junjie luo

On Sep 22, 2013

  • Jin J, He K, Tang X, Li Z, Lv L, Zhao Y, Luo J,Kong L, Gao G. An Arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors. Mol Biol Evol. 2015 Mar 6. pii: msv058.
  • Hu B, Jin J, Guo A, Zhang H, Luo J, Gao G. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. (2015) 31 (8): 1296-1297
  • Zhao Y, Tang L, Li Z, Jin J, Luo J, Gao G. Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics. BMC Evol Biology. 2015 15:66
  • Wu J, Mao X, Cai T, Luo J, Wei L: KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res 2006, 34(Web Server issue):W720-724.
  • Jin JP, Zhang H, Kong L, Gao G and Luo JC. PlantTFDB 3.0: a portal for the functional and evolutionary study of plant tran1111ion factors. Nucleic Acids Research 2013.
  • Wang J, Kong L, Zhao S, Zhang H, Tang L, Li Z, Gu X, Luo J, Gao G. Rice-Map: a new-generation rice genome browser. BMC Genomics. 2011 Mar 30;12:165.
  • Chen ZX, Zhang YE, Vibranovski M, Luo J, Gao G, Long M. Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome. Mol Biol Evol. 2011 May 5
  • Wang J, Kong L, Gao G, Luo J. A brief introduction to web-based genome browsers. Briefings in Bioinformatics. 2012 Jul 3
  • Kong L, Wang J, Zhao S, Gu X, Luo J, Gao G. ABrowse--a customizable next-generation genome browser framework. BMC Bioinformatics. 2012 Jan 5;13:2
  • Zhang H, Jin J, Tang L, Zhao Y, Gu X, Gao G, Luo J. PlantTFDB 2.0: update and improvement of the comprehensive plant tran1111ion factor database. Nucleic Acids Res. 2011 Jan;39(Database issue):D1114-7
  • Liu X, Li Z, Jiang Z, Zhao Y, Peng J, Jin J, Guo H, Luo J. LSD: a leaf senescence database. Nucleic Acids Res. 2011 Jan;39(Database issue):D1103-7
  • Jiang Z, Liu X, Peng Z, Wan Y, Ji Y, He W, Wan W, Luo J, Guo H. AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies. Nucleic Acids Res. 2011 Jan;39(Database issue):D1123-9
  • He K, Guo AY, Gao G, Zhu QH, Liu XC, Zhang H, Chen X, Gu X, Luo J. Computational identification of plant tran1111ion factors and the construction of the PlantTFDB database. Methods Mol Biol. 2010;674:351-68.
  • He K, Li X, Zhou J, Deng XW, Zhao H, Luo J. NTAP: for NimbleGen tiling array ChIP-chip data analysis. Bioinformatics. 2009 Jul 15;25(14):1838-40
  • Li Z, Zhang H, Ge S, Gu X, Gao G, Luo J. Expression pattern divergence of duplicated genes in rice. BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S8
  • Liu X, Wu J, Wang J, Liu X, Zhao S, Li Z, Kong L, Gu X, Luo J, Gao G., WebLab: a data-centric, knowledge-sharing bioinformatic platform., Nucleic Acids Research, doi:10.1093/nar/gkp428
  • Guo AY, Chen X, Gao G, Zhang H, Zhu QH, Liu XC, Zhong YF, Gu X, He K, Luo J. PlantTFDB: a comprehensive plant tran1111ion factor database. Nucleic Acids Research, 2007 Oct 12, doi:10.1093/nar/gkm841
  • Zhong Y, Guo A, Li C, Zhuang B, Lai M, Wei C, Luo J, Li Y: Identification of a naturally occurring recombinant isolate of Sugarcane mosaic virus causing maize dwarf mosaic disease. Virus Genes 2005, 30(1):75-83
  • Yin YB, Zhang Y, Yu P, Luo JC, Jiang Y, Li SG: Comparative study of apoptosis-related gene loci in human, mouse and rat genomes. Acta Biochim Biophys Sin (Shanghai) 2005, 37(5):341-348
  • Wu X, Walker MG, Luo J, Wei L: GBA server: EST-based digital gene expression profiling. Nucleic Acids Res 2005, 33(Web Server issue):W673-676.
