{"id":"https://openalex.org/W4414874463","doi":"https://doi.org/10.1093/bioinformatics/btaf539","title":"DeNoFo: a file format and toolkit for standardized, comparable <i>de novo</i> gene annotation","display_name":"DeNoFo: a file format and toolkit for standardized, comparable <i>de novo</i> gene annotation","publication_year":2025,"publication_date":"2025-10-01","ids":{"openalex":"https://openalex.org/W4414874463","doi":"https://doi.org/10.1093/bioinformatics/btaf539","pmid":"https://pubmed.ncbi.nlm.nih.gov/41051215"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf539","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf539","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf539/64518926/btaf539.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf539/64518926/btaf539.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075803222","display_name":"Elias Dohmen","orcid":"https://orcid.org/0000-0002-7203-2314"},"institutions":[{"id":"https://openalex.org/I22465464","display_name":"University of M\u00fcnster","ror":"https://ror.org/00pd74e08","country_code":"DE","type":"education","lineage":["https://openalex.org/I22465464"]},{"id":"https://openalex.org/I4210096541","display_name":"Institute for Biodiversity","ror":"https://ror.org/01n8ggb71","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I4210096541"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Elias Dohmen","raw_affiliation_strings":["Institute for Evolution and Biodiversity, University of M\u00fcnster , M\u00fcnster 48151,","University of M\u00fcnster Institute for Evolution and Biodiversity, , M\u00fcnster, 48151,"],"affiliations":[{"raw_affiliation_string":"Institute for Evolution and Biodiversity, University of M\u00fcnster , M\u00fcnster 48151,","institution_ids":["https://openalex.org/I4210096541","https://openalex.org/I22465464"]},{"raw_affiliation_string":"University of M\u00fcnster Institute for Evolution and Biodiversity, , M\u00fcnster, 48151,","institution_ids":["https://openalex.org/I4210096541","https://openalex.org/I22465464"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090830940","display_name":"Margaux Aubel","orcid":"https://orcid.org/0000-0003-1653-9441"},"institutions":[{"id":"https://openalex.org/I22465464","display_name":"University of M\u00fcnster","ror":"https://ror.org/00pd74e08","country_code":"DE","type":"education","lineage":["https://openalex.org/I22465464"]},{"id":"https://openalex.org/I4210096541","display_name":"Institute for Biodiversity","ror":"https://ror.org/01n8ggb71","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I4210096541"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Margaux Aubel","raw_affiliation_strings":["Institute for Evolution and Biodiversity, University of M\u00fcnster , M\u00fcnster 48151,","University of M\u00fcnster Institute for Evolution and Biodiversity, , M\u00fcnster, 48151,"],"affiliations":[{"raw_affiliation_string":"Institute for Evolution and Biodiversity, University of M\u00fcnster , M\u00fcnster 48151,","institution_ids":["https://openalex.org/I4210096541","https://openalex.org/I22465464"]},{"raw_affiliation_string":"University of M\u00fcnster Institute for Evolution and Biodiversity, , M\u00fcnster, 48151,","institution_ids":["https://openalex.org/I4210096541","https://openalex.org/I22465464"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078782253","display_name":"Lars A. Eicholt","orcid":"https://orcid.org/0000-0002-3985-3698"},"institutions":[{"id":"https://openalex.org/I22465464","display_name":"University of M\u00fcnster","ror":"https://ror.org/00pd74e08","country_code":"DE","type":"education","lineage":["https://openalex.org/I22465464"]},{"id":"https://openalex.org/I4210096541","display_name":"Institute for Biodiversity","ror":"https://ror.org/01n8ggb71","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I4210096541"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lars A Eicholt","raw_affiliation_strings":["Institute for Evolution and Biodiversity, University of M\u00fcnster , M\u00fcnster 48151,","University of M\u00fcnster Institute for Evolution and Biodiversity, , M\u00fcnster, 48151,"],"affiliations":[{"raw_affiliation_string":"Institute for Evolution and Biodiversity, University of M\u00fcnster , M\u00fcnster 48151,","institution_ids":["https://openalex.org/I4210096541","https://openalex.org/I22465464"]},{"raw_affiliation_string":"University of M\u00fcnster Institute for Evolution and Biodiversity, , M\u00fcnster, 48151,","institution_ids":["https://openalex.org/I4210096541","https://openalex.org/I22465464"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035280068","display_name":"Paul Roginski","orcid":"https://orcid.org/0000-0003-0297-723X"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2738703131","display_name":"Commissariat \u00e0 l'\u00c9nergie Atomique et aux \u00c9nergies Alternatives","ror":"https://ror.org/00jjx8s55","country_code":"FR","type":"government","lineage":["https://openalex.org/I2738703131"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210106617","display_name":"Institut de Biologie Int\u00e9grative de la Cellule","ror":"https://ror.org/01fftxe08","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I2738703131","https://openalex.org/I2738703131","https://openalex.org/I277688954","https://openalex.org/I4210106617","https://openalex.org/I4210113668"]},{"id":"https://openalex.org/I4210128565","display_name":"CEA