{"id":"https://openalex.org/W4285533641","doi":null,"title":"Optimal Scaffolding for Chloroplasts' Inverted Repeats","display_name":"Optimal Scaffolding for Chloroplasts' Inverted Repeats","publication_year":2022,"publication_date":"2022-07-05","ids":{"openalex":"https://openalex.org/W4285533641"},"language":"fr","primary_location":{"id":"pmh:oai:HAL:hal-03625229v1","doi":null,"is_oa":true,"landing_page_url":"https://inria.hal.science/hal-03625229","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://jobim2022.sciencesconf.org","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://inria.hal.science/hal-03625229","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064046379","display_name":"Victor Epain","orcid":"https://orcid.org/0000-0003-0049-0954","observed_orcids":["https://orcid.org/0000-0003-0049-0954"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Epain, Victor","raw_affiliation_strings":["Scalable, Optimized and Parallel Algorithms for Genomics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Scalable, Optimized and Parallel Algorithms for Genomics","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040381671","display_name":"Rumen Andonov","orcid":"https://orcid.org/0000-0003-4842-7102","observed_orcids":["https://orcid.org/0000-0003-4842-7102"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Andonov, Rumen","raw_affiliation_strings":["Scalable, Optimized and Parallel Algorithms for Genomics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Scalable, Optimized and Parallel Algorithms for Genomics","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008215565","display_name":"Dominique D. Lavenier","orcid":"https://orcid.org/0000-0003-2557-680X","observed_orcids":["https://orcid.org/0000-0003-2557-680X"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lavenier, Dominique","raw_affiliation_strings":["Scalable, Optimized and Parallel Algorithms for Genomics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Scalable, Optimized and Parallel Algorithms for Genomics","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":0.09099265,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.5810999870300293,"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":0.5810999870300293,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3686999976634979,"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/T11269","display_name":"Algorithms and Data Compression","score":0.027499999850988388,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/scaffolding","display_name":"scaffolding","score":0.8360000252723694},{"id":"https://openalex.org/keywords/chloroplast-genome","display_name":"chloroplast genome","score":0.7789999842643738},{"id":"https://openalex.org/keywords/inverted-repeats","display_name":"inverted repeats","score":0.9739999771118164},{"id":"https://openalex.org/keywords/np-hardness","display_name":"NP-hardness","score":0.871999979019165},{"id":"https://openalex.org/keywords/genome-assembly","display_name":"genome assembly","score":0.8149999976158142},{"id":"https://openalex.org/keywords/directed-graphs","display_name":"directed graphs","score":0.6740000247955322},{"id":"https://openalex.org/keywords/read-filtering","display_name":"read filtering","score":0.4959999918937683},{"id":"https://openalex.org/keywords/chloroplast-genome-structure","display_name":"plastome structure","score":0.45100000500679016}],"concepts":[{"id":"https://openalex.org/C89429830","wikidata":"https://www.wikidata.org/wiki/Q735710","display_name":"Scaffold","level":2,"score":0.6478471755981445},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.54362952709198},{"id":"https://openalex.org/C69305403","wikidata":"https://www.wikidata.org/wiki/Q47263","display_name":"Chloroplast","level":3,"score":0.5408447980880737},{"id":"https://openalex.org/C51603236","wikidata":"https://www.wikidata.org/wiki/Q4852694","display_name":"Inverted repeat","level":4,"score":0.5209585428237915},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3770589828491211},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26693838834762573},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.20997703075408936},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17735639214515686},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12129303812980652},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:HAL:hal-03625229v1","doi":null,"is_oa":true,"landing_page_url":"https://inria.hal.science/hal-03625229","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://jobim2022.sciencesconf.org","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-03625229v1","doi":null,"is_oa":true,"landing_page_url":"https://inria.hal.science/hal-03625229","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://jobim2022.sciencesconf.org","raw_type":"info:eu-repo/semantics/conferenceObject"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4288044945","https://openalex.org/W4390849332","https://openalex.org/W7054838164","https://openalex.org/W4391575695","https://openalex.org/W4393395633","https://openalex.org/W4300539066","https://openalex.org/W2945963500","https://openalex.org/W2780320090","https://openalex.org/W2232213387","https://openalex.org/W4291585212"],"abstract_inverted_index":{"Scaffolding":[0,40],"step":[1],"in":[2,49],"the":[3,9,12,68,77,85,101,106],"genome":[4],"assembly":[5],"aims":[6],"to":[7,99,104],"determine":[8],"order":[10],"and":[11,33,91,103],"orientation":[13],"of":[14,18,30,53,108],"a":[15,27,50,96],"huge":[16],"number":[17],"previously":[19],"assembled":[20],"genomic":[21],"fractions":[22],"(contigs/scaffolds).":[23],"Here":[24],"we":[25,57,65,94],"introduce":[26],"particular":[28,51],"case":[29],"this":[31],"problem":[32,48,70],"denote":[34],"it":[35,44],"by":[36,83],"Nested":[37],"Inverted":[38],"Fragments":[39],"(NIFS).":[41],"We":[42,73],"formulate":[43],"as":[45],"an":[46],"optimisation":[47],"kind":[52],"directed":[54],"graph":[55,97],"that":[56,67],"call":[58],"Multiplied":[59],"Doubled":[60],"Contigs":[61],"Graph":[62],"(MDCG).":[63],"Furthermore,":[64],"prove":[66],"NIFS":[69],"is":[71],"NP-Hard.":[72],"also":[74],"discuss":[75],"how":[76],"chloroplast":[78],"data":[79],"have":[80],"been":[81],"generated":[82],"filtering":[84],"reads":[86],"sequenced":[87],"both":[88],"from":[89],"plants":[90],"chloroplasts.":[92],"Moreover,":[93],"propose":[95],"structure":[98],"visualise":[100],"solution":[102],"highlight":[105],"particularity":[107],"chloroplast's":[109],"regions":[110],"structure.":[111]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2022-07-16T00:00:00"}
