{"id":"https://openalex.org/W2075867703","doi":"https://doi.org/10.1186/1471-2105-15-s1-s7","title":"Reducing bias in RNA sequencing data: a novel approach to compute counts","display_name":"Reducing bias in RNA sequencing data: a novel approach to compute counts","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2075867703","doi":"https://doi.org/10.1186/1471-2105-15-s1-s7","mag":"2075867703","pmid":"https://pubmed.ncbi.nlm.nih.gov/24564404"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-s1-s7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s1-s7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S1-S7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S1-S7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033275131","display_name":"Francesca Finotello","orcid":"https://orcid.org/0000-0003-0712-4658"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Francesca Finotello","raw_affiliation_strings":["Department of Information Engineering, University of Padova, Padova, 35131, Italy","Department of Information Engineering; University of Padova; Padova; Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Engineering, University of Padova, Padova, 35131, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Department of Information Engineering; University of Padova; Padova; Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021297661","display_name":"Enrico Lavezzo","orcid":"https://orcid.org/0000-0002-3902-8356"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Enrico Lavezzo","raw_affiliation_strings":["Department of Molecular Medicine, University of Padova, Padova, 35131, Italy","Department of Molecular Medicine , University of Padova , Padova , Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine, University of Padova, Padova, 35131, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Department of Molecular Medicine , University of Padova , Padova , Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035748127","display_name":"Luca Bianco","orcid":"https://orcid.org/0000-0002-0196-8422"},"institutions":[{"id":"https://openalex.org/I103225651","display_name":"Fondazione Edmund Mach","ror":"https://ror.org/0381bab64","country_code":"IT","type":"other","lineage":["https://openalex.org/I103225651"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Luca Bianco","raw_affiliation_strings":["Research and Innovation Centre, Edmund Mach Foundation, Trento, 38010, Italy","Research and Innovation Centre, Edmund Mach Foundation, Trento, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research and Innovation Centre, Edmund Mach Foundation, Trento, 38010, Italy","institution_ids":["https://openalex.org/I103225651"]},{"raw_affiliation_string":"Research and Innovation Centre, Edmund Mach Foundation, Trento, Italy","institution_ids":["https://openalex.org/I103225651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083698836","display_name":"Luisa Barzon","orcid":"https://orcid.org/0000-0003-0720-8456"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Luisa Barzon","raw_affiliation_strings":["Department of Molecular Medicine, University of Padova, Padova, 35131, Italy","Department of Molecular Medicine , University of Padova , Padova , Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine, University of Padova, Padova, 35131, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Department of Molecular Medicine , University of Padova , Padova , Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065236106","display_name":"Paolo Emilio Mazzon","orcid":null},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paolo Mazzon","raw_affiliation_strings":["Department of Information Engineering, University of Padova, Padova, 35131, Italy","Department of Information Engineering; University of Padova; Padova; Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Engineering, University of Padova, Padova, 35131, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Department of Information Engineering; University of Padova; Padova; Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042600667","display_name":"Paolo Fontana","orcid":"https://orcid.org/0000-0002-4523-4818"},"institutions":[{"id":"https://openalex.org/I103225651","display_name":"Fondazione Edmund Mach","ror":"https://ror.org/0381bab64","country_code":"IT","type":"other","lineage":["https://openalex.org/I103225651"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paolo Fontana","raw_affiliation_strings":["Research and Innovation Centre, Edmund Mach Foundation, Trento, 38010, Italy","Research and Innovation Centre, Edmund Mach Foundation, Trento, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research and Innovation Centre, Edmund Mach Foundation, Trento, 38010, Italy","institution_ids":["https://openalex.org/I103225651"]},{"raw_affiliation_string":"Research and Innovation Centre, Edmund Mach Foundation, Trento, Italy","institution_ids":["https://openalex.org/I103225651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071924678","display_name":"Stefano Toppo","orcid":"https://orcid.org/0000-0002-0246-3119"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Stefano Toppo","raw_affiliation_strings":["Department of Molecular Medicine, University of Padova, Padova, 35131, Italy","Department of Molecular Medicine , University of