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To see my lab notebook, please see my Open Notebook Science page.

Below are some of the ideas/projects I've worked on (most recent is at the top).

Predicting a mammalian microbiota's response to changes in host diet. Gordon Lab WashU
I developed a RNA-Seq method for assaying microbial transciption in microbial gut communities. I'm currently developing predictive models of defined human gut microbial communities in gnotobiotic mice.
Determination of prokaryotic transcriptional regulatory networks Gardner Lab Boston University
My Ph.D. was focused on technology and algorithm development for inferring transcriptional regulatory networks in microbes. This work was in the lab of Tim Gardner with some collaboration with people in Jim Collins synthetic and systems biology lab and Simon Kasif.
Large-scale RNAi, protein-protein interactions, and haplotypes Ravi Lab Cold Spring Harbor Laboratory
At CSHL, I was a bioinformatics odd-jobs person. Together with the Hannon Lab, we created many tools for large-scale RNAi knockdowns in human and mouse. Along with this, we developed a widely-used webpage for designing RNAi hairpin oligonucleotides (which has since been updated by Jason Lee). Along other lines, Ravi and I developed tools for exploring protein-protein interaction data using graph theoretic and spectral methods. Lastly, we collaborated with many labs worldwide in creating a large human chromosome 19 linkage map across diverse ethnic groups.
Mitochondrial genomics Pollock Lab Louisiana State University
This project began as a purely bioinformatics effort: how to organize the genomic data from an ongoing mitochondrial genomics project into a useful form for evolutionary biologists. However, once the data was organized, it provided a platform for evolutionary hypothesis testing and led to a refined model of the evolutionary dynamics of mitochondrial mutations that may have an effect on how future phylogenetic inference programs are written allowing incorporation of more precise models that take into consideration the assymetical mutation process inherent in vertebrate mitochondrial genomes.
Additional information
For an overview of the science behind my research, you might check out the synthetic biology wiki page I'm working on (which Drew Endy took from a crappy sketch to a beautiful reference) and the biology textbook section of NCBI. Also, GNN has a nice up-to-date list of sequenced genomes.