Aleksandra Ola Tarkowska | Senior Software Engineer / Solution Architect

Aleksandra Ola Tarkowska

aleksandra.tarkowska@sanger.ac.uk
Cellular Genetics Informatics

I work in Cellular Genetics Informatics group as a Solution Architect building a large-scale data infrastructure to provide fast and easy access to petabytes of heterogeneous imaging data sets for Human Cell Atlas. I hold Master degree in Software Engineering obtained from University of Technology in Lodz. My main interest of research and development is in the area of data resources for life science.

Publications

  • A new genomic blueprint of the human gut microbiota.

    Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB et al.

    Nature 2019;568;7753;499-504

    PUBMED: 30745586; PMC: 6784870; DOI: 10.1038/s41586-019-0965-1

  • Eleven quick tips to build a usable REST API for life sciences.

    Tarkowska A, Carvalho-Silva D, Cook CE, Turner E, Finn RD and Yates AD

    PLoS computational biology 2018;14;12;e1006542

    PUBMED: 30543619; PMC: 6292566; DOI: 10.1371/journal.pcbi.1006542

  • The Image Data Resource: A Bioimage Data Integration and Publication Platform.

    Williams E, Moore J, Li SW, Rustici G, Tarkowska A et al.

    Nature methods 2017;14;8;775-781

    PUBMED: 28775673; PMC: 5536224; DOI: 10.1038/nmeth.4326

  • Metadata management for high content screening in OMERO.

    Li S, Besson S, Blackburn C, Carroll M, Ferguson RK et al.

    Methods (San Diego, Calif.) 2016;96;27-32

    PUBMED: 26476368; PMC: 4773399; DOI: 10.1016/j.ymeth.2015.10.006

  • Publishing and sharing multi-dimensional image data with OMERO.

    Burel JM, Besson S, Blackburn C, Carroll M, Ferguson RK et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2015;26;9-10;441-7

    PUBMED: 26223880; PMC: 4602067; DOI: 10.1007/s00335-015-9587-6

  • OMERO: flexible, model-driven data management for experimental biology.

    Allan C, Burel JM, Moore J, Blackburn C, Linkert M et al.

    Nature methods 2012;9;3;245-53

    PUBMED: 22373911; PMC: 3437820; DOI: 10.1038/nmeth.1896

  • Metadata matters: access to image data in the real world.

    Linkert M, Rueden CT, Allan C, Burel JM, Moore W et al.

    The Journal of cell biology 2010;189;5;777-82

    PUBMED: 20513764; PMC: 2878938; DOI: 10.1083/jcb.201004104

  • Bioimage informatics for experimental biology.

    Swedlow JR, Goldberg IG, Eliceiri KW and OME Consortium

    Annual review of biophysics 2009;38;327-46

    PUBMED: 19416072; PMC: 3522875; DOI: 10.1146/annurev.biophys.050708.133641

  • Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments.

    Almeida A, Mitchell AL, Tarkowska A and Finn RD

    GigaScience 2018;7;5

    PUBMED: 29762668; PMC: 5967554; DOI: 10.1093/gigascience/giy054

  • EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.

    Mitchell AL, Scheremetjew M, Denise H, Potter S, Tarkowska A et al.

    Nucleic acids research 2018;46;D1;D726-D735

    PUBMED: 29069476; PMC: 5753268; DOI: 10.1093/nar/gkx967

  • Eleven quick tips to build a usable REST API for life sciences.

    Tarkowska A, Carvalho-Silva D, Cook CE, Turner E, Finn RD and Yates AD

    PLoS computational biology 2018;14;12;e1006542

    PUBMED: 30543619; PMC: 6292566; DOI: 10.1371/journal.pcbi.1006542

  • Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments.

    Almeida A, Mitchell AL, Tarkowska A and Finn RD

    GigaScience 2018;7;5

    PUBMED: 29762668; PMC: 5967554; DOI: 10.1093/gigascience/giy054

  • EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.

    Mitchell AL, Scheremetjew M, Denise H, Potter S, Tarkowska A et al.

    Nucleic acids research 2018;46;D1;D726-D735

    PUBMED: 29069476; PMC: 5753268; DOI: 10.1093/nar/gkx967

  • The Image Data Resource: A Bioimage Data Integration and Publication Platform.

    Williams E, Moore J, Li SW, Rustici G, Tarkowska A et al.

    Nature methods 2017;14;8;775-781

    PUBMED: 28775673; PMC: 5536224; DOI: 10.1038/nmeth.4326

  • Metadata management for high content screening in OMERO.

    Li S, Besson S, Blackburn C, Carroll M, Ferguson RK et al.

    Methods (San Diego, Calif.) 2016;96;27-32

    PUBMED: 26476368; PMC: 4773399; DOI: 10.1016/j.ymeth.2015.10.006

  • Publishing and sharing multi-dimensional image data with OMERO.

    Burel JM, Besson S, Blackburn C, Carroll M, Ferguson RK et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2015;26;9-10;441-7

    PUBMED: 26223880; PMC: 4602067; DOI: 10.1007/s00335-015-9587-6

  • OMERO: flexible, model-driven data management for experimental biology.

    Allan C, Burel JM, Moore J, Blackburn C, Linkert M et al.

    Nature methods 2012;9;3;245-53

    PUBMED: 22373911; PMC: 3437820; DOI: 10.1038/nmeth.1896

  • Metadata matters: access to image data in the real world.

    Linkert M, Rueden CT, Allan C, Burel JM, Moore W et al.

    The Journal of cell biology 2010;189;5;777-82

    PUBMED: 20513764; PMC: 2878938; DOI: 10.1083/jcb.201004104

Aleksandra Ola Tarkowska

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