{"id":"https://openalex.org/W4390073119","doi":null,"title":"Comparative microbial pangenomics to explore mobilome dynamics","display_name":"Comparative microbial pangenomics to explore mobilome dynamics","publication_year":2019,"publication_date":"2019-07-02","ids":{"openalex":"https://openalex.org/W4390073119"},"language":"en","primary_location":{"id":"pmh:oai:HAL:hal-04358338v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.science/hal-04358338","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"JOBIM 2019 Journ\u00e9es Ouvertes Biologie, Informatique et Math\u00e9matiques, Jul 2019, Nantes, France","raw_type":"info:eu-repo/semantics/conferenceObject"},"volume":null,"type":"conference-paper","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hal.science/hal-04358338","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057798554","display_name":"Adelme Bazin","orcid":"https://orcid.org/0000-0002-5656-4708","observed_orcids":["https://orcid.org/0000-0002-5656-4708"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bazin, Adelme","raw_affiliation_strings":["LABGeM - Analyse Bio-Informatique pour la G\u00e9nomique et le M\u00e9tabolisme (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LABGeM - Analyse Bio-Informatique pour la G\u00e9nomique et le M\u00e9tabolisme (France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021690242","display_name":"Guillaume Gautreau","orcid":"https://orcid.org/0000-0002-0970-9361","observed_orcids":["https://orcid.org/0000-0002-0970-9361"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gautreau, Guillaume","raw_affiliation_strings":["LABGeM - Analyse Bio-Informatique pour la G\u00e9nomique et le M\u00e9tabolisme (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LABGeM - Analyse Bio-Informatique pour la G\u00e9nomique et le M\u00e9tabolisme (France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028317703","display_name":"Claudine M\u00e9digue","orcid":"https://orcid.org/0000-0002-3905-1054","observed_orcids":["https://orcid.org/0000-0002-3905-1054"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M\u00e9digue, Claudine","raw_affiliation_strings":["LABGeM - Analyse Bio-Informatique pour la G\u00e9nomique et le M\u00e9tabolisme (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LABGeM - Analyse Bio-Informatique pour la G\u00e9nomique et le M\u00e9tabolisme (France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034741393","display_name":"Alexandra Calteau","orcid":"https://orcid.org/0000-0002-5871-9347","observed_orcids":["https://orcid.org/0000-0002-5871-9347"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Calteau, Alexandra","raw_affiliation_strings":["LABGeM - Analyse Bio-Informatique pour la G\u00e9nomique et le M\u00e9tabolisme (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LABGeM - Analyse Bio-Informatique pour la G\u00e9nomique et le M\u00e9tabolisme (France)","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072154324","display_name":"David Vallenet","orcid":"https://orcid.org/0000-0001-6648-0332","observed_orcids":["https://orcid.org/0000-0001-6648-0332"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vallenet, David","raw_affiliation_strings":["LABGeM - Analyse Bio-Informatique pour la G\u00e9nomique et le M\u00e9tabolisme (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LABGeM - Analyse Bio-Informatique pour la G\u00e9nomique et le M\u00e9tabolisme (France)","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9916999936103821,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9916999936103821,"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"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.0020000000949949026,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.0012000000569969416,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/core-genome","display_name":"core genome","score":0.5580000281333923},{"id":"https://openalex.org/keywords/accessory-genome","display_name":"accessory genome","score":0.9879999756813049},{"id":"https://openalex.org/keywords/gene-family-classification","display_name":"gene family classification","score":0.5609999895095825},{"id":"https://openalex.org/keywords/allele-frequency","display_name":"allele frequency","score":0.6359999775886536},{"id":"https://openalex.org/keywords/network-alignment","display_name":"network