{"id":"https://openalex.org/W2112885819","doi":"https://doi.org/10.1186/1756-0381-5-12","title":"Finding biomarkers in non-model species: literature mining of transcription factors involved in bovine embryo development","display_name":"Finding biomarkers in non-model species: literature mining of transcription factors involved in bovine embryo development","publication_year":2012,"publication_date":"2012-08-29","ids":{"openalex":"https://openalex.org/W2112885819","doi":"https://doi.org/10.1186/1756-0381-5-12","mag":"2112885819","pmid":"https://pubmed.ncbi.nlm.nih.gov/22931563"},"language":"en","primary_location":{"id":"doi:10.1186/1756-0381-5-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-5-12","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-5-12","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-5-12","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082665913","display_name":"Nicolas Turenne","orcid":"https://orcid.org/0000-0003-1229-5590"},"institutions":[{"id":"https://openalex.org/I4210137407","display_name":"Sciences en Soci\u00e9t\u00e9","ror":"https://ror.org/045bzvb60","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210115779","https://openalex.org/I4210137407"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Nicolas Turenne","raw_affiliation_strings":["INRA, SenS, UR1326, IFRIS, Champs-sur-Marne, F-77420, France","SenS - Sciences en Soci\u00e9t\u00e9 (Bois de l'Etang, 5 Bd Descartes, Champs sur Marne, F-77454 Marne-la-Vall\u00e9e - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRA, SenS, UR1326, IFRIS, Champs-sur-Marne, F-77420, France","institution_ids":[]},{"raw_affiliation_string":"SenS - Sciences en Soci\u00e9t\u00e9 (Bois de l'Etang, 5 Bd Descartes, Champs sur Marne, F-77454 Marne-la-Vall\u00e9e - France)","institution_ids":["https://openalex.org/I4210137407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065497862","display_name":"Evgeny Tiys","orcid":"https://orcid.org/0000-0001-5820-8646"},"institutions":[{"id":"https://openalex.org/I4210116466","display_name":"Institute of Cytology and Genetics","ror":"https://ror.org/0277xgb12","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1313323035","https://openalex.org/I188973947","https://openalex.org/I4210116466","https://openalex.org/I4210127387","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Evgeniy Tiys","raw_affiliation_strings":["Sector of Computational Proteomics, Institute of Cytology and Genetics, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia","Sector of Computational Proteomic (Russia)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sector of Computational Proteomics, Institute of Cytology and Genetics, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]},{"raw_affiliation_string":"Sector of Computational Proteomic (Russia)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014655081","display_name":"\u0412. \u0410. \u0418\u0432\u0430\u043d\u0438\u0441\u0435\u043d\u043a\u043e","orcid":"https://orcid.org/0000-0002-1859-4631"},"institutions":[{"id":"https://openalex.org/I4210116466","display_name":"Institute of Cytology and Genetics","ror":"https://ror.org/0277xgb12","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1313323035","https://openalex.org/I188973947","https://openalex.org/I4210116466","https://openalex.org/I4210127387","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Vladimir Ivanisenko","raw_affiliation_strings":["Sector of Computational Proteomics, Institute of Cytology and Genetics, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia","Sector of Computational Proteomic (Russia)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sector of Computational Proteomics, Institute of Cytology and Genetics, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]},{"raw_affiliation_string":"Sector of Computational Proteomic (Russia)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042500646","display_name":"N. S. Yudin","orcid":"https://orcid.org/0000-0002-1947-5554"},"institutions":[{"id":"https://openalex.org/I4210116466","display_name":"Institute of Cytology and Genetics","ror":"https://ror.org/0277xgb12","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1313323035","https://openalex.org/I188973947","https://openalex.org/I4210116466","https://openalex.org/I4210127387","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I4210131892","display_name":"Institute of Molecular Genetics","ror":"https://ror.org/03apz2q12","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210131892"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Nikolay