1.Liu JZ, Li Y, Li J, Chen W, Pan BZ, Liu AZ, Xu ZF, Xu W, Liu CN: EupDB: An integrative and comprehensive functional genomics data hub for Euphorbiaceae plants. Plant Commun 2024, 5(1).
2.He LL, Liu Y, Mao YW, Wu XY, Zheng XL, Zhao WY, Mo XY, Wang RR, Wu Q, Wang DF et al: GRAS transcription factor PINNATE-LIKE PENTAFOLIATA2 controls compound leaf morphogenesis in Medicago truncatula. Plant Cell 2024.
3.Zhao JX, Wang S, Liu JZ, Jiang XD, Wen J, Suo ZQ, Liu J, Zhong MC, Wang Q, Gu ZR et al: A comparative full-length transcriptomic resource provides insight into the perennial monocarpic mass flowering. Plant Journal 2023.
4.Yang WJ, Bai QZ, Li Y, Chen JH, Liu CN: Epigenetic modifications: Allusive clues of lncRNA functions in plants. Computational and Structural Biotechnology Journal 2023, 21:1989-1994.
5.Mao YW, Zhou SL, Yang J, Wen JQ, Wang DF, Zhou X, Wu XY, He LL, Liu ML, Wu H et al: The MIO1-MtKIX8 module regulates the organ size in <i>Medicago truncatula</i>. Physiologia Plantarum 2023, 175(5).
6.Jiang LH, Yao BL, Zhang XY, Wu LX, Fu QJ, Zhao YT, Cao YX, Zhu RM, Lu XQ, Huang WY et al: Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal 2023, 115(1):155-174.
7.Zhao JP, Jiang LH, Bai HR, Dai YL, Li KX, Li SJ, Wang XR, Wu LX, Fu QJ, Yang YF et al: Characteristics of members of IGT family genes in controlling rice root system architecture and tiller development. Frontiers in Plant Science 2022, 13.
8.Wang RR, Lu N, Liu CG, Dixon RA, Wu Q, Mao YW, Yang YT, Zheng XL, He LL, Zhao BL et al: <i>MtGSTF7</i>, a TT19-like GST gene, is essential for accumulation of anthocyanins, but not proanthocyanins in <i>Medicago truncatula</i>. Journal of Experimental Botany 2022, 73(12):4129-4146.
9.Wang RR, Lu N, Liu CG, Dixon RA, Wu Q, Mao YW, Yang YT, Zheng XL, He LL, Zhao BL et al: MtGSTF7, a TT19-like GST gene, is essential for accumulation of anthocyanins, but not proanthocyanins in Medicago truncatula. Journal of Experimental Botany 2022, 73(12):4129-4146.
10.Wang J, Jiang XK, Bai HR, Liu CN: Genome-wide identification, classification and expression analysis of the JmjC domain-containing histone demethylase gene family in <i>Jatropha curcas</i> L. Scientific Reports 2022, 12(1).
11.Wang J, Jiang XK, Bai HR, Liu CN: Genome-wide identification, classification and expression analysis of the JmjC domain-containing histone demethylase gene family in Jatropha curcas L. Scientific Reports 2022, 12(1).
12.Su QX, Zhang X, Li J, Yang WJ, Ren Q, Gao XY, Liu CN: PPDP: A Data Portal of <i>Paris polyphylla</i> for Polyphyllin Biosynthesis and Germplasm Resource Exploration. Diversity-Basel 2022, 14(12).
13.Jin Q, Yang ZT, Yang WJ, Gao XY, Liu CN: Genome-Wide Identification and Analysis of Lbd Transcription Factor Genes in <i>Jatropha curcas</i> and Related Species. Plants-Basel 2022, 11(18).
14.Gao XY, Su QX, Yao BL, Yang WJ, Ma WS, Yang B, Liu CN: Development of EST-SSR Markers Related to Polyphyllin Biosynthesis Reveals Genetic Diversity and Population Structure in <i>Paris polyphylla</i>. Diversity-Basel 2022, 14(8).
15.Gao XY, Su QX, Yao BL, Yang WJ, Ma WS, Yang B, Liu CN: Development of EST-SSR Markers Related to Polyphyllin Biosynthesis Reveals Genetic Diversity and Population Structure in Paris polyphylla. Diversity-Basel 2022, 14(8).
16.Gao XY, Su QX, Li J, Yang WJ, Yao BL, Guo JW, Li SY, Liu CN: RNA-Seq analysis reveals the important co-expressed genes associated with polyphyllin biosynthesis during the developmental stages of <i>Paris polyphylla</i>. Bmc Genomics 2022, 23(SUPPL 1).
