Andrew Warren

  • Research Assistant Professor
Andrew Warren headshot


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
Cucinell C; Dickerman A; Kenyon R; Machi D; Mao C; Warren A; Wattam A; Olson R; Assaf R; Brettin T; Conrad N; Davis J; Dempsey D; Dietrich E; Kuscuoglo M; Lefkowitz E; Lu J; Macken C; Niewiadomska A; Nguyen M; Olsen G; Overbeek R; Parrello B; Porter J; Pusch G; Shukla M; Singh I; Stewart L; Tan G; Thomas C; VanOeffelen M; Wallace Z; Xia F; Yoo H; Zhang Y; Zmasek C; Scheuermann R; Stevens R . Nucleic Acids Res.. 2023; 51(D1):D678–D689
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
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