Padova , Padova , Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine, University of Padova, Padova, 35131, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Department of Molecular Medicine , University of Padova , Padova , Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077821068","display_name":"Barbara Di Camillo","orcid":"https://orcid.org/0000-0001-8415-4688"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Barbara Di Camillo","raw_affiliation_strings":["Department of Information Engineering, University of Padova, Padova, 35131, Italy","Department of Information Engineering; University of Padova; Padova; Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Engineering, University of Padova, Padova, 35131, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Department of Information Engineering; University of Padova; Padova; Italy","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5077821068"],"corresponding_institution_ids":["https://openalex.org/I138689650"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.7035,"has_fulltext":true,"cited_by_count":59,"citation_normalized_percentile":{"value":0.90598928,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"15","issue":"S1","first_page":"S7","last_page":"S7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6714000105857849,"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":0.6714000105857849,"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":0.1437000036239624,"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":0.03590000048279762,"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/dna-microarray","display_name":"DNA microarray","score":0.575096845626831},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5663232803344727},{"id":"https://openalex.org/keywords/gc-content","display_name":"GC-content","score":0.49710801243782043},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.4768615663051605},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47232311964035034},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4662878215312958},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.43486952781677246},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3559882640838623},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34573835134506226},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3134780526161194},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2334883213043213},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.15996837615966797},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.13753271102905273}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.575096845626831},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5663232803344727},{"id":"https://openalex.org/C42251679","wikidata":"https://www.wikidata.org/wiki/Q933491","display_name":"GC-content","level":4,"score":0.49710801243782043},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.4768615663051605},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47232311964035034},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4662878215312958},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43486952781677246},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3559882640838623},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34573835134506226},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3134780526161194},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2334883213043213},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.15996837615966797},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.13753271102905273},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-15-s1-s7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s1-s7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S1-S7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24564404","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24564404","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3005885","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4016203","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:openpub.fmach.it:10449/90377","is_oa":true,"landing_page_url":"https://hdl.handle.net/10449/90377","pdf_url":null,"source":{"id":"https://openalex.org/S4377196413","display_name":"CINECA IRIS Institutional Research Information System (Fondazione Edmund Mach)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I103225651","host_organization_name":"Fondazione Edmund Mach","host_organization_lineage":["https://openalex.org/I103225651"],"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":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:www.research.unipd.it:11577/2668299","is_oa":false,"landing_page_url":"http://hdl.handle.net/11577/2668299","pdf_url":null,"source":{"id":"https://openalex.org/S4377196283","display_name":"Research Padua  Archive (University of Padua)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-s1-s7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s1-s7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S1-S7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309832","display_name":"Fondazione Cassa di Risparmio di Padova e Rovigo","ror":"https://ror.org/02jecj653"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2075867703.pdf","grobid_xml":"https://content.openalex.org/works/W2075867703.