17.Gao XY, Su QX, Li J, Yang WJ, Yao BL, Guo JW, Li SY, Liu CN: RNA-Seq analysis reveals the important co-expressed genes associated with polyphyllin biosynthesis during the developmental stages of Paris polyphylla. Bmc Genomics 2022, 23(SUPPL 1).
18.Chen W, Li J, Huang SL, Li XD, Zhang X, Hu X, Xiang SL, Liu CN: GCEN: An Easy-to-Use Toolkit for Gene Co-Expression Network Analysis and lncRNAs Annotation. Current Issues in Molecular Biology 2022, 44(4):1479-1487.
19.Bai QZ, Yang WJ, Qin GC, Zhao BL, He LL, Zhang X, Zhao WY, Zhou DA, Liu Y, Liu Y et al: Multidimensional Gene Regulatory Landscape of Motor Organ Pulvinus in the Model Legume <i>Medicago truncatula</i>. International Journal of Molecular Sciences 2022, 23(8).
20.Bai QZ, Yang WJ, Qin GC, Zhao BL, He LL, Zhang X, Zhao WY, Zhou DA, Liu Y, Liu Y et al: Multidimensional Gene Regulatory Landscape of Motor Organ Pulvinus in the Model Legume Medicago truncatula. International Journal of Molecular Sciences 2022, 23(8).
21.Zhao YT, Wu LX, Fu QJ, Wang D, Li J, Yao BL, Yu S, Jiang L, Qian J, Zhou X et al: <i>INDITTO2</i> transposon conveys auxin-mediated <i>DRO1</i> transcription for rice drought avoidance. Plant Cell and Environment 2021, 44(6):1846-1857.
22.Zhao YT, Wu LX, Fu QJ, Wang D, Li J, Yao BL, Yu S, Jiang L, Qian J, Zhou X et al: INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant Cell and Environment 2021, 44(6):1846-1857.
23.Zhang X, Li J, Pan BZ, Chen W, Chen MS, Tang MY, Xu ZF, Liu CN: Extended mining of the oil biosynthesis pathway in biofuel plant <i>Jatropha curcas</i> by combined analysis of transcriptome and gene interactome data. Bmc Bioinformatics 2021, 22(SUPPL 6).
24.Zhang X, Li J, Pan BZ, Chen W, Chen MS, Tang MY, Xu ZF, Liu CN: Extended mining of the oil biosynthesis pathway in biofuel plant Jatropha curcas by combined analysis of transcriptome and gene interactome data. Bmc Bioinformatics 2021, 22(SUPPL 6).
25.Sang SY, Chen W, Zhang D, Zhang X, Yang WJ, Liu CN: Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants. Bmc Genomics 2021, 22(SUPPL 3).
26.Chen L, Li HM, Xie LX, Zuo ZJ, Tian LQ, Liu CN, Guo XQ: Editorial: Big Data and Machine Learning in Cancer Genomics. Frontiers in Genetics 2021, 12.
27.Wang J, Zhang X, Chen W, Hu X, Li J, Liu CN: Regulatory roles of long noncoding RNAs implicated in cancer hallmarks. International Journal of Cancer 2020, 146(4):906-916.
28.Li J, Zhang X, Liu CN: The computational approaches of lncRNA identification based on coding potential: Status quo and challenges. Computational and Structural Biotechnology Journal 2020, 18:3666-3677.
29.Li J, Gao XY, Zhang XA, Liu CN: Dynamic Expansion and Functional Evolutionary Profiles of Plant Conservative Gene Family SBP-Box in Twenty Two Flowering Plants and the Origin of miR156. Biomolecules 2020, 10(5).
30.Gao XY, Zhang X, Chen W, Li J, Yang WJ, Zhang XW, Li SY, Liu CN: Transcriptome analysis of Paris polyphylla var. yunnanensis illuminates the biosynthesis and accumulation of steroidal saponins in rhizomes and leaves. Phytochemistry 2020, 178.
31.Zhang X, Pan BZ, Chen MS, Chen W, Li J, Xu ZF, Liu CN: JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants. Bmc Genomics 2019, 20.
32.Zhang X, Li TJ, Wang J, Li J, Chen L, Liu CN: Identification of Cancer-Related Long Non-Coding RNAs Using XGBoost With High Accuracy. Frontiers in Genetics 2019, 10.
33.Zhang W, Du L, Qu ZP, Zhang XW, Li FW, Li Z, Qi FF, Wang X, Jiang YY, Men P et al: Compartmentalized biosynthesis of mycophenolic acid. Proceedings of the National Academy of Sciences of the United States of America 2019, 116(27):13305-13310.
