{"id":"https://openalex.org/W1585889856","doi":"https://doi.org/10.3233/fi-2011-526","title":"Directed Overlap-inclusion Graphs as Representations of Ciliate Genes","display_name":"Directed Overlap-inclusion Graphs as Representations of Ciliate Genes","publication_year":2011,"publication_date":"2011-01-01","ids":{"openalex":"https://openalex.org/W1585889856","doi":"https://doi.org/10.3233/fi-2011-526","mag":"1585889856"},"language":"en","primary_location":{"id":"doi:10.3233/fi-2011-526","is_oa":false,"landing_page_url":"https://doi.org/10.3233/fi-2011-526","pdf_url":null,"source":{"id":"https://openalex.org/S39012697","display_name":"Fundamenta Informaticae","issn_l":"0169-2968","issn":["0169-2968","1875-8681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Fundamenta Informaticae","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082298867","display_name":"Sepinoud Azimi","orcid":"https://orcid.org/0000-0002-4739-9560"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Sepinoud Azimi","raw_affiliation_strings":["Computational Biomodeling Laboratory, Turku Centre for Computer Science, \u00c5bo Akademi University, Turku, Finland. sepinoud.azimi@abo.fi"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biomodeling Laboratory, Turku Centre for Computer Science, \u00c5bo Akademi University, Turku, Finland. sepinoud.azimi@abo.fi","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054372678","display_name":"Tero Harju","orcid":"https://orcid.org/0000-0002-9640-6309"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Tero Harju","raw_affiliation_strings":["Department of Mathematics, University of Turku, Turku, Finland. tero.harju@utu.fi"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Turku, Turku, Finland. tero.harju@utu.fi","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053223351","display_name":"Miika Langille","orcid":null},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Miika Langille","raw_affiliation_strings":["Computational Biomodeling Laboratory, Turku Centre for Computer Science, \u00c5bo Akademi University, Turku, Finland. miika.langille@gmail.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biomodeling Laboratory, Turku Centre for Computer Science, \u00c5bo Akademi University, Turku, Finland. miika.langille@gmail.com","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047091186","display_name":"Ion Petre","orcid":"https://orcid.org/0000-0002-5014-5529"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Ion Petre","raw_affiliation_strings":["Computational Biomodeling Laboratory, Turku Centre for Computer Science, \u00c5bo Akademi University, Turku, Finland. ion.petre@abo.fi"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biomodeling Laboratory, Turku Centre for Computer Science, \u00c5bo Akademi University, Turku, Finland. ion.petre@abo.fi","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I130217899"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079232711","display_name":"Vladimir Rogojin","orcid":null},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Vladimir Rogojin","raw_affiliation_strings":["Computational Systems Biology Laboratory, University of Helsinki, Helsinki, Finland. vladimir.rogojin@helsinki.fi"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Laboratory, University of Helsinki, Helsinki, Finland. vladimir.rogojin@helsinki.fi","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5082298867"],"corresponding_institution_ids":["https://openalex.org/I130217899","https://openalex.org/I183173800"],"apc_list":null,"apc_paid":null,"fwci":0.133,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.51145547,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"110","issue":"1-4","first_page":"29","last_page":"44"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11879","display_name":"Protist diversity and phylogeny","score":0.9988999962806702,"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/T11879","display_name":"Protist diversity and phylogeny","score":0.9988999962806702,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9973999857902527,"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/T12012","display_name":"Diatoms and Algae