Shurong Liu+, Junhong Huang+, Jie Zhou, Siyan Chen, Wujian Zheng, Chang Liu, Qiao Lin, Ping Zhang, Di Wu, Simeng He, Jiayi Ye, Shun Liu, Keren Zhou, Bin Li*, Lianghu Qu* & Jianhua Yang* . NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions. Nat Commun 15, 2425 (2024). https://doi.org/10.1038/s41467-024-46596-y (* Correspondence Author, +Co-first author)

Xuan J, Chen L, Chen Z, Pang J, Huang J, Lin J, Zheng L, Li B*, Qu L*, Yang J*. RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications. Nucleic Acids Res. 2024 Jan 5;52(D1):D273-D284. doi: 10.1093/nar/gkad1070. (* Correspondence Author)

Li B+, Liu S+, Zheng W+, Liu A+, Yu P+, Wu D, Zhou J, Zhang P, Liu C, Lin Q, Ye J, He S, Huang Q, Zhou H, Chen J, Qu L*, Yang J*. (2023). RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators. Nature Biotechnology. 2024 Jan;42(1):119-131. doi: 10.1038/s41587-023-01749-0. Epub 2023 Apr 10. (* Correspondence Author, +Co-first author)

Li B, Qu L*, Yang J*. RNA-Guided RNA Modifications: Biogenesis, Functions, and Applications. Accounts of Chemical Research, 2023 Nov 21;56(22):3198-3210. doi: 10.1021/acs.accounts.3c00474. Epub 2023 Nov 6.(* Correspondence Author, Invited review paper)

Zhang P+, Huang J+, Zheng W, Chen L, Liu S, Liu A, Ye J, Zhou J, Chen Z, Huang Q, Liu S, Zhou K, Qu L*, Li B*, Yang J*. Single-base resolution mapping of 2'-O-methylation sites by an exoribonuclease-enriched chemical method. Sci China Life Sci. 2023 Apr;66(4):800-818. (* Correspondence Author, +Co-first author)

Xu W+, Liu C+, Deng B+, Lin P+, Sun Z, Liu A, Xuan J, Li Y, Zhou K, Zhang X, Huang Q, Zhou H, He Q, Li B*, Qu L*, Yang J*. TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation. Genome Res. 2022 Jun;32(6):1026-1041. (* Correspondence Author, +Co-first author)

Liu S, Li B, Liang Q, Liu A, Qu L*, Yang J*. Classification and function of RNA-protein interactions. Wiley Interdiscip Rev RNA. 2020 Nov;11(6):e1601. doi: 10.1002/wrna.1601.(* Correspondence Author, Invited review paper)

Huang H+, Weng H+, Zhou K+, Wu T+, Zhao B. S+, Sun M, Chen Z, Deng X, Xiao G, Auer F, Klemm L, Wu H, Zuo Z, Qin X, Dong Y, Zhou Y, Qin H, Tao S, Du J, Liu J, Lu Z, Yin H, Mesquita A, Yuan C. L, Hu Y.-C, Sun W, Su R, Dong L, Shen C, Li C, Qing Y, Jiang X, Wu X, Sun M, Guan J.-L, Qu L, Wei M, Müschen M, Huang G*, He C*, Yang J*, Chen J*. Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally. Nature. 2019 Mar;567(7748):414-419. (* Correspondence Author, +Co-first author) Highlight in Nature Reviews Genetics & Highlight in Nature Chemical Biology.

Deng B+, Xu W+, Wang Z, Liu C, Lin P, Li B, Huang Q, Yang J*, Zhou H*, Qu L*. An LTR retrotransposon-derived lncRNA interacts with RNF169 to promote homologous recombination.EMBO Rep. 2019 Sep 5:e47650. (* Correspondence Author, +Co-first author) Highlight in EMBO Reports.

Huang H+, Weng H+, Sun W+, Qin X+, Shi H+, Wu H, Zhao BS, Mesquita A, Liu C, Yuan CL, Hu YC, Hüttelmaier S, Skibbe JR, Su R, Deng X, Dong L, Sun M, Li C, Nachtergaele S, Wang Y, Hu C, Ferchen K, Greis KD, Jiang X, Wei M, Qu L, Guan JL, He C*, Yang J*, Chen J*. Recognition of RNA N(6)-methyladenosine by IGF2BP proteins enhances mRNA stability and translation. Nature Cell Biology. 2018 Mar;20(3):285-295. (* Correspondence Author, +Co-first author) ESI Highly Cited Paper, News & Views in Nature Cell Biology.

