{"id":"https://openalex.org/W2120835288","doi":"https://doi.org/10.1093/bioinformatics/btv425","title":"Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment","display_name":"Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment","publication_year":2015,"publication_date":"2015-07-23","ids":{"openalex":"https://openalex.org/W2120835288","doi":"https://doi.org/10.1093/bioinformatics/btv425","mag":"2120835288","pmid":"https://pubmed.ncbi.nlm.nih.gov/26206307"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv425","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv425","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/22/3625/49036194/bioinformatics_31_22_3625.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":"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":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/22/3625/49036194/bioinformatics_31_22_3625.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013433142","display_name":"Marek Gierli\u0144ski","orcid":"https://orcid.org/0000-0001-9149-3514"},"institutions":[{"id":"https://openalex.org/I177639307","display_name":"University of Dundee","ror":"https://ror.org/03h2bxq36","country_code":"GB","type":"education","lineage":["https://openalex.org/I177639307"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Marek Gierli\u0144ski","raw_affiliation_strings":["1 Division of Computational Biology and","2 Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street Dundee, DD1 5EH, UK,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Division of Computational Biology and","institution_ids":[]},{"raw_affiliation_string":"2 Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street Dundee, DD1 5EH, UK,","institution_ids":["https://openalex.org/I177639307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087385117","display_name":"Christian Cole","orcid":"https://orcid.org/0000-0002-2560-2484"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Christian Cole","raw_affiliation_strings":["1 Division of Computational Biology and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Division of Computational Biology and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035568718","display_name":"Piet\u00e1 Schofield","orcid":"https://orcid.org/0000-0002-6398-2537"},"institutions":[{"id":"https://openalex.org/I177639307","display_name":"University of Dundee","ror":"https://ror.org/03h2bxq36","country_code":"GB","type":"education","lineage":["https://openalex.org/I177639307"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Piet\u00e0 Schofield","raw_affiliation_strings":["1 Division of Computational Biology and","2 Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street Dundee, DD1 5EH, UK,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Division of Computational Biology and","institution_ids":[]},{"raw_affiliation_string":"2 Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street Dundee, DD1 5EH, UK,","institution_ids":["https://openalex.org/I177639307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048534433","display_name":"Nick Schurch","orcid":"https://orcid.org/0000-0001-9068-9654"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nicholas J. Schurch","raw_affiliation_strings":["1 Division of Computational Biology and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Division of Computational Biology and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032236750","display_name":"Alexander Sherstnev","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alexander Sherstnev","raw_affiliation_strings":["1 Division of Computational Biology and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Division of Computational Biology and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081804980","display_name":"Vijender Singh","orcid":"https://orcid.org/0000-0002-9382-269X"},"institutions":[{"id":"https://openalex.org/I177639307","display_name":"University of Dundee","ror":"https://ror.org/03h2bxq36","country_code":"GB","type":"education","lineage":["https://openalex.org/I177639307"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Vijender Singh","raw_affiliation_strings":["2 Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street Dundee, DD1 5EH, UK,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street Dundee, DD1 5EH, UK,","institution_ids":["https://openalex.org/I177639307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053867506","display_name":"Nicola Wrobel","orcid":"https://orcid.org/0000-0001-9995-8662"},"institutions":[{"id":"https://openalex.org/I4210137845","display_name":"Edinburgh Genomics","ror":"https://ror.org/02z3r7t23","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210137845"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicola Wrobel","raw_affiliation_strings":["3 Edinburgh Genomics and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Edinburgh Genomics