{"id":"https://openalex.org/W2898336517","doi":"https://doi.org/10.1093/bioinformatics/bty902","title":"ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles","display_name":"ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles","publication_year":2018,"publication_date":"2018-10-25","ids":{"openalex":"https://openalex.org/W2898336517","doi":"https://doi.org/10.1093/bioinformatics/bty902","mag":"2898336517","pmid":"https://pubmed.ncbi.nlm.nih.gov/30364927"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty902","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty902","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1974/48935056/bioinformatics_35_11_1974.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1974/48935056/bioinformatics_35_11_1974.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079804568","display_name":"Tiago C. Silva","orcid":"https://orcid.org/0000-0003-1343-6850"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]},{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]}],"countries":["BR","US"],"is_corresponding":false,"raw_author_name":"Tiago C Silva","raw_affiliation_strings":["Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA","Department of Genetics, Ribeir\u00e3o Preto Medical School, University of S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Department of Genetics, Ribeir\u00e3o Preto Medical School, University of S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil","institution_ids":["https://openalex.org/I17974374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015262217","display_name":"Simon G. Coetzee","orcid":"https://orcid.org/0000-0003-4267-5930"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Simon G Coetzee","raw_affiliation_strings":["Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072186475","display_name":"Nicole Gull","orcid":null},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicole Gull","raw_affiliation_strings":["Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111967552","display_name":"Lijing Yao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lijing Yao","raw_affiliation_strings":["Bioinformatics Research & Early Development, Roche Sequencing Solutions, Belmont, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research & Early Development, Roche Sequencing Solutions, Belmont, CA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050826378","display_name":"Dennis J. Hazelett","orcid":"https://orcid.org/0000-0003-0749-9935"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dennis J Hazelett","raw_affiliation_strings":["Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078471371","display_name":"Houtan Noushmehr","orcid":"https://orcid.org/0000-0003-4051-8114"},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]},{"id":"https://openalex.org/I2803043754","display_name":"Henry Ford Hospital","ror":"https://ror.org/0193sb042","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I154057602","https://openalex.org/I2803043754"]}],"countries":["BR","US"],"is_corresponding":false,"raw_author_name":"Houtan Noushmehr","raw_affiliation_strings":["Department of Genetics, Ribeir\u00e3o Preto Medical School, University of S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil","Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Ribeir\u00e3o Preto Medical School, University of S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil","institution_ids":["https://openalex.org/I17974374"]},{"raw_affiliation_string":"Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA","institution_ids":["https://openalex.org/I2803043754"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022303526","display_name":"De\u2010Chen Lin","orcid":"https://orcid.org/0000-0002-1951-367X"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"De-Chen Lin","raw_affiliation_strings":["Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032108534","display_name":"Benjamin P. Berman","orcid":"https://orcid.org/0000-0002-2099-9005"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Benjamin P Berman","raw_affiliation_strings":["Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA","Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5022303526","https://openalex.org/A5032108534"],"corresponding_institution_ids":["https://openalex.org/I1282927834"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.0827,"has_fulltext":true,"cited_by_count":161,"citation_normalized_percentile":{"value":0.95083971,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"35","issue":"11","first_page":"1974","last_page":"1977"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13426","display_name":"Kruppel-like factors research","score":0.40070000290870667,"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/T13426","display_name":"Kruppel-like factors research","score":0.40070000290870667,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.1678999960422516,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.10459999740123749,"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/bioconductor","display_name":"Bioconductor","score":0.962242603302002},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.7566050887107849},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.7118258476257324},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5494076013565063},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5322116613388062},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.5093456506729126},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.49489325284957886},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4709908366203308},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4268912672996521},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4206130802631378},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.251065194606781}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.962242603302002},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7566050887107849},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.7118258476257324},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5494076013565063},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5322116613388062},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.5093456506729126},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.49489325284957886},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4709908366203308},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4268912672996521},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4206130802631378},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.251065194606781}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bty902","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty902","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1974/48935056/bioinformatics_35_11_1974.