{"id":"https://openalex.org/W2963013324","doi":"https://doi.org/10.1186/s13015-019-0149-4","title":"A general framework for genome rearrangement with biological constraints","display_name":"A general framework for genome rearrangement with biological constraints","publication_year":2019,"publication_date":"2019-07-19","ids":{"openalex":"https://openalex.org/W2963013324","doi":"https://doi.org/10.1186/s13015-019-0149-4","mag":"2963013324","pmid":"https://pubmed.ncbi.nlm.nih.gov/31360217"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-019-0149-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-019-0149-4","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-019-0149-4","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-019-0149-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059966107","display_name":"Pijus Simonaitis","orcid":"https://orcid.org/0000-0003-3576-8098"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pijus Simonaitis","raw_affiliation_strings":["1CNRS, LIRMM, Universit\u00e9 Montpellier, 161 Rue Ada, 34392 Montpellier, France","CNRS, LIRMM, Universit\u00e9 Montpellier, Montpellier, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1CNRS, LIRMM, Universit\u00e9 Montpellier, 161 Rue Ada, 34392 Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I4210101743"]},{"raw_affiliation_string":"CNRS, LIRMM, Universit\u00e9 Montpellier, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001451722","display_name":"Annie Ch\u00e2teau","orcid":"https://orcid.org/0000-0003-4760-8171"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210097156","display_name":"Biologie Computationnelle, Quantitative et Synth\u00e9tique","ror":"https://ror.org/00pcqj134","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210097156"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Annie Chateau","raw_affiliation_strings":["1CNRS, LIRMM, Universit\u00e9 Montpellier, 161 Rue Ada, 34392 Montpellier, France","2Institut de Biologie Computationnelle (IBC), Montpellier, France","Institut de Biologie Computationnelle (IBC), Montpellier, France","CNRS, LIRMM, Universit\u00e9 Montpellier, Montpellier, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1CNRS, LIRMM, Universit\u00e9 Montpellier, 161 Rue Ada, 34392 Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I4210101743"]},{"raw_affiliation_string":"2Institut de Biologie Computationnelle (IBC), Montpellier, France","institution_ids":["https://openalex.org/I4210097156"]},{"raw_affiliation_string":"Institut de Biologie Computationnelle (IBC), Montpellier, France","institution_ids":[]},{"raw_affiliation_string":"CNRS, LIRMM, Universit\u00e9 Montpellier, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014999428","display_name":"Krister M. Swenson","orcid":"https://orcid.org/0000-0001-8690-1261"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210097156","display_name":"Biologie Computationnelle, Quantitative et Synth\u00e9tique","ror":"https://ror.org/00pcqj134","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210097156"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Krister M. Swenson","raw_affiliation_strings":["1CNRS, LIRMM, Universit\u00e9 Montpellier, 161 Rue Ada, 34392 Montpellier, France","2Institut de Biologie Computationnelle (IBC), Montpellier, France","Institut de Biologie Computationnelle (IBC), Montpellier, France","CNRS, LIRMM, Universit\u00e9 Montpellier, Montpellier, France"],"raw_orcid":"https://orcid.org/0000-0001-8690-1261","affiliations":[{"raw_affiliation_string":"1CNRS, LIRMM, Universit\u00e9 Montpellier, 161 Rue Ada, 34392 Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I4210101743"]},{"raw_affiliation_string":"2Institut de Biologie Computationnelle (IBC), Montpellier, France","institution_ids":["https://openalex.org/I4210097156"]},{"raw_affiliation_string":"Institut de Biologie Computationnelle (IBC), Montpellier, France","institution_ids":[]},{"raw_affiliation_string":"CNRS, LIRMM, Universit\u00e9 Montpellier, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014999428"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210097156","https://openalex.org/I4210101743"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":0.18,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.63050061,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"14","issue":"1","first_page":"15","last_page":"15"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9994999766349792,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.939300000667572,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.655667245388031},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.507206916809082},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34336432814598083},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2526552975177765},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15380257368087769},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11171624064445496}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.655667245388031},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.507206916809082},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