Publication List

• 2007
• 2006
• 2005
• Earlier Research

2007

• Wei L, Yu J., Bioinformatics in china: a personal perspective., Plos Computational Biology, 2008 Apr 25;4(4):e1000020 [Full Text]
• Li CY, Mao X, Wei L. Genes and (Common) Pathways Underlying Drug Addiction. Plos Computational Biology, 2008, 4(1): e2. doi:10.1371/journal.pcbi.0040002, [PubMed]
• Guo AY, Chen X, Gao G, Zhang H, Zhu QH, Liu XC, Zhong YF, Gu X, He K, Luo J. PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Research, 2007 Oct 12, doi:10.1093/nar/gkm841
• Kong, L., Y. Zhang, Z.Q. Ye, X.Q. Liu, S.Q. Zhao, L. Wei, and G. Gao. 2007. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 36: W345-349. [Abstract] [Full Text]
• Li, C.Y., et al., A nonsynonymous SNP in human cytosolic sialidase in a small Asian population results in reduced enzyme activity: potential link with severe adverse reactions to oseltamivir. Cell Research (2007) 17: 357–362. doi: 10.1038/cr.2007.27; published online 10 April 2007 [Abstract]
• Sun, Y., et al., ABCGrid: Application for Bioinformatics Computing Grid. Bioinformatics.2007; 23: 1175-1177 [Abstract]
• Ye, Z.Q., et al., Finding New Structural and Sequence Attributes to Predict Possible Disease-Association of Single Amino Acid Polymorphism (SAP). Bioinformatics 2007 23(12):1444-1450; doi:10.1093/bioinformatics/btm119 [Abstract] [Full Text]
• Zhang Y, Li J, Kong L, Gao G, Liu QR, Wei L, NATsDB: Natural Antisense Transcripts DataBase. Nucleic Acids Res. 2007 Jan;35(Database issue):D156-61.[Abstract] [Full Text]
• Zhang, W., et al., SynDB: a Synapse protein DataBase based on synapse ontology. Nucleic Acids Res, 2007. 35(Database issue): p. D737-41. [Abstract] [Full Text]
• Zhu, Q.H., et al., DPTF: a database of poplar transcription factors. Bioinformatics, 2007. [Abstract]

2006

• Cai Z, Mao X, Li S, Wei L: Genome comparison using Gene Ontology (GO) with statistical testing. BMC Bioinformatics 2006, 7:374. [Abstract] [Full Text]
• Cheng HP, Wei S, Wei LP, Verkhratsky A: Calcium signaling in physiology and pathophysiology. Acta Pharmacol Sin 2006, 27(7):767-772. [Abstract] [Full Text]
• Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J: DRTF: a database of rice transcription factors. Bioinformatics 2006, 22(10):1286-1287. [Abstract] [Full Text]
• Ji X, Li W, Song J, Wei L, Liu XS: CEAS: cis-regulatory element annotation system. Nucleic Acids Res 2006, 34(Web Server issue):W551-554. [Abstract] [Full Text]
• Li J, Li X, Guo L, Lu F, Feng X, He K, Wei L, Chen Z, Qu LJ, Gu H: A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice. J Exp Bot 2006, 57(6):1263-1273. [Abstract] [Full Text]
• Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J et al: Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 2006, 38(1):124-129. [Abstract]
• Lu XC, Gong HQ, Huang ML, Bai SL, He YB, Mao X, Geng Z, Li SG, Wei L, Yuwen JS et al: Molecular analysis of early rice stamen development using organ-specific gene expression profiling. Plant Mol Biol 2006, 61(6):845-861. [Abstract]
• 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. [Abstract]
• Shi YH, Zhu SW, Mao XZ, Feng JX, Qin YM, Zhang L, Cheng J, Wei LP, Wang ZY, Zhu YX: Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 2006, 18(3):651-664. [Abstract] [Full Text]
• 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. [Abstract] [Full Text]
• Zhang Y, Liu XS, Liu QR, Wei L: Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res 2006, 34(12):3465-3475. [Abstract] [Full Text]
• Zhou M, Xu H, Wei X, Ye Z, Wei L, Gong W, Wang Y, Zhu Z: Identification of a glyphosate-resistant mutant of rice 5-enolpyruvylshikimate 3-phosphate synthase using a directed evolution strategy. Plant Physiol 2006, 140(1):184-195. [Abstract] [Full Text]

