{"id":"https://openalex.org/W2900906861","doi":"https://doi.org/10.1093/bioinformatics/bty903","title":"CAARS: comparative assembly and annotation of RNA-Seq data","display_name":"CAARS: comparative assembly and annotation of RNA-Seq data","publication_year":2018,"publication_date":"2018-11-17","ids":{"openalex":"https://openalex.org/W2900906861","doi":"https://doi.org/10.1093/bioinformatics/bty903","mag":"2900906861","pmid":"https://pubmed.ncbi.nlm.nih.gov/30452539"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty903","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty903","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6596894","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075826396","display_name":"Carine Rey","orcid":"https://orcid.org/0000-0003-4871-8110"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Carine Rey","raw_affiliation_strings":["UnivLyon, Universit\u00e9 Claude Bernard Lyon 1, ENS de Lyon, CNRS UMR, INSERM U1210, LBMC, F-69007, Lyon, France"],"affiliations":[{"raw_affiliation_string":"UnivLyon, Universit\u00e9 Claude Bernard Lyon 1, ENS de Lyon, CNRS UMR, INSERM U1210, LBMC, F-69007, Lyon, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I154526488","https://openalex.org/I113428412","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112813196","display_name":"Philippe Veber","orcid":"https://orcid.org/0000-0003-0328-0143"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I4210135640","display_name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive","ror":"https://ror.org/03skt0t88","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I203339264","https://openalex.org/I4210100596","https://openalex.org/I4210107625","https://openalex.org/I4210135640"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Philippe Veber","raw_affiliation_strings":["UnivLyon, Universit\u00e9 Claude Bernard Lyon 1, CNRS, UMR, LBBE, F-69100, Villeurbanne, France"],"affiliations":[{"raw_affiliation_string":"UnivLyon, Universit\u00e9 Claude Bernard Lyon 1, CNRS, UMR, LBBE, F-69100, Villeurbanne, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I4210135640","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079299227","display_name":"Bastien Boussau","orcid":"https://orcid.org/0000-0003-0776-4460"},"institutions":[{"id":"https://openalex.org/I4210135640","display_name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive","ror":"https://ror.org/03skt0t88","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I203339264","https://openalex.org/I4210100596","https://openalex.org/I4210107625","https://openalex.org/I4210135640"]},{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Bastien Boussau","raw_affiliation_strings":["UnivLyon, Universit\u00e9 Claude Bernard Lyon 1, CNRS, UMR, LBBE, F-69100, Villeurbanne, France"],"affiliations":[{"raw_affiliation_string":"UnivLyon, Universit\u00e9 Claude Bernard Lyon 1, CNRS, UMR, LBBE, F-69100, Villeurbanne, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I4210135640","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091156775","display_name":"Marie S\u00e9mon","orcid":"https://orcid.org/0000-0003-3479-7524"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Marie S\u00e9mon","raw_affiliation_strings":["UnivLyon, Universit\u00e9 Claude Bernard Lyon 1, ENS de Lyon, CNRS UMR, INSERM U1210, LBMC, F-69007, Lyon, France"],"affiliations":[{"raw_affiliation_string":"UnivLyon, Universit\u00e9 Claude Bernard Lyon 1, ENS de Lyon, CNRS UMR, INSERM U1210, LBMC, F-69007, Lyon, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I154526488","https://openalex.org/I113428412","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5075826396"],"corresponding_institution_ids":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590","https://openalex.org/I154526488"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0928,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.49323948,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"35","issue":"13","first_page":"2199","last_page":"2207"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":1.0,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9961000084877014,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9878000020980835,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6697862148284912},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5596555471420288},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5560417771339417},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5464611649513245},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.5193004012107849},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5000100135803223},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.449621319770813},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.44833144545555115},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31064027547836304}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6697862148284912},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5596555471420288},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5560417771339417},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5464611649513245},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.5193004012107849},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5000100135803223},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.449621319770813},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.44833144545555115},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31064027547836304}],"mesh":[{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bty903","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty903","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30452539","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30452539","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:hal-02330682v1","is_oa":false,"landing_page_url":"https://cnrs.hal.science/hal-02330682","pdf_url":null,"source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","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":"Bioinformatics, 2019, 35 (13), pp.2199-2207. &#x27E8;10.1093/bioinformatics/bty903&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:6596894","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6596894","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:6596894","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6596894","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.44999998807907104,"display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320329934","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1966056950","https://openalex.org/W1972157500","https://openalex.org/W1973537909","https://openalex.org/W1981509058","https://openalex.org/W1995701890","https://openalex.org/W2009234149","https://openalex.org/W2012034410","https://openalex.org/W2013067928","https://openalex.org/W2044886350","https://openalex.org/W2055770801","https://openalex.org/W2059123697","https://openalex.org/W2060842569","https://openalex.org/W2070029696","https://openalex.org/W2081531294","https://openalex.org/W2097065948","https://openalex.org/W2099321785","https://openalex.org/W2106114901","https://openalex.org/W2114676910","https://openalex.org/W2117260150","https://openalex.org/W2120892748","https://openalex.org/W2121052765","https://openalex.org/W2126419817","https://openalex.org/W2127774996","https://openalex.org/W2130807368","https://openalex.org/W2140737953","https://openalex.org/W2141458291","https://openalex.org/W2142678478","https://openalex.org/W2143335572","https://openalex.org/W2143592941","https://openalex.org/W2147526198","https://openalex.org/W2153116581","https://openalex.org/W2155839887","https://openalex.org/W2157363486","https://openalex.org/W2163249996","https://openalex.org/W2166265186","https://openalex.org/W2167898988","https://openalex.org/W2170747616","https://openalex.org/W2236822143","https://openalex.org/W2239969570","https://openalex.org/W2281248875","https://openalex.org/W2281531600","https://openalex.org/W2310259903","https://openalex.org/W2310622210","https://openalex.org/W2323326409","https://openalex.org/W2333071592","https://openalex.org/W2403922294","https://openalex.org/W2425763960","https://openalex.org/W2469868269","https://openalex.org/W2587686048","https://openalex.org/W2755196863","https://openalex.org/W3106505504","https://openalex.org/W4252232449","https://openalex.org/W6697974936","https://openalex.org/W6732929663"],"related_works":["https://openalex.org/W2059565715","https://openalex.org/W2901823680","https://openalex.org/W2009940763","https://openalex.org/W2946410450","https://openalex.org/W4361192415","https://openalex.org/W2126804125","https://openalex.org/W2162782320","https://openalex.org/W4386637333","https://openalex.org/W2137318037","https://openalex.org/W1760213857"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-03-22T08:09:32.410652","created_date":"2025-10-10T00:00:00"}
