Research Topics
| Zhenjun HuSummaryAffiliation: Boston University Country: USA Publications
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Detail Information
Publications
Analysis strategy of protein-protein interaction networksZhenjun 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...
SeqVISTA: a graphical tool for sequence feature visualization and comparisonZhenjun 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...- VisANT: an online visualization and analysis tool for biological interaction dataZhenjun 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... - VisANT 3.0: new modules for pathway visualization, editing, prediction and constructionZhenjun 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... 
Analyzing networks with VisANTZhenjun 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)...- VisANT: data-integrating visual framework for biological networks and modulesZhenjun 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... - Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage networkBolan 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... - VisANT: an integrative framework for networks in systems biologyZhenjun 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... - VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontologyZhenjun 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... - Gene annotation and network inference by phylogenetic profilingJie 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... - Towards zoomable multidimensional maps of the cellZhenjun Hu
Program in Bioinformatics and Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
Nat Biotechnol 25:547-54. 2007.... - SeqVISTA: a new module of integrated computational tools for studying transcriptional regulationZhenjun 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... - Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancerDaichi 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... - Identification of functional modules that correlate with phenotypic difference: the influence of network topologyJui 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... - Dynamic visual data mining: biological sequence analysis and annotation using SeqVISTATianhua Niu
Department of Meidcine, Brigham and Women s Hospital, Boston, MA 02215, USA
Int J Bioinform Res Appl 1:18-30. 2005.... - Gene set enrichment analysis: performance evaluation and usage guidelinesJui Hung Hung
Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
Brief Bioinform 13:281-91. 2012.... - SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assaysTianhua 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... - hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genesPhilippe 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... - COMBREX: a project to accelerate the functional annotation of prokaryotic genomesRichard 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...