I am a Research Assistant Professor at the Biocomplexity Institute and Initiative at the University of Virginia, a Senior Scientist and Senior Software Engineer for BVBRC under NIAID. Recently I was Principal Investigator for a Functional Genomic and Computational Assessment of Threats (FunGCAT) team, an IARPA project, where I led a team of over 60 individuals to develop analysis tools to screen nucleotide synthesis requests. As PI of this project I oversaw creating novel methods for organism prediction, threat assessment, and functional prediction using a number of deep learning methods. Previous projects include developments in genome annotation, organism prediction, RNA-Seq analysis, comparative genomics, algorithmics, modeling genomes as graphs, and graph theory. Since 2011 I have worked with the PATRIC project during which time I created core concepts of the current resource to facilitate comparative genomics research as well as popular tools for processing research data. For NIAID I created RNA-Rocket, a popular tool, with thousands of registered users, for processing RNA-Seq data related to infectious disease whose technology has been integrated into the Bioinformatic Resource Centers. I recently created the concept of pan-synteny graphs, a new graph-based model for quickly comparing thousands of bacterial genomes. As a scientist in the Network Systems Science and Advanced Computing group, I work with a trans-disciplinary team of experts in modeling different levels of infectious disease spread for medical and defense research.
Metagenomics processing, pan-genomes, genome graphs, RNA-Seq algorithms, barcode systems for organism identification, ontology analysis/expansion/assignment, genome annotation
I have research expertise in developing and applying algorithms for processing biological data for insight and hypothesis testing using comparative genomics, experimental analysis, machine learning, data mining, and graph modeling.
- PATRIC as a unique resource for studying antimicrobial resistance
Briefings in bioinformatics, (2017) Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S, Kenyon RW, Machi D, Mao C, Murphy-Olson DE, Nordberg EK, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Santerre J, Shukla M, Stevens RL, VanOeffelen M, Vonstein V, Warren AS, Wattam AR, Xia F, Yoo H
- Improvements to PATRIC, the allbacterial Bioinformatics Database and Analysis Resource Center
Nucleic Acids Res, 45(D1):D535-D542. (2017) Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL, Gerdes S, Henry CS, Kenyon RW, Machi D, Mao C, Nordberg EK, Olsen GJ, Murphy-Olson DE, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens RL
Virginia Polytechnic Institute and State University, Blacksburg, VA; Computer Science, Ph.D., 2017
Virginia Polytechnic Institute and State University, Blacksburg, VA; Computer Science, M.S., 2007
Virginia Polytechnic Institute and State University, Blacksburg, VA; Biochemistry, B.S., 2004