Jinyu Wu

Summary

Country: China

Publications

  1. ncbi CSCDB: the cAMP and cGMP signaling components database
    Jianxin Lu
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325003, China
    Genomics 92:60-4. 2008
  2. pmc De novo transcriptome of safflower and the identification of putative genes for oleosin and the biosynthesis of flavonoids
    Haiyan Li
    Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China
    PLoS ONE 7:e30987. 2012
  3. pmc cTFbase: a database for comparative genomics of transcription factors in cyanobacteria
    Jinyu Wu
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325000, China
    BMC Genomics 8:104. 2007
  4. pmc Characterization of the stress associated microRNAs in Glycine max by deep sequencing
    Haiyan Li
    Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin 130118, China
    BMC Plant Biol 11:170. 2011
  5. pmc FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families
    Jinyu Wu
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, PR China
    BMC Bioinformatics 10:123. 2009
  6. doi Investigation of the microRNAs in safflower seed, leaf, and petal by high-throughput sequencing
    Haiyan Li
    Engineering Research Center of Bioreactor and Pharmaceutical Development, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
    Planta 233:611-9. 2011
  7. pmc mirTools: microRNA profiling and discovery based on high-throughput sequencing
    Erle Zhu
    Institute of Genomic Medicine Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou, China
    Nucleic Acids Res 38:W392-7. 2010
  8. doi proTF: a comprehensive data and phylogenomics resource for prokaryotic transcription factors
    Jie Bai
    Institute of Genomic Medicine Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325035, China
    Bioinformatics 26:2493-5. 2010
  9. pmc MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation
    Huabin Hou
    Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou 325035, China
    Nucleic Acids Res 38:W732-6. 2010
  10. doi Insights into the evolution of gene organization and multidrug resistance from Klebsiella pneumoniae plasmid pKF3-140
    Jie Bai
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, and The First Affiliated Hospital of Wenzhou Medical College, Wenzhou 325000, China
    Gene 519:60-6. 2013