alignment","score":0.6880000233650208}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.525551438331604},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.4351646304130554},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07951974868774414},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:HAL:hal-04358338v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.science/hal-04358338","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"JOBIM 2019 Journ\u00e9es Ouvertes Biologie, Informatique et Math\u00e9matiques, Jul 2019, Nantes, France","raw_type":"info:eu-repo/semantics/conferenceObject"},{"id":"pmh:oai:HAL:hal-04359455v1","doi":null,"is_oa":false,"landing_page_url":"https://hal.science/hal-04359455","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"The 8th Congress of European Microbiologists, FEMS 2019, Jul 2019, Glasgow, United Kingdom","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-04358338v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.science/hal-04358338","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"JOBIM 2019 Journ\u00e9es Ouvertes Biologie, Informatique et Math\u00e9matiques, Jul 2019, Nantes, France","raw_type":"info:eu-repo/semantics/conferenceObject"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4390073196","https://openalex.org/W3012393121","https://openalex.org/W4200449582","https://openalex.org/W4390287042","https://openalex.org/W4390552733","https://openalex.org/W7171557944","https://openalex.org/W4414633514","https://openalex.org/W2794172458","https://openalex.org/W4205745870","https://openalex.org/W7167937359"],"abstract_inverted_index":{"Background:For":[0],"the":[1,27,34,43,50,108,122,126,151,212],"last":[2],"decade,":[3],"pangenomics":[4,149],"has":[5],"provided":[6,154],"new":[7,69,103],"tools":[8],"for":[9,173],"researchers":[10],"to":[11,33,75,84,211,219],"estimate":[12],"genomic":[13],"diversity":[14],"by":[15,155,163],"partitioning":[16,95],"gene":[17,78,82,86],"content":[18],"in":[19,39,116,146],"terms":[20],"of":[21,36,45,52,65,96,110,125,194,198],"\u201ccore\u201d":[22],"and":[23,81,99,131,167,205],"\u201caccessory\u201d":[24],"genome.":[25],"However,":[26],"\u201dcore":[28],"genome\u201d":[29],"is":[30],"highly":[31],"related":[32],"number":[35,193],"genomes":[37],"included":[38],"a":[40,62,68,89,93,120,147,191],"study":[41],"limiting":[42],"relevance":[44],"comparisons":[46],"between":[47,139,176,226],"studies.":[48],"Moreover,":[49],"concept":[51],"accessory":[53],"genome":[54],"lacks":[55],"subtlety":[56],"as":[57],"it":[58],"gathers":[59],"genes":[60],"with":[61,190,200,228],"large":[63],"range":[64],"frequencies.":[66],"Recently,":[67],"tool":[70],"named":[71],"PPanGGOLiN":[72],"was":[73],"developed":[74,182],"exploit":[76],"both":[77,165],"neighborhood":[79],"topology":[80],"frequency":[83],"classify":[85],"families":[87],"using":[88,178],"graph-based":[90],"approach":[91],"into":[92,133],"3-class":[94],"\u201dpersistent\u201d,":[97],"\u201dshell\u201d":[98],"\u201dcloud\u201d":[100],"genome.Objectives:Using":[101],"this":[102],"approach,":[104],"we":[105,141,171],"are":[106,158,224],"establishing":[107],"pangenomes":[109,127,199],"all":[111],"microbial":[112],"species":[113,177,189,227],"sufficiently":[114],"represented":[115],"databanks.":[117],"With":[118],"such":[119],"resource,":[121],"variable":[123,203],"regions":[124,204],"can":[128,142,184],"be":[129,185,208],"detected":[130,159],"split":[132],"modules.":[134],"By":[135],"studying":[136],"module":[137],"conservation":[138],"species,":[140],"explore":[143],"mobilome":[144],"dynamics":[145],"comparative":[148],"approach.Methods:Using":[150],"graph":[152],"structure":[153],"PPanGGOLiN,":[156],"modules":[157,175,206,222],"within":[160],"each":[161],"pangenome":[162],"integrating":[164],"co-occurrence":[166],"co-localization":[168],"information.":[169],"Then":[170],"search":[172],"conserved":[174],"network":[179],"alignment":[180],"methods.Results:The":[181],"method":[183],"applied":[186],"on":[187],"any":[188],"sufficient":[192],"genomes.":[195],"The":[196],"collection":[197],"their":[201],"predicted":[202],"will":[207],"made":[209],"available":[210],"research":[213],"community.":[214],"This":[215],"resource":[216],"may":[217],"help":[218],"associate":[220],"functional":[221],"that":[223],"shared":[225],"common":[229],"environmental":[230],"factors":[231],"or":[232],"phenotypic":[233],"traits.":[234]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2023-12-22T00:00:00"}
