Bayesian modeling of recombination events in bacterial populations View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-12

AUTHORS

Pekka Marttinen, Adam Baldwin, William P Hanage, Chris Dowson, Eshwar Mahenthiralingam, Jukka Corander

ABSTRACT

BACKGROUND: We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currently available methods for recombination detection capable of probabilistic characterization of uncertainty have a limited applicability in practice as the number of strains in a data set increases. RESULTS: We introduce a Bayesian spatial structural model representing the continuum of origins over sites within the observed sequences, including a probabilistic characterization of uncertainty related to the origin of any particular site. To enable a statistically accurate and practically feasible approach to the analysis of large-scale data sets representing a single genus, we have developed a novel software tool (BRAT, Bayesian Recombination Tracker) implementing the model and the corresponding learning algorithm, which is capable of identifying the posterior optimal structure and to estimate the marginal posterior probabilities of putative origins over the sites. CONCLUSION: A multitude of challenging simulation scenarios and an analysis of real data from seven housekeeping genes of 120 strains of genus Burkholderia are used to illustrate the possibilities offered by our approach. The software is freely available for download at URL http://web.abo.fi/fak/mnf//mate/jc/software/brat.html. More... »

PAGES

421

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-9-421

DOI

http://dx.doi.org/10.1186/1471-2105-9-421

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1008209350

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18840286


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/2008/0801", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Artificial Intelligence and Image Processing", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/08", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information and Computing Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Base Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Bayes Theorem", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Burkholderia", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromosome Mapping", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Information Storage and Retrieval", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Pattern Recognition, Automated", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Phylogeny", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Recombination, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Alignment", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Uncertainty", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of Helsinki", 
          "id": "https://www.grid.ac/institutes/grid.7737.4", 
          "name": [
            "Department of Mathematics and statistics, University of Helsinki, FIN-00014, 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 Warwick", 
          "id": "https://www.grid.ac/institutes/grid.7372.1", 
          "name": [
            "Department of Biological Sciences, Warwick University, CV4 7AL, Coventry, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Baldwin", 
        "givenName": "Adam", 
        "id": "sg:person.01273175115.30", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01273175115.30"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Imperial College London", 
          "id": "https://www.grid.ac/institutes/grid.7445.2", 
          "name": [
            "Department of Infectious Disease Epidemiology, Imperial College, W2 1PG, London, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hanage", 
        "givenName": "William P", 
        "id": "sg:person.01022047017.82", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01022047017.82"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Warwick", 
          "id": "https://www.grid.ac/institutes/grid.7372.1", 
          "name": [
            "Department of Biological Sciences, Warwick University, CV4 7AL, Coventry, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Dowson", 
        "givenName": "Chris", 
        "id": "sg:person.0707172503.96", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0707172503.96"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Cardiff University", 
          "id": "https://www.grid.ac/institutes/grid.5600.3", 
          "name": [
            "Cardiff School of Biosciences, Cardiff University, CF10 3TL, Cardiff, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mahenthiralingam", 
        "givenName": "Eshwar", 
        "id": "sg:person.0756134565.97", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0756134565.97"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "\u00c5bo Akademi University", 
          "id": "https://www.grid.ac/institutes/grid.13797.3b", 
          "name": [
            "Department of Mathematics, Abo Akademi University, FIN-20500, Finland"
          ], 
          "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/10.1534/genetics.106.066258", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005555335"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1534/genetics.106.066258", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005555335"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/oxfordjournals.molbev.a025960", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010278768"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0022-5193(74)90129-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010769677"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/iai.72.3.1537-1547.2004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011570372"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jcm.43.9.4665-4673.2005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011915617"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1534/genetics.106.063305", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012919594"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1534/genetics.106.063305", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012919594"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bth250", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016574435"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1741-7007-3-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017758777", 
          "https://doi.org/10.1186/1741-7007-3-6"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0022-2836(68)90230-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018109109"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/tpbi.2002.1587", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021034039"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/oxfordjournals.molbev.a025760", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022245988"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msg039", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023461557"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-4612-4250-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024387799", 
          "https://doi.org/10.1007/978-1-4612-4250-5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-4612-4250-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024387799", 
