Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-09-16

AUTHORS

John A. Lees, Minna Vehkala, Niko Välimäki, Simon R. Harris, Claire Chewapreecha, Nicholas J. Croucher, Pekka Marttinen, Mark R. Davies, Andrew C. Steer, Steven Y. C. Tong, Antti Honkela, Julian Parkhill, Stephen D. Bentley, Jukka Corander

ABSTRACT

Bacterial genomes vary extensively in terms of both gene content and gene sequence. This plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. Here we introduce a computationally scalable and widely applicable statistical method (SEER) for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to tens of thousands of genomes by counting variable-length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogens Streptococcus pneumoniae and Streptococcus pyogenes, SEER identifies relevant previously characterized resistance determinants for several antibiotics and discovers potential novel factors related to the invasiveness of S. pyogenes. We thus demonstrate that our method can answer important biologically and medically relevant questions. More... »

PAGES

12797

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/ncomms12797

DOI

http://dx.doi.org/10.1038/ncomms12797

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1047980738

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27633831


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Computer Simulation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome-Wide Association Study", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Nucleic Acid Amplification Techniques", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Streptococcus pneumoniae", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Streptococcus pyogenes", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Wellcome Sanger Institute", 
          "id": "https://www.grid.ac/institutes/grid.10306.34", 
          "name": [
            "Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lees", 
        "givenName": "John A.", 
        "id": "sg:person.016027633411.82", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016027633411.82"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Helsinki", 
          "id": "https://www.grid.ac/institutes/grid.7737.4", 
          "name": [
            "Department of Mathematics and Statistics, University of Helsinki, Helsinki FI-00014, Finland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Vehkala", 
        "givenName": "Minna", 
        "id": "sg:person.01106574512.01", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01106574512.01"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Helsinki", 
          "id": "https://www.grid.ac/institutes/grid.7737.4", 
          "name": [
            "Department of Medical and Clinical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki FI-00014, Finland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "V\u00e4lim\u00e4ki", 
        "givenName": "Niko", 
        "id": "sg:person.01130615551.21", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01130615551.21"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Wellcome Sanger Institute", 
          "id": "https://www.grid.ac/institutes/grid.10306.34", 
          "name": [
            "Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Harris", 
        "givenName": "Simon R.", 
        "id": "sg:person.014130257112.00", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014130257112.00"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Cambridge", 
          "id": "https://www.grid.ac/institutes/grid.5335.0", 
          "name": [
            "Department of Medicine, University of Cambridge, Cambridge CB2 0SP, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Chewapreecha", 
        "givenName": "Claire", 
        "id": "sg:person.01273660161.10", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01273660161.10"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Imperial College London", 
          "id": "https://www.grid.ac/institutes/grid.7445.2", 
          "name": [
            "Department of Infectious Disease Epidemiology, Imperial College, London W2 1NY, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Croucher", 
        "givenName": "Nicholas J.", 
        "id": "sg:person.01355254423.20", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01355254423.20"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Aalto University", 
          "id": "https://www.grid.ac/institutes/grid.5373.2", 
          "name": [
            "Department of Computer Science, Aalto University, Espoo FI-00076, Finland", 
            "Helsinki Institute of Information Technology HIIT, Department of Computer Science, Aalto University, Espoo FI-00076, Finland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Marttinen", 
        "givenName": "Pekka", 
        "id": "sg:person.0753733617.28", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0753733617.28"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Melbourne", 
          "id": "https://www.grid.ac/institutes/grid.1008.9", 
          "name": [
            "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3010, Australia"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Davies", 
        "givenName": "Mark R.", 
        "id": "sg:person.01062356656.48", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01062356656.48"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Murdoch Childrens Research Institute", 
          "id": "https://www.grid.ac/institutes/grid.1058.c", 
          "name": [
            "Centre for International Child Health, Department of Paediatrics, University of Melbourne, Melbourne, Victoria 3052, Australia", 
            "Group A Streptococcal Research Group, Murdoch Children\u2019s Research Institute, Parkville, Victoria 3052, Australia"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Steer", 
        "givenName": "Andrew C.", 
        "id": "sg:person.01247427574.29", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01247427574.29"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Menzies School of Health Research", 
          "id": "https://www.grid.ac/institutes/grid.271089.5", 
          "name": [
            "Menzies School of Health Research, Darwin, Northern Territory 0811, Australia"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Tong", 
        "givenName": "Steven Y. C.", 
        "id": "sg:person.015775213232.74", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015775213232.74"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Helsinki", 
          "id": "https://www.grid.ac/institutes/grid.7737.4", 
          "name": [
            "Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki FI-00014, Finland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Honkela", 
        "givenName": "Antti", 
        "id": "sg:person.0675465056.12", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0675465056.12"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Wellcome Sanger Institute", 
          "id": "https://www.grid.ac/institutes/grid.10306.34", 
          "name": [
            "Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Parkhill", 
        "givenName": "Julian", 
        "id": "sg:person.01273656103.87", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01273656103.87"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Wellcome Sanger Institute", 
          "id": "https://www.grid.ac/institutes/grid.10306.34", 
          "name": [
            "Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bentley", 
        "givenName": "Stephen D.", 
        "id": "sg:person.01305165520.99", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01305165520.99"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Helsinki", 
          "id": "https://www.grid.ac/institutes/grid.7737.4", 
          "name": [
            "Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK", 
            "Department of Mathematics and Statistics, University of Helsinki, Helsinki FI-00014, Finland", 
            "Department of Biostatistics, University of Oslo, 0317 Oslo, Norway"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Corander", 
        "givenName": "Jukka", 
        "id": "sg:person.01125514227.61", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01125514227.61"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1093/molbev/mst028", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000292919"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/iai.71.10.6079-6082.2003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001949246"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkg509", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002198958"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msr268", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004713377"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg3472", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004746414", 