Yudin","raw_affiliation_strings":["Laboratory of Animal Molecular Genetics, Institute of Cytology and Genetics, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia","Laboratory of Animal Molecular Genetic (Russia)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Animal Molecular Genetics, Institute of Cytology and Genetics, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]},{"raw_affiliation_string":"Laboratory of Animal Molecular Genetic (Russia)","institution_ids":["https://openalex.org/I4210131892"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075720865","display_name":"E. V. Ignatieva","orcid":"https://orcid.org/0000-0002-8588-6511"},"institutions":[{"id":"https://openalex.org/I4210116466","display_name":"Institute of Cytology and Genetics","ror":"https://ror.org/0277xgb12","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1313323035","https://openalex.org/I188973947","https://openalex.org/I4210116466","https://openalex.org/I4210127387","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Elena Ignatieva","raw_affiliation_strings":["Laboratory of Evolutionary Bioinformatics and Theoretical, Institute of Cytology and Genetics, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia","Laboratory of Theoretic al Genetic (Russia)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Evolutionary Bioinformatics and Theoretical, Institute of Cytology and Genetics, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]},{"raw_affiliation_string":"Laboratory of Theoretic al Genetic (Russia)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039884066","display_name":"Damien Valour","orcid":"https://orcid.org/0000-0002-7292-7003"},"institutions":[{"id":"https://openalex.org/I17606148","display_name":"\u00c9cole Nationale V\u00e9t\u00e9rinaire d'Alfort","ror":"https://ror.org/04k031t90","country_code":"FR","type":"education","lineage":["https://openalex.org/I17606148","https://openalex.org/I197681013"]},{"id":"https://openalex.org/I4210103770","display_name":"Laboratoire de Biologie du D\u00e9veloppement","ror":"https://ror.org/024hnwe62","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210103770"]},{"id":"https://openalex.org/I4210135462","display_name":"Agence Nationale des Fr\u00e9quences","ror":"https://ror.org/03qtr7n72","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210135462"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Damien Valour","raw_affiliation_strings":["ENVA, Maisons Alfort, F-94704, France","INRA, UMR1198 Biologie du D\u00e9veloppement et Reproduction, Jouy-en-Josas, F-78352, France","ENVA - \u00c9cole nationale v\u00e9t\u00e9rinaire d'Alfort (7 avenue du G\u00e9n\u00e9ral de Gaulle - 94700 Maisons-Alfort - France)","BDR - Biologie du d\u00e9veloppement et reproduction (B\u00e2timent 440 Domaine Vilvert 78352 JOUY EN JOSAS CEDEX - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ENVA, Maisons Alfort, F-94704, France","institution_ids":["https://openalex.org/I17606148","https://openalex.org/I4210135462"]},{"raw_affiliation_string":"INRA, UMR1198 Biologie du D\u00e9veloppement et Reproduction, Jouy-en-Josas, F-78352, France","institution_ids":["https://openalex.org/I4210103770"]},{"raw_affiliation_string":"ENVA - \u00c9cole nationale v\u00e9t\u00e9rinaire d'Alfort (7 avenue du G\u00e9n\u00e9ral de Gaulle - 94700 Maisons-Alfort - France)","institution_ids":["https://openalex.org/I17606148"]},{"raw_affiliation_string":"BDR - Biologie du d\u00e9veloppement et reproduction (B\u00e2timent 440 Domaine Vilvert 78352 JOUY EN JOSAS CEDEX - France)","institution_ids":["https://openalex.org/I4210103770"]}]},{"author_position":"middle","author":{"id":null,"display_name":"S\u00e9verine A Degrelle","orcid":null},"institutions":[{"id":"https://openalex.org/I17606148","display_name":"\u00c9cole Nationale V\u00e9t\u00e9rinaire d'Alfort","ror":"https://ror.org/04k031t90","country_code":"FR","type":"education","lineage":["https://openalex.org/I17606148","https://openalex.org/I197681013"]},{"id":"https://openalex.org/I4210103770","display_name":"Laboratoire de Biologie du D\u00e9veloppement","ror":"https://ror.org/024hnwe62","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210103770"]},{"id":"https://openalex.org/I4210135462","display_name":"Agence Nationale des Fr\u00e9quences","ror":"https://ror.org/03qtr7n72","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210135462"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"S\u00e9verine A Degrelle","raw_affiliation_strings":["ENVA, Maisons