          "https://doi.org/10.1007/978-1-4612-4250-5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00239-001-0034-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028269619", 
          "https://doi.org/10.1007/s00239-001-0034-9"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.mbs.2006.09.015", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029406893"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cub.2007.03.032", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031668828"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1127573", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033824448"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btl411", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034012279"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1751-5823.2001.tb00465.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034920734"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cub.2006.12.048", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035487853"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf02101694", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039008589", 
          "https://doi.org/10.1007/bf02101694"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf02101694", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039008589", 
          "https://doi.org/10.1007/bf02101694"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf00182187", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039411850", 
          "https://doi.org/10.1007/bf00182187"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bti459", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039458980"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1214/ss/1028905933", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040962441"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-8-458", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042638835", 
          "https://doi.org/10.1186/1471-2105-8-458"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrmicro1085", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042690574", 
          "https://doi.org/10.1038/nrmicro1085"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrmicro1085", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042690574", 
          "https://doi.org/10.1038/nrmicro1085"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/tpbi.2002.1596", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042756207"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s11222-006-9391-y", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042853180", 
          "https://doi.org/10.1007/s11222-006-9391-y"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.3201/eid1303.060403", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043010811"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrmicro1385", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044061226", 
          "https://doi.org/10.1038/nrmicro1385"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrmicro1385", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044061226", 
          "https://doi.org/10.1038/nrmicro1385"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/13.3.235", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044605581"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-412", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045603319", 
          "https://doi.org/10.1186/1471-2105-7-412"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-412", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045603319", 
          "https://doi.org/10.1186/1471-2105-7-412"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-294x.2006.02994.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048622172"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1099/0022-1317-51-7-533", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060354234"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1198/016214503000215", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1064198111"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1198/016214505000000664", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1064198398"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1075335894", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1076835742", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/oxfordjournals.molbev.a040567", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1079212537"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2008-12", 
    "datePublishedReg": "2008-12-01", 
    "description": "BACKGROUND: We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currently available methods for recombination detection capable of probabilistic characterization of uncertainty have a limited applicability in practice as the number of strains in a data set increases.\nRESULTS: We introduce a Bayesian spatial structural model representing the continuum of origins over sites within the observed sequences, including a probabilistic characterization of uncertainty related to the origin of any particular site. To enable a statistically accurate and practically feasible approach to the analysis of large-scale data sets representing a single genus, we have developed a novel software tool (BRAT, Bayesian Recombination Tracker) implementing the model and the corresponding learning algorithm, which is capable of identifying the posterior optimal structure and to estimate the marginal posterior probabilities of putative origins over the sites.\nCONCLUSION: A multitude of challenging simulation scenarios and an analysis of real data from seven housekeeping genes of 120 strains of genus Burkholderia are used to illustrate the possibilities offered by our approach. The software is freely available for download at URL http://web.abo.fi/fak/mnf//mate/jc/software/brat.html.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2105-9-421", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1023786", 
        "issn": [
          "1471-2105"
        ], 
        "name": "BMC Bioinformatics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "9"
      }
    ], 
    "name": "Bayesian modeling of recombination events in bacterial populations", 
    "pagination": "421", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "271c61dd070cc82fa0ab7618fd8074bc86bf1582d89cb47f6de81cdc907b18ef"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "18840286"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965194"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2105-9-421"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1008209350"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2105-9-421", 
      "https://app.dimensions.ai/details/publication/pub.1008209350"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T10:00", 
    "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/v90/0000000347_0000000347/records_89816_00000000.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://link.springer.com/10.1186%2F1471-2105-9-421"
  }
]
 

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.10.1186/1471-2105-9-421'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-421'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-421'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-421'


 