          "https://doi.org/10.1038/nrg3472"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.229202", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006260064"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/aac.45.4.1104-1108.2001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008327062"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/hmg/ddv260", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015966089"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1534/genetics.108.098863", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016552150"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1534/genetics.108.098863", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016552150"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1198545", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017237439"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bth471", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018284836"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btu340", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018398611"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0378-1097(02)01184-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021740920"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btr509", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022904685"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2007-8-5-r71", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023243160", 
          "https://doi.org/10.1186/gb-2007-8-5-r71"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.3201/eid2202.151358", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024957091"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.tim.2009.03.002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025642026"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.2656", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026226151", 
          "https://doi.org/10.1038/ng.2656"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0081760", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026743571"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jcm.00312-09", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029464337"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msm064", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029850425"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/sim.1047", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031330449"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1847", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031429813", 
          "https://doi.org/10.1038/ng1847"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1847", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031429813", 
          "https://doi.org/10.1038/ng1847"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.2747", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034222991", 
          "https://doi.org/10.1038/ng.2747"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.165415.113", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034850872"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmicrobiol.2016.59", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035046492", 
          "https://doi.org/10.1038/nmicrobiol.2016.59"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.bpg.2014.04.009", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035800913"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.micro.53.1.217", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036692682"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.2895", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037018769", 
          "https://doi.org/10.1038/ng.2895"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.mib.2015.03.002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037370858"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btt020", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038110157"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bts187", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039045908"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pgen.1004547", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039447206"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.01343-08", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040452434"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bti1200", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040834749"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-015-0866-z", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042902494", 
          "https://doi.org/10.1186/s13059-015-0866-z"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.4161/fly.19695", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046734556"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1305559110", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047807069"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-016-0997-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050687712", 
          "https://doi.org/10.1186/s13059-016-0997-x"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-016-0997-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050687712", 
          "https://doi.org/10.1186/s13059-016-0997-x"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.074492.107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051720574"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/cmr.00101-13", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051998097"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msp063", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052677007"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msp063", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052677007"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ncomms7740", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053370903", 
          "https://doi.org/10.1038/ncomms7740"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.21105/joss.00026", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1068918725"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1082423803", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1082813051", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/0471272612", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1098661018"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/0471272612", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1098661018"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2016-09-16", 
    "datePublishedReg": "2016-09-16", 
    "description": "Bacterial genomes vary extensively in terms of both gene content and gene sequence. This plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. Here we introduce a computationally scalable and widely applicable statistical method (SEER) for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to tens of thousands of genomes by counting variable-length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogens Streptococcus pneumoniae and Streptococcus pyogenes, SEER identifies relevant previously characterized resistance determinants for several antibiotics and discovers potential novel factors related to the invasiveness of S. pyogenes. We thus demonstrate that our method can answer important biologically and medically relevant questions.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/ncomms12797", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.3778831", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.4247274", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.4580145", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1043282", 
        "issn": [
          "2041-1723"
        ], 
        "name": "Nature Communications", 
        "type": "Periodical"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "7"
      }
    ], 
    "name": "Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes", 
    "pagination": "12797", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "e49214a2f27bedb877673a251f37399269d24751a1e3d96d8b026cdc9ab2c10e"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "27633831"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101528555"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/ncomms12797"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1047980738"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/ncomms12797", 
      "https://app.dimensions.ai/details/publication/pub.1047980738"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T01:14", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8697_00000551.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://www.nature.com/articles/ncomms12797"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/ncomms12797'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/ncomms12797'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/ncomms12797'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/ncomms12797'


