{"id":"https://openalex.org/W2767006528","doi":"https://doi.org/10.1093/bioinformatics/btx690","title":"DIEGO: detection of differential alternative splicing using Aitchison\u2019s geometry","display_name":"DIEGO: detection of differential alternative splicing using Aitchison\u2019s geometry","publication_year":2017,"publication_date":"2017-10-27","ids":{"openalex":"https://openalex.org/W2767006528","doi":"https://doi.org/10.1093/bioinformatics/btx690","mag":"2767006528","pmid":"https://pubmed.ncbi.nlm.nih.gov/29088309"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx690","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx690","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/6/1066/48914346/bioinformatics_34_6_1066.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/34/6/1066/48914346/bioinformatics_34_6_1066.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005070498","display_name":"Gero Doose","orcid":null},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Gero Doose","raw_affiliation_strings":["Chair of Bioinformatics, Faculty of Mathematics and Computer Science, Leipzig University, Leipzig, Germany","Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany","ecSeq Bioinformatics, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chair of Bioinformatics, Faculty of Mathematics and Computer Science, Leipzig University, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"ecSeq Bioinformatics, Leipzig, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Stephan H Bernhart","orcid":null},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Stephan H Bernhart","raw_affiliation_strings":["Chair of Bioinformatics, Faculty of Mathematics and Computer Science, Leipzig University, Leipzig, Germany","Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chair of Bioinformatics, Faculty of Mathematics and Computer Science, Leipzig University, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078518274","display_name":"Rabea Wagener","orcid":"https://orcid.org/0000-0002-5394-0907"},"institutions":[{"id":"https://openalex.org/I196349391","display_name":"Universit\u00e4t Ulm","ror":"https://ror.org/032000t02","country_code":"DE","type":"education","lineage":["https://openalex.org/I196349391"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Rabea Wagener","raw_affiliation_strings":["Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany","institution_ids":["https://openalex.org/I196349391"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025429291","display_name":"Steve Hoffman","orcid":"https://orcid.org/0000-0002-2379-8081"},"institutions":[{"id":"https://openalex.org/I4210127789","display_name":"Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)","ror":"https://ror.org/039a53269","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210127789"]},{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Steve Hoffmann","raw_affiliation_strings":["Chair of Bioinformatics, Faculty of Mathematics and Computer Science, Leipzig University, Leipzig, Germany","Computational Biology Group, Leibniz Institute on Ageing - Fritz Lipmann Institute (FLI) and Friedrich-Schiller-University Jena, Jena, Germany","Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chair of Bioinformatics, Faculty of Mathematics and Computer Science, Leipzig University, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Computational Biology Group, Leibniz Institute on Ageing - Fritz Lipmann Institute (FLI) and Friedrich-Schiller-University Jena, Jena, Germany","institution_ids":["https://openalex.org/I4210127789","https://openalex.org/I76198965"]},{"raw_affiliation_string":"Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025429291"],"corresponding_institution_ids":["https://openalex.org/I4210127789","https://openalex.org/I76198965","https://openalex.org/I926574661"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.3045,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.57377103,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"34","issue":"6","first_page":"1066","last_page":"1068"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.3165000081062317,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.3165000081062317,"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":0.18140000104904175,"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":0.13840000331401825,"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/computer-science","display_name":"Computer science","score":0.5551552176475525},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.5389360785484314},{"id":"https://openalex.org/keywords/differential-geometry","display_name":"Differential geometry","score":0.44206225872039795},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4391588866710663},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.4231044054031372},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2740700840950012},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14489296078681946},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12511911988258362}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5551552176475525},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.5389360785484314},{"id":"https://openalex.org/C192939610","wikidata":"https://www.wikidata.org/wiki/Q188444","display_name":"Differential geometry","level":2,"score":0.44206225872039795},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4391588866710663},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.4231044054031372},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2740700840950012},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14489296078681946},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12511911988258362},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"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":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","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},{"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx690","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx690","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/6/1066/48914346/bioinformatics_34_6_1066.