{"id":"https://openalex.org/W3108241513","doi":"https://doi.org/10.1371/journal.pcbi.1008482","title":"Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages","display_name":"Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages","publication_year":2020,"publication_date":"2020-12-04","ids":{"openalex":"https://openalex.org/W3108241513","doi":"https://doi.org/10.1371/journal.pcbi.1008482","mag":"3108241513","pmid":"https://pubmed.ncbi.nlm.nih.gov/33275597"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008482","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008482","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008482&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.1008482&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101976218","display_name":"Amjad Khan","orcid":"https://orcid.org/0000-0001-7691-4608"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Amjad Khan","raw_affiliation_strings":["Department of Applied Mathematics, Western University, London, Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics, Western University, London, Ontario, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038707028","display_name":"Alita R. Burmeister","orcid":"https://orcid.org/0000-0003-4304-5551"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alita R. Burmeister","raw_affiliation_strings":["BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA","Department of Ecology and Evolution, Yale University, New Haven, Connecticut, USA"],"raw_orcid":"https://orcid.org/0000-0003-4304-5551","affiliations":[{"raw_affiliation_string":"BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA","institution_ids":[]},{"raw_affiliation_string":"Department of Ecology and Evolution, Yale University, New Haven, Connecticut, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077870673","display_name":"Lindi M. Wahl","orcid":"https://orcid.org/0000-0003-1163-0940"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Lindi M. Wahl","raw_affiliation_strings":["Department of Applied Mathematics, Western University, London, Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics, Western University, London, Ontario, Canada","institution_ids":["https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5077870673"],"corresponding_institution_ids":["https://openalex.org/I125749732"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.6086,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.83022251,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"16","issue":"12","first_page":"e1008482","last_page":"e1008482"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11688","display_name":"Microbial infections and disease research","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9907000064849854,"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/prophage","display_name":"Prophage","score":0.9736550450325012},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.772799015045166},{"id":"https://openalex.org/keywords/lytic-cycle","display_name":"Lytic cycle","score":0.7456883788108826},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6782857179641724},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5409013628959656},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5247136354446411},{"id":"https://openalex.org/keywords/transposase","display_name":"Transposase","score":0.4705795645713806},{"id":"https://openalex.org/keywords/lysogenic-cycle","display_name":"Lysogenic cycle","score":0.46021783351898193},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37185031175613403},{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.3492221236228943},{"id":"https://openalex.org/keywords/bacteriophage","display_name":"Bacteriophage","score":0.33377206325531006},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.07645472884178162},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.06752395629882812}],"concepts":[{"id":"https://openalex.org/C73445445","wikidata":"https://www.wikidata.org/wiki/Q1712327","display_name":"Prophage","level":5,"score":0.9736550450325012},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.772799015045166},{"id":"https://openalex.org/C182615771","wikidata":"https://www.wikidata.org/wiki/Q1369386","display_name":"Lytic cycle","level":3,"score":0.7456883788108826},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6782857179641724},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5409013628959656},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5247136354446411},{"id":"https://openalex.org/C172510086","wikidata":"https://www.wikidata.org/wiki/Q410629","display_name":"Transposase","level":5,"score":0.4705795645713806},{"id":"https://openalex.org/C136199206","wikidata":"https://www.wikidata.org/wiki/Q1148110","display_name":"Lysogenic