34.Li J, Liu CN: Coding or Noncoding, the Converging Concepts of RNAs. Frontiers in Genetics 2019, 10.
35.Li J, Gao XY, Sang SY, Liu CN: Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae. Bmc Genomics 2019, 20.
36.Chen W, Zhang GQ, Li J, Zhang X, Huang SL, Xiang SL, Hu X, Liu CN: CRISPRlnc: a manually curated database of validated sgRNAs for lncRNAs. Nucleic Acids Research 2019, 47(D1):D63-D68.
37.Zhang X, Wang J, Li J, Chen W, Liu CN: CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features. Bmc Medical Genomics 2018, 11.
38.Wang PP, Li J, Gao XY, Zhang D, Li AL, Liu CN: Genome-Wide Screening and Characterization of the Dof Gene Family in Physic Nut (Jatropha curcas L.). International Journal of Molecular Sciences 2018, 19(6).
39.Wang J, Zhang X, Chen W, Li J, Liu CN: CRlncRNA: a manually curated database of cancer-related long non-coding RNAs with experimental proof of functions on clinicopathological and molecular features. Bmc Medical Genomics 2018, 11.
40.Li YY, He LL, Li J, Chen JH, Liu CN: Genome-Wide Identification, Characterization, and Expression Profiling of the Legume BZR Transcription Factor Gene Family. Frontiers in Plant Science 2018, 9.
41.Hu X, Chen W, Li J, Huang SL, Xu XL, Zhang X, Xiang SL, Liu CN: ZFLNC: a comprehensive and well-annotated database for zebrafish lncRNA. Database-the Journal of Biological Databases and Curation 2018.
42.Gao XY, Zhang X, Meng HH, Li J, Zhang D, Liu CN: Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications. Bmc Genomics 2018, 19.
43.Chen W, Zhang X, Li J, Huang SL, Xiang SL, Hu X, Liu CN: Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish. Bmc Genomics 2018, 19.
44.Li X, Liang FJ, Liu CN, Zhang LC, Li YH, Li Y, Chen SG, Xiong JH: Comparison of the Prognostic Utility of Diverse Molecular Data among lncRNA, DNA Methylation, microRNA and mRNA across Five Human Cancers (vol 10, e0142433, 2015). Plos One 2016, 11(3).
45.Zhang W, Cao SN, Qiu L, Qi FX, Li Z, Yang Y, Huang SH, Bai FL, Liu CN, Wan XB et al: Functional Characterization of MpaG ', the O-Methyltransferase Involved in the Biosynthesis of Mycophenolic Acid. Chembiochem 2015, 16(4):565-569.
46.Li X, Liang FJ, Liu CN, Zhang LC, Li YH, Li Y, Chen SG, Xiong JH: Comparison of the Prognostic Utility of the Diverse Molecular Data among lncRNA, DNA Methylation, microRNA, and mRNA across Five Human Cancers. Plos One 2015, 10(11).
47.Sun L, Luo HT, Liao Q, Bu DC, Zhao GG, Liu CN, Liu YN, Zhao Y: Systematic study of human long intergenic non-coding RNAs and their impact on cancer. Science China-Life Sciences 2013, 56(4):324-334.
48.Lin D, He F, Liao Y, Lin JT, Liu CN, Song JX, Cheng Y: Three-dimensional staggered herringbone mixer fabricated by femtosecond laser direct writing. Journal of Optics 2013, 15(2).
49.Li J, Xuan ZY, Liu CN: Long Non-Coding RNAs and Complex Human Diseases. International Journal of Molecular Sciences 2013, 14(9):18790-18808.
50.Zhao GG, Bu DC, Liu CN, Li J, Yang J, Liu ZY, Zhao Y, Chen RS: CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing. Protein & Cell 2012, 3(2):148-152.
51.Liu CN, Liao Y, He F, Shen YL, Chen DP, Cheng Y, Xu ZZ, Sugioka K, Midorikawa K: Fabrication of three-dimensional microfluidic channels inside glass using nanosecond laser direct writing. Optics Express 2012, 20(4):4291-4296.
52.Bu DC, Yu KT, Sun SL, Xie CY, Skogerbo G, Miao RY, Xiao H, Liao Q, Luo HT, Zhao GG et al: NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Research 2012, 40(D1):D210-D215.
53.Yuan XY, Zhao Y, Liu CN, Bu DB: LEX-SVM: EXPLORING THE POTENTIAL OF EXON EXPRESSION PROFILING FOR DISEASE CLASSIFICATION. Journal of Bioinformatics and Computational Biology 2011, 9(2):299-316.