Alfort, F-94704, France","INRA, UMR1198 Biologie du D\u00e9veloppement et Reproduction, Jouy-en-Josas, F-78352, France","ENVA - \u00c9cole nationale v\u00e9t\u00e9rinaire d'Alfort (7 avenue du G\u00e9n\u00e9ral de Gaulle - 94700 Maisons-Alfort - France)","BDR - Biologie du d\u00e9veloppement et reproduction (B\u00e2timent 440 Domaine Vilvert 78352 JOUY EN JOSAS CEDEX - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ENVA, Maisons Alfort, F-94704, France","institution_ids":["https://openalex.org/I17606148","https://openalex.org/I4210135462"]},{"raw_affiliation_string":"INRA, UMR1198 Biologie du D\u00e9veloppement et Reproduction, Jouy-en-Josas, F-78352, France","institution_ids":["https://openalex.org/I4210103770"]},{"raw_affiliation_string":"ENVA - \u00c9cole nationale v\u00e9t\u00e9rinaire d'Alfort (7 avenue du G\u00e9n\u00e9ral de Gaulle - 94700 Maisons-Alfort - France)","institution_ids":["https://openalex.org/I17606148"]},{"raw_affiliation_string":"BDR - Biologie du d\u00e9veloppement et reproduction (B\u00e2timent 440 Domaine Vilvert 78352 JOUY EN JOSAS CEDEX - France)","institution_ids":["https://openalex.org/I4210103770"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001237277","display_name":"Isabelle Hue","orcid":"https://orcid.org/0000-0002-3873-9738"},"institutions":[{"id":"https://openalex.org/I17606148","display_name":"\u00c9cole Nationale V\u00e9t\u00e9rinaire d'Alfort","ror":"https://ror.org/04k031t90","country_code":"FR","type":"education","lineage":["https://openalex.org/I17606148","https://openalex.org/I197681013"]},{"id":"https://openalex.org/I4210103770","display_name":"Laboratoire de Biologie du D\u00e9veloppement","ror":"https://ror.org/024hnwe62","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210103770"]},{"id":"https://openalex.org/I4210135462","display_name":"Agence Nationale des Fr\u00e9quences","ror":"https://ror.org/03qtr7n72","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210135462"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Isabelle Hue","raw_affiliation_strings":["ENVA, Maisons Alfort, F-94704, France","INRA, UMR1198 Biologie du D\u00e9veloppement et Reproduction, Jouy-en-Josas, F-78352, France","ENVA - \u00c9cole nationale v\u00e9t\u00e9rinaire d'Alfort (7 avenue du G\u00e9n\u00e9ral de Gaulle - 94700 Maisons-Alfort - France)","BDR - Biologie du d\u00e9veloppement et reproduction (B\u00e2timent 440 Domaine Vilvert 78352 JOUY EN JOSAS CEDEX - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ENVA, Maisons Alfort, F-94704, France","institution_ids":["https://openalex.org/I17606148","https://openalex.org/I4210135462"]},{"raw_affiliation_string":"INRA, UMR1198 Biologie du D\u00e9veloppement et Reproduction, Jouy-en-Josas, F-78352, France","institution_ids":["https://openalex.org/I4210103770"]},{"raw_affiliation_string":"ENVA - \u00c9cole nationale v\u00e9t\u00e9rinaire d'Alfort (7 avenue du G\u00e9n\u00e9ral de Gaulle - 94700 Maisons-Alfort - France)","institution_ids":["https://openalex.org/I17606148"]},{"raw_affiliation_string":"BDR - Biologie du d\u00e9veloppement et reproduction (B\u00e2timent 440 Domaine Vilvert 78352 JOUY EN JOSAS CEDEX - France)","institution_ids":["https://openalex.org/I4210103770"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5082665913"],"corresponding_institution_ids":["https://openalex.org/I4210137407"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.9406,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.74251842,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"5","issue":"1","first_page":"12","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9642000198364258,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9642000198364258,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.00930000003427267,"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/T11063","display_name":"Rough Sets and Fuzzy