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

288 TRIPLES      21 PREDICATES      80 URIs      33 LITERALS      21 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2105-9-421 schema:about N126f4a17d450472e972169149c4bc905
2 N12734616dee740659e22b34dc713b5b6
3 N1d5b6b4f0066431d96dcf3be8e7cd155
4 N377c6077817641e39bc45cff4c17542e
5 N4c7ff82fc1fd4518b792fd1318815072
6 N6116eafcc4384d13aac10b8afad89f3d
7 N7b2558085c1748f58badaa4938e1b3b8
8 N7ecbbd960cf94d11b5b6505114421539
9 N803dcf00788e4d9c90261bf8e4142cc2
10 N8a4d68db347242f782ca9c0f368aa75b
11 N9c49709ede834749b23187e9916dfb19
12 Na6a2280eff6a4a8d9f91b9f0dcdff4cc
13 anzsrc-for:08
14 anzsrc-for:0801
15 schema:author N42b5be73815d4fdbaee2812f0ae73de0
16 schema:citation sg:pub.10.1007/978-1-4612-4250-5
17 sg:pub.10.1007/bf00182187
18 sg:pub.10.1007/bf02101694
19 sg:pub.10.1007/s00239-001-0034-9
20 sg:pub.10.1007/s11222-006-9391-y
21 sg:pub.10.1038/nrmicro1085
22 sg:pub.10.1038/nrmicro1385
23 sg:pub.10.1186/1471-2105-7-412
24 sg:pub.10.1186/1471-2105-8-458
25 sg:pub.10.1186/1741-7007-3-6
26 https://app.dimensions.ai/details/publication/pub.1075335894
27 https://app.dimensions.ai/details/publication/pub.1076835742
28 https://doi.org/10.1006/tpbi.2002.1587
29 https://doi.org/10.1006/tpbi.2002.1596
30 https://doi.org/10.1016/0022-2836(68)90230-1
31 https://doi.org/10.1016/0022-5193(74)90129-5
32 https://doi.org/10.1016/j.cub.2006.12.048
33 https://doi.org/10.1016/j.cub.2007.03.032
34 https://doi.org/10.1016/j.mbs.2006.09.015
35 https://doi.org/10.1093/bioinformatics/13.3.235
36 https://doi.org/10.1093/bioinformatics/bth250
37 https://doi.org/10.1093/bioinformatics/bti459
38 https://doi.org/10.1093/bioinformatics/btl411
39 https://doi.org/10.1093/molbev/msg039
40 https://doi.org/10.1093/oxfordjournals.molbev.a025760
41 https://doi.org/10.1093/oxfordjournals.molbev.a025960
42 https://doi.org/10.1093/oxfordjournals.molbev.a040567
43 https://doi.org/10.1099/0022-1317-51-7-533
44 https://doi.org/10.1111/j.1365-294x.2006.02994.x
45 https://doi.org/10.1111/j.1751-5823.2001.tb00465.x
46 https://doi.org/10.1126/science.1127573
47 https://doi.org/10.1128/iai.72.3.1537-1547.2004
48 https://doi.org/10.1128/jcm.43.9.4665-4673.2005
49 https://doi.org/10.1198/016214503000215
50 https://doi.org/10.1198/016214505000000664
51 https://doi.org/10.1214/ss/1028905933
52 https://doi.org/10.1534/genetics.106.063305
53 https://doi.org/10.1534/genetics.106.066258
54 https://doi.org/10.3201/eid1303.060403
55 schema:datePublished 2008-12
56 schema:datePublishedReg 2008-12-01
57 schema:description BACKGROUND: We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currently available methods for recombination detection capable of probabilistic characterization of uncertainty have a limited applicability in practice as the number of strains in a data set increases. RESULTS: We introduce a Bayesian spatial structural model representing the continuum of origins over sites within the observed sequences, including a probabilistic characterization of uncertainty related to the origin of any particular site. To enable a statistically accurate and practically feasible approach to the analysis of large-scale data sets representing a single genus, we have developed a novel software tool (BRAT, Bayesian Recombination Tracker) implementing the model and the corresponding learning algorithm, which is capable of identifying the posterior optimal structure and to estimate the marginal posterior probabilities of putative origins over the sites. CONCLUSION: A multitude of challenging simulation scenarios and an analysis of real data from seven housekeeping genes of 120 strains of genus Burkholderia are used to illustrate the possibilities offered by our approach. The software is freely available for download at URL http://web.abo.fi/fak/mnf//mate/jc/software/brat.html.
58 schema:genre research_article
59 schema:inLanguage en
60 schema:isAccessibleForFree true
61 schema:isPartOf N55e6c7479f994f1abd63eaccac2fc532
62 Nb50424a0593a4173935fe183ad61f3c6
63 sg:journal.1023786
64 schema:name Bayesian modeling of recombination events in bacterial populations
65 schema:pagination 421
66 schema:productId N54b18fa67fc64c01855c43c48ed352a6
67 N78ccb8afb6dc46edb4b5fbc0d64fba12
68 Nb1bb0997703a433091de394179f54f9c