cycle","level":5,"score":0.46021783351898193},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37185031175613403},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.3492221236228943},{"id":"https://openalex.org/C2776441376","wikidata":"https://www.wikidata.org/wiki/Q165028","display_name":"Bacteriophage","level":4,"score":0.33377206325531006},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.07645472884178162},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.06752395629882812}],"mesh":[{"descriptor_ui":"D005814","descriptor_name":"Genes, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005814","descriptor_name":"Genes, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005814","descriptor_name":"Genes, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1008482","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008482","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008482&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:33275597","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33275597","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:doaj.org/article:0ff286b88d364e118e008b05f455c8f1","is_oa":true,"landing_page_url":"https://doaj.org/article/0ff286b88d364e118e008b05f455c8f1","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 16, Iss 12, p e1008482 (2020)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:6687366","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC7744054","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7744054","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7744054","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.1008482","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008482","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008482&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":[{"id":"https://metadata.un.org/sdg/15","score":0.41999998688697815,"display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G2290218358","display_name":null,"funder_award_id":"R21AI144345","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5417603641","display_name":null,"funder_award_id":"06294-2019-RGPIN","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3108241513.pdf","grobid_xml":"https://content.openalex.org/works/W3108241513.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1585692887","https://openalex.org/W1902011974","https://openalex.org/W1921607560","https://openalex.org/W1971178500","https://openalex.org/W2016588572","https://openalex.org/W2017569339","https://openalex.org/W2027831845","https://openalex.org/W2036134563","https://openalex.org/W2040416009","https://openalex.org/W2044530165","https://openalex.org/W2068613608","https://openalex.org/W2077637320","https://openalex.org/W2082883430","https://openalex.org/W2104791774","https://openalex.org/W2108210068","https://openalex.org/W2119585200","https://openalex.org/W2135796236","https://openalex.org/W2144109966","https://openalex.org/W2146966776","https://openalex.org/W2149559438","https://openalex.org/W2166985142","https://openalex.org/W2269668178","https://openalex.org/W2345791363","https://openalex.org/W2524644896","https://openalex.org/W2557121075","https://openalex.org/W2589558686","https://openalex.org/W2605159790","https://openalex.org/W2763831277","https://openalex.org/W2800439744","https://openalex.org/W2808027486","https://openalex.org/W2810810788","https://openalex.org/W2901099141","https://openalex.org/W2990021576"],"related_works":["https://openalex.org/W1965668149","https://openalex.org/W2006903599","https://openalex.org/W2065225242","https://openalex.org/W2047426655","https://openalex.org/W2014337967","https://openalex.org/W1924790022","https://openalex.org/W4242876064","https://openalex.org/W2171019569","https://openalex.org/W95610762","https://openalex.org/W2059368236"],"abstract_inverted_index":{"Integrated":[0],"into":[1],"their":[2],"bacterial":[3],"hosts'":[4],"genomes,":[5],"prophage":[6,62,67],"sequences":[7,21,174],"exhibit":[8],"a":[9,28,170,178],"wide":[10],"diversity":[11,171],"of":[12,31,48,58,73,90,153,172],"length":[13],"and":[14,40,75,88,104,116,155,166],"gene":[15,46,71],"content,":[16],"from":[17],"highly":[18],"degraded":[19],"cryptic":[20,159,167],"to":[22],"intact,":[23],"functional":[24,165],"prophages":[25,133,168],"that":[26,81,120,134,138,164,175],"retain":[27,136],"full":[29],"complement":[30],"lytic-function":[32],"genes.":[33],"We":[34],"apply":[35],"three":[36],"approaches-bioinformatics,":[37],"analytical":[38],"modelling":[39],"computational":[41,117],"simulation-to":[42],"understand":[43],"the":[44,51,56,70,85,140,151],"diverse":[45],"content":[47],"prophages.":[49,77,160],"In":[50],"bioinformatics":[52],"work,":[53],"we":[54,146,162],"examine":[55],"distributions":[57],"over":[59],"50,000":[60],"annotated":[61],"genes":[63,82,106,121,137,157],"identified":[64],"in":[65,84,97,123,131,158],"1384":[66],"sequences,":[68],"comparing":[69],"repertoires":[72],"intact":[74],"incomplete":[76,98],"These":[78],"data":[79],"indicate":[80],"involved":[83,122],"replication,":[86],"packaging,":[87],"release":[89],"phage":[91,124],"particles":[92],"have":[93],"been":[94],"preferentially":[95,128],"lost":[96],"prophages,":[99],"while":[100],"tail":[101],"fiber,":[102],"transposase":[103,156],"integrase":[105,154],"are":[107,127],"significantly":[108],"enriched.":[109],"Consistent":[110],"with":[111],"these":[112,144],"results,":[113],"our":[114],"mathematical":[115],"approaches":[118],"predict":[119],"lytic":[125],"function":[126],"lost,":[129],"resulting":[130],"shorter":[132],"often":[135],"benefit":[139],"host.":[141],"Informed":[142],"by":[143],"models,":[145],"offer":[147],"novel":[148],"hypotheses":[149],"for":[150],"enrichment":[152],"Overall,":[161],"demonstrate":[163],"represent":[169],"genetic":[173],"evolve":[176],"along":[177],"parasitism-mutualism":[179],"continuum.":[180]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}