chen Lab in BMC Genomics. Congratulations to Xiao-Ou and Li.

May: Rui and Qin of our group have passed the mid-term review. Congratulations to Rui and Qin!

April: Welcome new graduate student Zheng to join our group!

March: We have published a collaborative work with Chen Lab in BMC Genomics. Congratulations to Xiao-Ou and Li.

2013

December: Rui and Qin of our group have passed their prelim. Congratulations to Rui and Qin!

October: Hua-Hong has a cute baby boy. Cheer up!

September: We have published a collaborative work on circular intronic RNAs with Chen Lab in Mol Cell. Congratulations to Xiao-Ou, Shanshan and Li.

August: Our sno-lncRNA paper published in Mol Cell was recently selected as one of Best of 2012 by Mol Cell.

June: Xiao-Ou has obtained the Best Poster Awards in The 2013 CAS-MPG Partner Institute for Computational Biology Scientific Exchange Meeting. Congratulations to Xiao-Ou!

March: Xiao-Ou has passed his mid-term evaluation. Congratulations to Xiao-Ou!

April: We have published a collaborative work on RNA editing with Chen Lab in BMC Genomics. Congratulations to Shanshan and Li.

April: We welcome new graduate students Rui and Qin to join our group!

February: Our invited review on long noncoding RNAs was published. Congratulations to Shanshan, Xiao-Ou, Li!

2012

December: Li was invited to give comments on Diffculties in RNA editing study in Nat Biotechnol. Congratulations to Li!

December: Congratulations to Xiao-Ou for passing his prelim!

October: We published a collaborative work on sno-lncRNA with Chen Lab in Mol Cell. Congratulations to Li.

October: Chen Lab and our lab had an enjoyable joint lab retreat in Suzhou.


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