54.Liao Q, Yuan XY, Xiao H, Liu CN, Lv ZY, Zhao Y, Wu ZD: Identifying Schistosoma japonicum Excretory/Secretory Proteins and Their Interactions with Host Immune System. Plos One 2011, 6(8).
55.Liao Q, Xiao H, Bu DC, Xie CY, Miao RY, Luo HT, Zhao GG, Yu KT, Zhao HT, Skogerbo G et al: ncFANs: a web server for functional annotation of long non-coding RNAs. Nucleic Acids Research 2011, 39:W118-W124.
56.Liao Q, Liu CN, Yuan XY, Kang SL, Miao RY, Xiao H, Zhao GG, Luo HT, Bu DC, Zhao HT et al: Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Research 2011, 39(9):3864-3878.
57.Yang Z, Ren F, Liu CN, He SM, Sun G, Gao QA, Yao L, Zhang YD, Miao RY, Cao Y et al: dbDEMC: a database of differentially expressed miRNAs in human cancers. Bmc Genomics 2010, 11.
58.Miao RY, Zhao HT, Yang HY, Mao YL, Lu X, Zhao Y, Liu CN, Zhong SX, Sang XT, Huang JF: Postoperative adjuvant antiviral therapy for hepatitis B/C virus-related hepatocellular carcinoma: A meta-analysis. World Journal of Gastroenterology 2010, 16(23):2931-2942.
59.Liu CN, Li J, Zhao Y: Exploring hierarchical and overlapping modular structure in the yeast protein interaction network. Bmc Genomics 2010, 11.
60.Yuan XY, Liu CN, Yang PC, He SM, Liao Q, Kang SL, Zhao Y: Clustered microRNAs' coordination in regulating protein-protein interaction network. Bmc Systems Biology 2009, 3.
61.Zhao Y, He SM, Liu CN, Ru SW, Zha HT, Yang Z, Yang PC, Yuan XY, Sun SW, Bu DB et al: MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control. Trends in Genetics 2008, 24(7):323-327.
62.Sun SW, Yu CG, Qiao YT, Lin Y, Dong GJ, Liu CN, Zhang LF, Zhang Z, Cai JJ, Zhang H et al: Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra. Journal of Proteome Research 2008, 7(1):202-208.
63.He SM, Su H, Liu CN, Skogerbo G, He HS, He DD, Zhu XP, Liu T, Zhao Y, Chen RS: MicroRNA-encoding long non-coding RNAs. Bmc Genomics 2008, 9.
64.He SM, Liu CN, Skogerbo G, Zhao HT, Wang J, Liu T, Bai BY, Zhao Y, Chen RS: NONCODE v2.0: decoding the non-coding. Nucleic Acids Research 2008, 36:D170-D172.
65.Yin YF, Zhao Y, Wang J, Liu CN, Chen SG, Chen RS, Zhao HT: antiCODE: a natural sense-antisense transcripts database. Bmc Bioinformatics 2007, 8.
66.Zhang ZH, Liu CN, Skogerbo G, Zhu XP, Lu HC, Chen L, Shi BC, Zhang Y, Wang J, Wu T et al: Dynamic changes in subgraph preference profiles of crucial transcription factors. Plos Computational Biology 2006, 2(5):383-391.
67.Wu T, Wang J, Liu CN, Zhang Y, Shi BC, Zhu XP, Zhang ZH, Skogerbo G, Chen L, Lu HC et al: NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. Nucleic Acids Research 2006, 34:D150-D152.
68.Wang XS, Zhao HT, Xu QW, Jin WB, Liu CN, Zhang HG, Huang ZB, Zhang XY, Zhang Y, Xin DQ et al: HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma. Nucleic Acids Research 2006, 34:D607-D612.
69.Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y et al: The DNA sequence, annotation and analysis of human chromosome 3. Nature 2006, 440(7088):1194-1198.
70.Lu HC, Shi BC, Wu GW, Zhang Y, Zhu XP, Zhang ZH, Liu CN, Zhao Y, Wu T, Wang J et al: Integrated analysis of multiple data sources reveals modular structure of biological networks. Biochemical and Biophysical Research Communications 2006, 345(1):302-309.
71.Deng W, Zhu XP, Skogerbo G, Zhao Y, Fu Z, Wang YD, He HS, Cai L, Sun H, Liu CN et al: Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression. Genome Research 2006, 16(1):20-29.
72.Liu CN, Bai BY, Skogerbo G, Cai L, Deng W, Zhang Y, Bu DB, Zhao Y, Chen RS: NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Research 2005, 33:D112-D115.
