{"id":"https://openalex.org/W4382631187","doi":"https://doi.org/10.1093/bioinformatics/btad264","title":"isONform: reference-free transcriptome reconstruction from Oxford Nanopore data","display_name":"isONform: reference-free transcriptome reconstruction from Oxford Nanopore data","publication_year":2023,"publication_date":"2023-06-01","ids":{"openalex":"https://openalex.org/W4382631187","doi":"https://doi.org/10.1093/bioinformatics/btad264","pmid":"https://pubmed.ncbi.nlm.nih.gov/37387174"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad264","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad264","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i222/50741745/btad264.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i222/50741745/btad264.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111000965","display_name":"Alexander J. Petri","orcid":null},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Alexander J Petri","raw_affiliation_strings":["Department of Mathematics, Science for Life Laboratory, Stockholm University , Stockholm 106 91, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Science for Life Laboratory, Stockholm University , Stockholm 106 91, Sweden","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I161593684"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082939519","display_name":"Kristoffer Sahlin","orcid":"https://orcid.org/0000-0001-7378-2320"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Kristoffer Sahlin","raw_affiliation_strings":["Department of Mathematics, Science for Life Laboratory, Stockholm University , Stockholm 106 91, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Science for Life Laboratory, Stockholm University , Stockholm 106 91, Sweden","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I161593684"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5111000965"],"corresponding_institution_ids":["https://openalex.org/I161593684","https://openalex.org/I2800139495"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.4362,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.89037353,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"39","issue":"Supplement_1","first_page":"i222","last_page":"i231"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9965000152587891,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9923999905586243,"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/computational-biology","display_name":"Computational biology","score":0.5859186053276062},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.5846396684646606},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5716771483421326},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5677198767662048},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5140079259872437},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5100579857826233},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49460527300834656},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.47101983428001404},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4627644419670105},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.46151280403137207},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4597821831703186},{"id":"https://openalex.org/keywords/de-novo-transcriptome-assembly","display_name":"De novo transcriptome assembly","score":0.44102567434310913},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.348432719707489},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.335899293422699},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3281462490558624},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11894446611404419}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5859186053276062},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.5846396684646606},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5716771483421326},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5677198767662048},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5140079259872437},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5100579857826233},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49460527300834656},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.47101983428001404},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4627644419670105},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.46151280403137207},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4597821831703186},{"id":"https://openalex.org/C50489715","wikidata":"https://www.wikidata.org/wiki/Q5244960","display_name":"De novo transcriptome assembly","level":5,"score":0.44102567434310913},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.348432719707489},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.335899293422699},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3281462490558624},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11894446611404419}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018076","descriptor_name":"DNA, Complementary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018076","descriptor_name":"DNA, Complementary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018076","descriptor_name":"DNA, Complementary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018076","descriptor_name":"DNA, Complementary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad264","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad264","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i222/50741745/btad264.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37387174","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37387174","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:pubmedcentral.nih.gov:10311309","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10311309","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10311309/pdf/btad264.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad264","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad264","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i222/50741745/btad264.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1364868472","display_name":null,"funder_award_id":"2018-05973","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G3321450376","display_name":null,"funder_award_id":"05973","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G5356226767","display_name":null,"funder_award_id":"2018-0597","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G5732281853","display_name":null,"funder_award_id":"021-04000","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G712881263","display_name":null,"funder_award_id":"2018-","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G7395996006","display_name":null,"funder_award_id":"2021-04000","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"}],"funders":[{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320336376","display_name":"Uppsala Multidisciplinary Center for Advanced Computational Science","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4382631187.pdf"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W958219903","https://openalex.org/W2141408763","https://openalex.org/W2144560237","https://openalex.org/W2160969485","https://openalex.org/W2260037449","https://openalex.org/W2575750030","https://openalex.org/W2617273082","https://openalex.org/W2789843538","https://openalex.org/W2804628144","https://openalex.org/W2899345312","https://openalex.org/W2952666313","https://openalex.org/W2978728885","https://openalex.org/W2995527562","https://openalex.org/W2995642161","https://openalex.org/W2995995746","https://openalex.org/W2999510651","https://openalex.org/W3010772070","https://openalex.org/W3011428862","https://openalex.org/W3017368919","https://openalex.org/W3045473232","https://openalex.org/W3119188679","https://openalex.org/W3125399386","https://openalex.org/W3128964673","https://openalex.org/W3177776373","https://openalex.org/W3186338429","https://openalex.org/W3191132797","https://openalex.org/W3200242814","https://openalex.org/W3206657624","https://openalex.org/W4284885445","https://openalex.org/W4310960769","https://openalex.org/W4311803917","https://openalex.org/W4313454274","https://openalex.org/W4377291096","https://openalex.org/W4380319111","https://openalex.org/W4384559024","https://openalex.org/W4399437507","https://openalex.org/W6773153462","https://openalex.org/W6799364060","https://openalex.org/W6846935355"],"related_works":["https://openalex.org/W2584868213","https://openalex.org/W2607669908","https://openalex.org/W3090794301","https://openalex.org/W233273322","https://openalex.org/W2480204629","https://openalex.org/W334260928","https://openalex.org/W1996370379","https://openalex.org/W2800773082","https://openalex.org/W2524794421","https://openalex.org/W2745892572"],"abstract_inverted_index":{"https://github.com/aljpetri/isONform.":[0]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