Collaborators

Detail Information

Publications27

  1. ncbi CSCDB: the cAMP and cGMP signaling components database
    Jianxin Lu
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325003, China
    Genomics 92:60-4. 2008
    ..Currently, CSCDB contains 4234 entries covering 466 organisms, including 35 eukaryotes, 382 bacteria, and 29 archaea. CSCDB can be freely accessible on the web at http://cscdb.com.cn...
  2. pmc De novo transcriptome of safflower and the identification of putative genes for oleosin and the biosynthesis of flavonoids
    Haiyan Li
    Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China
    PLoS ONE 7:e30987. 2012
    ....
  3. pmc cTFbase: a database for comparative genomics of transcription factors in cyanobacteria
    Jinyu Wu
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325000, China
    BMC Genomics 8:104. 2007
    ..6 to 9.1 Mb and little is known about their TF repertoires. Therefore, we constructed the cTFbase database to classify and analyze all the putative TFs in cyanobacterial genomes, followed by genome-wide comparative analysis...
  4. pmc Characterization of the stress associated microRNAs in Glycine max by deep sequencing
    Haiyan Li
    Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin 130118, China
    BMC Plant Biol 11:170. 2011
    ..MicroRNAs (miRNAs) have recently emerged as key regulators in gene regulation, developmental processes and stress tolerance in plants...
  5. pmc FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families
    Jinyu Wu
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, PR China
    BMC Bioinformatics 10:123. 2009
    ..However, all of these resources are gene-centric and lack the information of the gene families in Drosophila...
  6. doi Investigation of the microRNAs in safflower seed, leaf, and petal by high-throughput sequencing
    Haiyan Li
    Engineering Research Center of Bioreactor and Pharmaceutical Development, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
    Planta 233:611-9. 2011
    ..In addition, 13 putative novel miRNAs have been identified in safflower. The small RNA transcriptomes obtained in this study provide a basis for further investigation of the physiological roles of identified miRNAs in safflower...
  7. pmc mirTools: microRNA profiling and discovery based on high-throughput sequencing
    Erle Zhu
    Institute of Genomic Medicine Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou, China
    Nucleic Acids Res 38:W392-7. 2010
    ..mirTools can be accessed at http://centre.bioinformatics.zj.cn/mirtools/ and http://59.79.168.90/mirtools...
  8. doi proTF: a comprehensive data and phylogenomics resource for prokaryotic transcription factors
    Jie Bai
    Institute of Genomic Medicine Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325035, China
    Bioinformatics 26:2493-5. 2010
    ..In conclusion, proTF dedicates to the prokaryotic TFs with integrated multi-function, which will become a valuable resource for prokaryotic transcriptional regulatory network in the post-genomic era...
  9. pmc MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation
    Huabin Hou
    Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou 325035, China
    Nucleic Acids Res 38:W732-6. 2010
    ..MagicViewer is freely available at http://bioinformatics.zj.cn/magicviewer/...
  10. doi Insights into the evolution of gene organization and multidrug resistance from Klebsiella pneumoniae plasmid pKF3-140
    Jie Bai
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, and The First Affiliated Hospital of Wenzhou Medical College, Wenzhou 325000, China
    Gene 519:60-6. 2013
    ..coli and acquired the resistance genes from a variety of enteric bacteria and underscores the importance of a further understanding of horizontal gene transfer among enteric bacteria...
  11. doi Codon usage patterns and adaptive evolution of marine unicellular cyanobacteria Synechococcus and Prochlorococcus
    Tonghai Yu
    Institute of Genomic Medicine Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325000, China
    Mol Phylogenet Evol 62:206-13. 2012
    ..Our evolutionary genomic analysis provides the first insight into codon usage, evolutionary genetic mechanisms and environmental adaptation of Synechococcus and Prochlorococcus after divergence...
  12. doi PGA4genomics for comparative genome assembly based on genetic algorithm optimization
    Fangqing Zhao
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325035, China
    Genomics 94:284-6. 2009
    ..The availability of such a platform would greatly benefit the research community working on bacterial genomics. PGA4genomics can be accessed at two mirror sites http://centre.bioinformatics.zj.cn:8080/pga or http://59.79.168.90:8080/pga...
  13. doi PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families
    Xiang Xu
    School of Pharmaceutical Science Zhejiang Provincial Key Laboratory of Biotechnology Pharmaceutical Engineering, Wenzhou Medical College, Wenzhou 325035, PR China
    Bioinformatics 24:1217-20. 2008
    ..falciparum, P. berghei, P. knowlesi, P. chabaudi, P. vivax and P. yoelii. The availability of such a highly integrated system would be of great interest for the community of researchers working on malaria parasite phylogenomics...
  14. pmc Characterization of the small RNA transcriptomes of androgen dependent and independent prostate cancer cell line by deep sequencing
    Gang Xu
