{"id":"https://openalex.org/W2913762507","doi":"https://doi.org/10.1093/bioinformatics/btz089","title":"How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in <i>Arabidopsis thaliana</i>","display_name":"How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in <i>Arabidopsis thaliana</i>","publication_year":2019,"publication_date":"2019-02-05","ids":{"openalex":"https://openalex.org/W2913762507","doi":"https://doi.org/10.1093/bioinformatics/btz089","mag":"2913762507","pmid":"https://pubmed.ncbi.nlm.nih.gov/30726870"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz089","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz089","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3372/30024558/btz089.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":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3372/30024558/btz089.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052150756","display_name":"Kimon Froussios","orcid":"https://orcid.org/0000-0003-2812-0525"},"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":"Kimon Froussios","raw_affiliation_strings":["Division of Computational Biology, University of Dundee , Dundee, UK"],"raw_orcid":"https://orcid.org/0000-0003-2812-0525","affiliations":[{"raw_affiliation_string":"Division of Computational Biology, University of Dundee , Dundee, 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":[{"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":"Nick J Schurch","raw_affiliation_strings":["Division of Computational Biology, University of Dundee , Dundee, UK"],"raw_orcid":"https://orcid.org/0000-0001-9068-9654","affiliations":[{"raw_affiliation_string":"Division of Computational Biology, University of Dundee , Dundee, UK","institution_ids":["https://openalex.org/I177639307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048867422","display_name":"Katarzyna Mackinnon","orcid":null},"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":"Katarzyna Mackinnon","raw_affiliation_strings":["Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK","institution_ids":["https://openalex.org/I177639307"]}]},{"author_position":"middle","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":["Division of Computational Biology, University of Dundee , Dundee, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Computational Biology, University of Dundee , Dundee, UK","institution_ids":["https://openalex.org/I177639307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021059142","display_name":"C\u00e9line Duc","orcid":"https://orcid.org/0000-0001-7426-4541"},"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":"C\u00e9line Duc","raw_affiliation_strings":["Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK","GReD, Facult\u00e9 de M\u00e9decine 28 , place Henri Dunant BP 38 - 63001 CLERMONT-FERRAND"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK","institution_ids":["https://openalex.org/I177639307"]},{"raw_affiliation_string":"GReD, Facult\u00e9 de M\u00e9decine 28 , place Henri Dunant BP 38 - 63001 CLERMONT-FERRAND","institution_ids":[]}]},{"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/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":"Gordon G Simpson","raw_affiliation_strings":["Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK","Division of Plant Sciences, School of Life Sciences, University of Dundee , Dundee, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK","institution_ids":["https://openalex.org/I177639307"]},{"raw_affiliation_string":"Division of Plant Sciences, School of Life Sciences, University of Dundee , Dundee, UK","institution_ids":["https://openalex.org/I177639307"]}]},{"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":["Division of Computational Biology, University of Dundee , Dundee, UK"],"raw_orcid":"https://orcid.org/0000-0002-9014-5355","affiliations":[{"raw_affiliation_string":"Division of Computational Biology, University of Dundee , Dundee, UK","institution_ids":["https://openalex.org/I177639307"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5023223230","https://openalex.org/A5082043302"],"corresponding_institution_ids":["https://openalex.org/I177639307"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":1971,"currency":"EUR","value_usd":2125},"fwci":0.6629,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.67254436,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"35","issue":"18","first_page":"3372","last_page":"3377"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.34540000557899475,"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":0.34540000557899475,"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":0.27410000562667847,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.05790000036358833,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/arabidopsis-thaliana","display_name":"Arabidopsis thaliana","score":0.7845285534858704},{"id":"https://openalex.org/keywords/eukaryote","display_name":"Eukaryote","score":0.6688838005065918},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.6499742269515991},{"id":"https://openalex.org/keywords/arabidopsis","display_name":"Arabidopsis","score":0.6294536590576172},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6171769499778748},{"id":"https://openalex.org/keywords/negative-binomial-distribution","display_name":"Negative binomial distribution","score":0.5795273184776306},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5661918520927429},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5120332837104797},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4591926634311676},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4330786168575287},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.42288023233413696},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3818938136100769},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.15911313891410828},{"id":"https://openalex.org/keywords/poisson-distribution","display_name":"Poisson distribution","score":0.11120149493217468},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.08117648959159851},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08089515566825867}],"concepts":[{"id":"https://openalex.org/C2775988993","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Arabidopsis thaliana","level":4,"score":0.7845285534858704},{"id":"https://openalex.org/C2779413310","wikidata":"https://www.wikidata.org/wiki/Q19088","display_name":"Eukaryote","level":4,"score":0.6688838005065918},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6499742269515991},{"id":"https://openalex.org/C2779491563","wikidata":"https://www.wikidata.org/wiki/Q157892","display_name":"Arabidopsis","level":4,"score":0.6294536590576172},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6171769499778748},{"id":"https://openalex.org/C199335787","wikidata":"https://www.wikidata.org/wiki/Q743364","display_name":"Negative binomial distribution","level":3,"score":0.5795273184776306},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5661918520927429},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5120332837104797},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4591926634311676},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4330786168575287},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.42288023233413696},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3818938136100769},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.15911313891410828},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.11120149493217468},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.08117648959159851},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08089515566825867},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz089","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz089","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3372/30024558/btz089.