69 Nc3b0921bc9d04948a19c9b7f46645d60
70 Ne2a400c8b78a4ca0af62a3f34195671f
71 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008209350
72 https://doi.org/10.1186/1471-2105-9-421
73 schema:sdDatePublished 2019-04-11T10:00
74 schema:sdLicense https://scigraph.springernature.com/explorer/license/
75 schema:sdPublisher N535fe0a8d1b34615918f93a823f25646
76 schema:url https://link.springer.com/10.1186%2F1471-2105-9-421
77 sgo:license sg:explorer/license/
78 sgo:sdDataset articles
79 rdf:type schema:ScholarlyArticle
80 N126f4a17d450472e972169149c4bc905 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Chromosome Mapping
82 rdf:type schema:DefinedTerm
83 N12734616dee740659e22b34dc713b5b6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
84 schema:name Sequence Analysis, DNA
85 rdf:type schema:DefinedTerm
86 N16ea037087f24342abf276774322107c rdf:first sg:person.01273175115.30
87 rdf:rest N698fc61df0f94b7ea6dddcda71816329
88 N1d5b6b4f0066431d96dcf3be8e7cd155 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
89 schema:name Information Storage and Retrieval
90 rdf:type schema:DefinedTerm
91 N251b85b609d1422a9119a3063b9ab3da rdf:first sg:person.0756134565.97
92 rdf:rest N9bf5a7247f00419a955d41fc16e6cda2
93 N377c6077817641e39bc45cff4c17542e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
94 schema:name Recombination, Genetic
95 rdf:type schema:DefinedTerm
96 N401cc111d1ae476b965c6ba698b3b3d2 rdf:first sg:person.0707172503.96
97 rdf:rest N251b85b609d1422a9119a3063b9ab3da
98 N42b5be73815d4fdbaee2812f0ae73de0 rdf:first sg:person.0753733617.28
99 rdf:rest N16ea037087f24342abf276774322107c
100 N4c7ff82fc1fd4518b792fd1318815072 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
101 schema:name Software
102 rdf:type schema:DefinedTerm
103 N535fe0a8d1b34615918f93a823f25646 schema:name Springer Nature - SN SciGraph project
104 rdf:type schema:Organization
105 N54b18fa67fc64c01855c43c48ed352a6 schema:name nlm_unique_id
106 schema:value 100965194
107 rdf:type schema:PropertyValue
108 N55e6c7479f994f1abd63eaccac2fc532 schema:volumeNumber 9
109 rdf:type schema:PublicationVolume
110 N6116eafcc4384d13aac10b8afad89f3d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
111 schema:name Pattern Recognition, Automated
112 rdf:type schema:DefinedTerm
113 N698fc61df0f94b7ea6dddcda71816329 rdf:first sg:person.01022047017.82
114 rdf:rest N401cc111d1ae476b965c6ba698b3b3d2
115 N78ccb8afb6dc46edb4b5fbc0d64fba12 schema:name readcube_id
116 schema:value 271c61dd070cc82fa0ab7618fd8074bc86bf1582d89cb47f6de81cdc907b18ef
117 rdf:type schema:PropertyValue
118 N7b2558085c1748f58badaa4938e1b3b8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
119 schema:name Base Sequence
120 rdf:type schema:DefinedTerm
121 N7ecbbd960cf94d11b5b6505114421539 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
122 schema:name Phylogeny
123 rdf:type schema:DefinedTerm
124 N803dcf00788e4d9c90261bf8e4142cc2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
125 schema:name Burkholderia
126 rdf:type schema:DefinedTerm
127 N8a4d68db347242f782ca9c0f368aa75b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
128 schema:name Bayes Theorem
129 rdf:type schema:DefinedTerm
130 N9bf5a7247f00419a955d41fc16e6cda2 rdf:first sg:person.01125514227.61
131 rdf:rest rdf:nil
132 N9c49709ede834749b23187e9916dfb19 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
133 schema:name Uncertainty
134 rdf:type schema:DefinedTerm
135 Na6a2280eff6a4a8d9f91b9f0dcdff4cc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
136 schema:name Sequence Alignment
137 rdf:type schema:DefinedTerm
138 Nb1bb0997703a433091de394179f54f9c schema:name pubmed_id
139 schema:value 18840286
140 rdf:type schema:PropertyValue
141 Nb50424a0593a4173935fe183ad61f3c6 schema:issueNumber 1
142 rdf:type schema:PublicationIssue
143 Nc3b0921bc9d04948a19c9b7f46645d60 schema:name dimensions_id
144 schema:value pub.1008209350
145 rdf:type schema:PropertyValue
146 Ne2a400c8b78a4ca0af62a3f34195671f schema:name doi
147 schema:value 10.1186/1471-2105-9-421
148 rdf:type schema:PropertyValue
149 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
150 schema:name Information and Computing Sciences
151 rdf:type schema:DefinedTerm
152 anzsrc-for:0801 schema:inDefinedTermSet anzsrc-for:
153 schema:name Artificial Intelligence and Image Processing