 

This table displays all metadata directly associated to this object as RDF triples.

370 TRIPLES      21 PREDICATES      82 URIs      27 LITERALS      16 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/ncomms12797 schema:about N169f9fd4bcaf474d8daacb6de474f4a2
2 N1f0fbba2a27042ada77cdb8c3bc715e4
3 N4e96e1371cfe4d83986d2f02989c8c31
4 N5bedee94bd2a4aee894e2e09ba903776
5 N5cb1097283fc43c093a4e946757cc6bd
6 N8be00b9368ef494080a5dc4e7373e52c
7 Nd2b5a4301f1640d99384510781c3d180
8 Nf9753102f22e43969cfce65ca9bae63e
9 anzsrc-for:06
10 anzsrc-for:0604
11 schema:author N409aaff9c9ee42ee8443fa81bbefc97e
12 schema:citation sg:pub.10.1038/ncomms7740
13 sg:pub.10.1038/ng.2656
14 sg:pub.10.1038/ng.2747
15 sg:pub.10.1038/ng.2895
16 sg:pub.10.1038/ng1847
17 sg:pub.10.1038/nmicrobiol.2016.59
18 sg:pub.10.1038/nrg3472
19 sg:pub.10.1186/gb-2007-8-5-r71
20 sg:pub.10.1186/s13059-015-0866-z
21 sg:pub.10.1186/s13059-016-0997-x
22 https://app.dimensions.ai/details/publication/pub.1082423803
23 https://app.dimensions.ai/details/publication/pub.1082813051
24 https://doi.org/10.1002/0471272612
25 https://doi.org/10.1002/sim.1047
26 https://doi.org/10.1016/j.bpg.2014.04.009
27 https://doi.org/10.1016/j.mib.2015.03.002
28 https://doi.org/10.1016/j.tim.2009.03.002
29 https://doi.org/10.1016/s0378-1097(02)01184-9
30 https://doi.org/10.1073/pnas.1305559110
31 https://doi.org/10.1093/bioinformatics/bth471
32 https://doi.org/10.1093/bioinformatics/bti1200
33 https://doi.org/10.1093/bioinformatics/btr509
34 https://doi.org/10.1093/bioinformatics/bts187
35 https://doi.org/10.1093/bioinformatics/btt020
36 https://doi.org/10.1093/bioinformatics/btu340
37 https://doi.org/10.1093/hmg/ddv260
38 https://doi.org/10.1093/molbev/msm064
39 https://doi.org/10.1093/molbev/msp063
40 https://doi.org/10.1093/molbev/msr268
41 https://doi.org/10.1093/molbev/mst028
42 https://doi.org/10.1093/nar/gkg509
43 https://doi.org/10.1101/gr.074492.107
44 https://doi.org/10.1101/gr.165415.113
45 https://doi.org/10.1101/gr.229202
46 https://doi.org/10.1126/science.1198545
47 https://doi.org/10.1128/aac.45.4.1104-1108.2001
48 https://doi.org/10.1128/cmr.00101-13
49 https://doi.org/10.1128/iai.71.10.6079-6082.2003
50 https://doi.org/10.1128/jb.01343-08
51 https://doi.org/10.1128/jcm.00312-09
52 https://doi.org/10.1146/annurev.micro.53.1.217
53 https://doi.org/10.1371/journal.pgen.1004547
54 https://doi.org/10.1371/journal.pone.0081760
55 https://doi.org/10.1534/genetics.108.098863
56 https://doi.org/10.21105/joss.00026
57 https://doi.org/10.3201/eid2202.151358
58 https://doi.org/10.4161/fly.19695
59 schema:datePublished 2016-09-16
60 schema:datePublishedReg 2016-09-16
61 schema:description Bacterial genomes vary extensively in terms of both gene content and gene sequence. This plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. Here we introduce a computationally scalable and widely applicable statistical method (SEER) for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to tens of thousands of genomes by counting variable-length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogens Streptococcus pneumoniae and Streptococcus pyogenes, SEER identifies relevant previously characterized resistance determinants for several antibiotics and discovers potential novel factors related to the invasiveness of S. pyogenes. We thus demonstrate that our method can answer important biologically and medically relevant questions.
62 schema:genre research_article
63 schema:inLanguage en
64 schema:isAccessibleForFree true
65 schema:isPartOf N6c2201ffb7194ac7852bb1036e0b461a
66 sg:journal.1043282
