{"id":"https://openalex.org/W2786675980","doi":"https://doi.org/10.1371/journal.pcbi.1005931","title":"Predicting pathogenicity behavior in Escherichia coli population through a state dependent model and TRS profiling","display_name":"Predicting pathogenicity behavior in Escherichia coli population through a state dependent model and TRS profiling","publication_year":2018,"publication_date":"2018-01-31","ids":{"openalex":"https://openalex.org/W2786675980","doi":"https://doi.org/10.1371/journal.pcbi.1005931","mag":"2786675980","pmid":"https://pubmed.ncbi.nlm.nih.gov/29385125"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005931","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005931","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005931&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005931&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056335921","display_name":"Krzysztof Bartoszek","orcid":"https://orcid.org/0000-0002-5816-4345"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Krzysztof Bartoszek","raw_affiliation_strings":["Department of Mathematics, Uppsala University, Uppsala, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-5816-4345","affiliations":[{"raw_affiliation_string":"Department of Mathematics, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038778264","display_name":"Marta Majchrzak","orcid":null},"institutions":[{"id":"https://openalex.org/I4210124861","display_name":"Institute for Medical Biology","ror":"https://ror.org/02kstzn75","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210124861","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"government","lineage":["https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Marta Majchrzak","raw_affiliation_strings":["Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland","institution_ids":["https://openalex.org/I4210124861","https://openalex.org/I99542240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077512966","display_name":"Sebastian Sakowski","orcid":"https://orcid.org/0000-0002-6127-3403"},"institutions":[{"id":"https://openalex.org/I34250744","display_name":"University of \u0141\u00f3d\u017a","ror":"https://ror.org/05cq64r17","country_code":"PL","type":"education","lineage":["https://openalex.org/I34250744"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Sebastian Sakowski","raw_affiliation_strings":["Faculty of Mathematics and Computer Science, University of Lodz, Lodz, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Computer Science, University of Lodz, Lodz, Poland","institution_ids":["https://openalex.org/I34250744"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034586875","display_name":"Anna B. Kubiak-Szeligowska","orcid":"https://orcid.org/0000-0001-5672-9018"},"institutions":[{"id":"https://openalex.org/I4210124861","display_name":"Institute for Medical Biology","ror":"https://ror.org/02kstzn75","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210124861","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"government","lineage":["https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Anna B. Kubiak-Szeligowska","raw_affiliation_strings":["Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland","institution_ids":["https://openalex.org/I4210124861","https://openalex.org/I99542240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087188031","display_name":"Ingemar Kaj","orcid":"https://orcid.org/0000-0002-7672-190X"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Ingemar Kaj","raw_affiliation_strings":["Department of Mathematics, Uppsala University, Uppsala, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069809917","display_name":"Pawe\u0142 Parniewski","orcid":"https://orcid.org/0000-0002-9074-2758"},"institutions":[{"id":"https://openalex.org/I4210124861","display_name":"Institute for Medical Biology","ror":"https://ror.org/02kstzn75","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210124861","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"government","lineage":["https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Pawel Parniewski","raw_affiliation_strings":["Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland"],"raw_orcid":"https://orcid.org/0000-0002-9074-2758","affiliations":[{"raw_affiliation_string":"Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland","institution_ids":["https://openalex.org/I4210124861","https://openalex.org/I99542240"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5069809917"],"corresponding_institution_ids":["https://openalex.org/I4210124861","https://openalex.org/I99542240"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.3801,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.59987051,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"14","issue":"1","first_page":"e1005931","last_page":"e1005931"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10943","display_name":"Escherichia coli research studies","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1310","display_name":"Endocrinology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10943","display_name":"Escherichia coli research studies","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1310","display_name":"Endocrinology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pathogenicity","display_name":"Pathogenicity","score":0.7742888331413269},{"id":"https://openalex.org/keywords/virulence","display_name":"Virulence","score":0.6691906452178955},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.640504777431488},{"id":"https://openalex.org/keywords/trait","display_name":"Trait","score":0.5383682250976562},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5108672976493835},{"id":"https://openalex.org/keywords/microsatellite","display_name":"Microsatellite","score":0.47844910621643066},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4737547039985657},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43487492203712463},{"id":"https://openalex.org/keywords/pathogenicity-island","display_name":"Pathogenicity island","score":0.41480785608291626},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1769692301750183},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.16438409686088562},{"id":"https://openalex.org/keywords/microbiology","display_name":"Microbiology","score":0.15842872858047485}],"concepts":[{"id":"https://openalex.org/C64502627","wikidata":"https://www.wikidata.org/wiki/Q170065","display_name":"Pathogenicity","level":2,"score":0.7742888331413269},{"id":"https://openalex.org/C60987743","wikidata":"https://www.wikidata.org/wiki/Q1460232","display_name":"Virulence","level":3,"score":0.6691906452178955},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.640504777431488},{"id":"https://openalex.org/C106934330","wikidata":"https://www.wikidata.org/wiki/Q1971873","display_name":"Trait","level":2,"score":0.5383682250976562},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5108672976493835},{"id":"https://openalex.org/C61320498","wikidata":"https://www.wikidata.org/wiki/Q265193","display_name":"Microsatellite","level":4,"score":0.47844910621643066},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4737547039985657},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43487492203712463},{"id":"https://openalex.org/C62130838","wikidata":"https://www.wikidata.org/wiki/Q5196163","display_name":"Pathogenicity island","level":4,"score":0.41480785608291626},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1769692301750183},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.16438409686088562},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.15842872858047485},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003967","descriptor_name":"Diarrhea","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D003967","descriptor_name":"Diarrhea","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D003967","descriptor_name":"Diarrhea","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D003967","descriptor_name":"Diarrhea","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D003967","descriptor_name":"Diarrhea","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D004927","descriptor_name":"Escherichia