34336432814598083},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2526552975177765},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15380257368087769},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11171624064445496}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13015-019-0149-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-019-0149-4","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-019-0149-4","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:31360217","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31360217","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:HAL:lirmm-02410420v1","is_oa":true,"landing_page_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-02410420","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"Algorithms for Molecular Biology, 2019, 14 (1), &#x27E8;10.1186/s13015-019-0149-4&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:6c1212496f084629aba36380f88c62f7","is_oa":false,"landing_page_url":"https://doaj.org/article/6c1212496f084629aba36380f88c62f7","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 14, Iss 1, Pp 1-14 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6642580","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6642580","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":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-019-0149-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-019-0149-4","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-019-0149-4","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.44999998807907104,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G6115547468","display_name":"Institut de biologie Computationnelle","funder_award_id":"ANR-11-BINF-0002","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8192438173","display_name":"Digital and Hardware Solutions and Modeling for the Environement and Life Sciences","funder_award_id":"ANR-10-LABX-0020","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2963013324.pdf","grobid_xml":"https://content.openalex.org/works/W2963013324.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1491688952","https://openalex.org/W1501691050","https://openalex.org/W1510141990","https://openalex.org/W1553145333","https://openalex.org/W1647106508","https://openalex.org/W1835951843","https://openalex.org/W1932436296","https://openalex.org/W1969393824","https://openalex.org/W1969575089","https://openalex.org/W1975922463","https://openalex.org/W1985530443","https://openalex.org/W1993481783","https://openalex.org/W1994384119","https://openalex.org/W2004237294","https://openalex.org/W2009353698","https://openalex.org/W2021503576","https://openalex.org/W2054345649","https://openalex.org/W2070449673","https://openalex.org/W2076186660","https://openalex.org/W2090037139","https://openalex.org/W2102626883","https://openalex.org/W2135123683","https://openalex.org/W2149628296","https://openalex.org/W2154555409","https://openalex.org/W2157622572","https://openalex.org/W2160389343","https://openalex.org/W2161080683","https://openalex.org/W2270929032","https://openalex.org/W2345748362","https://openalex.org/W2367820173","https://openalex.org/W2405206615","https://openalex.org/W2552354420","https://openalex.org/W2561675875","https://openalex.org/W2613781255","https://openalex.org/W2622515803","https://openalex.org/W2804961397","https://openalex.org/W2952039867","https://openalex.org/W2964035435","https://openalex.org/W3098488744","https://openalex.org/W4229487902"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"This":[0],"paper":[1],"generalizes":[2],"previous":[3,124],"studies":[4],"on":[5,41,63,111,126],"genome":[6,66],"rearrangement":[7],"under":[8],"biological":[9],"constraints,":[10],"using":[11],"double":[12],"cut":[13],"and":[14,84,87,109,116,121],"join":[15],"(DCJ).":[16],"We":[17,44],"propose":[18],"a":[19,26,64],"model":[20],"for":[21],"weighted":[22],"DCJ,":[23],"along":[24],"with":[25,67],"family":[27],"of":[28,53,71,82,93,106],"optimization":[29],"problems":[30],"called":[31],"$$\\varphi$$":[32,54,61],"-MCPS":[33,62],"(Minimum":[34],"Cost":[35],"Parsimonious":[36,130],"Scenario),":[37],"that":[38,102,122],"are":[39],"based":[40],"labeled":[42],"graphs.":[43],"show":[45],"how":[46],"to":[47,50,59],"compute":[48,60],"solutions":[49],"general":[51,75],"instances":[52,76],"-MCPS,":[55],"given":[56],"an":[57,79],"algorithm":[58],"circular":[65,83],"exactly":[68],"one":[69],"occurrence":[70],"each":[72],"gene.":[73],"These":[74],"can":[77],"have":[78],"arbitrary":[80,88],"number":[81],"linear":[85],"chromosomes,":[86],"gene":[89],"content.":[90],"The":[91],"practicality":[92],"the":[94,104,112,127],"framework":[95],"is":[96],"displayed":[97],"by":[98,114],"presenting":[99],"polynomial-time":[100],"algorithms":[101],"generalize":[103,123],"results":[105,125],"Bulteau,":[107],"Fertin,":[108],"Tannier":[110],"Sorting":[113],"wDCJs":[115],"indels":[117],"in":[118],"intergenes":[119],"problem,":[120],"Minimum":[128],"Local":[129],"Scenario":[131],"problem.":[132]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}
