A core strength in the PROOF Centre is its award-winning Computation Team, a group of highly skilled people who bring together the many resources necessary for biomarker development. The Computation Team, a winner at the Bio-IT World’s Best Practices Awards Program in 2010, includes database specialists, clinical statisticians, biostatisticians, bioinformaticians, mathematicians, computer scientists, and systems scientists. From statistical evaluation of complex data and clinical trial statistics, to high throughput platform analysis, the Computational Team excels in data integration and management, data mining, bioinformatics, statistics, and tool development.

In particular, the Computation Team provides expertise and tools to support:

  • Experimental design review including sample size calculations and randomized sample layout
  • Analysis of proteomic, genomic, and metabolomic data from a variety of high throughput biomarker discovery and development platforms; examples include Affymetrix microarrays, RNA sequencing data, mass spectrometry, and immunoassays
  • Integration and analysis of data from different sources including administrative, clinical, proteomic, genomic, and metabolomic data
  • Single time point and time course data analyses
  • One group, two group, and multi-group analyses
  • Classification and feature selection using a variety of techniques:
  1. Analytical methods including moderated t-tests (robust and non-robust eBayes) and Significance Analysis of Microarrays (SAM)
  2. Classification algorithms including Linear Discriminant Analysis (LDA), Support Vector Machines (SVM), Elastic Net and Random Forests
  3. Algorithms are built and operated in R, BioConductor and SAS
  • Linkage of data to web resources and to frame ontologies using IO Informatics Sentient software (www.io-informatics.com)
  • Biological pathway analysis performed using MetaCore and Ingenuity pathway analysis software and FatiGO functional enrichment analysis software
  • Systems analysis of global expression profiles in the context of diseases, drugs, and targets

Click here to view a list of academic publications from the PROOF Centre.