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1977957409","https://openalex.org/W1981509058","https://openalex.org/W1983253191","https://openalex.org/W1984708728","https://openalex.org/W1985484001","https://openalex.org/W2009458183","https://openalex.org/W2012016911","https://openalex.org/W2018604728","https://openalex.org/W2021704169","https://openalex.org/W2023621259","https://openalex.org/W2027455260","https://openalex.org/W2028925572","https://openalex.org/W2052297861","https://openalex.org/W2053057991","https://openalex.org/W2061537056","https://openalex.org/W2061680337","https://openalex.org/W2096760403","https://openalex.org/W2097065948","https://openalex.org/W2097647914","https://openalex.org/W2098832713","https://openalex.org/W2099320873","https://openalex.org/W2102619694","https://openalex.org/W2107018762","https://openalex.org/W2107060225","https://openalex.org/W2108234281","https://openalex.org/W2114104545","https://openalex.org/W2123497973","https://openalex.org/W2131088968","https://openalex.org/W2134199796","https://openalex.org/W2146436369","https://openalex.org/W2151529515","https://openalex.org/W2152239989","https://openalex.org/W2154431984","https://openalex.org/W2154537630","https://openalex.org/W2156631105","https://openalex.org/W2160164696","https://openalex.org/W2161106528","https://openalex.org/W2167699390","https://openalex.org/W2168342464","https://openalex.org/W2170219300","https://openalex.org/W2616754551"],"related_works":["https://openalex.org/W2591697403","https://openalex.org/W2953716828","https://openalex.org/W2904857019","https://openalex.org/W2944728705","https://openalex.org/W3011538607","https://openalex.org/W2904022177","https://openalex.org/W4321441197","https://openalex.org/W2359348847","https://openalex.org/W4294432981","https://openalex.org/W2096302356"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1,234],"the":[2,57,107,114,128,135,172,210,229,242,247,250,260,268,277],"last":[3],"decade,":[4],"Next-Generation":[5],"Sequencing":[6],"technologies":[7],"have":[8,33],"been":[9,34],"extensively":[10],"applied":[11],"to":[12,21,36,71,89,105,110,141,181,209,226,259,273,276],"quantitative":[13,299],"transcriptomics,":[14],"making":[15],"RNA":[16],"sequencing":[17,90],"a":[18,100,286],"valuable":[19],"alternative":[20,296],"microarrays":[22],"for":[23,298],"measuring":[24],"and":[25,92,120,153,166,169,177,192,222,256,282],"comparing":[26],"gene":[27],"transcription":[28],"levels.":[29],"Although":[30],"several":[31,155],"methods":[32],"proposed":[35],"provide":[37],"an":[38,53,111,142,295],"unbiased":[39],"estimate":[40],"of":[41,48,56,60,116,138,174,179,183,231,249,263,280],"transcript":[42],"abundances":[43],"through":[44],"data":[45,151],"normalization,":[46],"all":[47],"them":[49],"are":[50,79,147,253,257,271,283],"based":[51],"on":[52,63,195,246],"initial":[54],"count":[55],"total":[58,136],"number":[59,137],"reads":[61,78,139,264,281],"mapping":[62],"each":[64],"transcript.":[65],"This":[66],"procedure,":[67],"in":[68,94,125,171,228],"principle":[69],"robust":[70,225,272],"random":[72],"noise,":[73],"is":[74,201,223],"actually":[75],"error-prone":[76],"if":[77],"not":[80],"uniformly":[81],"distributed":[82],"along":[83,265],"sequences,":[84],"as":[85,113,163,294],"happens":[86],"indeed":[87],"due":[88,275],"errors":[91],"ambiguity":[93],"read":[95],"mapping.":[96],"Here":[97],"we":[98,121,236,291],"propose":[99,292],"new":[101],"approach,":[102],"called":[103],"maxcounts,":[104],"quantify":[106],"expression":[108,199],"assigned":[109],"exon":[112,164],"maximum":[115],"its":[117,123],"per-base":[118],"counts,":[119],"assess":[122],"performance":[124],"comparison":[126],"with":[127,207,241],"standard":[129,211,243],"approach":[130,244,297],"described":[131],"above,":[132],"which":[133],"considers":[134],"aligned":[140],"exon.":[143],"The":[144],"two":[145],"measures":[146,188],"compared":[148],"using":[149],"multiple":[150],"sets":[152],"considering":[154],"evaluation":[156],"criteria:":[157],"independence":[158],"from":[159],"gene-specific":[160],"covariates,":[161],"such":[162],"length":[165,248],"GC-content,":[167],"accuracy":[168,191],"precision":[170],"quantification":[173,200],"true":[175],"concentrations":[176],"robustness":[178],"measurements":[180],"variations":[182,227],"alignments":[184],"quality.":[185],"RESULTS:":[186],"Both":[187],"show":[189],"high":[190],"low":[193,220],"dependency":[194],"GC-content.":[196],"However,":[197],"maxcounts":[198,270,293],"less":[202],"biased":[203],"towards":[204],"long":[205],"exons":[206],"respect":[208],"approach.":[212],"Moreover,":[213],"it":[214],"shows":[215],"lower":[216,287],"technical":[217,288],"variability":[218],"at":[219],"expressions":[221],"more":[224],"quality":[230],"alignments.":[232],"CONCLUSIONS:":[233],"summary,":[235],"confirm":[237],"that":[238],"counts":[239],"computed":[240],"depend":[245],"feature":[251],"they":[252],"summarized":[254],"on,":[255],"sensitive":[258],"non-uniform":[261],"distribution":[262,279],"transcripts.":[266],"On":[267],"opposite,":[269],"biases":[274],"non-uniformity":[278],"characterized":[284],"by":[285],"variability.":[289],"Hence,":[290],"RNA-sequencing":[300],"applications.":[301]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