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29088309","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29088309","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:europepmc.org:4775875","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860559","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:frl.publisso.de:frl:6414366","is_oa":true,"landing_page_url":"https://repository.publisso.de/resource/frl:6414366","pdf_url":null,"source":{"id":"https://openalex.org/S4377196269","display_name":"PUBLISSO (German National Library of Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210112663","host_organization_name":"ZB MED - Information Centre for Life Sciences","host_organization_lineage":["https://openalex.org/I4210112663"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 34(6):1066-1068","raw_type":"Zeitschriftenartikel"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx690","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx690","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/6/1066/48914346/bioinformatics_34_6_1066.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1882903657","display_name":null,"funder_award_id":"HNPCCSys 031 6065A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2362642933","display_name":null,"funder_award_id":"01KU1505","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2688163272","display_name":null,"funder_award_id":"01KU1505-C","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G3037562619","display_name":null,"funder_award_id":"01KU1002A-J","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G3145041415","display_name":null,"funder_award_id":"031 6065A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G6920464129","display_name":null,"funder_award_id":"01KU1002A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2767006528.pdf","grobid_xml":"https://content.openalex.org/works/W2767006528.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2009258895","https://openalex.org/W2012284471","https://openalex.org/W2047452386","https://openalex.org/W2066231767","https://openalex.org/W2075318911","https://openalex.org/W2106352274","https://openalex.org/W2119204091","https://openalex.org/W2141458291","https://openalex.org/W2255131131","https://openalex.org/W2395491655","https://openalex.org/W6712067400"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4388322895","https://openalex.org/W2032618524","https://openalex.org/W2587202202","https://openalex.org/W1975748241","https://openalex.org/W2026745357"],"abstract_inverted_index":{"Motivation:":[0],"Alternative":[1],"splicing":[2,55],"is":[3,107,133],"a":[4,15,29,69,78],"biological":[5],"process":[6],"of":[7,31,37,45,90],"fundamental":[8],"importance":[9],"in":[10,18],"most":[11,50,65],"eukaryotes.":[12],"It":[13],"plays":[14],"pivotal":[16],"role":[17],"cell":[19],"differentiation":[20],"and":[21,24,106,117,122,129],"gene":[22],"regulation":[23],"has":[25],"been":[26],"associated":[27],"with":[28],"number":[30],"different":[32],"diseases.":[33],"The":[34,98,131],"widespread":[35],"availability":[36],"RNA-Sequencing":[38],"capacities":[39],"allows":[40],"an":[41],"ever":[42],"closer":[43],"investigation":[44],"differentially":[46],"expressed":[47],"isoforms.":[48],"However,":[49],"tools":[51],"for":[52,68,125],"differential":[53],"alternative":[54],"(DAS)":[56],"analysis":[57,81],"do":[58],"not":[59],"take":[60],"split":[61,95],"reads,":[62],"i.e.":[63],"the":[64],"direct":[66],"evidence":[67],"splice":[70],"event,":[71],"into":[72],"account.":[73],"Here,":[74],"we":[75],"present":[76],"DIEGO,":[77],"compositional":[79],"data":[80,142],"method":[82],"able":[83],"to":[84,110],"detect":[85],"DAS":[86],"between":[87],"two":[88],"sets":[89],"RNA-Seq":[91],"samples":[92],"based":[93],"on":[94],"reads.":[96],"Results:":[97],"python":[99,121],"tool":[100],"DIEGO":[101],"works":[102],"without":[103],"isoform":[104],"annotations":[105],"fast":[108],"enough":[109],"analyze":[111],"large":[112],"experiments":[113],"while":[114],"being":[115],"robust":[116],"accurate.":[118],"We":[119],"provide":[120],"perl":[123],"parsers":[124],"common":[126],"formats.":[127],"Availability":[128],"implementation:":[130],"software":[132],"available":[134,144],"at:":[135],"www.bioinf.uni-leipzig.de/Software/DIEGO.":[136],"Contact:":[137],"steve@bioinf.uni-leipzig.de.":[138],"Supplementary":[139,141],"information:":[140],"are":[143],"at":[145],"Bioinformatics":[146],"online.":[147]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-08-10T07:06:39.071514","created_date":"2025-10-10T00:00:00"}