Paris-Saclay","ror":"https://ror.org/03n15ch10","country_code":"FR","type":"government","lineage":["https://openalex.org/I2738703131","https://openalex.org/I277688954","https://openalex.org/I4210128565"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Paul Roginski","raw_affiliation_strings":["Institute for Integrative Biology of the Cell (I2BC), Universit\u00e9 Paris-Saclay, CEA, CNRS , Gif-sur-Yvette 91198,","Universit\u00e9 Paris-Saclay, CEA, CNRS Institute for Integrative Biology of the Cell (I2BC), , Gif-sur-Yvette, 91198,"],"affiliations":[{"raw_affiliation_string":"Institute for Integrative Biology of the Cell (I2BC), Universit\u00e9 Paris-Saclay, CEA, CNRS , Gif-sur-Yvette 91198,","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210128565","https://openalex.org/I4210106617","https://openalex.org/I277688954","https://openalex.org/I2738703131"]},{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, CEA, CNRS Institute for Integrative Biology of the Cell (I2BC), , Gif-sur-Yvette, 91198,","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210128565","https://openalex.org/I4210106617","https://openalex.org/I277688954","https://openalex.org/I2738703131"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030280915","display_name":"Victor Luria","orcid":"https://orcid.org/0000-0003-0558-0983"},"institutions":[{"id":"https://openalex.org/I1288882113","display_name":"Boston Children's Hospital","ror":"https://ror.org/00dvg7y05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1288882113"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Victor Luria","raw_affiliation_strings":["Department of Neuroscience, Yale School of Medicine , New Haven, CT 06510,","Department of Systems Biology, Harvard Medical School , Boston, MA 02115,","Division of Genetics and Genomics, Boston Children\u2019s Hospital, Harvard Medical School , Boston, MA 02115,","Department of Systems Biology, Harvard Medical School, Boston, MA 02115, United States","Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, United States","Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, United States"],"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, Yale School of Medicine , New Haven, CT 06510,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School , Boston, MA 02115,","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]},{"raw_affiliation_string":"Division of Genetics and Genomics, Boston Children\u2019s Hospital, Harvard Medical School , Boston, MA 02115,","institution_ids":["https://openalex.org/I1288882113"]},{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School, Boston, MA 02115, United States","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, United States","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, United States","institution_ids":["https://openalex.org/I1288882113","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065781368","display_name":"Amir Karger","orcid":"https://orcid.org/0000-0002-4561-3850"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amir Karger","raw_affiliation_strings":["IT-Research Computing, Harvard Medical School , Boston, MA 02115,","IT-Research Computing, Harvard Medical School, Boston, MA 02115, United States"],"affiliations":[{"raw_affiliation_string":"IT-Research Computing, Harvard Medical School , Boston, MA 02115,","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"IT-Research Computing, Harvard Medical School, Boston, MA 02115, United States","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027195013","display_name":"Anna Grandchamp","orcid":"https://orcid.org/0000-0003-3018-3138"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I21491767","display_name":"Aix-Marseille Universit\u00e9","ror":"https://ror.org/035xkbk20","country_code":"FR","type":"education","lineage":["https://openalex.org/I21491767"]},{"id":"https://openalex.org/I4210112918","display_name":"Theories and Approaches of Genomic Complexity","ror":"https://ror.org/025sfbe73","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I21491767","https://openalex.org/I4210112918"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Anna Grandchamp","raw_affiliation_strings":["Aix Marseille University, INSERM, TAGC, UMR_S1090 , Marseille 13288,","Aix Marseille University, INSERM, TAGC,UMR_S1090, Marseille, France"],"affiliations":[{"raw_affiliation_string":"Aix Marseille University, INSERM, TAGC, UMR_S1090 , Marseille 13288,","institution_ids":["https://openalex.org/I21491767","https://openalex.org/I4210112918"]},{"raw_affiliation_string":"Aix Marseille University, INSERM, TAGC,UMR_S1090, Marseille, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210112918","https://openalex.org/I21491767"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5075803222"],"corresponding_institution_ids":["https://openalex.org/I22465464","https://openalex.org/I4210096541"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.2876,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.89223008,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"41","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9975000023841858,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9912999868392944,"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/python","display_name":"Python (programming