Gary J. Olsen

About

Gary J. Olsen is a Professor of Microbiology at the University of Illinois, affiliated with the Carl R. Woese Institute for Genomic Biology. His research primarily focuses on the functions, evolutionary histories, and structures of genes and proteins, with a significant emphasis on genomics, comparative genomics, and genome evolution. His approach combines experimental work and computational analyses to study genomes and proteins, contributing to the development of tools and resources such as the SEED genome analysis environment, the RAST genome annotation server, and the PATRIC bioinformatics resource center. His work explores the role of lateral gene transfer in evolution, revealing that most genes in a genome can be acquired by transfer, which influences the understanding of gene inheritance and genome dynamics. Olsen also develops bioinformatics tools for analyzing sequence data, codon usage, and gene transfer, enhancing the ability to interpret genomic information. His contributions extend to the integration of bioinformatics resources and the study of antimicrobial resistance, making significant impacts in microbial genomics and bioinformatics.

Research topics

• Computer Science
• Virology
• Database
• Biology
• Genetics
• Bioinformatics
• Computational biology

Selected publications

• RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

  Scientific Reports · 2015-02-10 · 2873 citations

  articleOpen access

  The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In t…

  PublisherOA PDFDOI

• Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

  Nucleic Acids Research · 2016-11-09 · 1695 citations

  articleOpen access

  The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the…

  PublisherOA PDFDOI

• KBase: The United States Department of Energy Systems Biology Knowledgebase

  Nature Biotechnology · 2018-07-01 · 1647 citations

  articleOpen access

  The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) is an open-source software and data platform designed to tackle the grand challenge of systems biology—predicting and designing biological function at scales ranging from the biomolecular to the ecological. KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large analyses on scalable computing infrastr…

  PublisherOA PDFDOI

• Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR

  Nucleic Acids Research · 2022 · 1168 citations

  The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BR…

  PublisherDOI

• The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

  Nucleic Acids Research · 2019-10-12 · 958 citations

  articleOpen access

  The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization…

  PublisherDOI

Frequent coauthors

• Claudia I. Reich

  58 shared

• Carl R. Woese

  University of Tübingen

  36 shared

• Mitchell L. Sogin

  Marine Biological Laboratory

  34 shared

• Aaron A. Best

  31 shared

• Ross Overbeek

  University of Chicago

  30 shared

• Norman R. Pace

  University of Colorado Boulder

  29 shared

• Andrew G. McArthur

  Berkeley College

  26 shared

• Hilary G. Morrison

  Marine Biological Laboratory

  26 shared

Labs

• Molecular EvolutionPI

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