Research","score":0.9805999994277954,"subfield":{"id":"https://openalex.org/subfields/2502","display_name":"Biomaterials"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ciliate","display_name":"Ciliate","score":0.7916901111602783},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5152900218963623},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4918825626373291},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.43350690603256226},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.42165929079055786},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.40484336018562317},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.394160658121109},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38813507556915283},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37996935844421387}],"concepts":[{"id":"https://openalex.org/C2777334866","wikidata":"https://www.wikidata.org/wiki/Q106345","display_name":"Ciliate","level":2,"score":0.7916901111602783},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5152900218963623},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4918825626373291},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.43350690603256226},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.42165929079055786},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.40484336018562317},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.394160658121109},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38813507556915283},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37996935844421387}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3233/fi-2011-526","is_oa":false,"landing_page_url":"https://doi.org/10.3233/fi-2011-526","pdf_url":null,"source":{"id":"https://openalex.org/S39012697","display_name":"Fundamenta Informaticae","issn_l":"0169-2968","issn":["0169-2968","1875-8681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Fundamenta Informaticae","raw_type":"journal-article"},{"id":"pmh:oai:pure.atira.dk:publications/9689e9ae-3441-48f6-a610-c97b6e951a12","is_oa":false,"landing_page_url":"https://research.abo.fi/en/publications/9689e9ae-3441-48f6-a610-c97b6e951a12","pdf_url":null,"source":{"id":"https://openalex.org/S4406923060","display_name":"\u00c5bo Akademi University Research Portal","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":"Azimi Rashti, S, Harju, T, Langille, M, Petre, I & Rogojin, V 2011, 'Directed Overlap-Inclusion Graphs as Representations of Ciliate Genes', Fundamenta Informaticae, vol. 110, no. 1-4, pp. 29\u201344. https://doi.org/10.3233/FI-2011-526","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Reduced inequalities","score":0.5199999809265137,"id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W50054097","https://openalex.org/W86835110","https://openalex.org/W184595725","https://openalex.org/W1480899281","https://openalex.org/W1493657730","https://openalex.org/W1508520710","https://openalex.org/W1513391222","https://openalex.org/W1517921658","https://openalex.org/W1527280207","https://openalex.org/W1718591406","https://openalex.org/W1822599926","https://openalex.org/W1838041811","https://openalex.org/W1879527074","https://openalex.org/W1974684756","https://openalex.org/W1979909102","https://openalex.org/W2002300035","https://openalex.org/W2035047050","https://openalex.org/W2046026042","https://openalex.org/W2048249183","https://openalex.org/W2058999747","https://openalex.org/W2143474538","https://openalex.org/W2168918166","https://openalex.org/W2689903631","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2028415712","https://openalex.org/W2011868592","https://openalex.org/W2169569642","https://openalex.org/W2375513588","https://openalex.org/W3150283808","https://openalex.org/W2524700259","https://openalex.org/W2040460572","https://openalex.org/W2060038942","https://openalex.org/W1977068657"],"abstract_inverted_index":{"The":[0],"simple":[1,55],"intramolecular":[2],"model":[3,84],"for":[4],"gene":[5,32,56],"assembly":[6,26,57],"in":[7,36,46,62,91,103,135],"ciliates":[8],"consists":[9],"of":[10,27,38,49,53,64,78,82,96,99,105,111,115,125,128,137],"three":[11,80],"molecular":[12],"operations":[13,81],"based":[14],"on":[15],"local":[16],"DNA":[17],"manipulations.":[18],"It":[19],"was":[20],"shown":[21],"to":[22,75],"predict":[23],"correctly":[24],"the":[25,50,54,79,83,97,112,116],"all":[28],"currently":[29],"known":[30],"ciliate":[31,117],"patterns.":[33],"Mathematical":[34],"models":[35],"terms":[37,63,104,136],"signed":[39,42],"permutations":[40],"and":[41,71,85,101],"strings":[43],"proved":[44,73],"limited":[45],"capturing":[47],"some":[48],"combinatorial":[51,87,126],"details":[52],"process.":[58],"A":[59],"different":[60],"formalization":[61],"overlap-inclusion":[65,107],"graphs,":[66,130],"recently":[67],"introduced":[68],"by":[69],"Brijder":[70,100],"Hoogeboom,":[72],"well-suited":[74],"describe":[76],"two":[77],"their":[86],"properties.":[88],"We":[89,121],"introduce":[90],"this":[92],"paper":[93],"an":[94],"extension":[95],"framework":[98],"Hoogeboom":[102],"directed":[106],"graphs":[108],"where":[109],"more":[110],"linear":[113],"structure":[114],"genes":[118],"is":[119],"described.":[120],"investigate":[122],"a":[123,132],"number":[124],"properties":[127],"these":[129],"including":[131],"necessary":[133],"property":[134],"forbidden":[138],"induced":[139],"subgraphs.":[140]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-02T06:04:40.494371","created_date":"2025-10-10T00:00:00"}
