{"id":"https://openalex.org/W2906064383","doi":"https://doi.org/10.1093/bioinformatics/bty1052","title":"Curse: building expression atlases and co-expression networks from public RNA-Seq data","display_name":"Curse: building expression atlases and co-expression networks from public RNA-Seq data","publication_year":2018,"publication_date":"2018-12-20","ids":{"openalex":"https://openalex.org/W2906064383","doi":"https://doi.org/10.1093/bioinformatics/bty1052","mag":"2906064383","pmid":"https://pubmed.ncbi.nlm.nih.gov/30590391"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty1052","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty1052","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039018487","display_name":"Dries Vaneechoutte","orcid":"https://orcid.org/0000-0002-8975-2801"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210098178","display_name":"VIB-UGent Center for Plant Systems Biology","ror":"https://ror.org/01qnqmc89","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I32597200","https://openalex.org/I4210098178"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Dries Vaneechoutte","raw_affiliation_strings":["Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B, Belgium","VIB Center for Plant Systems Biology, VIB, Ghent B, Belgium"],"raw_orcid":"https://orcid.org/0000-0002-8975-2801","affiliations":[{"raw_affiliation_string":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"VIB Center for Plant Systems Biology, VIB, Ghent B, Belgium","institution_ids":["https://openalex.org/I4210098178"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052680833","display_name":"Klaas Vandepoele","orcid":"https://orcid.org/0000-0003-4790-2725"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210098178","display_name":"VIB-UGent Center for Plant Systems Biology","ror":"https://ror.org/01qnqmc89","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I32597200","https://openalex.org/I4210098178"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Klaas Vandepoele","raw_affiliation_strings":["Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium","Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B, Belgium","VIB Center for Plant Systems Biology, VIB, Ghent B, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"VIB Center for Plant Systems Biology, VIB, Ghent B, Belgium","institution_ids":["https://openalex.org/I4210098178"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5052680833"],"corresponding_institution_ids":["https://openalex.org/I32597200","https://openalex.org/I4210098178"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.4841,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.82956962,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"35","issue":"16","first_page":"2880","last_page":"2881"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.20839999616146088,"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":0.20839999616146088,"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/T10604","display_name":"RNA Research and Splicing","score":0.16099999845027924,"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":0.11789999902248383,"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/expression","display_name":"Expression (computer science)","score":0.7355444431304932},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.6744476556777954},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5152371525764465},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4855944514274597},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4106300473213196},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.3878522217273712},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32353514432907104},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31140458583831787},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1944323480129242},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1292392611503601}],"concepts":[{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.7355444431304932},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6744476556777954},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5152371525764465},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4855944514274597},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4106300473213196},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3878522217273712},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32353514432907104},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31140458583831787},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1944323480129242},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1292392611503601},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":true},{"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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty1052","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty1052","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30590391","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30590391","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:archive.ugent.be:8587983","is_oa":false,"landing_page_url":"http://hdl.handle.net/1854/LU-8587983","pdf_url":null,"source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1367-4811","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321732","display_name":"Agentschap voor Innovatie door Wetenschap en Technologie","ror":"https://ror.org/01antkr91"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1490161904","https://openalex.org/W1980948656","https://openalex.org/W2131271579","https://openalex.org/W2152379610","https://openalex.org/W2165446840","https://openalex.org/W2175297783","https://openalex.org/W2323326409","https://openalex.org/W2624572223","https://openalex.org/W2761771578","https://openalex.org/W2763876357","https://openalex.org/W2765268771","https://openalex.org/W2769591387","https://openalex.org/W2793855015","https://openalex.org/W2917207851"],"related_works":["https://openalex.org/W4394359997","https://openalex.org/W4362511652","https://openalex.org/W4362511917","https://openalex.org/W4362511922","https://openalex.org/W4362485688","https://openalex.org/W4362530184","https://openalex.org/W4362530193","https://openalex.org/W2904597490","https://openalex.org/W4362485661","https://openalex.org/W4394365953"],"abstract_inverted_index":{"SUMMARY:":[0],"Public":[1],"RNA-Sequencing":[2],"(RNA-Seq)":[3],"datasets":[4],"are":[5,105,118],"a":[6,66],"valuable":[7],"resource":[8],"for":[9],"transcriptome":[10],"analyses,":[11],"but":[12],"their":[13,24,103],"accessibility":[14],"is":[15],"hindered":[16],"by":[17,27],"the":[18,28,61,75,95],"imperfect":[19],"quality":[20],"and":[21,26,65,73,81,102],"presentation":[22],"of":[23,30,46,57,89],"metadata":[25],"complexity":[29],"processing":[31],"raw":[32],"sequencing":[33],"data.":[34],"The":[35],"Curse":[36,52,84],"suite":[37],"was":[38,110],"created":[39],"to":[40,53,71,94],"alleviate":[41],"these":[42],"problems.":[43],"It":[44],"consists":[45],"an":[47],"online":[48],"curation":[49],"tool":[50],"named":[51,69],"efficiently":[54],"build":[55],"compendia":[56],"experiments":[58],"hosted":[59],"on":[60],"Sequence":[62],"Read":[63],"Archive,":[64],"lightweight":[67],"pipeline":[68],"Prose":[70,101,109],"download":[72],"process":[74],"RNA-Seq":[76],"data":[77,117],"into":[78],"expression":[79],"atlases":[80],"co-expression":[82],"networks.":[83],"networks":[85],"showed":[86],"improved":[87],"linking":[88],"functionally":[90],"related":[91],"genes":[92],"compared":[93],"state-of-the-art.":[96],"AVAILABILITY":[97],"AND":[98],"IMPLEMENTATION:":[99],"Curse,":[100],"manuals":[104],"available":[106,119],"at":[107,120],"http://bioinformatics.psb.ugent.be/webtools/Curse/.":[108],"implemented":[111],"in":[112],"Java.":[113],"SUPPLEMENTARY":[114],"INFORMATION:":[115],"Supplementary":[116],"Bioinformatics":[121],"online.":[122]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
