{"id":"https://openalex.org/W2912623135","doi":"https://doi.org/10.1093/bioinformatics/btz116","title":"Explore, edit and leverage genomic annotations using Python GTF toolkit","display_name":"Explore, edit and leverage genomic annotations using Python GTF toolkit","publication_year":2019,"publication_date":"2019-02-15","ids":{"openalex":"https://openalex.org/W2912623135","doi":"https://doi.org/10.1093/bioinformatics/btz116","mag":"2912623135","pmid":"https://pubmed.ncbi.nlm.nih.gov/30768152"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz116","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz116","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3487/48975776/bioinformatics_35_18_3487.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":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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3487/48975776/bioinformatics_35_18_3487.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014227566","display_name":"Florent Lopez","orcid":"https://orcid.org/0000-0002-8479-5749"},"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"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"F Lopez","raw_affiliation_strings":["Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France","institution_ids":["https://openalex.org/I21491767","https://openalex.org/I154526488"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104519974","display_name":"Guillaume Charbonnier","orcid":"https://orcid.org/0000-0001-5615-1287"},"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"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"G Charbonnier","raw_affiliation_strings":["Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France","institution_ids":["https://openalex.org/I21491767","https://openalex.org/I154526488"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061777864","display_name":"Yasmina Kermezli","orcid":"https://orcid.org/0000-0001-8445-6360"},"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/I233209018","display_name":"University of Abou Bekr Belka\u00efd","ror":"https://ror.org/00jsjm362","country_code":"DZ","type":"education","lineage":["https://openalex.org/I233209018"]}],"countries":["DZ","FR"],"is_corresponding":false,"raw_author_name":"Y Kermezli","raw_affiliation_strings":["Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France","The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University , Algeria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France","institution_ids":["https://openalex.org/I21491767","https://openalex.org/I154526488"]},{"raw_affiliation_string":"The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University , Algeria","institution_ids":["https://openalex.org/I233209018"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035030607","display_name":"Mohamed Belhocine","orcid":"https://orcid.org/0000-0001-9523-0658"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M Belhocine","raw_affiliation_strings":["Molecular Biology and Genetics Laboratory , Dubai, United Arab Emirates"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Biology and Genetics Laboratory , Dubai, United Arab Emirates","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021580640","display_name":"Quentin Ferr\u00e9","orcid":"https://orcid.org/0000-0003-4750-0355"},"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"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Q Ferr\u00e9","raw_affiliation_strings":["Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France","institution_ids":["https://openalex.org/I21491767","https://openalex.org/I154526488"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065699840","display_name":"Nathanael Zweig","orcid":null},"institutions":[{"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"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"N Zweig","raw_affiliation_strings":["Aix Marseille Univ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aix Marseille Univ","institution_ids":["https://openalex.org/I21491767"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046980798","display_name":"Mourad Aribi","orcid":"https://orcid.org/0000-0002-6522-7252"},"institutions":[{"id":"https://openalex.org/I233209018","display_name":"University of Abou Bekr Belka\u00efd","ror":"https://ror.org/00jsjm362","country_code":"DZ","type":"education","lineage":["https://openalex.org/I233209018"]}],"countries":["DZ"],"is_corresponding":false,"raw_author_name":"M Aribi","raw_affiliation_strings":["The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University , Algeria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University , Algeria","institution_ids":["https://openalex.org/I233209018"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107597052","display_name":"Aitor Gonz\u00e1lez","orcid":"https://orcid.org/0000-0002-8402-1655"},"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"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"A Gonzalez","raw_affiliation_strings":["Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France","institution_ids":["https://openalex.org/I21491767","https://openalex.org/I154526488"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091488339","display_name":"Salvatore