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30364927","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30364927","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:6546131","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6546131","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:002983461","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1093/bioinformatics/bty902","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"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":"reponame:Reposit\u00f3rio Institucional da USP (Biblioteca Digital da Produ\u00e7\u00e3o Intelectual)","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty902","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty902","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1974/48935056/bioinformatics_35_11_1974.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.7699999809265137,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G2102285915","display_name":null,"funder_award_id":"R01CA190182","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3175236564","display_name":null,"funder_award_id":"2015/07925-5","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G4090764117","display_name":null,"funder_award_id":"R01CA190182","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4189589827","display_name":null,"funder_award_id":"2016/01389-7","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G4402799499","display_name":null,"funder_award_id":"2015/","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G5494573714","display_name":null,"funder_award_id":"1U24CA210969","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7240922459","display_name":null,"funder_award_id":"1U01CA184826","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320313996","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90"},{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2898336517.pdf","grobid_xml":"https://content.openalex.org/works/W2898336517.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1908864745","https://openalex.org/W1984562049","https://openalex.org/W2011463791","https://openalex.org/W2034032177","https://openalex.org/W2038838073","https://openalex.org/W2073759231","https://openalex.org/W2097626332","https://openalex.org/W2119393622","https://openalex.org/W2131050852","https://openalex.org/W2167996825","https://openalex.org/W2230320310","https://openalex.org/W2286341552","https://openalex.org/W2343269778","https://openalex.org/W2521492299","https://openalex.org/W2551771259","https://openalex.org/W2593831845","https://openalex.org/W2739552221","https://openalex.org/W2766463108","https://openalex.org/W2767572999","https://openalex.org/W2767749844","https://openalex.org/W2785792383","https://openalex.org/W2795867722","https://openalex.org/W2951303652","https://openalex.org/W2952626686"],"related_works":["https://openalex.org/W2898448758","https://openalex.org/W2902329290","https://openalex.org/W2802827720","https://openalex.org/W2139872319","https://openalex.org/W2052355316","https://openalex.org/W2046964473","https://openalex.org/W2107880877","https://openalex.org/W2151182744","https://openalex.org/W2024490794","https://openalex.org/W1998349112"],"abstract_inverted_index":{"MOTIVATION:":[0],"DNA":[1],"methylation":[2,47],"has":[3],"been":[4],"used":[5],"to":[6,84],"identify":[7],"functional":[8],"changes":[9],"at":[10,126,134],"transcriptional":[11],"enhancers":[12],"and":[13,20,48,78,98,102,109],"other":[14,21],"cis-regulatory":[15],"modules":[16],"(CRMs)":[17],"in":[18,111],"tumors":[19],"disease":[22],"tissues.":[23],"Our":[24],"R/Bioconductor":[25,124],"package":[26,125],"ELMER":[27,67,118],"(Enhancer":[28],"Linking":[29],"by":[30,44],"Methylation/Expression":[31],"Relationships)":[32],"provides":[33,69],"a":[34,61,79],"systematic":[35],"approach":[36],"that":[37,68,91],"reconstructs":[38],"altered":[39],"gene":[40,49],"regulatory":[41],"networks":[42],"(GRNs)":[43],"combining":[45],"enhancer":[46],"expression":[50],"data":[51,131],"derived":[52],"from":[53],"the":[54],"same":[55],"sample":[56,87],"set.":[57],"RESULTS:":[58],"We":[59,89],"present":[60],"completely":[62],"revised":[63],"version":[64],"2":[65],"of":[66],"numerous":[70],"new":[71,80],"features":[72],"including":[73],"an":[74,123],"optional":[75],"web-based":[76],"interface":[77],"Supervised":[81,92],"Analysis":[82],"mode":[83,93],"use":[85],"pre-defined":[86],"groupings.":[88],"show":[90],"significantly":[94],"increases":[95],"statistical":[96],"power":[97],"identifies":[99],"additional":[100],"GRNs":[101],"associated":[103],"Master":[104],"Regulators,":[105],"such":[106],"as":[107,122],"SOX11":[108],"KLF5":[110],"Basal-like":[112],"breast":[113],"cancer.":[114],"AVAILABILITY":[115],"AND":[116],"IMPLEMENTATION:":[117],"v.2":[119],"is":[120],"available":[121,133],"http://bioconductor.org/packages/ELMER/.":[127],"SUPPLEMENTARY":[128],"INFORMATION:":[129],"Supplementary":[130],"are":[132],"Bioinformatics":[135],"online.":[136]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":37},{"year":2023,"cited_by_count":34},{"year":2022,"cited_by_count":27},{"year":2021,"cited_by_count":18},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":11},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-20T22:02:38.213706","created_date":"2025-10-10T00:00:00"}
