{"id":"https://openalex.org/W2782480057","doi":"https://doi.org/10.1371/journal.pcbi.1005921","title":"Probing instructions for expression regulation in gene nucleotide compositions","display_name":"Probing instructions for expression regulation in gene nucleotide compositions","publication_year":2018,"publication_date":"2018-01-02","ids":{"openalex":"https://openalex.org/W2782480057","doi":"https://doi.org/10.1371/journal.pcbi.1005921","mag":"2782480057","pmid":"https://pubmed.ncbi.nlm.nih.gov/29293496"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005921","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005921","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005921&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005921&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067491911","display_name":"Chlo\u00e9 Bessi\u00e8re","orcid":"https://orcid.org/0000-0001-7518-3559"},"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210114166","display_name":"Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier","ror":"https://ror.org/02785qs39","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210096427","https://openalex.org/I4210114166"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Chlo\u00e9 Bessi\u00e8re","raw_affiliation_strings":["IBC, Univ. Montpellier, CNRS, Montpellier, France","Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier, University of Montpellier, CNRS, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"IBC, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier, University of Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I4210114166","https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060688018","display_name":"May Taha","orcid":"https://orcid.org/0000-0001-9592-449X"},"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210114166","display_name":"Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier","ror":"https://ror.org/02785qs39","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210096427","https://openalex.org/I4210114166"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"May Taha","raw_affiliation_strings":["IBC, Univ. Montpellier, CNRS, Montpellier, France","IMAG, Univ. Montpellier, CNRS, Montpellier, France","Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier, University of Montpellier, CNRS, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"IBC, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"IMAG, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier, University of Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I4210114166","https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010029786","display_name":"Florent Petitprez","orcid":"https://orcid.org/0000-0002-5117-6466"},"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210114166","display_name":"Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier","ror":"https://ror.org/02785qs39","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210096427","https://openalex.org/I4210114166"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Florent Petitprez","raw_affiliation_strings":["IBC, Univ. Montpellier, CNRS, Montpellier, France","Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier, University of Montpellier, CNRS, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"IBC, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier, University of Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I4210114166","https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032193494","display_name":"Jimmy Vandel","orcid":"https://orcid.org/0000-0003-0189-0220"},"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Jimmy Vandel","raw_affiliation_strings":["IBC, Univ. Montpellier, CNRS, Montpellier, France","LIRMM, Univ. Montpellier, CNRS, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"IBC, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LIRMM, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I4210101743","https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033156491","display_name":"Jean\u2010Michel Marin","orcid":"https://orcid.org/0000-0001-7451-9719"},"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Jean-Michel Marin","raw_affiliation_strings":["IBC, Univ. Montpellier, CNRS, Montpellier, France","IMAG, Univ. Montpellier, CNRS, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"IBC, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"IMAG, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049393621","display_name":"Laurent Br\u00e9h\u00e9lin","orcid":"https://orcid.org/0000-0002-2582-2831"},"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Laurent Br\u00e9h\u00e9lin","raw_affiliation_strings":["IBC, Univ. Montpellier, CNRS, Montpellier, France","LIRMM, Univ. Montpellier, CNRS, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"IBC, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LIRMM, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I4210101743","https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044919124","display_name":"Sophie L\u00e8bre","orcid":"https://orcid.org/0000-0003-3444-2416"},"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I208215962","display_name":"Universit\u00e9 Paul-Val\u00e9ry Montpellier","ror":"https://ror.org/00qhdy563","country_code":"FR","type":"education","lineage":["https://openalex.org/I208215962"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Sophie L\u00e8bre","raw_affiliation_strings":["IBC, Univ. Montpellier, CNRS, Montpellier, France","IMAG, Univ. Montpellier, CNRS, Montpellier, France","Univ. Paul-Val\u00e9ry-Montpellier 3, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"IBC, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"IMAG, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Univ. Paul-Val\u00e9ry-Montpellier 3, Montpellier, France","institution_ids":["https://openalex.org/I208215962"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038496499","display_name":"Charles\u2010Henri Lecellier","orcid":"https://orcid.org/0000-0002-0229-5434"},"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210114166","display_name":"Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier","ror":"https://ror.org/02785qs39","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210096427","https://openalex.org/I4210114166"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Charles-Henri Lecellier","raw_affiliation_strings":["IBC, Univ. Montpellier, CNRS, Montpellier, France","Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier, University of Montpellier, CNRS, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"IBC, Univ. Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier, University of Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I4210114166","https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5010029786","https://openalex.org/A5032193494","https://openalex.org/A5033156491","https://openalex.org/A5038496499","https://openalex.org/A5044919124","https://openalex.org/A5049393621","https://openalex.org/A5060688018","https://openalex.org/A5067491911"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I208215962","https://openalex.org/I4210101743","https://openalex.org/I4210114166"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":1912,"currency":"EUR","value_usd":2062},"fwci":0.9309,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.73566438,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"14","issue":"1","first_page":"e1005921","last_page":"e1005921"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10604","display_name":"RNA Research and Splicing","score":0.9983999729156494,"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/computational-biology","display_name":"Computational biology","score":0.6923937797546387},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6458073258399963},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6275473833084106},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.6187435388565063},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.6094753742218018},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5806850790977478},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.5634860992431641},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5248344540596008},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.5213093161582947},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4350668787956238}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6923937797546387},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6458073258399963},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6275473833084106},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.6187435388565063},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.6094753742218018},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5806850790977478},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.5634860992431641},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5248344540596008},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.5213093161582947},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4350668787956238}],"mesh":[{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","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":"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":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1005921","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005921","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005921&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:29293496","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29293496","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:HAL:lirmm-01744469v1","is_oa":true,"landing_page_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-01744469","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, 2018, 14 (1), pp.e1005921. &#x27E8;10.1371/journal.pcbi.1005921&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:HAL:tel-04908075v1","is_oa":true,"landing_page_url":"https://theses.hal.science/tel-04908075","pdf_url":null,"source":{"id":"https://openalex.org/S4406922440","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":"Computer Science [cs]. Universit\u00e9 de Montpellier, 2023","raw_type":"Accreditation to supervise research"},{"id":"pmh:oai:doaj.org/article:4364bca7da2c4e7485c066e824dc79f0","is_oa":true,"landing_page_url":"https://doaj.org/article/4364bca7da2c4e7485c066e824dc79f0","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 14, Iss 1, p e1005921 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4689622","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5766238","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"},{"id":"pmh:oai:figshare.com:article/5747715","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Probing_instructions_for_expression_regulation_in_gene_nucleotide_compositions/5747715","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1005921","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005921","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005921&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3335229504","display_name":null,"funder_award_id":"Avenir","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G4973929103","display_name":null,"funder_award_id":"funding","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"},{"id":"https://openalex.org/G6115547468","display_name":null,"funder_award_id":"ANR-11-BINF-0002","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7758152977","display_name":null,"funder_award_id":"support","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"}],"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/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2782480057.pdf","grobid_xml":"https://content.openalex.org/works/W2782480057.