154 rdf:type schema:DefinedTerm
155 sg:journal.1023786 schema:issn 1471-2105
156 schema:name BMC Bioinformatics
157 rdf:type schema:Periodical
158 sg:person.01022047017.82 schema:affiliation https://www.grid.ac/institutes/grid.7445.2
159 schema:familyName Hanage
160 schema:givenName William P
161 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01022047017.82
162 rdf:type schema:Person
163 sg:person.01125514227.61 schema:affiliation https://www.grid.ac/institutes/grid.13797.3b
164 schema:familyName Corander
165 schema:givenName Jukka
166 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01125514227.61
167 rdf:type schema:Person
168 sg:person.01273175115.30 schema:affiliation https://www.grid.ac/institutes/grid.7372.1
169 schema:familyName Baldwin
170 schema:givenName Adam
171 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01273175115.30
172 rdf:type schema:Person
173 sg:person.0707172503.96 schema:affiliation https://www.grid.ac/institutes/grid.7372.1
174 schema:familyName Dowson
175 schema:givenName Chris
176 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0707172503.96
177 rdf:type schema:Person
178 sg:person.0753733617.28 schema:affiliation https://www.grid.ac/institutes/grid.7737.4
179 schema:familyName Marttinen
180 schema:givenName Pekka
181 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0753733617.28
182 rdf:type schema:Person
183 sg:person.0756134565.97 schema:affiliation https://www.grid.ac/institutes/grid.5600.3
184 schema:familyName Mahenthiralingam
185 schema:givenName Eshwar
186 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0756134565.97
187 rdf:type schema:Person
188 sg:pub.10.1007/978-1-4612-4250-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024387799
189 https://doi.org/10.1007/978-1-4612-4250-5
190 rdf:type schema:CreativeWork
191 sg:pub.10.1007/bf00182187 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039411850
192 https://doi.org/10.1007/bf00182187
193 rdf:type schema:CreativeWork
194 sg:pub.10.1007/bf02101694 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039008589
195 https://doi.org/10.1007/bf02101694
196 rdf:type schema:CreativeWork
197 sg:pub.10.1007/s00239-001-0034-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028269619
198 https://doi.org/10.1007/s00239-001-0034-9
199 rdf:type schema:CreativeWork
200 sg:pub.10.1007/s11222-006-9391-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1042853180
201 https://doi.org/10.1007/s11222-006-9391-y
202 rdf:type schema:CreativeWork
203 sg:pub.10.1038/nrmicro1085 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042690574
204 https://doi.org/10.1038/nrmicro1085
205 rdf:type schema:CreativeWork
206 sg:pub.10.1038/nrmicro1385 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044061226
207 https://doi.org/10.1038/nrmicro1385
208 rdf:type schema:CreativeWork
209 sg:pub.10.1186/1471-2105-7-412 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045603319
210 https://doi.org/10.1186/1471-2105-7-412
211 rdf:type schema:CreativeWork
212 sg:pub.10.1186/1471-2105-8-458 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042638835
213 https://doi.org/10.1186/1471-2105-8-458
214 rdf:type schema:CreativeWork
215 sg:pub.10.1186/1741-7007-3-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017758777
216 https://doi.org/10.1186/1741-7007-3-6
217 rdf:type schema:CreativeWork
218 https://app.dimensions.ai/details/publication/pub.1075335894 schema:CreativeWork
219 https://app.dimensions.ai/details/publication/pub.1076835742 schema:CreativeWork
220 https://doi.org/10.1006/tpbi.2002.1587 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021034039
221 rdf:type schema:CreativeWork
222 https://doi.org/10.1006/tpbi.2002.1596 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042756207
223 rdf:type schema:CreativeWork
224 https://doi.org/10.1016/0022-2836(68)90230-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018109109
225 rdf:type schema:CreativeWork
226 https://doi.org/10.1016/0022-5193(74)90129-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010769677
227 rdf:type schema:CreativeWork
228 https://doi.org/10.1016/j.cub.2006.12.048 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035487853
229 rdf:type schema:CreativeWork
