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[59] Liu L, Liu Z, Liu Q, Wu W, Lin P, . . . Luo J, Rich JN, Xie Q, Jiang T,Chen R. LncRNA INHEG promotes glioma stem cell maintenance and tumorigenicity through regulating rRNA 2'-O-methylation.Nat Commun2023; 14(1): 7526.

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[57] Yue H, Li A, Tang Y,Chen R. TapHi-C for profiling genome-wide chromosome conformation capture.Trends Plant Sci2023; 28(10): 1192-3.

[56] Yang Z, Zeng X, Zhao Y,Chen R. AlphaFold2 and its applications in the fields of biology and medicine.Signal Transduct Target Ther2023; 8(1): 115.

[55] Zheng Y, Luo H, Teng X, . . . Zhao Y,Chen R, He S. NPInter v5.0: ncRNA interaction database in a new era.Nucleic Acids Res2023; 51(D1): D232-D9.

[54] Zhang L, Badai J, Wang G, Ru X, . . . Feng H,Chen R, Zhao Y, Chen Y. Discovering hematoma-stimulated circuits for secondary brain injury after intraventricular hemorrhage by spatial transcriptome analysis.Frontiers in immunology2023; 14: 1123652.

[53] Zhang C, Wang D, Hao Y, Wu S, Luo J, . . . Fu XD, Yang X,Chen R, Teng Y. LncRNA CCTT-mediated RNA-DNA and RNA-protein interactions facilitate the recruitment of CENP-C to centromeric DNA during kinetochore assembly.Mol Cell2022; 82(21): 4018-32 e9.

[52] Zhang Y, Qiao X, Liu L, . . . He S,Chen R, Chen C. Long noncoding RNA MAGI2-AS3 regulates the H2O2 level and cell senescence via HSPA8.Redox Biol2022; 54: 102383.

[51] Yang B, Zhang Y, Sun L, . . .Chen R, Luo J, Wang T, Jiang J, Qin Y. Modulated ultrasmall γ-Fe2O3 nanocrystal assembles for switchable magnetic resonance imaging and photothermal-ferroptotic-chemical synergistic cancer therapy.Advanced Functional Materials2022.

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[49] Cui X, Zhang R, Yang Y, Wu E, . . . Sun J, Luo J, Zhang S,Chen R, Xi JJ. Identification and characterization of long non-coding RNA Carip in modulating spatial learning and memory.Cell Rep2022; 38(8): 110398.

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[47] Zhang Q, Wu E, Tang Y, Cai T, . . . Luo J,Chen R, Yang F. Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs.Mol Cell Proteomics2021; 20: 100109.

[46] Xue H, Niu Y, Segraves K, Nie R, Hao Y, Zhang L, . . .Chen R, Yang X. The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae).BMC Genomics2021; 22(1): 243.

[45] Wu E, Guo X, Teng X, Zhang R, . . . Luo J, Wang J,Chen R. Discovery of Plasma Membrane-Associated RNAs through APEX-seq.Cell Biochem Biophys2021; 79(4): 905-917.

[44] Li Y, Zhou H, Chen X, Zheng Y, . . . Luo H, Hao Y,Chen R, Zhang P, He S. SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling.Genomics Proteomics Bioinformatics2021; 19(4): 602-610.

[43] Lai C, Liu L, Liu Q, Wang K, Cheng S, . . . Luo J, Wang X,Chen R, Yang P. Long noncoding RNA AVAN promotes antiviral innate immunity by interacting with TRIM25 and enhancing the transcription of FOXO3a.Cell Death Differ2021; 28(10): 2900-2915.

[42] Wang D, Zhou Z, Wu E, Ouyang C, Wei G, . . . Reed SH, Luo J,Chen R. LRIK interacts with the Ku70-Ku80 heterodimer enhancing the efficiency of NHEJ repair.Cell Death Differ2020; 27(12): 3337-3353.

[41] Fan Z, Chen X, Liu L, Zhu C, Xu J, . . . Cui Y, Zhang X,Chen R. Association of the Polymorphism rs13259960 in SLEAR With Predisposition to Systemic Lupus Erythematosus.Arthritis Rheumatol2020; 72(6): 985-996.

[40] Hao Y, Wang D, Wu S, Li X, . . . Fu XD,Chen R, He S. Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division.Genome Res2020; 30(11): 1570-1582.

