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Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.
Meisel, Jacquelyn S; Nasko, Daniel J; Brubach, Brian; Cepeda-Espinoza, Victoria; Chopyk, Jessica; Corrada-Bravo, Héctor; Fedarko, Marcus; Ghurye, Jay; Javkar, Kiran; Olson, Nathan D; Shah, Nidhi; Allard, Sarah M; Bazinet, Adam L; Bergman, Nicholas H; Brown, Alexis; Caporaso, J Gregory; Conlan, Sean; DiRuggiero, Jocelyne; Forry, Samuel P; Hasan, Nur A; Kralj, Jason; Luethy, Paul M; Milton, Donald K; Ondov, Brian D; Preheim, Sarah; Ratnayake, Shashikala; Rogers, Stephanie M; Rosovitz, M J; Sakowski, Eric G; Schliebs, Nils Oliver; Sommer, Daniel D; Ternus, Krista L; Uritskiy, Gherman; Zhang, Sean X; Pop, Mihai; Treangen, Todd J.
Afiliação
  • Meisel JS; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
  • Nasko DJ; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
  • Brubach B; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
  • Cepeda-Espinoza V; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
  • Chopyk J; School of Public Health, University of Maryland, College Park, College Park, MD, USA.
  • Corrada-Bravo H; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
  • Fedarko M; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
  • Ghurye J; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
  • Javkar K; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
  • Olson ND; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
  • Shah N; Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
  • Allard SM; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
  • Bazinet AL; School of Public Health, University of Maryland, College Park, College Park, MD, USA.
  • Bergman NH; National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA.
  • Brown A; National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA.
  • Caporaso JG; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
  • Conlan S; The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
  • DiRuggiero J; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • Forry SP; Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
  • Hasan NA; Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
  • Kralj J; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
  • Luethy PM; CosmosID, Inc., Rockville, MD, USA.
  • Milton DK; Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
  • Ondov BD; Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA.
  • Preheim S; Maryland Institute for Applied Environmental Health, School of Public Health, University of Maryland, College Park, College Park, MD, USA.
  • Ratnayake S; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
  • Rogers SM; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • Rosovitz MJ; Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA.
  • Sakowski EG; National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA.
  • Schliebs NO; B.Next, In-Q-Tel, Inc., Arlington, VA, USA.
  • Sommer DD; National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA.
  • Ternus KL; Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA.
  • Uritskiy G; Department of Computer Science, University of Tübingen, Tübingen, Germany.
  • Zhang SX; National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA.
  • Pop M; Signature Science, LLC, Arlington, VA, USA.
  • Treangen TJ; Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
Microbiome ; 6(1): 197, 2018 11 05.
Article em En | MEDLINE | ID: mdl-30396371
ABSTRACT
The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Biologia Computacional / Armas Biológicas / Metagenômica / Sequenciamento de Nucleotídeos em Larga Escala Tipo de estudo: Diagnostic_studies / Guideline Limite: Humans Idioma: En Ano de publicação: 2018 Tipo de documento: Article
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Biologia Computacional / Armas Biológicas / Metagenômica / Sequenciamento de Nucleotídeos em Larga Escala Tipo de estudo: Diagnostic_studies / Guideline Limite: Humans Idioma: En Ano de publicação: 2018 Tipo de documento: Article