Genomics Tools
  • GeneSpring
  • dChip
  • Affymetrix Gene Expression Console
  • GCOS
  • TM4
  • Bioconductor
  • GEXPAS (developed in house)
Proteomic Tools
  • Protein Forest
  • Protein Pilot
  • Mascot
  • SEQuest

Statistical Packages

  • R
  • SAS
  • SPSS
  • MATLab
Systems Biology Analysis
  • Pathway Analysis
    • Ingenuity, GeneGo, Pathway Assist, and Bioconductor
  • Geneset Enrichment Analysis
  • Interactive Network analysis using Cytoscape
  • Biomarker Prediction using GEXBio (developed in house)

The Bioinformatics Core will be the central portal of the Proteomics Core that will provide DF/HCC investigators with access to phenotypically annotated proteomics data as well as a large set of analytic procedures (i.e. unsupervised and supervised learning techniques, statistical analysis tools, automated clustering and classification procedures, pathway analysis and generation tools, protein identification database tools, data-visualization tools, annotation tools) with which to explore the data sets for further hypothesis generation.

Bioinformatics Analyses Offered

  • Personalized consulting
  • Customized data analysis and interpretation
  • Web-based bioinformatics tools
  • Comprehensive and innovative Bioinformatics and visualization tools
  • Comprehensive annotation tools
  • Identification of Global Relationships
  • Incorporation of Biological Knowledge
  • Pathway Analysis
  • miRNA Data Analysis
  • CGH and Genotype Array Analysis
  • Protein and DNA Sequence Analysis
  • Development of Prediction Models using Bayesian, SVM, ANN, KNN Algorithms
  • Publication ready figures
  • The Bioinformatics Core is also responsible for software support and development.

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