[39] Wu S, Wu E, Wang D, Niu Y, Yue H, Zhang D, Luo J,Chen R. LncRNA HRCEG, regulated by HDAC1, inhibits cells proliferation and epithelial-mesenchymal-transition in gastric cancer.Cancer Genet2020; 241: 25-33.

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[37] Fan Z,Chen R, Chen X. SpatialDB: a database for spatially resolved transcriptomes.Nucleic Acids Res2020; 48(D1): D233-D237.

[36] Wang Y, Zhu P, Luo J, Wang J, Liu Z, Wu W, . . .Chen R, Tian Y, Fan Z. LncRNA HAND2-AS1 promotes liver cancer stem cell self-renewal via BMP signaling.EMBO J2019: e101110.

[35] Chen X, Hao Y, Cui Y, Fan Z,Chen R. LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes.Methods Mol Biol2019; 1870: 189-198.

[34] Wang J, Zhang P, Lu Y, Li Y, Zheng Y, Kan Y,Chen R, He S. piRBase: a comprehensive database of piRNA sequences.Nucleic Acids Res2019; 47(D1): D175-D180.

[33] Ye B, Liu B, Yang L, Zhu X, Zhang D, Wu W, . . .Chen R, Tian Y, Fan Z. LncKdm2b controls self-renewal of embryonic stem cells via activating expression of transcription factor Zbtb3.EMBO J2018; 37(8).

[32] Wang Y, Zhu P, Wang J, Zhu X, Luo J, Meng S, . . .Chen R, Tian Y, Fan Z. Long noncoding RNA LncHand2 promotes liver repopulation via c-Met signaling.J Hepatol2018; 69(4): 861-872.

[31] Fang S, Zhang L, Guo J, Niu Y, Wu Y, Li H, . . .Chen R, Zhao Y. NONCODEV5: a comprehensive annotation database for long non-coding RNAs.Nucleic Acids Res2018; 46(D1): D308-D314.

[30] Hao Y, Zhang L, Niu Y, Cai T, Luo J, He S, . . .Chen R. SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci.Brief Bioinform2018; 19(4): 636-643.

[29] Cui Y, Chen X, Niu Y, Wang D, Luo H, Fan Z, . . .Chen R. Dynamic-BM: multispecies Dynamic BodyMap database from temporal RNA-seq data.Brief Bioinform2018; 19(6): 1302-1309.

[28] Yan X, Zhang D, Wu W, Wu S, Qian J, Hao Y, . . .Chen R, Fan Z. Mesenchymal Stem Cells Promote Hepatocarcinogenesis via lncRNA-MUF Interaction with ANXA2 and miR-34a.Cancer Res2017; 77(23): 6704-6716.

[27] Wang Z, Hao Y, Zhang C, Wang Z, Liu X, Li G, . . .Chen R, Jiang T. The Landscape of Viral Expression Reveals Clinically Relevant Viruses with Potential Capability of Promoting Malignancy in Lower-Grade Glioma.Clin Cancer Res2017; 23(9): 2177-2185.

[26] Sun Y, Wei G, Luo H, Wu W, Skogerbo G, Luo J,Chen R. The long noncoding RNA SNHG1 promotes tumor growth through regulating transcription of both local and distal genes.Oncogene2017; 36(49): 6774-6783.

[25] Liu B, Ye B, Yang L, Zhu X, Huang G, Zhu P, . . .Chen R, Tian Y, Fan Z. Long noncoding RNA lncKdm2b is required for ILC3 maintenance by initiation of Zfp292 expression.Nat Immunol2017; 18(5): 499-508.

[24] Chen X, Hao Y, Cui Y, Fan Z, He S, Luo J andChen R. LncVar: a database of genetic variation associated with long non-coding genes.Bioinformatics2017; 33: 112-118.

[23] Zhao Y, Li H, Fang S, Kang Y, Wu W, Hao Y, . . .Chen R. NONCODE 2016: an informative and valuable data source of long non-coding RNAs.Nucleic Acids Res2016; 44: D203-208.

[22] Liu L, Yue H, Liu Q, Yuan J, Li J, Wei G, . . .Chen R. LncRNA MT1JP functions as a tumor suppressor by interacting with TIAR to modulate the p53 pathway.Oncotarget2016; 7: 15787-15800.