and","institution_ids":["https://openalex.org/I4210137845"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042838621","display_name":"Karim Gharbi","orcid":"https://orcid.org/0000-0003-1092-4488"},"institutions":[{"id":"https://openalex.org/I4210137845","display_name":"Edinburgh Genomics","ror":"https://ror.org/02z3r7t23","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210137845"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Karim Gharbi","raw_affiliation_strings":["3 Edinburgh Genomics and","4 Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Edinburgh Genomics and","institution_ids":["https://openalex.org/I4210137845"]},{"raw_affiliation_string":"4 Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK,","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023223230","display_name":"Gordon G. Simpson","orcid":"https://orcid.org/0000-0001-6744-5889"},"institutions":[{"id":"https://openalex.org/I4210086649","display_name":"Planta","ror":"https://ror.org/001vw6n49","country_code":"RU","type":"other","lineage":["https://openalex.org/I4210086649"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Gordon Simpson","raw_affiliation_strings":["5 Division of Plant Sciences and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"5 Division of Plant Sciences and","institution_ids":["https://openalex.org/I4210086649"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007965740","display_name":"Tom Owen\u2010Hughes","orcid":"https://orcid.org/0000-0002-0618-8185"},"institutions":[{"id":"https://openalex.org/I177639307","display_name":"University of Dundee","ror":"https://ror.org/03h2bxq36","country_code":"GB","type":"education","lineage":["https://openalex.org/I177639307"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Tom Owen-Hughes","raw_affiliation_strings":["2 Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street Dundee, DD1 5EH, UK,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street Dundee, DD1 5EH, UK,","institution_ids":["https://openalex.org/I177639307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060637041","display_name":"Mark Blaxter","orcid":"https://orcid.org/0000-0003-2861-949X"},"institutions":[{"id":"https://openalex.org/I4210137845","display_name":"Edinburgh Genomics","ror":"https://ror.org/02z3r7t23","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210137845"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark Blaxter","raw_affiliation_strings":["3 Edinburgh Genomics and","4 Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Edinburgh Genomics and","institution_ids":["https://openalex.org/I4210137845"]},{"raw_affiliation_string":"4 Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK,","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082043302","display_name":"Geoffrey J. Barton","orcid":"https://orcid.org/0000-0002-9014-5355"},"institutions":[{"id":"https://openalex.org/I177639307","display_name":"University of Dundee","ror":"https://ror.org/03h2bxq36","country_code":"GB","type":"education","lineage":["https://openalex.org/I177639307"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Geoffrey J. Barton","raw_affiliation_strings":["1 Division of Computational Biology and","2 Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street Dundee, DD1 5EH, UK,","6 Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street Dundee, DD1 5EH, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Division of Computational Biology and","institution_ids":[]},{"raw_affiliation_string":"2 Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street Dundee, DD1 5EH, UK,","institution_ids":["https://openalex.org/I177639307"]},{"raw_affiliation_string":"6 Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street Dundee, DD1 5EH, UK","institution_ids":["https://openalex.org/I177639307"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5082043302"],"corresponding_institution_ids":["https://openalex.org/I177639307"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":2832,"currency":"EUR","value_usd":3054},"fwci":4.2692,"has_fulltext":true,"cited_by_count":97,"citation_normalized_percentile":{"value":0.95116256,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"31","issue":"22","first_page":"3625","last_page":"3630"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4715999960899353,"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":0.4715999960899353,"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":0.09549999982118607,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.044199999421834946,"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/replicate","display_name":"Replicate","score":0.9595537185668945},{"id":"https://openalex.org/keywords/negative-binomial-distribution","display_name":"Negative binomial distribution","score":0.8710871338844299},{"id":"https://openalex.org/keywords/count-data","display_name":"Count