Systems Biology

We are active both in bioinformatics as well as in computational systems biology. Very roughly defined, bioinformatics efforts intersect computer science with life science and computational systems biology efforts intersect applied mathematics with life science). In terms of bioinformatics, we have been involved in the development of tools that facilitate the analysis of shotgun proteomics datasets such as those obtained using isobaric tagging reagents. We developed a package called iTRAQPak which facilitates visualization of such datasets and addresses important issues related to protein versus peptide measurements during large scale shotgun proteomics studies.

We also have an interest in developing mathematical frameworks to describe molecular processes inside cells. We have been interested in the relationship between DNA sequence, mRNA expression, and protein expression in cells on a genome-wide scale. We developed a framework that describes (i.e. predicts) protein expression changes genome-wide when changes in mRNA expression are measured and when DNA sequence is known. There are several other key problems of interest to us as well. We are modeling programmed ribosomal frameshifting for both +1 and -1 frameshifts. We are modeling the aggregation of proteins expressed inside cells that should be secreted from the cells, but are not. And we are modeling the molecular basis of circadian rhythmicity in fruitfly. We generally perform experiments to guide our model development and to refine models as well. The balance between modeling and experiment is key to our approach.

iTraq labeling

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