Logic","score":0.0013000000035390258,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7393255829811096},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.582348644733429},{"id":"https://openalex.org/keywords/embryo","display_name":"Embryo","score":0.5773715376853943},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5233898758888245},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.45145025849342346},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4514176845550537},{"id":"https://openalex.org/keywords/embryogenesis","display_name":"Embryogenesis","score":0.43246597051620483},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.42583584785461426},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4160422682762146},{"id":"https://openalex.org/keywords/biotechnology","display_name":"Biotechnology","score":0.37626832723617554},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3437327444553375}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7393255829811096},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.582348644733429},{"id":"https://openalex.org/C196843134","wikidata":"https://www.wikidata.org/wiki/Q33196","display_name":"Embryo","level":2,"score":0.5773715376853943},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5233898758888245},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.45145025849342346},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4514176845550537},{"id":"https://openalex.org/C87073359","wikidata":"https://www.wikidata.org/wiki/Q33196","display_name":"Embryogenesis","level":3,"score":0.43246597051620483},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.42583584785461426},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4160422682762146},{"id":"https://openalex.org/C150903083","wikidata":"https://www.wikidata.org/wiki/Q7108","display_name":"Biotechnology","level":1,"score":0.37626832723617554},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3437327444553375}],"mesh":[],"locations_count":7,"locations":[{"id":"doi:10.1186/1756-0381-5-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-5-12","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-5-12","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:22931563","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22931563","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":"BioData mining","raw_type":null},{"id":"pmh:oai:HAL:hal-01189832v1","is_oa":true,"landing_page_url":"https://hal.science/hal-01189832","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":"http://www.biodatamining.org/","raw_type":"Journal articles"},{"id":"pmh:oai:HAL:inserm-02440326v1","is_oa":true,"landing_page_url":"https://www.hal.inserm.fr/inserm-02440326","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":"ISSN: 1756-0381","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:7393b396c5754c3591d964ab20a4374f","is_oa":false,"landing_page_url":"https://doaj.org/article/7393b396c5754c3591d964ab20a4374f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 5, Iss 1, p 12 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2567836","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3563503","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3563503","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3563503","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1756-0381-5-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-5-12","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-5-12","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321770","display_name":"Siberian Branch, Russian Academy of Sciences","ror":"https://ror.org/02frkq021"},{"id":"https://openalex.org/F4320323910","display_name":"Institut National de la Recherche Agronomique","ror":"https://ror.org/01x3gbx83"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2112885819.pdf","grobid_xml":"https://content.openalex.org/works/W2112885819.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1547855212","https://openalex.org/W1622668755","https://openalex.org/W1956559956","https://openalex.org/W1958077162","https://openalex.org/W1974139890","https://openalex.org/W1979567812","https://openalex.org/W1985748545","https://openalex.org/W1986553481","https://openalex.org/W1997094733","https://openalex.org/W2004369047","https://openalex.org/W2006937757","https://openalex.org/W2013856253","https://openalex.org/W2028885049","https://openalex.org/W2031445920","https://openalex.org/W2043748764","https://openalex.org/W2043819822","https://openalex.org/W2043901317","https://openalex.org/W2045106437","https://openalex.org/W2049460839","https://openalex.org/W2057301496","https://openalex.org/W2067274784","https://openalex.org/W2072325907","https://openalex.org/W2079647188","https://openalex.org/W2082029075","https://openalex.org/W2090615247","https://openalex.org/W2098154073","https://openalex.org/W2098412979","https://openalex.org/W2098754388","https://openalex.org/W2099794271","https://openalex.org/W2100963977","https://openalex.org/W2101727078","https://openalex.org/W2105389823","https://openalex.org/W2105469909","https://openalex.org/W2110680515","https://openalex.org/W2118074213","https://openalex.org/W2126276057","