{"id":"https://openalex.org/W2016757285","doi":"https://doi.org/10.1371/journal.pcbi.1003449","title":"Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data","display_name":"Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data","publication_year":2014,"publication_date":"2014-01-30","ids":{"openalex":"https://openalex.org/W2016757285","doi":"https://doi.org/10.1371/journal.pcbi.1003449","mag":"2016757285","pmid":"https://pubmed.ncbi.nlm.nih.gov/24499934"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003449","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003449","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003449&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003449&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076325815","display_name":"Geetu Tuteja","orcid":"https://orcid.org/0000-0002-8726-9955"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Geetu Tuteja","raw_affiliation_strings":["Department of Developmental Biology, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Developmental Biology, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110779024","display_name":"Karen Betancourt Moreira","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karen Betancourt Moreira","raw_affiliation_strings":["Department of Developmental Biology, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Developmental Biology, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033373582","display_name":"Tisha Chung","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tisha Chung","raw_affiliation_strings":["Department of Developmental Biology, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Developmental Biology, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032529120","display_name":"Jenny Chen","orcid":"https://orcid.org/0000-0002-6664-2597"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jenny Chen","raw_affiliation_strings":["Biomedical Informatics Program, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Program, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083782077","display_name":"Aaron M. Wenger","orcid":"https://orcid.org/0000-0003-1183-0432"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron M. Wenger","raw_affiliation_strings":["Department of Computer Science, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085525898","display_name":"Gill Bejerano","orcid":"https://orcid.org/0000-0001-5179-3635"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gill Bejerano","raw_affiliation_strings":["Department of Developmental Biology, Stanford University, Stanford, California, United States of America ; Department of Computer Science, Stanford University, Stanford, California, United States of America","Department of Computer Science, Stanford University, Stanford, California, United States of America","Department of Developmental Biology, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Developmental Biology, Stanford University, Stanford, California, United States of America ; Department of Computer Science, Stanford University, Stanford, California, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Developmental Biology, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5085525898"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.4278,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.63189341,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"10","issue":"1","first_page":"e1003449","last_page":"e1003449"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9977999925613403,"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/enhancer","display_name":"Enhancer","score":0.9152756333351135},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.716758131980896},{"id":"https://openalex.org/keywords/epigenomics","display_name":"Epigenomics","score":0.6359447240829468},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6298828721046448},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5204046964645386},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.44339919090270996},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.38220158219337463},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.30932173132896423},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.19477146863937378}],"concepts":[{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.9152756333351135},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.716758131980896},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.6359447240829468},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6298828721046448},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5204046964645386},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.44339919090270996},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38220158219337463},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.30932173132896423},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.19477146863937378}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010920","descriptor_name":"Placenta","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D010920","descriptor_name":"Placenta","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D010920","descriptor_name":"Placenta","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011247","descriptor_name":"Pregnancy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011247","descriptor_name":"Pregnancy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011247","descriptor_name":"Pregnancy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014327","descriptor_name":"Trophoblasts","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D014327","descriptor_name":"Trophoblasts","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D014327","descriptor_name":"Trophoblasts","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1003449","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003449","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003449&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:24499934","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24499934","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:doaj.org/article:0c75bcd8e1ce41ae845f7e9346db71f9","is_oa":true,"landing_page_url":"https://doaj.org/article/0c75bcd8e1ce41ae845f7e9346db71f9","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 