  • Wang X, Shi X, Hao B, Ge S, Luo J: Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol 2005, 165(3):937-946.
  • Guo A, He K, Liu D, Bai S, Gu X, Wei L, Luo J: DATF: a database of Arabidopsis tran1111ion factors. Bioinformatics 2005, 21(10):2568-2569.
  • Feng JX, Liu D, Pan Y, Gong W, Ma LG, Luo JC, Deng XW, Zhu YX: An annotation update via cDNA sequence analysis and comprehensive profiling of developmental, hormonal or environmental responsiveness of the Arabidopsis AP2/EREBP tran1111ion factor gene fami
  • Dai X, Chen Q, Lian M, Zhou Y, Zhou M, Lu S, Chen Y, Luo J, Gu X, Jiang Y et al: Systematic high-yield production of human secreted proteins in Escherichia coli. Biochem Biophys Res Commun 2005, 332(2):593-601.
  • Chen Y, Zhang Y, Yin Y, Gao G, Li S, Jiang Y, Gu X, Luo J: SPD--a web-based secreted protein database. Nucleic Acids Res 2005, 33(Database issue):D169-173.
  • Zhu Y, Zhang Y, Luo J, Davies PJ, Ho DT: PPF-1, a post-floral-specific gene expressed in short-day-grown G2 pea, may be important for its never-senescing phenotype. Gene 1998, 208(1):1-6.
  • Lu S, Deng P, Liu X, Luo J, Han R, Gu X, Liang S, Wang X, Li F, Lozanov V et al: Solution structure of the major alpha-amylase inhibitor of the crop plant amaranth. J Biol Chem 1999, 274(29):20473-20478.
  • Li JM, Han JS, Huang Y, Tain PK, Qu SM, Yao M, Jiang HQ, Wan DF, Luo JC, Gu CX et al: A novel gene delivery system targeting cells expressing VEGF receptors. Cell Res 1999, 9(1):11-25.
  • Liu Y, Luo J, Xu C, Ren F, Peng C, Wu G, Zhao J: Purification, characterization, and molecular cloning of the gene of a seed-specific antimicrobial protein from pokeweed. Plant Physiol 2000, 122(4):1015-1024.
  • Zhang G, Zhang S, Chen W, Qiu W, Wu H, Wang J, Luo J, Gu X, Cotton RG: Go!Poly: A gene-oriented polymorphism database. Hum Mutat 2001, 18(5):382-387
  • Carugo O, Lu S, Luo J, Gu X, Liang S, Strobl S, Pongor S: Structural analysis of free and enzyme-bound amaranth alpha-amylase inhibitor: classification within the knottin fold superfamily and analysis of its functional flexibility. Protein Eng 2001, 14(9)
  • Yu Z, Li T, Zhao J, Luo J: PGAAS: a prokaryotic genome assembly assistant system. Bioinformatics 2002, 18(5):661-665.
  • Zhang Y, Yin Y, Chen Y, Gao G, Yu P, Luo J, Jiang Y: PCAS--a precomputed proteome annotation database resource. BMC Genomics 2003, 4(1):42.
  • Jiang Y, Gao G, Fang G, Gustafson EL, Laverty M, Yin Y, Zhang Y, Luo J, Greene JR, Bayne ML et al: PepPat, a pattern-based oligopeptide homology search method and the identification of a novel tachykinin-like peptide. Mamm Genome 2003, 14(5):341-349
  • Ji SJ, Lu YC, Feng JX, Wei G, Li J, Shi YH, Fu Q, Liu D, Luo JC, Zhu YX: Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array. Nucleic Acids Res 2003, 31(10):2534-2543
  • Shi X, Wang X, Li Z, Zhu Q, Tang W, Ge S, Luo J: Nucleotide substitution pattern in rice paralogues: implication for negative correlation between the synonymous substitution rate and codon usage bias. Gene 2006, 376(2):199-206
  • Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J: DRTF: a database of rice tran1111ion factors. Bioinformatics 2006, 22(10):1286-1287
  • Chen Y, Yu P, Luo J, Jiang Y: Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT. Mamm Genome 2003, 14(12):859-865
  • Ying X, Luo H, Luo J, Li W: RDfolder: a web server for prediction of RNA secondary structure. Nucleic Acids Res 2004, 32(Web Server issue):W150-153.