67 schema:name Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
68 schema:pagination 12797
69 schema:productId N7dfccaa40acd4866bdeae9ee1cddf353
70 N9fb67e709950445cbf0f48d21b78f928
71 Ne2051381307e463dab71e7319763d866
72 Nf59b552c721e43cda29e4483f89ec8ce
73 Nfbe7366abf2a4e21b181a3dd33300883
74 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047980738
75 https://doi.org/10.1038/ncomms12797
76 schema:sdDatePublished 2019-04-11T01:14
77 schema:sdLicense https://scigraph.springernature.com/explorer/license/
78 schema:sdPublisher N4709b2d2128043fabd59a995a433e39f
79 schema:url http://www.nature.com/articles/ncomms12797
80 sgo:license sg:explorer/license/
81 sgo:sdDataset articles
82 rdf:type schema:ScholarlyArticle
83 N169f9fd4bcaf474d8daacb6de474f4a2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
84 schema:name Streptococcus pneumoniae
85 rdf:type schema:DefinedTerm
86 N1f0fbba2a27042ada77cdb8c3bc715e4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
87 schema:name DNA, Bacterial
88 rdf:type schema:DefinedTerm
89 N327c43c202b34cc690cf4e809ee53d86 rdf:first sg:person.01355254423.20
90 rdf:rest N3e861b75ae3a4ee28a93470cdc22b732
91 N3a43cc5c1ae64fa6b352799aa6ba2b2d rdf:first sg:person.01305165520.99
92 rdf:rest Nd0abdc34fae041f2aae4c500a0aa02ed
93 N3e861b75ae3a4ee28a93470cdc22b732 rdf:first sg:person.0753733617.28
94 rdf:rest N9c9701799bde487194c92353491304bc
95 N409aaff9c9ee42ee8443fa81bbefc97e rdf:first sg:person.016027633411.82
96 rdf:rest Nc621c3925e914348bb954cb45ec6ab92
97 N4709b2d2128043fabd59a995a433e39f schema:name Springer Nature - SN SciGraph project
98 rdf:type schema:Organization
99 N4e96e1371cfe4d83986d2f02989c8c31 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
100 schema:name Models, Genetic
101 rdf:type schema:DefinedTerm
102 N588858e11fed4bada449a1a4aa2e7991 rdf:first sg:person.01130615551.21
103 rdf:rest Nda0b9762dc0041b78c1cca12c1064958
104 N5bedee94bd2a4aee894e2e09ba903776 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
105 schema:name Nucleic Acid Amplification Techniques
106 rdf:type schema:DefinedTerm
107 N5cb1097283fc43c093a4e946757cc6bd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
108 schema:name Genome, Bacterial
109 rdf:type schema:DefinedTerm
110 N658a302a98854ffebb1b3c351e926127 rdf:first sg:person.015775213232.74
111 rdf:rest N94ecd03f6c5a4da7b5059af64c951cf8
112 N6c2201ffb7194ac7852bb1036e0b461a schema:volumeNumber 7
113 rdf:type schema:PublicationVolume
114 N7dfccaa40acd4866bdeae9ee1cddf353 schema:name dimensions_id
115 schema:value pub.1047980738
116 rdf:type schema:PropertyValue
117 N8be00b9368ef494080a5dc4e7373e52c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
118 schema:name Streptococcus pyogenes
119 rdf:type schema:DefinedTerm
120 N94ecd03f6c5a4da7b5059af64c951cf8 rdf:first sg:person.0675465056.12
121 rdf:rest Nfacc11bc869141e7b2540cda8583004f
122 N9c9701799bde487194c92353491304bc rdf:first sg:person.01062356656.48
123 rdf:rest Nf9de27c3a49d416298206098c9bc3bf0
124 N9fb67e709950445cbf0f48d21b78f928 schema:name doi
125 schema:value 10.1038/ncomms12797
126 rdf:type schema:PropertyValue
127 Nc621c3925e914348bb954cb45ec6ab92 rdf:first sg:person.01106574512.01
128 rdf:rest N588858e11fed4bada449a1a4aa2e7991
129 Nd0abdc34fae041f2aae4c500a0aa02ed rdf:first sg:person.01125514227.61
130 rdf:rest rdf:nil
131 Nd2b5a4301f1640d99384510781c3d180 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
132 schema:name Computer Simulation
133 rdf:type schema:DefinedTerm
134 Nda0b9762dc0041b78c1cca12c1064958 rdf:first sg:person.014130257112.00