https://openalex.org/W2129937015","https://openalex.org/W2133023924","https://openalex.org/W2133075481","https://openalex.org/W2133790733","https://openalex.org/W2135030836","https://openalex.org/W2136804337","https://openalex.org/W2145330293","https://openalex.org/W2150415225","https://openalex.org/W2151875636","https://openalex.org/W2156310826","https://openalex.org/W2164381236","https://openalex.org/W2170165366","https://openalex.org/W2171283231","https://openalex.org/W2171385037","https://openalex.org/W2181179863","https://openalex.org/W2236252949","https://openalex.org/W2323375945","https://openalex.org/W2325227998","https://openalex.org/W2335572799","https://openalex.org/W2410792048","https://openalex.org/W4233415899","https://openalex.org/W4297953593"],"related_works":["https://openalex.org/W4223896405","https://openalex.org/W2059629050","https://openalex.org/W2074740504","https://openalex.org/W3013644380","https://openalex.org/W1996935079","https://openalex.org/W3210243923","https://openalex.org/W2145833061","https://openalex.org/W2258998699","https://openalex.org/W1998405066","https://openalex.org/W2377533390"],"abstract_inverted_index":{"BACKGROUND:":[0],"Since":[1],"processes":[2,135],"in":[3,13,27,53,58,88,122,136,168,284,323,364,375,500,585,640,655,674,721,740,783],"well-known":[4],"model":[5,89,287,302,646],"organisms":[6],"have":[7],"specific":[8],"features":[9],"different":[10,676,686,690],"from":[11,149,301,386,445,454,539,567,689],"those":[12,594],"Bos":[14],"taurus,":[15],"the":[16,65,183,223,239,265,350,371,397,406,418,423,435,470,476,496,540,545,548,579,604,612,651,660,683,732,747,752,756,759],"organism":[17],"under":[18],"study,":[19],"a":[20,32,48,61,246,285,317,328,431,521,568,597,709,716,766,786],"good":[21],"way":[22],"to":[23,39,63,68,156,175,308,344,361,403,416,513,593,611,715,772],"describe":[24],"gene":[25,51,66,86,235,362,497],"regulation":[26,363],"ruminant":[28,365],"embryos":[29,243],"would":[30,200,268],"be":[31,69,146,201,565,781],"species-specific":[33],"consideration":[34],"of":[35,82,113,186,225,231,241,248,299,346,370,393,422,438,447,475,524,547,599,702,711,727,735,746,755,769,785,789],"closely":[36,101,656],"related":[37,102,657],"species":[38,193,658,671,688],"cattle,":[40,59],"sheep":[41,74],"and":[42,103,117,124,171,192,196,203,217,244,296,325,333,377,409,420,441,465,472,485,509,517,620,693,695,705,723,778],"pig.":[43],"However,":[44,182],"as":[45,259,272,274,354,356,531,699,765],"highlighted":[46],"by":[47,482,487,751],"recent":[49,569],"report,":[50],"dictionaries":[52],"pig":[54],"are":[55,96,373],"smaller":[56],"than":[57,729],"bringing":[60],"risk":[62],"reduce":[64],"resources":[67],"mined":[70],"(and":[71],"so":[72,553,738],"for":[73,130,188,213,390,405,555,636],"dictionaries).":[75],"Bioinformatics":[76],"approaches":[77],"that":[78,233,256,319,433,582,648],"allow":[79],"an":[80,291,725],"integration":[81],"available":[83,378,543],"information":[84,159,178,684],"on":[85,160,179,281,294,379,495,685,758,774],"function":[87],"organisms,":[90],"taking":[91],"into":[92],"account":[93],"their":[94,197],"specificity,":[95],"thus":[97,551,780],"needed.":[98],"Besides":[99],"these":[100,190],"biologically":[104],"relevant":[105],"species,":[106,126],"there":[107],"is":[108,194,207,320],"indeed":[109],"much":[110],"more":[111,728],"knowledge":[112,144,219,280],"(i)":[114,150,708],"trophoblast":[115],"proliferation":[116,132,170,704],"differentiation":[118,134],"or":[119,153,163,450,672],"(ii)":[120,172,724],"embryogenesis":[121,174],"human":[123,332,471],"mouse":[125,173,334,473],"which":[127,342],"provides":[128],"opportunities":[129],"reconstructing":[131],"and/or":[133],"other":[137],"mammalian":[138,687],"embryos,":[139],"including":[140,349],"ruminants.":[141],"The":[142,368,490,645,743,761],"necessary":[143],"can":[145,412,763,779],"obtained":[147],"partly":[148],"stem":[151],"cell":[152,169],"cancer":[154],"research":[155],"supply":[157,176],"useful":[158,177,782],"molecular":[161,164],"agents":[162],"interactions":[165],"at":[166,544],"work":[167,773],"embryo":[180,366,561,703],"differentiation.":[181],"total":[184],"number":[185],"publications":[187],"all":[189,387],"topics":[191],"great":[195],"manual":[198,753],"processing":[199,437],"tedious":[202],"time":[204,546],"consuming.":[205],"This":[206,304],"why":[208],"we":[209,228,257,289,336,411,429,589,681],"used":[210,258],"text":[211,215,483],"mining":[212],"automated":[214,218],"analysis":[216],"extraction.":[220],"To":[221,278,426],"evaluate":[222],"quality