{"id":"https://openalex.org/W2170449011","doi":"https://doi.org/10.1093/bioinformatics/bts400","title":"Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements","display_name":"Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements","publication_year":2012,"publication_date":"2012-09-03","ids":{"openalex":"https://openalex.org/W2170449011","doi":"https://doi.org/10.1093/bioinformatics/bts400","mag":"2170449011","pmid":"https://pubmed.ncbi.nlm.nih.gov/22962458"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts400","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts400","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/i395/48882881/bioinformatics_28_18_i395.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/28/18/i395/48882881/bioinformatics_28_18_i395.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008327195","display_name":"Slavica Dimitrieva","orcid":"https://orcid.org/0000-0002-0043-2677"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Slavica Dimitrieva","raw_affiliation_strings":["1 Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL)","2 Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"1 Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL)","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"2 Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103270230","display_name":"Philipp B\u00fccher","orcid":"https://orcid.org/0000-0003-4824-885X"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Philipp Bucher","raw_affiliation_strings":["1 Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL)","2 Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"1 Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL)","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"2 Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5008327195"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I5124864"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9412,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.74682261,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"28","issue":"18","first_page":"i395","last_page":"i401"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994000196456909,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7248852849006653},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.650489330291748},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5976145267486572},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5755307078361511},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5182628631591797},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.49305078387260437},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.4773143231868744},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43328022956848145},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.36772072315216064}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7248852849006653},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.650489330291748},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5976145267486572},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5755307078361511},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5182628631591797},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.49305078387260437},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.4773143231868744},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43328022956848145},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.36772072315216064},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005399","descriptor_name":"Fishes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005399","descriptor_name":"Fishes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005399","descriptor_name":"Fishes","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D007438","descriptor_name":"Introns","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D050437","descriptor_name":"Genes, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050437","descriptor_name":"Genes, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050437","descriptor_name":"Genes, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/bts400","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts400","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/i395/48882881/bioinformatics_28_18_i395.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:22962458","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22962458","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:doc.rero.ch:303674","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400148","display_name":"reroDoc Digital Library","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:europepmc.org:2440699","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3436827","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:infoscience.epfl.ch:181680","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/181680","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:infoscience.tind.io:181680","is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/85999","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"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":"","raw_type":"research article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts400","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts400","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/i395/48882881/bioinformatics_28_18_i395.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":"Life in Land","score":0.6000000238418579,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G4790295624","display_name":"Analysis and classification of conserved DNA elements by whole genome multiple alignment","funder_award_id":"120719","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2170449011.pdf","grobid_xml":"https://content.openalex.org/works/W2170449011.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1531954825","https://openalex.org/W1536270671","https://openalex.org/W1971846931","https://openalex.org/W2001233190","https://openalex.org/W2033555181","https://openalex.org/W2057545775","https://openalex.org/W2057885377","https://openalex.org/W2057912154","https://openalex.org/W2067410483","https://openalex.org/W2100990361","https://openalex.org/W2107717979","https://openalex.org/W2110481384","https://openalex.org/W2116251070","https://openalex.org/W2118910836","https://openalex.org/W2120030937","https://openalex.org/W2125539728","https://openalex.org/W2127640118","https://openalex.org/W2129509542","https://openalex.org/W2160856280","https://openalex.org/W4210450218","https://openalex.org/W4252706339"],"related_works":["https://openalex.org/W4388014327","https://openalex.org/W2115382138","https://openalex.org/W1979058569","https://openalex.org/W1883409887","https://openalex.org/W2367076742","https://openalex.org/W1968617170","https://openalex.org/W2077068888","https://openalex.org/W2080410528","https://openalex.org/W2144958703","https://openalex.org/W2529820324"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4,8],"Bioinformatics":[5],"online":[6],"and":[7],"http://ccg.vital-it.ch/ucne/":[9]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}