data","score":0.7376896142959595},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.6025963425636292},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.4891376793384552},{"id":"https://openalex.org/keywords/binomial-distribution","display_name":"Binomial distribution","score":0.4692779779434204},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44692322611808777},{"id":"https://openalex.org/keywords/multinomial-distribution","display_name":"Multinomial distribution","score":0.446390300989151},{"id":"https://openalex.org/keywords/variance","display_name":"Variance (accounting)","score":0.4352136254310608},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4295186400413513},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4228295087814331},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38015180826187134},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3459174633026123},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30102524161338806},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.24647599458694458},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.22633448243141174},{"id":"https://openalex.org/keywords/poisson-distribution","display_name":"Poisson distribution","score":0.146214097738266},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.11422917246818542}],"concepts":[{"id":"https://openalex.org/C2781162219","wikidata":"https://www.wikidata.org/wiki/Q26250693","display_name":"Replicate","level":2,"score":0.9595537185668945},{"id":"https://openalex.org/C199335787","wikidata":"https://www.wikidata.org/wiki/Q743364","display_name":"Negative binomial distribution","level":3,"score":0.8710871338844299},{"id":"https://openalex.org/C33643355","wikidata":"https://www.wikidata.org/wiki/Q5176731","display_name":"Count data","level":3,"score":0.7376896142959595},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6025963425636292},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.4891376793384552},{"id":"https://openalex.org/C41054675","wikidata":"https://www.wikidata.org/wiki/Q185547","display_name":"Binomial distribution","level":2,"score":0.4692779779434204},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44692322611808777},{"id":"https://openalex.org/C192065140","wikidata":"https://www.wikidata.org/wiki/Q1147928","display_name":"Multinomial distribution","level":2,"score":0.446390300989151},{"id":"https://openalex.org/C196083921","wikidata":"https://www.wikidata.org/wiki/Q7915758","display_name":"Variance (accounting)","level":2,"score":0.4352136254310608},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4295186400413513},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4228295087814331},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38015180826187134},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3459174633026123},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30102524161338806},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24647599458694458},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.22633448243141174},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.146214097738266},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.11422917246818542},{"id":"https://openalex.org/C121955636","wikidata":"https://www.wikidata.org/wiki/Q4116214","display_name":"Accounting","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[{"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016010","descriptor_name":"Binomial Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016010","descriptor_name":"Binomial Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016010","descriptor_name":"Binomial Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016010","descriptor_name":"Binomial Distribution","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1093/bioinformatics/btv425","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv425","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/22/3625/49036194/bioinformatics_31_22_3625.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":"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:26206307","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26206307","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:discovery.dundee.ac.uk:openaire_cris_publications/f7805eb4-538d-4a62-af55-d9e844c1df4f","is_oa":true,"landing_page_url":"https://discovery.dundee.ac.uk/en/publications/f7805eb4-538d-4a62-af55-d9e844c1df4f","pdf_url":null,"source":{"id":"https://openalex.org/S4306400523","display_name":"Discovery Research Portal (University of Dundee)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177639307","host_organization_name":"University of Dundee","host_organization_lineage":["https://openalex.org/I177639307"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Gierlinski, M, Cole, C, Schofield, P, Schurch, N J, Sherstnev, A, Singh, V, Wrobel, N, Gharbi, K, Simpson, G, Owen-Hughes, T, Blaxter, M & Barton, G J 2015, 'Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment', Bioinformatics, vol. 31, no. 22, pp. 3625-3630. https://doi.org/10.1093/bioinformatics/btv425","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:arXiv.org:1505.00588","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1505.00588","pdf_url":"https://arxiv.org/pdf/1505.00588","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},{"id":"pmh:oai:pure.ed.ac.uk:publications/c722448b-ec12-4124-8707-e99b9b7ca06b","is_oa":true,"landing_page_url":null,"pdf_url":"https://www.research.ed.ac.uk/en/publications/c722448b-ec12-4124-8707-e99b9b7ca06b","source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/22/3625","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/22/3625","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:4754627","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4754627","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/c722448b-ec12-4124-8707-e99b9b7ca06b","is_oa":true,"landing_page_url":"https://hdl.handle.net/20.500.11820/c722448b-ec12-4124-8707-e99b9b7ca06b","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"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":"Gierli\u0144ski, M, Cole, C, Schofield, P, Schurch, N J, Sherstnev, A, Singh, V, Wrobel, N, Gharbi, K, Simpson, G, Owen-Hughes, T, Blaxter, M & Barton, G J 2015, 'Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment', Bioinformatics. https://doi.org/10.1093/bioinformatics/btv425","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pure.ed.ac.uk:publications/c722448b-ec12-4124-8707-e99b9b7ca06b","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/c722448b-ec12-4124-8707-e99b9b7ca06b","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"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":"Gierli\u0144ski, M, Cole, C, Schofield, P, Schurch, N J, Sherstnev, A, Singh, V, Wrobel, N, Gharbi, K, Simpson, G, Owen-Hughes, T, Blaxter, M & Barton, G J 2015, 'Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment', Bioinformatics. https://doi.org/10.1093/bioinformatics/btv425","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv425","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv425","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/22/3625/49036194/bioinformatics_31_22_3625.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":"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/G1685360338","display_name":null,"funder_award_id":"WT09230","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G1840636133","display_name":"The evolutionary genomics of sexual recombination","funder_award_id":"NE/J011355/1","funder_id":"https://openalex.org/F4320334631","funder_display_name":"Natural Environment Research Council"},{"id":"https://openalex.org/G1857440627","display_name":null,"funder_award_id":"BB/J00247X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2051502268","display_name":null,"funder_award_id":"NBAF010003","funder_id":"https://openalex.org/F4320334631","funder_display_name":"Natural Environment Research Council"},{"id":"https://openalex.org/G2461636024","display_name":null,"funder_award_id":"NBAF010003","funder_id":"https://openalex.org/F4320320022","funder_display_name":"Sight Research UK"},{"id":"https://openalex.org/G2554117814","display_name":"Elucidating mechansims and roles of alternative polyadenylation","funder_award_id":"BB/H002286/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G3401237215","display_name":"NERC Biomolecular Analysis Facility - Edinburgh","funder_award_id":"NBAF010003","funder_id":"https://openalex.org/F4320334631","funder_display_name":"Natural Environment Research Council"},{"id":"https://openalex.org/G3508426160","display_name":null,"funder_award_id":"NE/J011355/1","funder_id":"https://openalex.org/F4320320022","funder_display_name":"Sight Research UK"},{"id":"https://openalex.org/G4257852179","display_name":null,"funder_award_id":"WT083481","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G428489134","display_name":null,"funder_award_id":"BB/M010066/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G444919172","display_name":"Mechanisms for Remodelling Chromatin.","funder_award_id":"095062","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G5364756690","display_name":null,"funder_award_id":"NE/J011355/1","funder_id":"https://openalex.org/F4320334631","funder_display_name":"Natural Environment Research Council"},{"id":"https://openalex.org/G6441813994","display_name":null,"funder_award_id":"92530/Z/10/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G6666146636","display_name":null,"funder_award_id":"095062/Z/10/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G6862723008","display_name":"Diversifying Transcription Termination Function","funder_award_id":"BB/M004155/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6887627516","display_name":"Centre