Zhenjun Hu

Summary

Publications

  1. pmc VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies
    Zhenjun Hu
    Center for Advanced Genomic Technology, Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 41:W225-31. 2013
  2. pmc VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
    Zhenjun Hu
    Center for Advanced Genomic Technology, Program in Bioinformatics, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 37:W115-21. 2009
  3. pmc VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
    Zhenjun Hu
    Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 35:W625-32. 2007
  4. doi request reprint Analyzing networks with VisANT
    Zhenjun Hu
    Boston University, Boston, Massachusetts, USA
    Curr Protoc Bioinformatics . 2004
  5. pmc SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation
    Zhenjun Hu
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:W235-41. 2004
  6. pmc VisANT: data-integrating visual framework for biological networks and modules
    Zhenjun Hu
    Program in Bioinformatics and Systems Biology, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 33:W352-7. 2005
  7. pmc Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network
    Bolan Linghu
    Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02215, USA
    Genome Biol 10:R91. 2009
  8. pmc VisANT: an integrative framework for networks in systems biology
    Zhenjun Hu
    Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02115, USA
    Brief Bioinform 9:317-25. 2008
  9. doi request reprint Analysis strategy of protein-protein interaction networks
    Zhenjun Hu
    Bioinformatics Program, Boston University, Boston, MA, USA
    Methods Mol Biol 939:141-81. 2013
  10. ncbi request reprint Dynamic visual data mining: biological sequence analysis and annotation using SeqVISTA
    Tianhua Niu
    Department of Meidcine, Brigham and Women s Hospital, Boston, MA 02215, USA
    Int J Bioinform Res Appl 1:18-30. 2005

Collaborators

Detail Information

Publications19

  1. pmc VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies
    Zhenjun Hu
    Center for Advanced Genomic Technology, Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 41:W225-31. 2013
    ..VisANT is freely available at: http://visant.bu.edu. ..
  2. pmc VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
    Zhenjun Hu
    Center for Advanced Genomic Technology, Program in Bioinformatics, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 37:W115-21. 2009
    ..Both algorithms take account of network topology (i.e. correlations between genes based on various sources of evidence). VisANT is freely available at http://visant.bu.edu...
  3. pmc VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
    Zhenjun Hu
    Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 35:W625-32. 2007
    ..Pathways in the format of VisML can be securely shared within an interested group or published online using a simple Web link. VisANT is freely available at http://visant.bu.edu...
  4. doi request reprint Analyzing networks with VisANT
    Zhenjun Hu
    Boston University, Boston, Massachusetts, USA
    Curr Protoc Bioinformatics . 2004
    ..g., KEGG/KGML, BioPAX (in progress), GenBank, Gene Ontology. Multiple species are supported to the extent that computed or experimental evidence of interactions or associations are available (i.e., public datasets or Predictome database)...
  5. pmc SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation
    Zhenjun Hu
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:W235-41. 2004
    ..bu.edu/SeqVISTA/web.jnlp, provided that Java Web Start has been installed. In addition, a stand-alone version of the program can be downloaded and run locally. It can be obtained at http://zlab.bu.edu/SeqVISTA...
  6. pmc VisANT: data-integrating visual framework for biological networks and modules
    Zhenjun Hu
    Program in Bioinformatics and Systems Biology, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 33:W352-7. 2005
    ..VisANT is distributed freely via the web at http://visant.bu.edu and can also be downloaded for individual use...
  7. pmc Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network
    Bolan Linghu
    Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02215, USA
    Genome Biol 10:R91. 2009
    ..Many of these disease-disease associations are supported by epidemiology, but with no previous genetic basis. Such associations can drive novel hypotheses on molecular mechanisms of diseases and therapies...
  8. pmc VisANT: an integrative framework for networks in systems biology
    Zhenjun Hu
    Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02115, USA
    Brief Bioinform 9:317-25. 2008
    ..bu.edu) which integrates, mines and displays hierarchical information. Challenges to integrating modeling (discrete or continuous) and simulation capabilities into such visual mining software are briefly discussed...
  9. doi request reprint Analysis strategy of protein-protein interaction networks
    Zhenjun Hu
    Bioinformatics Program, Boston University, Boston, MA, USA
    Methods Mol Biol 939:141-81. 2013
    ..VisANT (http://visant.bu.edu)-a free Web-based software platform for the integrative visualization, mining, analysis, and modeling of the biological networks-will be used as a main tool for all examples used in this section...
  10. ncbi request reprint Dynamic visual data mining: biological sequence analysis and annotation using SeqVISTA
    Tianhua Niu
    Department of Meidcine, Brigham and Women s Hospital, Boston, MA 02215, USA
    Int J Bioinform Res Appl 1:18-30. 2005
    ....
  11. ncbi request reprint Towards zoomable multidimensional maps of the cell
    Zhenjun Hu
    Program in Bioinformatics and Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Nat Biotechnol 25:547-54. 2007
    ....
  12. pmc Gene annotation and network inference by phylogenetic profiling
    Jie Wu
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    BMC Bioinformatics 7:80. 2006
    ..Current methods, though useful, perform at a level well below what is possible, largely because performance of the latter deteriorates rapidly as coverage increases...
  13. pmc Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancer
    Daichi Shigemizu
    Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 8:e1002347. 2012
    ..01. These findings indicate that the method presented here could lead to a substantial increase in efficiency in drug discovery and development, and has potential application for the personalized medicine...
  14. pmc Identification of functional modules that correlate with phenotypic difference: the influence of network topology
    Jui Hung Hung
    Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02215, USA
    Genome Biol 11:R23. 2010
    ..We present a method that takes account of such information - expressed in terms of the topology of a correlation network - and we apply the method in the context of current procedures for gene set enrichment analysis...
  15. ncbi request reprint SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assays
    Tianhua Niu
    Division of Preventive Medicine, Brigham and Women s Hospital, Harvard Medical School, 900 Commonwealth Avenue, MA 02215, USA
    Bioinformatics 20:3263-5. 2004
    ..The SNP assays designed using SNPicker were cross-validated using the MassARRAY technology...
  16. pmc VisANT: an online visualization and analysis tool for biological interaction data
    Zhenjun Hu
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    BMC Bioinformatics 5:17. 2004
    ..This networked view of biology brings the potential for systematic understanding of living molecular systems...
  17. ncbi request reprint hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes
    Philippe Lamesch
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genomics 89:307-15. 2007
    ..dfci.harvard.edu). This expansion of the original ORFeome resource greatly increases the potential experimental search space for large-scale proteomics studies, which will lead to the generation of more comprehensive datasets...
  18. pmc COMBREX: a project to accelerate the functional annotation of prokaryotic genomes
    Richard J Roberts
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 39:D11-4. 2011
    ..It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support successful bids...
  19. pmc SeqVISTA: a graphical tool for sequence feature visualization and comparison
    Zhenjun Hu
    Bioinformatics Program, Boston University, Boston, MA, 02215, USA
    BMC Bioinformatics 4:1. 2003
    ..But now you want to see what other features have been annotated close by, and this information is buried several screenfuls higher up the web page...