Qu L+, Wang ZL+, Chen Q+, Li YM+, He HW, Hsieh JJ, Xue S, Wu ZJ, Liu B, Tang H, Xu XF, Xu F, Wang J, Bao Y, Wang AB, Wang D, Yi XM, Zhou ZK, Shi CJ, Zhong K, Sheng ZC, Zhou YL, Jiang J, Chu XY, He J, Ge JP, Zhang ZY, Zhou WQ*, Chen C*, Yang JH*, Sun YH*, Wang LH*. Prognostic Value of a Long Non-coding RNA Signature in Localized Clear Cell Renal Cell Carcinoma. European Urology 2018 Dec;74(6):756-763. (* Correspondence Author, +Co-first author) Highlight in European Urology

Bao X, Guo X, Yin M, Tariq M, Lai Y, Kanwal S, Zhou J, Li N, Lv Y, Pulido-Quetglas C, Wang X, Ji L, Khan MJ, Zhu X, Luo Z, Shao C, Lim DH, Liu X, Li N, Wang W, He M, Liu YL, Ward C, Wang T, Zhang G, Wang D, Yang J, Chen Y, Zhang C, Jauch R, Yang YG, Wang Y, Qin B, Anko ML, Hutchins AP, Sun H, Wang H, Fu XD, Zhang B, Esteban MA. Capturing the interactome of newly transcribed RNA. Nat Methods. 2018 Mar;15(3):213-220.

Weng H, Huang H, Wu H, Qin X, Zhao BS, Dong L, Shi H, Skibbe J, Shen C, Hu C, Sheng Y, Wang Y, Wunderlich M, Zhang B, Dore LC, Su R, Deng X, Ferchen K, Li C, Sun M, Lu Z, Jiang X, Marcucci G, Mulloy JC, Yang J, Qian Z, Wei M, He C, Chen J. METTL14 Inhibits Hematopoietic Stem/Progenitor Differentiation and Promotes Leukemogenesis via mRNA m(6)A Modification. Cell Stem Cell.2018 Feb 1;22(2):191-205.ESI Highly Cited Paper, Highlight in Cell Stem Cell, Top 10 Papers of 2018 Cell Stem Cell.

Wang ZL+, Li B+, Luo YX, Lin Q, Liu SR, Zhang XQ, Zhou H, Yang JH*#, Qu LH*. Comprehensive Genomic Characterization of RNA-Binding Proteins across Human Cancers. Cell Reports. 2018 Jan 2;22(1):286-298. (* Correspondence Author & #Lead Contact, +Co-first author)

Zheng LL+, Zhou KR+, Liu S, Zhang DY, Wang ZL, Chen ZR, Yang JH*, Qu LH*. dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease. Nucleic Acids Res. 2018 Jan 4;46(D1):D85-D91. (* Correspondence Author, +Co-first author)

Xuan JJ, Sun WJ, Lin PH, Zhou KR, Liu S, Zheng LL, Qu LH*, Yang JH*. RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data. Nucleic Acids Res. 2018 Jan 4;46(D1):D327-D334. (* Correspondence Author)ESI Highly Cited Paper

Zhang XQ*+, Wang ZL+, Poon MW+, Yang JH*. Spatial-temporal transcriptional dynamics of long non-coding RNAs in human brain. Hum Mol Genet. 2017 Aug 15;26(16):3202-3211.(* Correspondence Author, +Co-first author)

Zheng LL, Deng KW, Deng AC, Wu J, Yang JH, Lun ZR, Qu LH. Exo-miRExplorer: A Comprehensive Resource for Exploring and Comparatively Analyzing Exogenous MicroRNAs. Front Microbiol. 2017 Feb 1;8:126.

Zhou KR, Liu S, Sun WJ, Zheng LL, Zhou H, Yang JH*, Qu LH*. ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. Nucleic Acids Res. 2017 Jan 4;45(D1):D43-D50. (* Correspondence Author)ESI Highly Cited Paper

Huang ZP, Ding Y, Chen J, Wu G, Kataoka M, Hu Y, Yang JH, Liu J, Drakos SG, Selzman CH, Kyselovic J, Qu LH, Dos Remedios CG, Pu WT, Wang DZ. Long non-coding RNAs link extracellular matrix gene expression to ischemic cardiomyopathy. Cardiovasc Res. 2016 Aug 24. pii: cvw201.

Guo YH, Wang LQ, Li B, Xu H, Yang JH, Zheng LS, Yu P, Zhou AD, Zhang Y, Xie SJ, Liang ZR, Zhang CM, Zhou H, Qu LH. Wnt/β-catenin pathway transactivates microRNA-150 that promotes EMT of colorectal cancer cells by suppressing CREB signaling. Oncotarget. 2016 Jul 5;7(27):42513-4252

Zheng LL, Xu WL, Liu S, Sun WJ, Li JH, Wu J, Yang JH*, Qu LH*. tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. Nucleic Acids Res. 2016 Jul 8;44(W1):W185-93. (* Correspondence Author)