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W1582471009","https://openalex.org/W1590857219","https://openalex.org/W1594031697","https://openalex.org/W1815645917","https://openalex.org/W1816176398","https://openalex.org/W1900337607","https://openalex.org/W1975111661","https://openalex.org/W1976209715","https://openalex.org/W1978883675","https://openalex.org/W1981331174","https://openalex.org/W1986223165","https://openalex.org/W1987122345","https://openalex.org/W1989650370","https://openalex.org/W1997535872","https://openalex.org/W2013321787","https://openalex.org/W2015845481","https://openalex.org/W2020433571","https://openalex.org/W2023342647","https://openalex.org/W2029530775","https://openalex.org/W2032200433","https://openalex.org/W2056103949","https://openalex.org/W2070021921","https://openalex.org/W2083073732","https://openalex.org/W2090037139","https://openalex.org/W2104116111","https://openalex.org/W2105694586","https://openalex.org/W2106352274","https://openalex.org/W2110065044","https://openalex.org/W2123921145","https://openalex.org/W2124343649","https://openalex.org/W2129795133","https://openalex.org/W2134868027","https://openalex.org/W2135046866","https://openalex.org/W2136430672","https://openalex.org/W2143172590","https://openalex.org/W2146940435","https://openalex.org/W2147947827","https://openalex.org/W2150782426","https://openalex.org/W2159942968","https://openalex.org/W2161212572","https://openalex.org/W2164035719","https://openalex.org/W2198606573","https://openalex.org/W2240027552","https://openalex.org/W2259283565","https://openalex.org/W2259938310","https://openalex.org/W2267877430","https://openalex.org/W2268267797","https://openalex.org/W2340540054","https://openalex.org/W2344560359","https://openalex.org/W2413043813","https://openalex.org/W2424483111","https://openalex.org/W2430846749","https://openalex.org/W2495238549","https://openalex.org/W2519244818","https://openalex.org/W2520717521","https://openalex.org/W2520864903","https://openalex.org/W2546542913","https://openalex.org/W2560311853","https://openalex.org/W2562162676","https://openalex.org/W2606285789","https://openalex.org/W2911964244","https://openalex.org/W2951218167","https://openalex.org/W2952220073","https://openalex.org/W3085162807","https://openalex.org/W6689988116","https://openalex.org/W6843735874"],"related_works":["https://openalex.org/W3145419749","https://openalex.org/W3038565614","https://openalex.org/W4313509691","https://openalex.org/W3108101741","https://openalex.org/W2043274041","https://openalex.org/W2277277196","https://openalex.org/W3131178456","https://openalex.org/W1988612397","https://openalex.org/W1847045739","https://openalex.org/W4234163953"],"abstract_inverted_index":{"Gene":[0],"expression":[1,51,165],"is":[2,20,129],"orchestrated":[3],"by":[4,48],"distinct":[5],"regulatory":[6,24,197],"regions":[7,25,63,198],"to":[8,21,87,92,138,170,195,200,228,236],"ensure":[9],"a":[10,168,185,204],"wide":[11],"variety":[12],"of":[13,60,121,127,150,155,188,207,222,238],"cell":[14,40,93],"types":[15],"and":[16,33,64,95,102,166,235],"functions.":[17],"A":[18],"challenge":[19],"identify":[22],"which":[23,84],"are":[26,29,69,85,114,135],"active,":[27],"what":[28],"their":[30,201],"associated":[31,65,230,242],"features":[32],"how":[34],"they":[35],"work":[36],"together":[37],"in":[38,72,74,116,212],"each":[39],"type.":[41],"Several":[42],"approaches":[43,113],"have":[44],"tackled":[45],"this":[46,125],"problem":[47],"modeling":[49],"gene":[50,118,164,189,209],"based":[52,174],"on":[53,81,176],"epigenetic":[54],"marks,":[55],"with":[56,231],"the":[57,144,148,153,156,208,220],"ultimate":[58],"goal":[59],"identifying":[61],"driving":[62],"genomic":[66],"variations":[67],"that":[68,219],"clinically":[70],"relevant":[71],"particular":[73,213],"precision":[75],"medicine.":[76],"However,":[77],"these":[78,112,133],"models":[79,128],"rely":[80],"experimental":[82],"data,":[83],"limited":[86],"specific":[88],"samples":[89],"(even":[90],"often":[91],"lines)":[94],"cannot":[96],"be":[97,226],"generated":[98],"for":[99,163],"all":[100,103],"regulators":[101,151],"patients.":[104],"In":[105],"addition,":[106],"we":[107,159],"show":[108],"here":[109],"that,":[110],"although":[111],"accurate":[115],"predicting":[117],"expression,":[119],"inference":[120],"TF":[122],"combinations":[123],"from":[124],"type":[126],"not":[130,136],"straightforward.":[131],"Furthermore":[132],"methods":[134],"designed":[137],"capture":[139],"regulation":[140],"instructions":[141,162],"present":[142],"at":[143],"sequence":[145],"level,":[146],"before":[147],"binding":[149],"or":[152],"opening":[154],"chromatin.":[157],"Here,":[158],"probe":[160],"sequence-level":[161],"develop":[167],"method":[169,180],"explain":[171],"mRNA":[172],"levels":[173],"solely":[175],"nucleotide":[177,182,223],"features.":[178],"Our":[179],"positions":[181],"composition":[183],"as":[184],"critical":[186],"component":[187],"expression.":[190],"Moreover,":[191],"our":[192],"approach,":[193],"able":[194],"rank":[196],"according":[199],"contribution,":[202],"unveils":[203],"strong":[205],"influence":[206],"body":[210],"sequence,":[211],"introns.":[214],"We":[215],"further":[216],"provide":[217],"evidence":[218],"contribution":[221],"content":[224],"can":[225],"linked":[227],"co-regulations":[229],"genome":[232],"3D":[233],"architecture":[234],"associations":[237],"genes":[239],"within":[240],"topologically":[241],"domains.":[243]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