Spicuglia","orcid":"https://orcid.org/0000-0002-8101-7108"},"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/I4210095243","display_name":"La Ligue Contre le Cancer","ror":"https://ror.org/00rkrv905","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I4210095243"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"S Spicuglia","raw_affiliation_strings":["Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France","Equipe Labellis\u00e9e LIGUE contre le Cancer"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France","institution_ids":["https://openalex.org/I21491767","https://openalex.org/I154526488"]},{"raw_affiliation_string":"Equipe Labellis\u00e9e LIGUE contre le Cancer","institution_ids":["https://openalex.org/I4210095243"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049857580","display_name":"Denis Puthier","orcid":"https://orcid.org/0000-0002-7240-5280"},"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"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"D Puthier","raw_affiliation_strings":["Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aix Marseille Univ, INSERM, TAGC , UMR U1090, Marseille, France","institution_ids":["https://openalex.org/I21491767","https://openalex.org/I154526488"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5049857580"],"corresponding_institution_ids":["https://openalex.org/I154526488","https://openalex.org/I21491767"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.7455,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.69322439,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"35","issue":"18","first_page":"3487","last_page":"3488"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3138999938964844,"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":0.3138999938964844,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.17509999871253967,"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":0.14159999787807465,"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":0.9234733581542969},{"id":"https://openalex.org/keywords/ensembl","display_name":"Ensembl","score":0.8151594400405884},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8150471448898315},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.7206423282623291},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.6426055431365967},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5693761706352234},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.5054452419281006},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4406304955482483},{"id":"https://openalex.org/keywords/gene-nomenclature","display_name":"Gene nomenclature","score":0.4266071021556854},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.38704895973205566},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.34247639775276184},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.2581075429916382},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18113228678703308},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15740886330604553},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.13984543085098267}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9234733581542969},{"id":"https://openalex.org/C141674004","wikidata":"https://www.wikidata.org/wiki/Q1344256","display_name":"Ensembl","level":5,"score":0.8151594400405884},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8150471448898315},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.7206423282623291},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.6426055431365967},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5693761706352234},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.5054452419281006},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4406304955482483},{"id":"https://openalex.org/C62177273","wikidata":"https://www.wikidata.org/wiki/Q5531556","display_name":"Gene nomenclature","level":4,"score":0.4266071021556854},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.38704895973205566},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.34247639775276184},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2581075429916382},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18113228678703308},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15740886330604553},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.13984543085098267},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C514705636","wikidata":"https://www.wikidata.org/wiki/Q863247","display_name":"Nomenclature","level":3,"score":0.0}],"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz116","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz116","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3487/48975776/bioinformatics_35_18_3487.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30768152","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30768152","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-02078147v1","is_oa":true,"landing_page_url":"https://amu.hal.science/hal-02078147","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2019, &#x27E8;10.1093/bioinformatics/btz116&#x27E9;","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz116","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz116","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3487/48975776/bioinformatics_35_18_3487.