{"id":"https://openalex.org/W4205840725","doi":"https://doi.org/10.1093/bioinformatics/btab873","title":"On the identifiability of the isoform deconvolution problem: application to select the proper fragment length in an RNA-seq library","display_name":"On the identifiability of the isoform deconvolution problem: application to select the proper fragment length in an RNA-seq library","publication_year":2021,"publication_date":"2021-12-30","ids":{"openalex":"https://openalex.org/W4205840725","doi":"https://doi.org/10.1093/bioinformatics/btab873","pmid":"https://pubmed.ncbi.nlm.nih.gov/34978563"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab873","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab873","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/6/1491/49008437/btab873.pdf","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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/6/1491/49008437/btab873.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079108277","display_name":"Juan A. Ferrer-Bonsoms","orcid":"https://orcid.org/0000-0002-1588-2195"},"institutions":[{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Juan A Ferrer-Bonsoms","raw_affiliation_strings":["Department of Biomedical Engineering and Sciences, TECNUN, University of Navarra , Pamplona, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering and Sciences, TECNUN, University of Navarra , Pamplona, Spain","institution_ids":["https://openalex.org/I88155538"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045630896","display_name":"Xabier Morales","orcid":"https://orcid.org/0000-0003-0303-9958"},"institutions":[{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Xabier Morales","raw_affiliation_strings":["Department of Biomedical Engineering and Sciences, TECNUN, University of Navarra , Pamplona, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering and Sciences, TECNUN, University of Navarra , Pamplona, Spain","institution_ids":["https://openalex.org/I88155538"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075133225","display_name":"Pegah Tootoonchi Afshar","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pegah T Afshar","raw_affiliation_strings":["Department of Statistics, Stanford University , Stanford, CA 94305-4020, USA"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, Stanford University , Stanford, CA 94305-4020, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015401462","display_name":"Wing Hung Wong","orcid":"https://orcid.org/0000-0001-7466-2339"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wing H Wong","raw_affiliation_strings":["Department of Statistics, Stanford University , Stanford, CA 94305-4020, USA"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, Stanford University , Stanford, CA 94305-4020, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046603247","display_name":"\u00c1ngel Rubio","orcid":"https://orcid.org/0000-0002-3274-2450"},"institutions":[{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Angel Rubio","raw_affiliation_strings":["Department of Biomedical Engineering and Sciences, TECNUN, University of Navarra , Pamplona, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering and Sciences, TECNUN, University of Navarra , Pamplona, Spain","institution_ids":["https://openalex.org/I88155538"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5079108277"],"corresponding_institution_ids":["https://openalex.org/I88155538"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13662646,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"38","issue":"6","first_page":"1491","last_page":"1496"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983999729156494,"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":0.9983999729156494,"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":0.9962000250816345,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9929999709129333,"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/identifiability","display_name":"Identifiability","score":0.8126741647720337},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.777024507522583},{"id":"https://openalex.org/keywords/deconvolution","display_name":"Deconvolution","score":0.7187245488166809},{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.6434413194656372},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5806818008422852},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5803829431533813},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5716187953948975},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.5566241145133972},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4401463568210602},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4272242784500122},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.333662211894989},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24439170956611633},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12992370128631592},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.10899132490158081},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.09283497929573059},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08002257347106934},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.06862393021583557}],"concepts":[{"id":"https://openalex.org/C122770356","wikidata":"https://www.wikidata.org/wiki/Q1656753","display_name":"Identifiability","level":2,"score":0.8126741647720337},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.777024507522583},{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.7187245488166809},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.6434413194656372},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5806818008422852},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5803829431533813},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5716187953948975},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.5566241145133972},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4401463568210602},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4272242784500122},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.333662211894989},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24439170956611633},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12992370128631592},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.10899132490158081},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.09283497929573059},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08002257347106934},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.06862393021583557},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","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":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","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":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab873","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab873","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/6/1491/49008437/btab873.pdf","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:34978563","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34978563","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:8896638","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8896638","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":"doi:10.1093/bioinformatics/btab873","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab873","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/6/1491/49008437/btab873.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4096213317","display_name":null,"funder_award_id":"Programme","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G42813494","display_name":null,"funder_award_id":"HG007735","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4757780819","display_name":null,"funder_award_id":"P50 HG007735","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5188720299","display_name":null,"funder_award_id":"R01HG007834","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6732693109","display_name":null,"funder_award_id":"C355/A26819","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"}],"funders":[{"id":"https://openalex.org/F4320319985","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67"},{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4205840725.pdf","grobid_xml":"https://content.openalex.org/works/W4205840725.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1988245212","https://openalex.org/W2010394934","https://openalex.org/W2068568257","https://openalex.org/W2100448568","https://openalex.org/W2117688129","https://openalex.org/W2133459862","https://openalex.org/W2143447881","https://openalex.org/W2593821392","https://openalex.org/W2731748842","https://openalex.org/W2888193242","https://openalex.org/W2950410184","https://openalex.org/W2951972570","https://openalex.org/W2994165170","https://openalex.org/W3038923756","https://openalex.org/W3041018134"],"related_works":["https://openalex.org/W2724847603","https://openalex.org/W2034041141","https://openalex.org/W2184661725","https://openalex.org/W2900187352","https://openalex.org/W2573470972","https://openalex.org/W2105626102","https://openalex.org/W2131038454","https://openalex.org/W112856298","https://openalex.org/W145130300","https://openalex.org/W2169056646"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
