{"id":"https://openalex.org/W2157770058","doi":"https://doi.org/10.1186/1471-2105-11-s3-s6","title":"Towards reliable isoform quantification using RNA-SEQ data","display_name":"Towards reliable isoform quantification using RNA-SEQ data","publication_year":2010,"publication_date":"2010-04-01","ids":{"openalex":"https://openalex.org/W2157770058","doi":"https://doi.org/10.1186/1471-2105-11-s3-s6","mag":"2157770058","pmid":"https://pubmed.ncbi.nlm.nih.gov/20438653"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-s3-s6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s3-s6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S3-S6","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/10.1186/1471-2105-11-S3-S6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011043085","display_name":"Brian E. Howard","orcid":"https://orcid.org/0000-0002-6123-7090"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brian E Howard","raw_affiliation_strings":["Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA. itsbehoward@hotmail.com","Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27606, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA. itsbehoward@hotmail.com","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27606, USA","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058462301","display_name":"Steffen Heber","orcid":"https://orcid.org/0000-0002-1050-3635"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steffen Heber","raw_affiliation_strings":["Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27606, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27606, USA","institution_ids":["https://openalex.org/I137902535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5011043085"],"corresponding_institution_ids":["https://openalex.org/I137902535"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.1202,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.92095359,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"11","issue":"S3","first_page":"S6","last_page":"S6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9670000076293945,"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/T10604","display_name":"RNA Research and Splicing","score":0.9670000076293945,"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":0.009999999776482582,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.006800000090152025,"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/alternative-splicing","display_name":"Alternative splicing","score":0.7446871995925903},{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.7224189639091492},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6888963580131531},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.6785699129104614},{"id":"https://openalex.org/keywords/splice","display_name":"splice","score":0.6631007790565491},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6285191774368286},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6222972869873047},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5633326768875122},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.5482662916183472},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5265929102897644},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5049393773078918},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.48990052938461304},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4824579358100891},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.48164239525794983}],"concepts":[{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.7446871995925903},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.7224189639091492},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6888963580131531},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6785699129104614},{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.6631007790565491},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6285191774368286},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6222972869873047},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5633326768875122},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.5482662916183472},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5265929102897644},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5049393773078918},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.48990052938461304},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4824579358100891},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.48164239525794983}],"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013312","descriptor_name":"Stress, Physiological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013312","descriptor_name":"Stress, Physiological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013312","descriptor_name":"Stress, Physiological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017343","descriptor_name":"Genes, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017343","descriptor_name":"Genes, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017343","descriptor_name":"Genes, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D018506","descriptor_name":"Gene Expression Regulation, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018506","descriptor_name":"Gene Expression Regulation, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018506","descriptor_name":"Gene Expression Regulation, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000032","qualifier_name":"analysis","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":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-11-s3-s6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s3-s6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S3-S6","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:20438653","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20438653","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:pubmedcentral.nih.gov:2863065","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2863065","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-s3-s6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s3-s6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S3-S6","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":[{"id":"https://openalex.org/G7970188386","display_name":"EAGER:   Role of alternative splicing in Arabidopsis immune response","funder_award_id":"0951512","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310013","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2157770058.pdf","grobid_xml":"https://content.openalex.org/works/W2157770058.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W144334492","https://openalex.org/W1979770972","https://openalex.org/W1981509058","https://openalex.org/W1996542013","https://openalex.org/W2001952613","https://openalex.org/W2020112525","https://openalex.org/W2067151470","https://openalex.org/W2077199821","https://openalex.org/W2087878206","https://openalex.org/W2088387316","https://openalex.org/W2097341408","https://openalex.org/W2097694304","https://openalex.org/W2100448568","https://openalex.org/W2103017472","https://openalex.org/W2110065044","https://openalex.org/W2111769691","https://openalex.org/W2111857777","https://openalex.org/W2114856549","https://openalex.org/W2133750801","https://openalex.org/W2137591261","https://openalex.org/W2154431984","https://openalex.org/W2155804510","https://openalex.org/W2158297569","https://openalex.org/W2167865654"],"related_works":["https://openalex.org/W2001319824","https://openalex.org/W2067501355","https://openalex.org/W2008389025","https://openalex.org/W2136950317","https://openalex.org/W2155793948","https://openalex.org/W2038617558","https://openalex.org/W4389398524","https://openalex.org/W1538327476","https://openalex.org/W2093378391","https://openalex.org/W2071218173"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1,104,135],"eukaryotes,":[2],"alternative":[3,229],"splicing":[4],"often":[5,177],"generates":[6],"multiple":[7],"splice":[8,35],"variants":[9],"from":[10],"a":[11,31,53,65,123,164,193],"single":[12],"gene.":[13],"Here":[14],"we":[15,110,184],"explore":[16],"the":[17,26,37,42,46,59,79,86,94,151,199,205],"use":[18],"of":[19,33,45,61,70,81,125,142,166,179,198],"RNA":[20],"sequencing":[21],"(RNA-Seq)":[22],"datasets":[23],"to":[24,40,57,191],"address":[25],"isoform":[27,133,159,167],"quantification":[28],"problem.":[29],"Given":[30,155],"set":[32],"known":[34,62],"variants,":[36],"goal":[38],"is":[39,73],"estimate":[41,58],"relative":[43],"abundance":[44],"individual":[47],"variants.":[48],"METHODS:":[49],"Our":[50],"method":[51,72],"employs":[52],"linear":[54],"models":[55],"framework":[56],"ratios":[60],"isoforms":[63],"in":[64,132,158,204,220,228],"sample.":[66],"A":[67],"key":[68],"feature":[69],"our":[71,187],"that":[74,93,128,156,174,186],"it":[75],"takes":[76],"into":[77],"account":[78],"non-uniformity":[80],"RNA-Seq":[82,108],"read":[83],"positions":[84],"along":[85],"targeted":[87],"transcripts.":[88],"RESULTS:":[89],"Preliminary":[90],"tests":[91],"indicate":[92],"model":[95],"performs":[96],"well":[97,121],"on":[98,217,226],"both":[99],"simulated":[100],"and":[101,173],"real":[102],"data.":[103],"two":[105],"publicly":[106],"available":[107],"datasets,":[109],"identified":[111],"several":[112],"alternatively-spliced":[113],"genes":[114,127,138,210],"with":[115],"switch-like,":[116],"on/off":[117],"expression":[118,141,160,182,222],"properties,":[119],"as":[120,122],"number":[124],"other":[126],"varied":[129],"more":[130],"subtly":[131],"expression.":[134],"many":[136],"cases,":[137],"exhibiting":[139],"differential":[140],"alternatively":[143],"spliced":[144],"transcripts":[145],"were":[146],"not":[147,215],"differentially":[148],"expressed":[149],"at":[150],"gene":[152,181,221],"level.":[153],"CONCLUSIONS:":[154],"changes":[157,219,227],"level":[161],"frequently":[162],"involve":[163],"continuum":[165],"ratios,":[168],"rather":[169],"than":[170],"all-or-nothing":[171],"expression,":[172],"they":[175],"are":[176],"independent":[178],"general":[180],"changes,":[183],"anticipate":[185],"research":[188],"will":[189,208],"contribute":[190],"revealing":[192],"so":[194],"far":[195],"uninvestigated":[196],"layer":[197],"transcriptome.":[200],"We":[201],"believe":[202],"that,":[203],"future,":[206],"researchers":[207],"prioritize":[209],"for":[211],"functional":[212],"analysis":[213],"based":[214],"only":[216],"observed":[218],"levels,":[223],"but":[224],"also":[225],"splicing.":[230]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":7}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}