Network Systems Science and Advanced Computing

Andrew Warren

  • Research Assistant Professor
Andrew Warren Headshot
Bio

Bio

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.

  • 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

Selected Publications
Network Systems Science and Advanced Computing
Nucleic Acids Research, 45(D1):D535-D542: (2017) Wattam A, Davis J, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich E, Disz T, Gabbard J, Gerdes S, Henry C, Kenyon R, Machi D, Mao C, Nordberg E, Olsen G, Murphy-Olson D, Olson R, Overbeek R, Parrello B, Pusch G, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens R.
Network Systems Science and Advanced Computing
Briefings in Bioinformatics, July 2019. 20(4):1094-1102.: (2017) Antonopoulos D, Assaf R, Aziz R, Brettin T, Bun C, Conrad N, Davis J, Dietrich E, Disz T, Gerdes S, Kenyon R, Machi D, Mao C, Murphy-Olson D, Nordberg E, Olsen G, Olson R, Overbeek R, Parrello B, Pusch G, Santerre J, Shukla M, Stevens R, VanOeffelen M, Vonstein V, Warren A, Wattam A, Xia F, Yoo H.
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