Group
Software Development Philosophy
Often the fastest way to develop software programs for research projects is utilizing Open Source software development projects like BioPerl and Bioconductor. The Open Source movement treats program source code in a similar manner to the way scientists publish their results: publicly and open to unfettered examination and discussion. We are extremely grateful for these projects and contribute our code that might be of broader use to the bioinformatic community under similar Open Source licenses.
Biological Relationship Analysis
To identify biologically significant patterns in microarray data we developed an approach called “Biological Relationship Analysis”. We have used this approach in two recently submitted manuscripts on the superoxide response network in E. coli. We have also used Biological Relationship Analysis to interpret genome sequence data. For more information and to download the software see the Biological Relationship Analysis home page.
Genome Flux Analysis
To quantitatively determine the source of genome variation in bacterial species, we developed a computational approach we call “Genome Flux Analysis” to place gene loss, gene duplication, horizontal gene transfer events, and the appearance of “unique” genes in a phylogenetic context. Although this software was originally developed to address a specific research question, our ability to quickly analyze groups of related genomes has led to the application of this software in nearly all of our projects and in collaborations with several other research groups. For more information and to download the software see the Genome Flux Analysis home page.
Other projects soon to be published or in development
We developed a phylogenetic focus group-based approach for filtering environmental shotgun sequence data for using in population level studies.
We are developing methods for analyzing DNA genomic tiling arrays for mutation detection, identification of small RNAs and measuring mRNA transcript levels.