    Center for Clinical Laboratory Diagnosis, The First Affiliated Hospital of Wenzhou Medical College, Wenzhou, China
    PLoS ONE 5:e15519. 2010
    ..The small RNA transcriptomes obtained in this study provide considerable insights into a better understanding of the expression and function of small RNAs in the development of androgen-independent prostate cancer...
  15. doi The repertoire and evolution of ATP-binding cassette systems in Synechococcus and Prochlorococcus
    Lijing Bu
    Zhejiang Provincial Key Laboratory of Medical Genetics, Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou, 325000, China
    J Mol Evol 69:300-10. 2009
    ..In conclusion, the comprehensive survey of ABC systems in Synechococcus and Prochlorococcus provides novel insights into their potential evolutionary mechanism and the basis for further investigation of their physiological roles...
  16. ncbi Evidence for positive Darwinian selection of Vip gene in Bacillus thuringiensis
    Jinyu Wu
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325000, China
    J Genet Genomics 34:649-60. 2007
    ..Sites identified to be under positive selection may be related to the insect host range, which may shed a light on the investigation of the Vip proteins' structural and functional relationships...
  17. ncbi ArchaeaTF: an integrated database of putative transcription factors in Archaea
    Jinyu Wu
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325035, China
    Genomics 91:102-7. 2008
    ..ArchaeaTF is accessible at http://bioinformatics.zj.cn/archaeatf...
  18. doi Lineage-specific domain fusion in the evolution of purine nucleotide cyclases in cyanobacteria
    Jinyu Wu
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325000, China
    J Mol Evol 67:85-94. 2008
    ..In conclusion, the comprehensive survey of cyclases in cyanobacteria provides novel insight into their potential evolutionary mechanisms and further functional implications...
  19. pmc Sequencing and genetic variation of multidrug resistance plasmids in Klebsiella pneumoniae
    Fangqing Zhao
    Institute of Biomedical Informatics, Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, China
    PLoS ONE 5:e10141. 2010
    ..Characterizing the genetic variation among plasmids from different bacterial species or strains is a key step towards understanding the mechanism of virulence and their evolution...
  20. doi Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer
    Qi Liu
    Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou, China
    Genomics 99:178-82. 2012
    ..In conclusion, SplicingViewer can be widely used for studying alternative splicing easily and efficiently. SplicingViewer can be freely accessed at http://bioinformatics.zj.cn/splicingviewer...
  21. ncbi RRBS-analyser: a comprehensive web server for reduced representation bisulfite sequencing data analysis
    Tao Wang
    Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325035, China
    Hum Mutat 34:1606-10. 2013
    ..RRBS-Analyser can be widely used by researchers wanting to unravel the complexities of DNA methylome in the epigenetic community. RRBS-Analyser is freely available at http://122.228.158.106/RRBSAnalyser/. ..
  22. pmc Sequence analysis of pKF3-70 in Klebsiella pneumoniae: probable origin from R100-like plasmid of Escherichia coli
    Huiguang Yi
    Institute of Biomedical Informatics Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, China
    PLoS ONE 5:e8601. 2010
    ..The resistance is largely due to the acquisition of plasmids carrying drug-resistant as well as pathogenic genes, and its conjugal transfer facilitates the spread of resistant phenotypes...
  23. pmc Exome-assistant: a rapid and easy detection of disease-related genes and genetic variations from exome sequencing
    Qi Liu
    Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou 325035, China
    BMC Genomics 13:692. 2012
    ..However, there remain great challenges in handling the huge data generated by exome sequencing and in identifying potential disease-related genetic variations...
  24. doi Small RNA transcriptome investigation based on next-generation sequencing technology
    LingLin Zhou
    Institute of Genomic Medicine, Wenzhou Medical College, China
    J Genet Genomics 38:505-13. 2011
    ..To provide some insight into the small RNA transcriptome investigation, this review describes the major small RNA classes, experimental methods to identify small RNAs, and available bioinformatics tools and databases...
  25. doi Identification of a novel Cys146X mutation of SOD1 in familial amyotrophic lateral sclerosis by whole-exome sequencing
    Jinyu Wu
    The Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou, China
    Genet Med 14:823-6. 2012
    ..Therefore, to quickly learn the causative gene for patients with familial amyotrophic lateral sclerosis in a Chinese pedigree, we opted to apply whole-exome sequencing as a diagnostic tool...
  26. doi Exome sequencing reveals CCDC111 mutation associated with high myopia
    Fuxin Zhao
    School of Ophthalmology and Optometry and Eye hospital, Wenzhou Medical College, 325003 Zhejiang, People s Republic of China
    Hum Genet 132:913-21. 2013
    ..In summary, our results suggested that the CCDC111 may be a susceptibility gene for high myopia. ..
  27. ncbi Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria
    Fangqing Zhao
    Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
    Physiol Genomics 24:181-90. 2006
    ..Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations...