{"id":"https://openalex.org/W3154796822","doi":"https://doi.org/10.1371/journal.pcbi.1008909","title":"Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes","display_name":"Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes","publication_year":2021,"publication_date":"2021-04-16","ids":{"openalex":"https://openalex.org/W3154796822","doi":"https://doi.org/10.1371/journal.pcbi.1008909","mag":"3154796822","pmid":"https://pubmed.ncbi.nlm.nih.gov/33861755"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008909","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008909","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1008909","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005552606","display_name":"Christophe Menichelli","orcid":"https://orcid.org/0000-0001-9161-3715"},"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":false,"raw_author_name":"Christophe Menichelli","raw_affiliation_strings":["LIRMM, Univ Montpellier, CNRS, Montpellier, France"],"affiliations":[{"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/A5026184243","display_name":"Vincent Guitard","orcid":"https://orcid.org/0000-0003-3025-0978"},"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/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"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":false,"raw_author_name":"Vincent Guitard","raw_affiliation_strings":["Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, INSERM, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, INSERM, Montpellier, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012316993","display_name":"Rafael M. Martins","orcid":"https://orcid.org/0000-0001-7449-0696"},"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/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"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":false,"raw_author_name":"Rafael M. Martins","raw_affiliation_strings":["Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, INSERM, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, INSERM, Montpellier, France","institution_ids":["https://openalex.org/I154526488","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":false,"raw_author_name":"Sophie L\u00e8bre","raw_affiliation_strings":["IMAG, Univ. Montpellier, CNRS, Montpellier, France","Univ. Paul-Val\u00e9ry-Montpellier 3, Montpellier, France"],"affiliations":[{"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":"middle","author":{"id":"https://openalex.org/A5089659156","display_name":"Jos\u00e9-Juan Lopez-Rubio","orcid":"https://orcid.org/0000-0002-0555-1122"},"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/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"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":"Jose-Juan Lopez-Rubio","raw_affiliation_strings":["Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, INSERM, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, INSERM, Montpellier, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]},{"author_position":"middle","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/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"]},{"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":["Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier, University of Montpellier, CNRS, Montpellier, France","LIRMM, Univ Montpellier, CNRS, Montpellier, France"],"affiliations":[{"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"]},{"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":"last","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":["LIRMM, Univ Montpellier, CNRS, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"LIRMM, Univ Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I4210101743","https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5038496499","https://openalex.org/A5049393621","https://openalex.org/A5089659156"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210114166"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.244,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.52083296,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"17","issue":"4","first_page":"e1008909","last_page":"e1008909"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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/biology","display_name":"Biology","score":0.815742015838623},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6422125101089478},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5530956387519836},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5510823130607605},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5501381754875183},{"id":"https://openalex.org/keywords/multicellular-organism","display_name":"Multicellular organism","score":0.54203861951828},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.5329329371452332},{"id":"https://openalex.org/keywords/plasmodium-falciparum","display_name":"Plasmodium falciparum","score":0.5219935178756714},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.47482001781463623},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"Transcriptional regulation","score":0.47300201654434204},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.43273305892944336}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.815742015838623},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6422125101089478},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5530956387519836},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5510823130607605},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5501381754875183},{"id":"https://openalex.org/C74318829","wikidata":"https://www.wikidata.org/wiki/Q36458","display_name":"Multicellular organism","level":3,"score":0.54203861951828},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.5329329371452332},{"id":"https://openalex.org/C2778371730","wikidata":"https://www.wikidata.org/wiki/Q311383","display_name":"Plasmodium falciparum","level":3,"score":0.5219935178756714},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.47482001781463623},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.47300201654434204},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.43273305892944336},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.0},{"id":"https://openalex.org/C2778048844","wikidata":"https://www.wikidata.org/wiki/Q12156","display_name":"Malaria","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012323","descriptor_name":"RNA Processing, Post-Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012323","descriptor_name":"RNA Processing, Post-Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012323","descriptor_name":"RNA Processing, Post-Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012323","descriptor_name":"RNA Processing, Post-Transcriptional","qualifier_ui":null,"qualifier_name":null,"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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016372","descriptor_name":"RNA, Antisense","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016372","descriptor_name":"RNA, Antisense","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016372","descriptor_name":"RNA, Antisense","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016372","descriptor_name":"RNA, Antisense","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017930","descriptor_name":"Genes, Reporter","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017930","descriptor_name":"Genes, Reporter","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017930","descriptor_name":"Genes, Reporter","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017930","descriptor_name":"Genes, Reporter","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018503","descriptor_name":"Genome, Protozoan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018503","descriptor_name":"Genome, Protozoan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018503","descriptor_name":"Genome, Protozoan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018503","descriptor_name":"Genome, Protozoan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1008909","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008909","pdf_url":null,"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:33861755","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33861755","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:hal-03253460v1","is_oa":true,"landing_page_url":"https://hal.science/hal-03253460","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":"PLoS Computational Biology, 2021, 17 (4), pp.e1008909. &#x27E8;10.1371/journal.pcbi.1008909&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:cf5822cce8d34a898e0891104f9f2d10","is_oa":true,"landing_page_url":"https://doaj.org/article/cf5822cce8d34a898e0891104f9f2d10","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 17, Iss 4, p e1008909 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8081344","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8081344","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1008909","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008909","pdf_url":null,"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":[{"score":0.5400000214576721,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"awards":[{"id":"https://openalex.org/G1230763932","display_name":null,"funder_award_id":"ATIP-Avenir","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"},{"id":"https://openalex.org/G1385750998","display_name":null,"funder_award_id":"ATIP-Avenir","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G1786932369","display_name":null,"funder_award_id":"DEQ2018033199","funder_id":"https://openalex.org/F4320321589","funder_display_name":"Fondation pour la Recherche M\u00e9dicale"},{"id":"https://openalex.org/G3036550691","display_name":null,"funder_award_id":"11-LABX-0024-01","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"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/G3807293409","display_name":null,"funder_award_id":"ANR-11-LABX-00","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G4110391279","display_name":null,"funder_award_id":"project,","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G4219701773","display_name":null,"funder_award_id":"ANR-11-LABX-0024","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"},{"id":"https://openalex.org/G4735198178","display_name":null,"funder_award_id":"ATIP-Avenir","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/G4767150528","display_name":null,"funder_award_id":"ANR-11-LABX-0024-01","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/G6135850535","display_name":null,"funder_award_id":"ANR-11-LABX-0024","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G6197543479","display_name":null,"funder_award_id":"ANR-11-LABX-0024","funder_id":"https://openalex.org/F4320317765","funder_display_name":"Alliance Fran\u00e7aise contre les Maladies Parasitaires"},{"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"},{"id":"https://openalex.org/G938947800","display_name":null,"funder_award_id":"ANR-11-LABX-0024-01","funder_id":"https://openalex.org/F4320317765","funder_display_name":"Alliance Fran\u00e7aise contre les Maladies Parasitaires"}],"funders":[{"id":"https://openalex.org/F4320317765","display_name":"Alliance Fran\u00e7aise contre les Maladies Parasitaires","ror":null},{"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/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":101,"referenced_works":["https://openalex.org/W1592870802","https://openalex.org/W1900337607","https://openalex.org/W1936728507","https://openalex.org/W1974091218","https://openalex.org/W1981093360","https://openalex.org/W1996065618","https://openalex.org/W1999659528","https://openalex.org/W2011622850","https://openalex.org/W2014677321","https://openalex.org/W2018838463","https://openalex.org/W2021868082","https://openalex.org/W2023160008","https://openalex.org/W2024774367","https://openalex.org/W2029229088","https://openalex.org/W2040149948","https://openalex.org/W2044125630","https://openalex.org/W2047849307","https://openalex.org/W2055730063","https://openalex.org/W2056103949","https://openalex.org/W2057692691","https://openalex.org/W2070021921","https://openalex.org/W2084547321","https://openalex.org/W2090128221","https://openalex.org/W2094381221","https://openalex.org/W2096496718","https://openalex.org/W2099343472","https://openalex.org/W2102606027","https://openalex.org/W2107646820","https://openalex.org/W2111407873","https://openalex.org/W2112047656","https://openalex.org/W2115992869","https://openalex.org/W2129897419","https://openalex.org/W2130410032","https://openalex.org/W2131355964","https://openalex.org/W2133040714","https://openalex.org/W2135046866","https://openalex.org/W2138019504","https://openalex.org/W2140952049","https://openalex.org/W2144710927","https://openalex.org/W2144720570","https://openalex.org/W2145994105","https://openalex.org/W2147794131","https://openalex.org/W2149435095","https://openalex.org/W2149991876","https://openalex.org/W2152007783","https://openalex.org/W2153432157","https://openalex.org/W2157009395","https://openalex.org/W2158005619","https://openalex.org/W2163443861","https://openalex.org/W2164365774","https://openalex.org/W2169431889","https://openalex.org/W2175162543","https://openalex.org/W2198606573","https://openalex.org/W2208364268","https://openalex.org/W2227356030","https://openalex.org/W2267877430","https://openalex.org/W2283570988","https://openalex.org/W2336509392","https://openalex.org/W2460436629","https://openalex.org/W2532816831","https://openalex.org/W2563384021","https://openalex.org/W2578154916","https://openalex.org/W2603460184","https://openalex.org/W2604150000","https://openalex.org/W2617318554","https://openalex.org/W2624820140","https://openalex.org/W2677447961","https://openalex.org/W2747545374","https://openalex.org/W2749891995","https://openalex.org/W2782480057","https://openalex.org/W2784484745","https://openalex.org/W2789731316","https://openalex.org/W2798157446","https://openalex.org/W2800245987","https://openalex.org/W2802090556","https://openalex.org/W2810075380","https://openalex.org/W2883945062","https://openalex.org/W2884291705","https://openalex.org/W2887722577","https://openalex.org/W2892295314","https://openalex.org/W2893891122","https://openalex.org/W2914480421","https://openalex.org/W2922894427","https://openalex.org/W2950844094","https://openalex.org/W2952220073","https://openalex.org/W2952239877","https://openalex.org/W2953106052","https://openalex.org/W2972439184","https://openalex.org/W2988655273","https://openalex.org/W2991383172","https://openalex.org/W2995175313","https://openalex.org/W3009954623","https://openalex.org/W3014679506","https://openalex.org/W3026475692","https://openalex.org/W3038965684","https://openalex.org/W3039386892","https://openalex.org/W3043091519","https://openalex.org/W3095586809","https://openalex.org/W3118468815","https://openalex.org/W3119077889","https://openalex.org/W3160972853"],"related_works":["https://openalex.org/W2912720016","https://openalex.org/W2791405408","https://openalex.org/W3102681775","https://openalex.org/W1976009923","https://openalex.org/W2102101252","https://openalex.org/W4313509691","https://openalex.org/W4245871433","https://openalex.org/W1983426369","https://openalex.org/W2014043692","https://openalex.org/W2056161765"],"abstract_inverted_index":{"Long":[0],"regulatory":[1],"elements":[2],"(LREs),":[3],"such":[4],"as":[5,23,133,135],"CpG":[6],"islands,":[7],"polydA:dT":[8],"tracts":[9],"or":[10],"AU-rich":[11],"elements,":[12],"are":[13,91,161,191,206],"thought":[14],"to":[15,25,37,58,68,183],"play":[16],"key":[17],"roles":[18],"in":[19,136,163,227,232],"gene":[20,55,98],"regulation":[21,213],"but,":[22],"opposed":[24],"conventional":[26],"binding":[27],"sites":[28],"of":[29,61,71,74,109,151,187,193,221,240],"transcription":[30,188],"factors,":[31,189],"few":[32],"methods":[33],"have":[34],"been":[35],"proposed":[36],"formally":[38],"and":[39,65,77,96,124,129,200,211],"automatically":[40],"characterize":[41],"them.":[42],"We":[43],"present":[44],"here":[45],"a":[46,167],"computational":[47],"approach":[48],"named":[49],"DExTER":[50,226,241],"(Domain":[51],"Exploration":[52],"To":[53],"Explain":[54],"Regulation)":[56],"dedicated":[57],"the":[59,69,72,107,139,152,158,218],"identification":[60],"candidate":[62],"LREs":[63],"(cLREs)":[64],"apply":[66],"it":[67],"analysis":[70],"genomes":[73,86],"P.":[75,127,177,228],"falciparum":[76,128,229],"other":[78,130],"eukaryotes.":[79],"Our":[80],"analyses":[81,202],"show":[82,203],"that":[83,90,97,204],"all":[84,164],"tested":[85],"contain":[87],"several":[88],"cLREs":[89,116,146,160,190],"somewhat":[92],"conserved":[93],"along":[94,172],"evolution,":[95],"expression":[99,194],"can":[100],"be":[101,184],"predicted":[102],"with":[103,144,195,208],"surprising":[104],"accuracy":[105,197],"on":[106,122],"basis":[108],"these":[110],"long":[111],"regions":[112],"only.":[113],"Regulation":[114],"by":[115,225],"exhibits":[117],"very":[118],"different":[119,145,149],"behaviours":[120],"depending":[121],"species":[123],"conditions.":[125],"In":[126,176],"Apicomplexan":[131],"organisms":[132],"well":[134],"Dictyostelium":[137],"discoideum,":[138],"process":[140],"appears":[141],"highly":[142],"dynamic,":[143],"involved":[147,162],"at":[148,244],"phases":[150],"life":[153],"cycle.":[154],"For":[155],"multicellular":[156],"organisms,":[157],"same":[159],"tissues,":[165],"but":[166],"dynamic":[168],"behavior":[169],"is":[170,181,242],"observed":[171],"embryonic":[173],"development":[174],"stages.":[175],"falciparum,":[178],"whose":[179],"genome":[180],"known":[182],"strongly":[185],"depleted":[186],"predictive":[192],"an":[196,231],"above":[198],"70%,":[199],"our":[201],"they":[205],"associated":[207],"both":[209],"transcriptional":[210],"post-transcriptional":[212],"signals.":[214],"Moreover,":[215],"we":[216],"assessed":[217],"biological":[219],"relevance":[220],"one":[222],"LRE":[223],"discovered":[224],"using":[230],"vivo":[233],"reporter":[234],"assay.":[235],"The":[236],"source":[237],"code":[238],"(python)":[239],"available":[243],"https://gite.lirmm.fr/menichelli/DExTER.":[245]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-04-15T08:11:43.952461","created_date":"2025-10-10T00:00:00"}