135 rdf:rest Nee6915d44b49447a95952e87ca566cf1
136 Ne2051381307e463dab71e7319763d866 schema:name nlm_unique_id
137 schema:value 101528555
138 rdf:type schema:PropertyValue
139 Nee6915d44b49447a95952e87ca566cf1 rdf:first sg:person.01273660161.10
140 rdf:rest N327c43c202b34cc690cf4e809ee53d86
141 Nf59b552c721e43cda29e4483f89ec8ce schema:name readcube_id
142 schema:value e49214a2f27bedb877673a251f37399269d24751a1e3d96d8b026cdc9ab2c10e
143 rdf:type schema:PropertyValue
144 Nf9753102f22e43969cfce65ca9bae63e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
145 schema:name Genome-Wide Association Study
146 rdf:type schema:DefinedTerm
147 Nf9de27c3a49d416298206098c9bc3bf0 rdf:first sg:person.01247427574.29
148 rdf:rest N658a302a98854ffebb1b3c351e926127
149 Nfacc11bc869141e7b2540cda8583004f rdf:first sg:person.01273656103.87
150 rdf:rest N3a43cc5c1ae64fa6b352799aa6ba2b2d
151 Nfbe7366abf2a4e21b181a3dd33300883 schema:name pubmed_id
152 schema:value 27633831
153 rdf:type schema:PropertyValue
154 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
155 schema:name Biological Sciences
156 rdf:type schema:DefinedTerm
157 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
158 schema:name Genetics
159 rdf:type schema:DefinedTerm
160 sg:grant.3778831 http://pending.schema.org/fundedItem sg:pub.10.1038/ncomms12797
161 rdf:type schema:MonetaryGrant
162 sg:grant.4247274 http://pending.schema.org/fundedItem sg:pub.10.1038/ncomms12797
163 rdf:type schema:MonetaryGrant
164 sg:grant.4580145 http://pending.schema.org/fundedItem sg:pub.10.1038/ncomms12797
165 rdf:type schema:MonetaryGrant
166 sg:journal.1043282 schema:issn 2041-1723
167 schema:name Nature Communications
168 rdf:type schema:Periodical
169 sg:person.01062356656.48 schema:affiliation https://www.grid.ac/institutes/grid.1008.9
170 schema:familyName Davies
171 schema:givenName Mark R.
172 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01062356656.48
173 rdf:type schema:Person
174 sg:person.01106574512.01 schema:affiliation https://www.grid.ac/institutes/grid.7737.4
175 schema:familyName Vehkala
176 schema:givenName Minna
177 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01106574512.01
178 rdf:type schema:Person
179 sg:person.01125514227.61 schema:affiliation https://www.grid.ac/institutes/grid.7737.4
180 schema:familyName Corander
181 schema:givenName Jukka
182 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01125514227.61
183 rdf:type schema:Person
184 sg:person.01130615551.21 schema:affiliation https://www.grid.ac/institutes/grid.7737.4
185 schema:familyName Välimäki
186 schema:givenName Niko
187 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01130615551.21
188 rdf:type schema:Person
189 sg:person.01247427574.29 schema:affiliation https://www.grid.ac/institutes/grid.1058.c
190 schema:familyName Steer
191 schema:givenName Andrew C.
192 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01247427574.29
193 rdf:type schema:Person
194 sg:person.01273656103.87 schema:affiliation https://www.grid.ac/institutes/grid.10306.34
195 schema:familyName Parkhill
196 schema:givenName Julian
197 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01273656103.87
198 rdf:type schema:Person
199 sg:person.01273660161.10 schema:affiliation https://www.grid.ac/institutes/grid.5335.0
200 schema:familyName Chewapreecha
201 schema:givenName Claire
202 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01273660161.10
203 rdf:type schema:Person
204 sg:person.01305165520.99 schema:affiliation https://www.grid.ac/institutes/grid.10306.34
205 schema:familyName Bentley
206 schema:givenName Stephen D.