2005

• 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. [Abstract] [Full Text]
• 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. [Abstract]
• 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 transcription factor gene family. Plant Mol Biol 2005, 59(6):853-868. [Abstract]
• Guo A, He K, Liu D, Bai S, Gu X, Wei L, Luo J: DATF: a database of Arabidopsis transcription factors. Bioinformatics 2005, 21(10):2568-2569. [Abstract]
• Han Y, Ni P, Lu H, Ye J, Hu J, Chen C, Huang X, Cong L, Li G, Wang J et al: Applications of the double-barreled data in whole-genome shotgun sequence assembly and analysis. Sci China C Life Sci 2005, 48(3):300-306. [Abstract]
• Li L, Wang X, Xia M, Stolc V, Su N, Peng Z, Li S, Wang J, Deng XW: Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol 2005, 6(6):R52. [Abstract] [Full Text]
• Li R, Ye J, Li S, Wang J, Han Y, Ye C, Yang H, Yu J, Wong GK: ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun. PLoS Comput Biol 2005, 1(4):e43. [Abstract] [Full Text]
• Mao X, Cai T, Olyarchuk JG, Wei L: Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 2005, 21(19):3787-3793. [Abstract] [Full Text]
• Wang J, Xia Q, He X, Dai M, Ruan J, Chen J, Yu G, Yuan H, Hu Y, Li R et al: SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Res 2005, 33(Database issue):D399-402. [Abstract] [Full Text]
• 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. [Abstract]
• 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. [Abstract] [Full Text]
• 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. [Abstract]
• Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C et al: The Genomes of Oryza sativa: a history of duplications. PLoS Biol 2005, 3(2):e38. [Abstract] [Full Text]
• 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. [Abstract]

Earlier Research

• Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS: A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Res 2004, 32(Web Server issue):W204-207. [Abstract] [Full Text]
• Wong GK, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J et al: A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 2004, 432(7018):717-722. [Abstract] [Full Text]
• 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. [Abstract] [Full Text]
• Bi S, Qin E, Xu Z, Li W, Wang J, Hu Y, Liu Y, Duan S, Hu J, Han Y et al: Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04). Genomics Proteomics Bioinformatics 2003, 1(3):180-192. [Abstract]
• 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. [Abstract]
• Hu J, Wang J, Xu J, Li W, Han Y, Li Y, Ji J, Ye J, Xu Z, Zhang Z et al: Evolution and variation of the SARS-CoV genome. Genomics Proteomics Bioinformatics 2003, 1(3):216-225. [Abstract]
• 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. [Abstract] [Full Text]
• 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. [Abstract]
• Su H, Qu LJ, He K, Zhang Z, Wang J, Chen Z, Gu H: The Great Wall of China: a physical barrier to gene flow? Heredity 2003, 90(3):212-219. [Abstract] [Full Text]
• Xu J, Hu J, Wang J, Han Y, Hu Y, Wen J, Li Y, Ji J, Ye J, Zhang Z et al: Genome organization of the SARS-CoV. Genomics Proteomics Bioinformatics 2003, 1(3):226-235. [Abstract]
• 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. [Abstract] [Full Text]
• Zhong L, Zhang K, Huang X, Ni P, Han Y, Wang K, Wang J, Li S: A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts. Genomics Proteomics Bioinformatics 2003, 1(1):43-51. [Abstract]
• Ding HT, Ren H, Chen Q, Fang G, Li LF, Li R, Wang Z, Jia XY, Liang YH, Hu MH et al: Parallel cloning, expression, purification and crystallization of human proteins for structural genomics. Acta Crystallogr D Biol Crystallogr 2002, 58(Pt 12):2102-2108. [Abstract]
• Wang J, Wong GK, Ni P, Han Y, Huang X, Zhang J, Ye C, Zhang Y, Hu J, Zhang K et al: RePS: a sequence assembler that masks exact repeats identified from the shotgun data. Genome Res 2002, 12(5):824-831. [Abstract] [Full Text]
• Yu Z, Li T, Zhao J, Luo J: PGAAS: a prokaryotic genome assembly assistant system. Bioinformatics 2002, 18(5):661-665. [Abstract] [Full Text]
• 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):639-646. [Abstract] [Full Text]
• 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. [Abstract] [Full Text]
• 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. [Abstract] [Full Text]
• 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. [Abstract] [Full Text]
• 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. [Abstract] [Full Text]
• 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. [Abstract]