[21] Cui Y, Chen X, Luo H, Fan Z, Luo J, He S, . . .Chen R. BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications.Bioinformatics2016; 32: 1740-1742.

[20] Xiao T, Liu L, Li H, Sun Y, Luo H, Li T, . . .Chen R. Long Noncoding RNA ADINR Regulates Adipogenesis by Transcriptionally Activating C/EBPalpha.Stem Cell Reports2015; 5: 856-865.

[19] Wang Y, He L, Du Y, Zhu P, Huang G, Luo J, . . .Chen R, Fan Z. The Long Noncoding RNA lncTCF7 Promotes Self-Renewal of Human Liver Cancer Stem Cells through Activation of Wnt Signaling.Cell Stem Cell2015; 16: 413-425.

[18] Yuan J, Wu W, Xie C, Zhao G, Zhao Y andChen R. NPInter v2.0: an updated database of ncRNA interactions.Nucleic Acids Res2014; 42: D104-108.

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[16] Lu X, Wang L, Chen S, He L, Yang X, Shi Y, . . .Chen R, . . . Coronary ADG-WR. Genome-wide association study in Han Chinese identifies four new susceptibility loci for coronary artery disease.Nature Genetics2012; 44: 890-4.

[15] Wang Y, Chen J, Wei G, He H, Zhu X, Xiao T, . . .Chen R. The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression.Nucleic Acids Res 2011; 39: 5203-5214.

[14] Zhao Y, He S, Liu C, Ru S, Zha H, Yang Z, . . .Chen R. MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control.Trends in Genetics2008; 24: 323-327.

[13] He S, Su H, Liu C, Skogerbo G, He H, He D, . . .Chen R. MicroRNA-encoding long non-coding RNAs.BMC Genomics2008; 9: 236

[12] Aftab MN, He H, Skogerbo G andChen R. Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins.BMC Genomics2008; 9: 278.

[11] He H, Wang J, Liu T, Liu XS, Li T, Wang Y, . . .Chen R. Mapping the C-elegans noncoding transcriptome with a whole-genome tiling microarray.Genome Res 2007; 17: 1471-1477.

[10] Zhang Z, Liu C, Skogerbo G, Zhu X, Lu H, Chen L, . . .Chen R. Dynamic changes in subgraph preference profiles of crucial transcription factors.Plos Computational Biology2006; 2: 383-391.

[9] Zhang Y, Li S, Skogerbo G, Zhang Z, Zhu X, Zhang Z, . . .Chen R. Phylophenetic properties of metabolic pathway topologies as revealed by global analysis.BMC Bioinformatics2006; 7:

[8] Muzny D, Scherer S, Kaul R, Wang J, Yu J, Sudbrak R, . . .Chen R, . . .Gibbs R. The DNA sequence, annotation and analysis of human chromosome 3.Nature2006; 440: 1194-1198.

[7] He H, Cai L, Skogerbo G, Deng W, Liu T, Zhu X, . . .Chen R. Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray.Nucleic Acids Res 2006; 34: 2976-2983.

[6] Deng W, Zhu X, Skogerbo G, Zhao Y, Fu Z, Wang Y, . . .Chen R. Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression.Genome Res 2006; 16: 20-29.

[5] Liu C, Bai B, Skogerbo G, Cai L, Deng W, Zhang Y, . . .Chen R. NONCODE: an integrated knowledge database of non-coding RNAs.Nucleic Acids Res 2005; 33: D112-D115.

[4] Yu J, Hu S, Wang J, Wong G, Li S, Liu B, . . .Chen R, . . . Yang H. A draft sequence of the rice genome (Oryza sativa L. ssp indica).Science2002; 296: 79-92.

[3] Bu D, Zhao Y, Cai L, Xue H, Zhu X, Lu H, . . .Chen R. Topological structure analysis of the protein-protein interaction network in budding yeast.Nucleic Acids Res2003; 31: 2443-2450.

[2] Bao Q, Tian Y, Li W, Xu Z, Xuan Z, Hu S, . . .Chen R, . . . Yang H. A complete sequence of the T tengcongensis genome.Genome Res 2002; 12: 689-700.

[1] Li W, Fang W, Ling L, Wang J, Xuan Z andChen R. Phylogeny Based on Whole Genome as inferred from Complete Information Set Analysis.Journal of Biological Physics2002; 28: 439-447.

（资料来源：陈润生院士，2024-07-30）