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:30726870","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30726870","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/c233b57c-d1ea-4908-9794-47522343e37f","is_oa":true,"landing_page_url":"https://discovery.dundee.ac.uk/en/publications/c233b57c-d1ea-4908-9794-47522343e37f","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":"Froussios, K, Schurch, N, Mackinnon, K, Gierlinski, M, Duc, C, Simpson, G G & Barton, G J 2019, 'How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana', Bioinformatics, vol. 35, no. 18, pp. 3372-3377. https://doi.org/10.1093/bioinformatics/btz089","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6748783","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6748783","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz089","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz089","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3372/30024558/btz089.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/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/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/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/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/G7198869819","display_name":null,"funder_award_id":"BB/M004155","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"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/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/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"}],"funders":[{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2913762507.pdf","grobid_xml":"https://content.openalex.org/works/W2913762507.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W107998980","https://openalex.org/W1490261451","https://openalex.org/W1494075612","https://openalex.org/W1539289781","https://openalex.org/W1569294608","https://openalex.org/W1843238398","https://openalex.org/W1974876578","https://openalex.org/W1975107026","https://openalex.org/W1989367702","https://openalex.org/W2002426853","https://openalex.org/W2057850011","https://openalex.org/W2070494252","https://openalex.org/W2072602203","https://openalex.org/W2074414424","https://openalex.org/W2098734857","https://openalex.org/W2100305481","https://openalex.org/W2110065044","https://openalex.org/W2114104545","https://openalex.org/W2119034410","https://openalex.org/W2120835288","https://openalex.org/W2123579165","https://openalex.org/W2124097252","https://openalex.org/W2132832769","https://openalex.org/W2135256913","https://openalex.org/W2137526110","https://openalex.org/W2138207763","https://openalex.org/W2140688313","https://openalex.org/W2142165994","https://openalex.org/W2146512944","https://openalex.org/W2152239989","https://openalex.org/W2154129128","https://openalex.org/W2154431984","https://openalex.org/W2156631105","https://openalex.org/W2161106528","https://openalex.org/W2161318011","https://openalex.org/W2163915946","https://openalex.org/W2165909549","https://openalex.org/W2168783201","https://openalex.org/W2169456326","https://openalex.org/W2179438025","https://openalex.org/W2321872593","https://openalex.org/W2334656801","https://openalex.org/W2582743722","https://openalex.org/W3104013713","https://openalex.org/W6632189097","https://openalex.org/W6638663015"],"related_works":["https://openalex.org/W3147805512","https://openalex.org/W1594012662","https://openalex.org/W75625030","https://openalex.org/W2106134872","https://openalex.org/W2269421989","https://openalex.org/W3147624048","https://openalex.org/W2006745274","https://openalex.org/W2355042192","https://openalex.org/W2391996571","https://openalex.org/W4392673618"],"abstract_inverted_index":{"MOTIVATION:":[0],"RNA-seq":[1,46],"experiments":[2],"are":[3,47,85,140,202,212],"usually":[4],"carried":[5],"out":[6],"in":[7,49,63,77,83,176],"three":[8],"or":[9,101,184],"fewer":[10],"replicates.":[11],"In":[12,36],"order":[13],"to":[14],"work":[15,62],"well":[16],"with":[17,74,87],"so":[18],"few":[19],"samples,":[20],"differential":[21],"gene":[22,33,43,80],"expression":[23,34,44,81],"(DGE)":[24],"tools":[25,128,138],"typically":[26],"assume":[27],"the":[28,31,39,50,58,64,75,107,112,118,134,143,154,163],"form":[29],"of":[30,42,60,111,123,136],"underlying":[32,92],"distribution.":[35,146],"this":[37],"paper,":[38],"statistical":[40],"properties":[41],"from":[45,90,162,204],"investigated":[48],"complex":[51],"eukaryote,":[52],"Arabidopsis":[53,157],"thaliana,":[54],"extending":[55],"and":[56,105,109,170,200],"generalizing":[57],"results":[59,76],"previous":[61],"simple":[65],"eukaryote":[66],"Saccharomyces":[67],"cerevisiae.":[68],"RESULTS:":[69],"We":[70,131],"show":[71],"that,":[72],"consistent":[73,86],"S.cerevisiae,":[78],"more":[79],"measurements":[82],"A.thaliana":[84,113],"being":[88],"drawn":[89],"an":[91],"negative":[93,144],"binomial":[94,145],"distribution":[95,100],"than":[96],"either":[97],"a":[98,102],"log-normal":[99],"normal":[103],"distribution,":[104],"that":[106,139],"size":[108],"complexity":[110],"transcriptome":[114],"does":[115],"not":[116],"influence":[117],"false":[119],"positive":[120],"rate":[121],"performance":[122],"nine":[124],"widely":[125],"used":[126],"DGE":[127,137],"tested":[129],"here.":[130],"therefore":[132],"recommend":[133],"use":[135],"based":[141],"on":[142],"AVAILABILITY":[147],"AND":[148],"IMPLEMENTATION:":[149],"The":[150,168],"raw":[151],"data":[152,172,211],"for":[153],"17":[155],"WT":[156],"thaliana":[158],"datasets":[159],"is":[160],"available":[161,190,203,213],"European":[164],"Nucleotide":[165],"Archive":[166],"(E-MTAB-5446).":[167],"processed":[169],"aligned":[171],"can":[173],"be":[174],"visualized":[175],"context":[177],"using":[178,187],"IGB":[179,191],"(Freese":[180],"et":[181],"al.,":[182],"2016),":[183],"downloaded":[185],"directly,":[186],"our":[188],"publicly":[189],"quickload":[192],"server":[193],"at":[194,206,214],"https://compbio.lifesci.dundee.ac.uk/arabidopsisQuickload/public_quickload/":[195],"under":[196],"'RNAseq>Froussios2019'.":[197],"All":[198],"scripts":[199],"commands":[201],"github":[205],"https://github.com/bartongroup/KF_arabidopsis-GRNA.":[207],"SUPPLEMENTARY":[208],"INFORMATION:":[209],"Supplementary":[210],"Bioinformatics":[215],"online.":[216]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2019-02-21T00:00:00"}