10, Iss 1, p e1003449 (2014)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2898376","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3907286","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/919631","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Automated_Discovery_of_Tissue_Targeting_Enhancers_and_Transcription_Factors_from_Binding_Motif_and_Gene_Function_Data_/919631","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003449","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003449","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003449&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306960","display_name":"A.P. Giannini Foundation","ror":"https://ror.org/01e3cnp62"},{"id":"https://openalex.org/F4320311186","display_name":"Giannini Foundation of Agricultural Economics","ror":"https://ror.org/00pjdza24"},{"id":"https://openalex.org/F4320332622","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2016757285.pdf","grobid_xml":"https://content.openalex.org/works/W2016757285.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1964963969","https://openalex.org/W1965181820","https://openalex.org/W1967071065","https://openalex.org/W1975751233","https://openalex.org/W1979594866","https://openalex.org/W1991485331","https://openalex.org/W1999810025","https://openalex.org/W2001848617","https://openalex.org/W2006118118","https://openalex.org/W2028875315","https://openalex.org/W2030613990","https://openalex.org/W2031333605","https://openalex.org/W2042930277","https://openalex.org/W2045362835","https://openalex.org/W2047405190","https://openalex.org/W2048350099","https://openalex.org/W2056916102","https://openalex.org/W2058250593","https://openalex.org/W2069592147","https://openalex.org/W2070806491","https://openalex.org/W2072994066","https://openalex.org/W2078059415","https://openalex.org/W2079501676","https://openalex.org/W2083906966","https://openalex.org/W2084100632","https://openalex.org/W2088934405","https://openalex.org/W2094382141","https://openalex.org/W2100978247","https://openalex.org/W2102130285","https://openalex.org/W2110093634","https://openalex.org/W2114436231","https://openalex.org/W2121271640","https://openalex.org/W2128295200","https://openalex.org/W2134874840","https://openalex.org/W2135030836","https://openalex.org/W2136354344","https://openalex.org/W2142570576","https://openalex.org/W2155066685","https://openalex.org/W2160856280","https://openalex.org/W2161849959","https://openalex.org/W2163378821","https://openalex.org/W2167173797","https://openalex.org/W2168867830","https://openalex.org/W3143443079","https://openalex.org/W7073635527"],"related_works":["https://openalex.org/W2113330652","https://openalex.org/W2061914098","https://openalex.org/W4393004084","https://openalex.org/W2118646732","https://openalex.org/W4387565139","https://openalex.org/W4303699336","https://openalex.org/W2152841149","https://openalex.org/W2586783543","https://openalex.org/W4387598842","https://openalex.org/W2973036402"],"abstract_inverted_index":{"Identifying":[0],"enhancers":[1,31,43],"regulating":[2],"gene":[3,57],"expression":[4],"remains":[5,25],"an":[6],"important":[7],"and":[8,107,115,144,179],"challenging":[9],"task.":[10],"While":[11],"recent":[12,139],"sequencing-based":[13],"methods":[14],"provide":[15],"epigenomic":[16,140],"characteristics":[17],"that":[18,161],"correlate":[19],"well":[20,137],"with":[21,55,89,138],"enhancer":[22],"activity,":[23],"it":[24,168],"onerous":[26],"to":[27,40,61,100,169],"comprehensively":[28],"identify":[29,41,62],"all":[30],"across":[32],"development.":[33],"Here":[34],"we":[35,49,103,159],"introduce":[36],"a":[37,69],"computational":[38],"framework":[39],"tissue-specific":[42],"evolving":[44],"under":[45],"purifying":[46],"selection.":[47],"First,":[48],"incorporate":[50],"high-confidence":[51],"binding":[52,80],"site":[53],"predictions":[54,135],"target":[56],"functional":[58],"enrichment":[59],"analysis":[60],"transcription":[63],"factors":[64],"(TFs)":[65],"likely":[66],"functioning":[67],"in":[68,112,131,142],"particular":[70],"context.":[71],"We":[72],"then":[73],"search":[74],"the":[75,101],"genome":[76],"for":[77,82],"clusters":[78],"of":[79,93],"sites":[81],"these":[83],"TFs,":[84],"overcoming":[85],"previous":[86],"constraints":[87],"associated":[88],"biased":[90],"manual":[91],"curation":[92],"TFs":[94,111],"or":[95],"enhancers.":[96,120],"Applying":[97],"our":[98,149,162],"method":[99,163],"placenta,":[102],"find":[104],"33":[105],"known":[106],"implicate":[108],"17":[109],"novel":[110],"placental":[113,132],"function,":[114],"discover":[116],"2,216":[117],"putative":[118],"placenta":[119],"Using":[121],"luciferase":[122],"reporter":[123],"assays,":[124],"31/36":[125],"(86%)":[126],"tested":[127,154],"candidates":[128],"drive":[129],"activity":[130],"cells.":[133],"Our":[134],"agree":[136],"data":[141],"human":[143],"mouse,":[145],"yet":[146],"over":[147],"half":[148],"loci,":[150],"including":[151],"7/8":[152],"(87%)":[153],"regions,":[155],"are":[156],"novel.":[157],"Finally,":[158],"establish":[160],"is":[164],"generalizable":[165],"by":[166],"applying":[167],"5":[170],"additional":[171],"tissues:":[172],"heart,":[173],"pancreas,":[174],"blood":[175],"vessel,":[176],"bone":[177],"marrow,":[178],"liver.":[180]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2015,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