207 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01305165520.99
208 rdf:type schema:Person
209 sg:person.01355254423.20 schema:affiliation https://www.grid.ac/institutes/grid.7445.2
210 schema:familyName Croucher
211 schema:givenName Nicholas J.
212 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01355254423.20
213 rdf:type schema:Person
214 sg:person.014130257112.00 schema:affiliation https://www.grid.ac/institutes/grid.10306.34
215 schema:familyName Harris
216 schema:givenName Simon R.
217 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014130257112.00
218 rdf:type schema:Person
219 sg:person.015775213232.74 schema:affiliation https://www.grid.ac/institutes/grid.271089.5
220 schema:familyName Tong
221 schema:givenName Steven Y. C.
222 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015775213232.74
223 rdf:type schema:Person
224 sg:person.016027633411.82 schema:affiliation https://www.grid.ac/institutes/grid.10306.34
225 schema:familyName Lees
226 schema:givenName John A.
227 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016027633411.82
228 rdf:type schema:Person
229 sg:person.0675465056.12 schema:affiliation https://www.grid.ac/institutes/grid.7737.4
230 schema:familyName Honkela
231 schema:givenName Antti
232 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0675465056.12
233 rdf:type schema:Person
234 sg:person.0753733617.28 schema:affiliation https://www.grid.ac/institutes/grid.5373.2
235 schema:familyName Marttinen
236 schema:givenName Pekka
237 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0753733617.28
238 rdf:type schema:Person
239 sg:pub.10.1038/ncomms7740 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053370903
240 https://doi.org/10.1038/ncomms7740
241 rdf:type schema:CreativeWork
242 sg:pub.10.1038/ng.2656 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026226151
243 https://doi.org/10.1038/ng.2656
244 rdf:type schema:CreativeWork
245 sg:pub.10.1038/ng.2747 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034222991
246 https://doi.org/10.1038/ng.2747
247 rdf:type schema:CreativeWork
248 sg:pub.10.1038/ng.2895 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037018769
249 https://doi.org/10.1038/ng.2895
250 rdf:type schema:CreativeWork
251 sg:pub.10.1038/ng1847 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031429813
252 https://doi.org/10.1038/ng1847
253 rdf:type schema:CreativeWork
254 sg:pub.10.1038/nmicrobiol.2016.59 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035046492
255 https://doi.org/10.1038/nmicrobiol.2016.59
256 rdf:type schema:CreativeWork
257 sg:pub.10.1038/nrg3472 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004746414
258 https://doi.org/10.1038/nrg3472
259 rdf:type schema:CreativeWork
260 sg:pub.10.1186/gb-2007-8-5-r71 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023243160
261 https://doi.org/10.1186/gb-2007-8-5-r71
262 rdf:type schema:CreativeWork
263 sg:pub.10.1186/s13059-015-0866-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1042902494
264 https://doi.org/10.1186/s13059-015-0866-z
265 rdf:type schema:CreativeWork
266 sg:pub.10.1186/s13059-016-0997-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1050687712
267 https://doi.org/10.1186/s13059-016-0997-x
268 rdf:type schema:CreativeWork
269 https://app.dimensions.ai/details/publication/pub.1082423803 schema:CreativeWork
270 https://app.dimensions.ai/details/publication/pub.1082813051 schema:CreativeWork
271 https://doi.org/10.1002/0471272612 schema:sameAs https://app.dimensions.ai/details/publication/pub.1098661018
272 rdf:type schema:CreativeWork
