Theoretical Genomics Studies

A. Computational Genomics

  • Noise analysis of various ‘omics’ platforms
  • Feature extraction, primary analysis, export in selective formats, organization of searchable dbases and deposit into NCBI and other public dbases
  • Normalization and filtration of ‘omics’ data
  • Determination of gene expression level, control and coordination
  • Regulome
  • Prominent Gene Analysis
  • Pair-Wise Relevant Analysis
  • Transcriptomic Distance Analysis
  • Transcriptomic Recovery Analysis

B. Bioinformatics:

  • Agilent Feature Extraction, Axon GenePix + Acuity, Illumina Genome Studio
  • Gene ontology (GO) analysis
  • Pathway analysis (KEGG, Amigo, Ingenuity, GeneMap, DAVID)
  • Identification and quantification of significantly altered functional pathways
  • Determine composition, topology and interplay of functional genomic fabrics
  • Determine remodeling of functional genomic fabrics and their interplay during development/hormonal cycle/disease progression/treatment
  • Quantify the overall transcriptomic recovery in response to a therapy


C. Hybridization of Illumina beadchips:

  • Optimize information-to-cost experimental design, select study population, define outcomes and determine sample size and number of technical and biological replicas;
  • Perform various statistical tests on experimental data
  • Normalize, filter and perform statistical analysis of pathophysiological and ‘omic’ data;
  • Collect, perform primary analysis, export in selective formats, organize in searchable dbases and prepare data for deposit into public repositories;
  • Assistance with Origin Pro, GraphPad Office, Excel and Mathematica


D. Computational Biology/Mathematical modeling:

  • Develop (classical/quantum) physics and (continuous/discrete, deterministic/stochastic) mathematical models of complex biological systems/phenomena
  • Run numerical simulations of mathematical models
  • Determine the dynamics of the overall pathophysiological and transcriptomic changes during development, hormonal cycle, progression of a disease and recovery in response to a therapy.