The Edwards lab conducts research in various aspects of computational biology and bioinformatics, particularly proteomics and mass spectrometry informatics and DNA and protein based signatures for pathogen detection.
Research in molecular biology has been revolutionized by the advent of high-throughput experimental protocols that conduct hundreds or thousands of simple experiments in parallel. By itself, each simple experiment means little, but the combined results of all of the experiments, when carefully analyzed using the tools of mathematics, statistics, scientific computing, and computer science, can give insight into biological processes that would not otherwise be observable by traditional experimental techniques.
Our primary area of research is the analysis of mass spectrometry experiments for proteomics. Proteomics, the qualitative and quantitative analysis of the expressed proteins of a cell, makes it possible to detect and compare the protein abundance profiles of different samples. Proteins observed to be under or over expressed in disease samples can lead to diagnostic markers or drug targets. The observation of mutated or alternatively spliced protein isoforms may provide domain experts with clues to the mechanisms by which a disease operates. The detection of proteins by mass spectrometry can even signal the presence of airborne microorganisms, such as anthrax, in the detect-to-protect time-frame. Recent research has focused on the discovery of novel peptides in proteomics datasets, improving the sensitivity and specificity of peptide identification using spectral matching with hidden Markov models, and unsupervised machine-learning based peptide identification result combining.
Outside of proteomics, we work on computational tools for the design of highly specific oligonucleotides useful for pathogen signatures and PCR assay design. Recent research has focused on precomputing all human oligos of length 20 that are unique up to 4 string edits; and all bacterial 20-mer oligos that are species specific up to 4 string edits.