Research Statement
Systems biology of microbial cultures and communities

- Pathway reconstruction and analysis of bacterial communities from *omics datasets with relevance to biogeochemical cycles, biofuels, and human health
- Development of techniques for analysis, comparison, and unification of transcriptomics and proteomics datasets

Biophysical chemistry software, methods and applications

- Author of in lucem Molecular Mechanics (ilmm, Beck, D.A.C., Alonso, D.O.V., & Daggett, V)
- Development of an XML schema for molecular mechanics parameter library: MMPL
- Methods and software development for in silico drug and protein design in high-performance computing (HPC) environments
- Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. All atom, explicit solvent native and thermal unfolding simulations for hundreds of target proteins whose folds represent about 80% of the known protein domains. For more information, see our website: http://www.dynameomics.org

eScience

- Workflow design and engineering for data-intensive analytics in biology and chemistry
- Data mining, management and sharing strategies for large biological datasets