Wang ZL+, Li B,+ Piccolo SR, Zhang XQ, Li JH, Zhou H, Yang JH*, Qu LH*. Integrative analysis reveals clinical phenotypes and oncogenic potentials of long non-coding RNAs across 15 cancer types. Oncotarget. 2016 Jun 7;7(23):35044-55. (* Correspondence Author,+Co-first author)

Zheng LL, Li JH, Wu J, Sun WJ, Liu S, Wang ZL, Zhou H, Yang JH*, Qu LH*. deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. Nucleic Acids Res. 2016 Jan 4;44(D1):D196-202. (* Correspondence Author) ESI Highly Cited Paper

Sun WJ, Li JH, Liu S, Wu J, Zhou H, Qu LH*, Yang JH*. RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data. Nucleic Acids Res. 2016 Jan 4;44(D1):D259-65. (* Correspondence Author)ESI Highly Cited Paper

Liu S, Li JH, Wu J, Zhou KR, Zhou H, Yang JH*, Qu LH*. StarScan: a web server for scanning small RNA targets from degradome sequencing data. Nucleic Acids Res. 2015 Jul 1;43(W1):W480-6. (* Correspondence Author)

Li JH, Liu S, Zheng LL, Wu J, Sun WJ, Wang ZL, Zhou H, Qu LH*, Yang JH*. Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets. Front Bioeng Biotechnol. 2015 Jan 14;2:88. (* Correspondence Author, research paper invited by Carlo Maria Croce)

Zhang YJ, Yang JH, Shi QS, Zheng LL, Liu J, Zhou H, Zhang H, Qu LH. Rapid birth-and-death evolution of imprinted snoRNAs in the Prader-Willi syndrome locus: implications for neural development in Euarchontoglires. PLoS One. 2014 Jun 19;9(6):e100329.

Gou LT+, Dai P+, Yang JH+, Xue Y, Hu YP, Zhou Y, Kang JY, Wang X, Li H, Hua MM, Zhao S, Hu SD, Wu LG, Shi HJ, Li Y, Fu XD, Qu LH, Wang ED, Liu MF. Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis. Cell Res. 2014 Jun;24(6):680-700. (+Co-first author)Cover Paper, Research Highlight in Cell Res

Wen JZ, Liao JY, Zheng LL, Xu H, Yang JH, Guan DG, Zhang SM, Zhou H, Qu LH. A contig-based strategy for the genome-wide discovery of microRNAs without complete genome resources. PLoS One. 2014 Feb 7;9(2):e88179.

Li JH, Liu S, Zhou H, Qu LH*, Yang JH*. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014 Jan;42:D92-7. (* Correspondence Author)ESI Highly Cited Paper

Wen JZ, Liao JY, Zheng LL, Xu H, Yang JH, Guan DG, Zhang SM, Zhou H, Qu LH. A Contig-Based Strategy for the Genome-Wide Discovery of MicroRNAs without Complete Genome Resources. PLoS One. 2014 Feb 7;9(2):e88179.

Yang JH, Li JH, Jiang S, Zhou H, Qu LH. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res. 2013 Jan;41:D177-87. ESI Highly Cited Paper

Xiao ZD, Diao LT, Yang JH, Xu H, Huang MB, Deng YJ, Zhou H, Qu LH. Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. Nucleic Acids Res. 2013 Jan 7;41(1):e5.

Zheng LL, Wen YZ, Yang JH, Liao JY, Shao P, Xu H, Zhou H, Wen JZ, Lun ZR, Ayala FJ, Qu LH. Comparative transcriptome analysis of small noncoding RNAs in different stages of Trypanosoma brucei. RNA. 2013 Jul;19(7):863-75.

Shao P, Liao JY, Guan DG, Yang JH, Zheng LL, Jing Q, Zhou H, Qu LH. Drastic expression change of transposon-derived piRNA-like RNAs and microRNAs in early stages of chicken embryos implies a role in gastrulation. RNA Biol. 2012 Feb;9(2):212-

Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res. 2011 Jan;39:D202-9. ESI Highly Cited Paper

Yang JH, Shao P, Zhou H, Chen YQ, Qu LH. deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res. 2010 Jan;38:D123-30.

Zhang Y, Guan DG, Yang JH, Shao P, Zhou H, Qu LH. ncRNAimprint: a comprehensive database of mammalian imprinted noncoding RNAs. RNA. 2010 Oct;16(10):1889-901.

Zhang H+, Yang JH+, Zheng YS+, Zhang P, Chen X, Wu J, Xu L, Luo XQ, Ke ZY, Zhou H, Qu LH, Chen YQ. Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach. PLoS One. 2009 4(9):e6849. (+ co-first author)

Shao P+, Yang JH+, Zhou H, Guan DG, Qu LH. Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs. BMC Genomics. 2009 Feb 22;10:86. (+ co-first author)

Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH. snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucleic Acids Res. 2006;34(18):5112-23.