230 https://doi.org/10.1016/j.cub.2007.03.032 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031668828
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1016/j.mbs.2006.09.015 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029406893
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1093/bioinformatics/13.3.235 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044605581
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1093/bioinformatics/bth250 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016574435
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1093/bioinformatics/bti459 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039458980
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1093/bioinformatics/btl411 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034012279
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1093/molbev/msg039 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023461557
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1093/oxfordjournals.molbev.a025760 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022245988
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1093/oxfordjournals.molbev.a025960 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010278768
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1093/oxfordjournals.molbev.a040567 schema:sameAs https://app.dimensions.ai/details/publication/pub.1079212537
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1099/0022-1317-51-7-533 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060354234
251 rdf:type schema:CreativeWork
252 https://doi.org/10.1111/j.1365-294x.2006.02994.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1048622172
253 rdf:type schema:CreativeWork
254 https://doi.org/10.1111/j.1751-5823.2001.tb00465.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1034920734
255 rdf:type schema:CreativeWork
256 https://doi.org/10.1126/science.1127573 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033824448
257 rdf:type schema:CreativeWork
258 https://doi.org/10.1128/iai.72.3.1537-1547.2004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011570372
259 rdf:type schema:CreativeWork
260 https://doi.org/10.1128/jcm.43.9.4665-4673.2005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011915617
261 rdf:type schema:CreativeWork
262 https://doi.org/10.1198/016214503000215 schema:sameAs https://app.dimensions.ai/details/publication/pub.1064198111
263 rdf:type schema:CreativeWork
264 https://doi.org/10.1198/016214505000000664 schema:sameAs https://app.dimensions.ai/details/publication/pub.1064198398
265 rdf:type schema:CreativeWork
266 https://doi.org/10.1214/ss/1028905933 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040962441
267 rdf:type schema:CreativeWork
268 https://doi.org/10.1534/genetics.106.063305 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012919594
269 rdf:type schema:CreativeWork
270 https://doi.org/10.1534/genetics.106.066258 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005555335
271 rdf:type schema:CreativeWork
272 https://doi.org/10.3201/eid1303.060403 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043010811
273 rdf:type schema:CreativeWork
274 https://www.grid.ac/institutes/grid.13797.3b schema:alternateName Åbo Akademi University
275 schema:name Department of Mathematics, Abo Akademi University, FIN-20500, Finland
276 rdf:type schema:Organization
277 https://www.grid.ac/institutes/grid.5600.3 schema:alternateName Cardiff University
278 schema:name Cardiff School of Biosciences, Cardiff University, CF10 3TL, Cardiff, UK
279 rdf:type schema:Organization
280 https://www.grid.ac/institutes/grid.7372.1 schema:alternateName University of Warwick
281 schema:name Department of Biological Sciences, Warwick University, CV4 7AL, Coventry, UK
282 rdf:type schema:Organization
283 https://www.grid.ac/institutes/grid.7445.2 schema:alternateName Imperial College London
284 schema:name Department of Infectious Disease Epidemiology, Imperial College, W2 1PG, London, UK
285 rdf:type schema:Organization
286 https://www.grid.ac/institutes/grid.7737.4 schema:alternateName University of Helsinki
287 schema:name Department of Mathematics and statistics, University of Helsinki, FIN-00014, Finland
288 rdf:type schema:Organization
 




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


...