273 https://doi.org/10.1002/sim.1047 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031330449
274 rdf:type schema:CreativeWork
275 https://doi.org/10.1016/j.bpg.2014.04.009 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035800913
276 rdf:type schema:CreativeWork
277 https://doi.org/10.1016/j.mib.2015.03.002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037370858
278 rdf:type schema:CreativeWork
279 https://doi.org/10.1016/j.tim.2009.03.002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025642026
280 rdf:type schema:CreativeWork
281 https://doi.org/10.1016/s0378-1097(02)01184-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021740920
282 rdf:type schema:CreativeWork
283 https://doi.org/10.1073/pnas.1305559110 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047807069
284 rdf:type schema:CreativeWork
285 https://doi.org/10.1093/bioinformatics/bth471 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018284836
286 rdf:type schema:CreativeWork
287 https://doi.org/10.1093/bioinformatics/bti1200 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040834749
288 rdf:type schema:CreativeWork
289 https://doi.org/10.1093/bioinformatics/btr509 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022904685
290 rdf:type schema:CreativeWork
291 https://doi.org/10.1093/bioinformatics/bts187 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039045908
292 rdf:type schema:CreativeWork
293 https://doi.org/10.1093/bioinformatics/btt020 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038110157
294 rdf:type schema:CreativeWork
295 https://doi.org/10.1093/bioinformatics/btu340 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018398611
296 rdf:type schema:CreativeWork
297 https://doi.org/10.1093/hmg/ddv260 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015966089
298 rdf:type schema:CreativeWork
299 https://doi.org/10.1093/molbev/msm064 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029850425
300 rdf:type schema:CreativeWork
301 https://doi.org/10.1093/molbev/msp063 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052677007
302 rdf:type schema:CreativeWork
303 https://doi.org/10.1093/molbev/msr268 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004713377
304 rdf:type schema:CreativeWork
305 https://doi.org/10.1093/molbev/mst028 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000292919
306 rdf:type schema:CreativeWork
307 https://doi.org/10.1093/nar/gkg509 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002198958
308 rdf:type schema:CreativeWork
309 https://doi.org/10.1101/gr.074492.107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051720574
310 rdf:type schema:CreativeWork
311 https://doi.org/10.1101/gr.165415.113 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034850872
312 rdf:type schema:CreativeWork
313 https://doi.org/10.1101/gr.229202 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006260064
314 rdf:type schema:CreativeWork
315 https://doi.org/10.1126/science.1198545 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017237439
316 rdf:type schema:CreativeWork
317 https://doi.org/10.1128/aac.45.4.1104-1108.2001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008327062
318 rdf:type schema:CreativeWork
319 https://doi.org/10.1128/cmr.00101-13 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051998097
320 rdf:type schema:CreativeWork
321 https://doi.org/10.1128/iai.71.10.6079-6082.2003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001949246
322 rdf:type schema:CreativeWork
323 https://doi.org/10.1128/jb.01343-08 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040452434