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1512583955","display_name":"INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE","funder_award_id":"ANR-11-IDEX-0001","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G4181824923","display_name":"Dissection of coordinated stress responses by novel promoter elements with enhancer activity","funder_award_id":"ANR-18-CE12-0019","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G4866930200","display_name":null,"funder_award_id":"ANR-11-IDEX","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G541215150","display_name":null,"funder_award_id":"ANR-11-IDEX-0001-02","funder_id":"https://openalex.org/F4320320893","funder_display_name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale"},{"id":"https://openalex.org/G7527776872","display_name":null,"funder_award_id":"11-IDEX-0001-02","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G782245399","display_name":null,"funder_award_id":"IDEX-0001-02","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7929012186","display_name":null,"funder_award_id":"ANR-11-IDEX-0001-02","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320320893","display_name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","ror":"https://ror.org/02vjkv261"},{"id":"https://openalex.org/F4320321589","display_name":"Fondation pour la Recherche M\u00e9dicale","ror":"https://ror.org/04w6kn183"},{"id":"https://openalex.org/F4320322363","display_name":"Ligue Contre le Cancer","ror":"https://ror.org/00rkrv905"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2912623135.pdf","grobid_xml":"https://content.openalex.org/works/W2912623135.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W2048194168","https://openalex.org/W2070342831","https://openalex.org/W2099143842","https://openalex.org/W2107133912","https://openalex.org/W2114850508","https://openalex.org/W2136430672","https://openalex.org/W2342249984","https://openalex.org/W4250359879"],"related_works":["https://openalex.org/W3023169329","https://openalex.org/W4389470870","https://openalex.org/W2782165897","https://openalex.org/W1582950852","https://openalex.org/W4300438041","https://openalex.org/W2054104202","https://openalex.org/W2139703748","https://openalex.org/W2761254753","https://openalex.org/W1024825291","https://openalex.org/W2188981919"],"abstract_inverted_index":{"MOTIVATION:":[0],"While":[1],"Python":[2,32,65,77],"has":[3],"become":[4],"very":[5],"popular":[6],"in":[7,21,46,207],"bioinformatics,":[8],"a":[9,58],"limited":[10],"number":[11],"of":[12,18,43,55,95,114,146,166],"libraries":[13],"exist":[14],"for":[15,71],"fast":[16],"manipulation":[17,42],"gene":[19,44,178],"coordinates":[20,45],"Ensembl":[22],"GTF":[23,30,47,96,167],"format.":[24,48],"RESULTS:":[25],"We":[26],"have":[27,80,186],"developed":[28,81],"the":[29,52,64,82,159,164,199],"toolkit":[31],"package":[33,161],"(pygtftk),":[34],"which":[35],"aims":[36],"at":[37],"providing":[38,173],"easy":[39],"and":[40,69,184,191,193],"powerful":[41],"For":[49],"optimal":[50],"performances,":[51],"core":[53],"engine":[54],"pygtftk":[56,160,183],"is":[57,209],"C":[59,208],"dynamic":[60,204],"library":[61,205],"(libgtftk)":[62],"while":[63,172],"API":[66],"provides":[67],"usability":[68],"readability":[70],"developing":[72],"scripts.":[73],"Based":[74],"on":[75,120,189],"this":[76],"package,":[78],"we":[79],"gtftk":[83,185],"command":[84],"line":[85],"interface":[86],"that":[87],"contains":[88],"57":[89],"sub-commands":[90],"(v0.9.10)":[91],"to":[92,103,152,176],"ease":[93],"handling":[94],"files.":[97],"These":[98],"commands":[99],"may":[100],"be":[101],"used":[102],"(i)":[104],"perform":[105,177],"basic":[106],"tasks":[107],"(e.g.":[108,123],"selections,":[109],"insertions,":[110],"updates":[111],"or":[112,135],"deletions":[113],"features/keys),":[115],"(ii)":[116],"select":[117],"genes/transcripts":[118],"based":[119],"various":[121],"criteria":[122],"size,":[124],"exon":[125],"number,":[126],"transcription":[127],"start":[128],"site":[129],"location,":[130],"intron":[131],"length,":[132],"GO":[133],"terms)":[134],"(iii)":[136],"carry":[137],"out":[138],"more":[139],"advanced":[140],"operations":[141],"such":[142],"as":[143],"coverage":[144],"analyses":[145],"genomic":[147],"features":[148],"using":[149],"bigWig":[150],"files":[151,168],"create":[153],"faceted":[154],"read-coverage":[155],"diagrams.":[156],"In":[157],"conclusion,":[158],"greatly":[162],"simplifies":[163],"annotation":[165],"with":[169],"external":[170],"information":[171],"advance":[174],"tools":[175],"analyses.":[179],"AVAILABILITY":[180],"AND":[181],"IMPLEMENTATION:":[182],"been":[187],"tested":[188],"Linux":[190],"MacOSX":[192],"are":[194],"available":[195,210],"from":[196,211],"https://github.com/dputhier/pygtftk":[197],"under":[198],"MIT":[200],"license.":[201],"The":[202],"libgtftk":[203],"written":[206],"https://github.com/dputhier/libgtftk.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