":[224],"this":[226,679],"\"mining\",":[227],"took":[229],"advantage":[230],"studies":[232,784],"reported":[234],"expression":[236],"profiles":[237],"during":[238,313,559],"elongation":[240,642],"bovine":[242,314,339,477,526,560,586,641],"defined":[245,720],"list":[247,598],"transcription":[249,311,347,503,532,605,637],"factors":[250,312,348,504,606,638],"(or":[251],"TF,":[252],"n":[253],"=":[254],"64)":[255],"biological":[260,394,442,717,790],"\"gold":[261],"standard\".":[262],"When":[263],"successful,":[264],"\"mining\"":[266],"approach":[267,292,305],"identify":[269,309],"them":[270],"all,":[271],"well":[273,355],"novel":[275,310,357],"ones.":[276],"METHODS:":[277],"gain":[279],"molecular-genetic":[282],"regulations":[283],"non":[286],"organism,":[288],"offer":[290],"based":[293,494],"literature-mining":[295],"score":[297,488,491],"arrangement":[298],"data":[300,383,398,414,440,542,776],"organisms.":[303],"was":[306,643,749],"applied":[307],"blastocyst":[315],"elongation,":[316,562],"process":[318],"not":[321,623],"observed":[322],"rodents":[324],"primates.":[326],"As":[327],"result,":[329],"searching":[330],"through":[331],"corpuses,":[335],"identified":[337,506,530,607],"numerous":[338],"homologs,":[340,527],"among":[341,520,670],"11":[343],"14%":[345],"gold":[351,613,718,733],"standard":[352,614,719,734],"TF":[353,358,515,557,581,698,736],"potentially":[359],"important":[360],"development.":[367],"scripts":[369],"workflow":[372,432,633,748,762],"written":[374],"Perl":[376],"demand.":[380],"They":[381,550],"require":[382],"input":[384],"coming":[385],"various":[388],"databases":[389,691],"any":[391],"kind":[392,768],"issue":[395],"once":[396],"has":[399],"been":[400],"prepared":[401],"according":[402],"keywords":[404],"studied":[407],"topic":[408],"species;":[410],"provide":[413],"sample":[415],"illustrate":[417],"use":[419],"functionality":[421],"workflow.":[424],"RESULTS:":[425],"do":[427],"so,":[428],"created":[430],"allowed":[434],"pipeline":[436],"literature":[439],"data,":[443],"extracted":[444],"Web":[446],"Science":[448],"(WoS)":[449],"PubMed":[451],"but":[452,563],"also":[453],"Gene":[455,459],"Expression":[456],"Omnibus":[457],"(GEO),":[458],"Ontology":[460],"(GO),":[461],"Uniprot,":[462],"HomoloGene,":[463],"TcoF-DB":[464,508],"TFe":[466,512],"(TF":[467],"encyclopedia).":[468],"First,":[469],"homologs":[474],"proteins":[478,649],"were":[479,493,505,529,537,667],"selected,":[480],"filtered":[481],"corpora":[484],"arranged":[486],"functions.":[489],"functions":[492],"name":[498],"frequencies":[499],"corpora.":[501],"Then,":[502],"using":[507,511],"double-checked":[510],"characterise":[514],"groups":[516],"families.":[518],"Thus,":[519],"search":[522,635],"space":[523],"18,670":[525],"489":[528,697],"factors.":[533],"Among":[534,603],"them,":[535],"243":[536],"absent":[538],"high-throughput":[541],"study.":[549],"stand":[552],"far":[554,739],"putative":[556],"acting":[558,639],"might":[564],"retrieved":[566],"RNA":[570],"sequencing":[571],"dataset":[572],"(Mamo":[573],"et":[574],"al.":[575],",":[576],"2012).":[577],"Beyond":[578],"246":[580],"appeared":[583],"expressed":[584],"elongating":[587,741],"tissues,":[588],"restricted":[590],"our":[591],"interpretation":[592],"occurring":[595],"within":[596],"50":[600],"top-ranked":[601],"genes.":[602],"therein,":[608],"half":[609,621],"belonged":[610],"(ASCL2,":[615],"c-FOS,":[616],"ETS2,":[617],"GATA3,":[618],"HAND1)":[619],"did":[622],"(ESR1,":[624],"HES1,":[625],"ID2,":[626],"NANOG,":[627],"PHB2,":[628],"TP53,":[629],"STAT3).":[630],"CONCLUSIONS:":[631],"A":[632],"providing":[634],"developed.":[644],"assumed":[647],"sharing":[650],"same":[652,661],"protein":[653,662],"domains":[654],"had":[659],"functionalities,":[663],"even":[664],"if":[665],"they":[666],"differently":[668],"regulated":[669],"involved":[673],"somewhat":[675],"pathways.":[677],"Under":[678],"assumption,":[680],"merged":[682],"(literature":[692],"biology)":[694],"proposed":[696],"potential":[700],"participants":[701],"differentiation,":[706],"with":[707,713],"recall":[710],"95%":[712],"regard":[714],"2011":[722],"extension":[726],"3":[730],"times":[731],"detected":[737],"tissues.":[742],"working":[744],"capacity":[745],"supported":[750],"expertise":[754],"biologists":[757],"results.":[760],"serve":[764],"new":[767],"bioinformatics":[770],"tool":[771],"fused":[775],"sources":[777],"wide":[787],"range":[788],"processes.":[791]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2013,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}