324 rdf:type schema:CreativeWork
325 https://doi.org/10.1128/jcm.00312-09 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029464337
326 rdf:type schema:CreativeWork
327 https://doi.org/10.1146/annurev.micro.53.1.217 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036692682
328 rdf:type schema:CreativeWork
329 https://doi.org/10.1371/journal.pgen.1004547 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039447206
330 rdf:type schema:CreativeWork
331 https://doi.org/10.1371/journal.pone.0081760 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026743571
332 rdf:type schema:CreativeWork
333 https://doi.org/10.1534/genetics.108.098863 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016552150
334 rdf:type schema:CreativeWork
335 https://doi.org/10.21105/joss.00026 schema:sameAs https://app.dimensions.ai/details/publication/pub.1068918725
336 rdf:type schema:CreativeWork
337 https://doi.org/10.3201/eid2202.151358 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024957091
338 rdf:type schema:CreativeWork
339 https://doi.org/10.4161/fly.19695 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046734556
340 rdf:type schema:CreativeWork
341 https://www.grid.ac/institutes/grid.1008.9 schema:alternateName University of Melbourne
342 schema:name Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3010, Australia
343 rdf:type schema:Organization
344 https://www.grid.ac/institutes/grid.10306.34 schema:alternateName Wellcome Sanger Institute
345 schema:name Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
346 rdf:type schema:Organization
347 https://www.grid.ac/institutes/grid.1058.c schema:alternateName Murdoch Childrens Research Institute
348 schema:name Centre for International Child Health, Department of Paediatrics, University of Melbourne, Melbourne, Victoria 3052, Australia
349 Group A Streptococcal Research Group, Murdoch Children’s Research Institute, Parkville, Victoria 3052, Australia
350 rdf:type schema:Organization
351 https://www.grid.ac/institutes/grid.271089.5 schema:alternateName Menzies School of Health Research
352 schema:name Menzies School of Health Research, Darwin, Northern Territory 0811, Australia
353 rdf:type schema:Organization
354 https://www.grid.ac/institutes/grid.5335.0 schema:alternateName University of Cambridge
355 schema:name Department of Medicine, University of Cambridge, Cambridge CB2 0SP, UK
356 rdf:type schema:Organization
357 https://www.grid.ac/institutes/grid.5373.2 schema:alternateName Aalto University
358 schema:name Department of Computer Science, Aalto University, Espoo FI-00076, Finland
359 Helsinki Institute of Information Technology HIIT, Department of Computer Science, Aalto University, Espoo FI-00076, Finland
360 rdf:type schema:Organization
361 https://www.grid.ac/institutes/grid.7445.2 schema:alternateName Imperial College London
362 schema:name Department of Infectious Disease Epidemiology, Imperial College, London W2 1NY, UK
363 rdf:type schema:Organization
364 https://www.grid.ac/institutes/grid.7737.4 schema:alternateName University of Helsinki
365 schema:name Department of Biostatistics, University of Oslo, 0317 Oslo, Norway
366 Department of Mathematics and Statistics, University of Helsinki, Helsinki FI-00014, Finland
367 Department of Medical and Clinical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki FI-00014, Finland
368 Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki FI-00014, Finland
369 Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
370 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...