language)","score":0.8672999739646912},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.774399995803833},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.7472000122070312},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4812000095844269},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.46399998664855957},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4603999853134155},{"id":"https://openalex.org/keywords/line","display_name":"Line (geometry)","score":0.3935000002384186}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8672999739646912},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8151000142097473},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.774399995803833},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.7472000122070312},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5210999846458435},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4812000095844269},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.46399998664855957},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4603999853134155},{"id":"https://openalex.org/C198352243","wikidata":"https://www.wikidata.org/wiki/Q37105","display_name":"Line (geometry)","level":2,"score":0.3935000002384186},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.3912999927997589},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.38960000872612},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.3885999917984009},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.3882000148296356},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.38429999351501465},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3562999963760376},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.3122999966144562},{"id":"https://openalex.org/C2984927552","wikidata":"https://www.wikidata.org/wiki/Q845734","display_name":"Graphical display","level":2,"score":0.30869999527931213},{"id":"https://openalex.org/C2984968299","wikidata":"https://www.wikidata.org/wiki/Q1077784","display_name":"Software tool","level":3,"score":0.2921999990940094},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29179999232292175},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.28040000796318054}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf539","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf539","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf539/64518926/btaf539.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:41051215","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41051215","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:HAL:hal-05500639v1","is_oa":true,"landing_page_url":"https://amu.hal.science/hal-05500639","pdf_url":null,"source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2025, 41 (10), pp.btaf539. &#x27E8;10.1093/bioinformatics/btaf539&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:europepmc.org:11324034","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12516307","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf539","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf539","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf539/64518926/btaf539.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/G1279712735","display_name":null,"funder_award_id":"SPP 2349","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G1897224819","display_name":null,"funder_award_id":"R01NS095654","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2227946163","display_name":null,"funder_award_id":"BO2544-22-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G3190572894","display_name":null,"funder_award_id":"BO 2544/20-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G4304115851","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320882","funder_display_name":"Volkswagen Foundation"},{"id":"https://openalex.org/G4373664287","display_name":null,"funder_award_id":"NS095654","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5106512922","display_name":null,"funder_award_id":"Deutsche Forschungsgemeinschaft (DFG","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6345853531","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G822436402","display_name":null,"funder_award_id":"503348080","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8468371028","display_name":null,"funder_award_id":"98183","funder_id":"https://openalex.org/F4320320882","funder_display_name":"Volkswagen Foundation"},{"id":"https://openalex.org/G8526424774","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320320882","display_name":"Volkswagen Foundation","ror":"https://ror.org/03bsmfz84"},{"id":"https://openalex.org/F4320322957","display_name":"Westf\u00e4lische Wilhelms-Universit\u00e4t M\u00fcnster","ror":"https://ror.org/00pd74e08"},{"id":"https://openalex.org/F4320327235","display_name":"Servier","ror":"https://ror.org/034e7c066"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414874463.pdf","grobid_xml":"https://content.openalex.org/works/W4414874463.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"DeNoFo":[0],"is":[1,27],"available":[2,31],"through":[3],"the":[4],"official":[5],"Python":[6],"Package":[7],"Index":[8],"(PyPI)":[9],"and":[10,20,36,40],"at":[11],"https://github.com/EDohmen/denofo.":[12],"All":[13],"tools":[14],"have":[15],"a":[16,21],"graphical":[17],"user":[18],"interface":[19],"command":[22],"line":[23],"interface.":[24],"The":[25],"toolkit":[26],"implemented":[28],"in":[29],"Python3,":[30],"for":[32],"all":[33],"major":[34],"platforms":[35],"installable":[37],"with":[38],"pip":[39],"uv.":[41]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-07T00:00:00"}
