Bioinformatics and Systems Biology

Systems Biology

• 3D Reconstruction Via Stereoscopy for the Study of Mosquito Swarms
• Dose Response Analysis Pipeline (DRAP)
• Immune Epitope Database and Analysis Resource (IEDB)
  • B Cell Epitope Prediction Tools
  • T Cell Epitope Prediction Tools
• Modeling Immunity for Biodefense
• Simmune
  • Simmune Modeler 
  • Simmune Network Browser 
  • Simmune Simulator 
• Systems Approach to Immunology
  • Computational Core
  • Signalling Core
• Systems Biology for Infectious Diseases
  • Systems Biology of Enteropathogens
    • COBRA Project: Physiochemical constraints to model a biological network.
    • Omics Datasets
  • Systems Influenza
    • Exon microarray data sets
    • SILAC Proteomic Data
    • Viral Host protein interactions
  • Mycobacterium tuberculosis Systems Biology
    • CSDeconv: computational method to locate TF binding from ChIP-seq data using blind deconvolution.
    • GenomeView: genome editor and viewer with dynamic visualization of aligned short read sequences.
    • E-Flux: method to model metabolic states using whole cell measurements and extend flux balance analysis.
    • Mycobacterium tuberculosis ChipSeq regulatory binding sites
  • Systems Virology
    • Systems Virology Agilent Microarray datasets:
    • Proteomics datasets:
    • Seqbias - graphical per-position bias correction of quantitative sequence abundance in RNA-Seq experiments:
    • Peptide Abundance Analysis Toolbox (PAAT):
    • QC workflow for Proteomics Data: RMD - statistical program to determine if LC-MS peptide abundance data are statistical outliers.