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
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 . Nucleic Acids Research. 2017; 45(D1):D535-542
Network Systems Science and Advanced Computing
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 . Briefings in Bioinformatics. 2017; 20(4):1094-1102
In the News
Warren