coli Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D004927","descriptor_name":"Escherichia coli Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D004927","descriptor_name":"Escherichia coli Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D004927","descriptor_name":"Escherichia coli Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D004927","descriptor_name":"Escherichia coli Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014552","descriptor_name":"Urinary Tract Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D014552","descriptor_name":"Urinary Tract Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D014552","descriptor_name":"Urinary Tract Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D014552","descriptor_name":"Urinary Tract Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D014552","descriptor_name":"Urinary Tract Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D014774","descriptor_name":"Virulence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014774","descriptor_name":"Virulence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014774","descriptor_name":"Virulence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014774","descriptor_name":"Virulence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014774","descriptor_name":"Virulence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018895","descriptor_name":"Microsatellite Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018895","descriptor_name":"Microsatellite Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018895","descriptor_name":"Microsatellite Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018895","descriptor_name":"Microsatellite Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018895","descriptor_name":"Microsatellite Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018911","descriptor_name":"Trinucleotide Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018911","descriptor_name":"Trinucleotide Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018911","descriptor_name":"Trinucleotide Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018911","descriptor_name":"Trinucleotide Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018911","descriptor_name":"Trinucleotide Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D037521","descriptor_name":"Virulence Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D037521","descriptor_name":"Virulence Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D037521","descriptor_name":"Virulence Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D037521","descriptor_name":"Virulence Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D037521","descriptor_name":"Virulence Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1005931","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005931","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005931&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:29385125","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29385125","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:DiVA.org:liu-145810","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-145810","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article in journal"},{"id":"pmh:oai:DiVA.org:uu-341023","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-341023","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:doaj.org/article:f95e593ba0eb469e888b96440638b98d","is_oa":true,"landing_page_url":"https://doaj.org/article/f95e593ba0eb469e888b96440638b98d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 14, Iss 1, p e1005931 (2018)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5809097","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5809097","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1005931","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005931","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005931&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320323344","display_name":"Uniwersytet \u0141\u00f3dzki","ror":"https://ror.org/05cq64r17"},{"id":"https://openalex.org/F4320334915","display_name":"Instytut Biologii Medycznej Polskiej Akademii Nauk","ror":"https://ror.org/02kstzn75"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2786675980.pdf","grobid_xml":"https://content.openalex.org/works/W2786675980.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W564619513","https://openalex.org/W1482160415","https://openalex.org/W1531740033","https://openalex.org/W1964553709","https://openalex.org/W1968371014","https://openalex.org/W1988199082","https://openalex.org/W1993542801","https://openalex.org/W1995879748","https://openalex.org/W2021412480","https://openalex.org/W2022178880","https://openalex.org/W2023956150","https://openalex.org/W2029588642","https://openalex.org/W2090732181","https://openalex.org/W2092872439","https://openalex.org/W2093941883","https://openalex.org/W2100104632","https://openalex.org/W2108398626","https://openalex.org/W2108992034","https://openalex.org/W2112334754","https://openalex.org/W2126730752","https://openalex.org/W2134275620","https://openalex.org/W2137678717","https://openalex.org/W2138139644","https://openalex.org/W2142489493","https://openalex.org/W2146907710","https://openalex.org/W2150581974","https://openalex.org/W2151062029","https://openalex.org/W2255408690","https://openalex.org/W2288363425","https://openalex.org/W2469170393","https://openalex.org/W2476982611","https://openalex.org/W2582743722","https://openalex.org/W2735207660","https://openalex.org/W2951758813","https://openalex.org/W4253451516"],"related_works":["https://openalex.org/W2139790819","https://openalex.org/W4213212980","https://openalex.org/W1985396638","https://openalex.org/W2355961013","https://openalex.org/W2376818183","https://openalex.org/W1554191723","https://openalex.org/W2358685355","https://openalex.org/W4378803659","https://openalex.org/W2353716672","https://openalex.org/W2025891339"],"abstract_inverted_index":{"The":[0,112],"Binary":[1],"State":[2],"Speciation":[3],"and":[4,96],"Extinction":[5],"(BiSSE)":[6],"model":[7,13,63,79],"is":[8,56],"a":[9,23,28,88,102],"branching":[10,61],"process":[11,62],"based":[12,31],"that":[14],"allows":[15],"the":[16,33,59,73,77],"diversification":[17],"rates":[18],"to":[19,117],"be":[20,115],"controlled":[21],"by":[22],"binary":[24],"trait.":[25],"We":[26,86],"develop":[27],"general":[29],"approach,":[30],"on":[32],"BiSSE":[34,78],"model,":[35],"for":[36,49,80],"predicting":[37,50],"pathogenicity":[38,51,119],"in":[39,52,108],"bacterial":[40,110,122],"populations":[41,55],"from":[42,83],"microsatellites":[43,66],"profiling":[44],"data.":[45,85],"A":[46],"comprehensive":[47],"approach":[48],"E.":[53,93],"coli":[54,94],"proposed":[57],"using":[58,76],"state-dependent":[60],"combined":[64],"with":[65],"TRS-PCR":[67],"profiling.":[68],"Additionally,":[69],"we":[70],"have":[71],"evaluated":[72],"possibility":[74],"of":[75,104,120],"estimating":[81],"parameters":[82],"genetic":[84],"analyzed":[87],"real":[89],"dataset":[90],"(from":[91],"251":[92],"strains)":[95],"confirmed":[97],"previous":[98],"biological":[99],"observations":[100],"demonstrating":[101],"prevalence":[103],"some":[105],"virulence":[106],"traits":[107],"specific":[109],"sub-groups.":[111],"method":[113],"may":[114],"used":[116],"predict":[118],"other":[121],"taxa.":[123]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}