for Immunity, Infection and Evolution.","funder_award_id":"095831","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G7561865055","display_name":"The non-coding Arabidopsis genome","funder_award_id":"BB/J00247X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G763531393","display_name":null,"funder_award_id":"097945/C/11/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G7661018485","display_name":"The Arabidopsis Epitranscriptome","funder_award_id":"BB/M010066/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7875091695","display_name":"Wellcome Trust Technology Platform","funder_award_id":"097945","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G8044590665","display_name":null,"funder_award_id":"BB/M004155/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8354192919","display_name":null,"funder_award_id":"BB/H002286/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8709544946","display_name":null,"funder_award_id":"MR/K001744/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320320022","display_name":"Sight Research UK","ror":"https://ror.org/03z2py885"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320334631","display_name":"Natural Environment Research Council","ror":"https://ror.org/02b5d8509"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2120835288.pdf"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1513618424","https://openalex.org/W1539289781","https://openalex.org/W1843238398","https://openalex.org/W1974611660","https://openalex.org/W1975107026","https://openalex.org/W1989367702","https://openalex.org/W1995070233","https://openalex.org/W2002426853","https://openalex.org/W2009458183","https://openalex.org/W2070494252","https://openalex.org/W2081098333","https://openalex.org/W2107018762","https://openalex.org/W2110065044","https://openalex.org/W2114104545","https://openalex.org/W2121044470","https://openalex.org/W2121211805","https://openalex.org/W2134526812","https://openalex.org/W2140729960","https://openalex.org/W2141425631","https://openalex.org/W2141458291","https://openalex.org/W2147109452","https://openalex.org/W2152239989","https://openalex.org/W2154431984","https://openalex.org/W2165909549","https://openalex.org/W2952535963","https://openalex.org/W4210450218","https://openalex.org/W4232513052","https://openalex.org/W4239657535","https://openalex.org/W6632189097","https://openalex.org/W6680267820"],"related_works":["https://openalex.org/W2599805416","https://openalex.org/W3210390693","https://openalex.org/W2971731486","https://openalex.org/W2974887920","https://openalex.org/W4214644238","https://openalex.org/W3135460725","https://openalex.org/W2138071539","https://openalex.org/W2355806151","https://openalex.org/W2485412231","https://openalex.org/W2586858414"],"abstract_inverted_index":{"MOTIVATION:":[0],"High-throughput":[1],"RNA":[2],"sequencing":[3],"(RNA-seq)":[4],"is":[5,41],"now":[6],"the":[7,36,44,52,98,102,128],"standard":[8],"method":[9],"to":[10,140],"determine":[11],"differential":[12],"gene":[13,85,129],"expression.":[14],"Identifying":[15],"differentially":[16],"expressed":[17],"genes":[18],"crucially":[19],"depends":[20],"on":[21,31,61],"estimates":[22,27],"of":[23,54,104,108,121],"read-count":[24,130],"variability.":[25],"These":[26],"are":[28],"typically":[29],"based":[30],"statistical":[32],"models":[33,56],"such":[34],"as":[35],"negative":[37,94],"binomial":[38,95],"distribution,":[39],"which":[40,124],"employed":[42],"by":[43],"tools":[45],"edgeR,":[46],"DESeq":[47],"and":[48,77,93,119],"cuffdiff.":[49],"Until":[50],"now,":[51],"validity":[53],"these":[55],"has":[57],"usually":[58],"been":[59,138],"tested":[60,79],"either":[62],"low-replicate":[63],"RNA-seq":[64,71,135],"data":[65,78,112,136],"or":[66],"simulations.":[67],"RESULTS:":[68],"A":[69],"48-replicate":[70],"experiment":[72],"in":[73],"yeast":[74],"was":[75],"performed":[76],"against":[80],"theoretical":[81],"models.":[82],"The":[83,110],"observed":[84],"read":[86],"counts":[87],"were":[88],"consistent":[89],"with":[90,143],"both":[91],"log-normal":[92],"distributions,":[96],"while":[97],"mean-variance":[99],"relation":[100],"followed":[101],"line":[103],"constant":[105],"dispersion":[106],"parameter":[107],"\u223c0.01.":[109],"high-replicate":[111],"also":[113],"allowed":[114],"for":[115],"strict":[116],"quality":[117],"control":[118],"screening":[120],"'bad'":[122],"replicates,":[123],"can":[125],"drastically":[126],"affect":[127],"distribution.":[131],"AVAILABILITY":[132],"AND":[133],"IMPLEMENTATION:":[134],"have":[137],"submitted":[139],"ENA":[141],"archive":[142],"project":[144],"ID":[145],"PRJEB5348.":[146],"CONTACT:":[147],"g.j.barton@dundee.ac.uk.":[148]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":22},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":8}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}