Skip to content

Research at St Andrews

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Research output: Contribution to journalArticle

DOI

Open Access permissions

Open

Author(s)

Silvia Argimón, Khalil Abudahab, Richard J. E. Goater, Artemij Fedosejev, Jyothish Bhai, Corinna Glasner, Edward J. Feil, Matthew T. G. Holden, Corin A. Yeats, Hajo Grundmann, Brian G. Spratt, David M. Aanensen

School/Research organisations

Abstract

Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets.
Close

Details

Original languageEnglish
Number of pages11
JournalMicrobial Genomics
Volume2
Issue number11
DOIs
Publication statusPublished - 30 Nov 2016

    Research areas

  • Open data, Trees, Phylogenomics, Population genomics, Phylogeography

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus

    Harrison, E. M., Ba, X., Coll, F., Blane, B., Restif, O., Carvell, H., Köser, C. U., Jamrozy, D., Reuter, S., Lovering, A., Gleadall, N., Bellis, K. L., Uhlemann, A. C., Lowy, F. D., Massey, R. C., Grilo, I. R., Sobral, R., Larsen, J., Rhod Larsen, A., Vingsbo Lundberg, C. & 5 othersParkhill, J., Paterson, G. K., Holden, M. T. G., Peacock, S. J. & Holmes, M. A., 24 Jun 2019, In : Nature Microbiology. 15 p.

    Research output: Contribution to journalArticle

  2. Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

    Davies, M. R., McIntyre, L., Mutreja, A., Lacey, J. A., Lees, J. A., Towers, R. J., Duchêne, S., Smeesters, P. R., Frost, H. R., Price, D. J., Holden, M. T. G., David, S., Giffard, P. M., Worthing, K. A., Seale, A. C., Berkley, J. A., Harris, S. R., Rivera-Hernandez, T., Berking, O., Cork, A. J. & 18 othersTorres, R. S. L. A., Lithgow, T., Strugnell, R. A., Bergmann, R., Nitsche-Schmitz, P., Chhatwal, G. S., Bentley, S. D., Fraser, J. D., Moreland, N. J., Carapetis, J. R., Steer, A. C., Parkhill, J., Saul, A., Williamson, D. A., Currie, B. J., Tong, S. Y. C., Dougan, G. & Walker, M. J., Jun 2019, In : Nature Genetics. 51, 6, p. 1035-1043

    Research output: Contribution to journalArticle

  3. Antimicrobial resistance in atopic dermatitis: need for an urgent rethink

    Harkins, C. P., Holden, M. T. G. & Irvine, A. D., Mar 2019, In : Annals of Allergy Asthma & Immunology. 122, 3, p. 236-240 5 p.

    Research output: Contribution to journalArticle

  4. Molecular epidemiology and expression of capsular polysaccharides in Staphylococcus aureus clinical isolates in the United States

    Mohamed, N., Timofeyeva, Y., Jamrozy, D., Rojas, E., Hao, L., Silmon de Monerri, N. C., Hawkins, J., Singh, G., Cai, B., Liberator, P., Sebastian, S., Donald, R. G. K., Scully, I. L., Jones, C. H., Creech, C. B., Thomsen, I., Parkhill, J., Peacock, S. J., Jansen, K. U., Holden, M. T. G. & 1 othersAnderson, A. S., 14 Jan 2019, In : PLoS ONE. 14, 1, 33 p., e0208356.

    Research output: Contribution to journalArticle

Related by journal

  1. Distinct evolutionary patterns of Neisseria meningitidis serogroup B disease outbreaks at two universities in the USA

    Hao, L., Holden, M. T. G., Wang, X., Andrew, L., Wellnitz, S., Hu, F., Whaley, M., Sammons, S., Knipe, K., Frace, M., McNamara, L. A., Liberator, P. & Anderson, A. S., Apr 2018, In : Microbial Genomics. 4, 4, 10 p., e000155.

    Research output: Contribution to journalArticle

  2. Genetic analysis of invasive Escherichia coli in Scotland reveals determinants of healthcare-associated versus community-acquired infections

    Goswami, C., Fox, S., Holden, M., Connor, M., Leanord, A. & Evans, T. J., 1 Jun 2018, In : Microbial Genomics. 4, 6, 15 p., 000190.

    Research output: Contribution to journalArticle

  3. Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns

    Donker, T., Reuter, S., Scriberras, J., Reynolds, R., Brown, N. M., Török, M. E., James, R., Network, E. O. E. M. R., Aanensen, D. M., Bentley, S. D., Holden, M. T. G., Parkhill, J., Spratt, B. G., Peacock, S. J., Feil, E. J. & Grundmann, H., 9 Jul 2017, In : Microbial Genomics. 3, 7, 12 p., e000113.

    Research output: Contribution to journalArticle

  4. Whole-genome sequencing to investigate a non-clonal melioidosis cluster on a remote Australian island

    Sarovich, D. S., Chapple, S. N. J., Price, E. P., Mayo, M., Holden, M. T. G., Peacock, S. J. & Currie, B. J., 31 Aug 2017, In : Microbial Genomics. 3, 8, 7 p., e000117.

    Research output: Contribution to journalArticle

ID: 248115969