Microbial Ecology & Evolution
My main research interest is the understanding of eco-evolutionary principles governing microbial communities: primary evolutionary and ecologic forces shaping populations and their metabolic potential, their interactions with other microbial species, their hosts, and the environment, and the role of stochasticity.
In the pursuit of these questions, I’ve garnered ample experience on genomic and metagenomic analyses in environmental, clinical, agricultural, and engineered settings, including the description, characterization, modeling, and simulation of microbial communities and populations. I’ve explored and discussed both theoretical and practical problems on microbiome analysis including the development and application of methods on phylogenomics, taxonomy of prokaryotes, metabolic modeling, statistical techniques, and sequence analyses.
I’ve authored over 50 papers and book chapters (about a third as first author) with over three thousand citations and an h-index of 24, presented multiple workshops, seminars, and symposia on microbiome analysis for researchers and undergraduate educators, and served as reviewer for several international journals. See my list of publications.
New ideas need implementation, and throughout my research I’ve made it a point to implement those ideas in efficient, high-quality, well-documented, and user-friendly software. I’ve developed tens of bioinformatic tools and web interfaces in a variety of programming languages and frameworks (Ruby, Rails, Perl, R, C++, etc) with over 10,000 downloads or online queries per month. See my software contributions.