{"id":"https://openalex.org/W2015900846","doi":"https://doi.org/10.1007/s12038-007-0084-2","title":"Incorporating evolution of transcription factor binding sites into annotated alignments","display_name":"Incorporating evolution of transcription factor binding sites into annotated alignments","publication_year":2007,"publication_date":"2007-08-01","ids":{"openalex":"https://openalex.org/W2015900846","doi":"https://doi.org/10.1007/s12038-007-0084-2","mag":"2015900846","pmid":"https://pubmed.ncbi.nlm.nih.gov/17914226"},"language":"en","primary_location":{"id":"doi:10.1007/s12038-007-0084-2","doi":"https://doi.org/10.1007/s12038-007-0084-2","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s12038-007-0084-2","pdf_url":null,"source":{"id":"https://openalex.org/S65171370","display_name":"Journal of Biosciences","issn_l":"0250-5991","issn":["0250-5991","0973-7138"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","jufo-1","medline","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biosciences","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071186147","display_name":"Abha Singh Bais","orcid":"https://orcid.org/0000-0001-5910-1306","observed_orcids":["https://orcid.org/0000-0001-5910-1306"]},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Abha S. Bais","raw_affiliation_strings":["Max Planck Institute for Molecular Genetics, Berlin, Germany. bais@molgen.mpg.de","Max Planck Institute  for Molecular Genetics, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Molecular Genetics, Berlin, Germany. bais@molgen.mpg.de","institution_ids":["https://openalex.org/I4210142260"]},{"raw_affiliation_string":"Max Planck Institute  for Molecular Genetics, Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Steffen Grossmann","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I149899117"]},{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Steffen Grossmann","raw_affiliation_strings":["Max Planck Institute for Molecular Genetics, Berlin, Germany","Max Planck Society"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Molecular Genetics, Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]},{"raw_affiliation_string":"Max Planck Society","institution_ids":["https://openalex.org/I149899117"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009628707","display_name":"Martin Vingron","orcid":"https://orcid.org/0000-0002-1765-4241","observed_orcids":["https://orcid.org/0000-0002-1765-4241","https://orcid.org/0000-0003-1064-3571"]},"institutions":[{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I149899117"]},{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Vingron","raw_affiliation_strings":["Max Planck Institute for Molecular Genetics, Berlin, Germany","Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Molecular Genetics, Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]},{"raw_affiliation_string":"Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society","institution_ids":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5071186147"],"corresponding_institution_ids":["https://openalex.org/I4210142260"],"apc_list":null,"apc_paid":null,"fwci":0.6528,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.62242463,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":93},"biblio":{"volume":"32","issue":"S1","first_page":"841","last_page":"850"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.5443999767303467,"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":0.5443999767303467,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4059999883174896,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.00559999980032444,"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/transcription-factor-binding-sites","display_name":"transcription factor binding sites","score":0.9919999837875366},{"id":"https://openalex.org/keywords/conserved-binding-sites","display_name":"conserved binding sites","score":0.8299999833106995},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"comparative genomics","score":0.6660000085830688},{"id":"https://openalex.org/keywords/binding-site-prediction","display_name":"binding site prediction","score":0.5839999914169312}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.7064467668533325},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5461883544921875},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5407945513725281},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5190406441688538},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4405127465724945},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.41405153274536133},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4059980809688568},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2892177999019623},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2383972704410553},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.208406001329422},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17135131359100342},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.10329079627990723},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D008957","descriptor_name":"Models, Genetic","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":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1007/s12038-007-0084-2","doi":"https://doi.org/10.1007/s12038-007-0084-2","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s12038-007-0084-2","pdf_url":null,"source":{"id":"https://openalex.org/S65171370","display_name":"Journal of Biosciences","issn_l":"0250-5991","issn":["0250-5991","0973-7138"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","jufo-1","medline","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biosciences","raw_type":"journal-article"},{"id":"pmid:17914226","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17914226","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,"listed_in":[],"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":"Journal of biosciences","raw_type":"Comparative Study"},{"id":"pmh:oai:edoc.mpg.de:335500","doi":null,"is_oa":false,"landing_page_url":"http://edoc.mpg.de/335500","pdf_url":null,"source":{"id":"https://openalex.org/S4406922265","display_name":"Max Planck Institute for Plasma Physics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"Journal of Bioscience, v.32, 841-850 (2007)","raw_type":"Article"},{"id":"pmh:oai:pure.mpg.de:item_1584796","doi":null,"is_oa":false,"landing_page_url":"https://hdl.handle.net/11858/00-001M-0000-0010-8198-D","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Bioscience","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1525734744","https://openalex.org/W1984053739","https://openalex.org/W1986841498","https://openalex.org/W1987122345","https://openalex.org/W2001706442","https://openalex.org/W2004232360","https://openalex.org/W2007969038","https://openalex.org/W2019896510","https://openalex.org/W2025665146","https://openalex.org/W2030640865","https://openalex.org/W2050296956","https://openalex.org/W2053276922","https://openalex.org/W2064442647","https://openalex.org/W2074530889","https://openalex.org/W2087064593","https://openalex.org/W2095901576","https://openalex.org/W2097386339","https://openalex.org/W2102159699","https://openalex.org/W2102424972","https://openalex.org/W2109314645","https://openalex.org/W2113833510","https://openalex.org/W2120248467","https://openalex.org/W2134591904","https://openalex.org/W2135722286","https://openalex.org/W2144857133","https://openalex.org/W2149769193","https://openalex.org/W2151907070","https://openalex.org/W2157076973","https://openalex.org/W2160659074","https://openalex.org/W2166898290","https://openalex.org/W2593075177","https://openalex.org/W3214380909","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W7140240753","https://openalex.org/W6887594516","https://openalex.org/W2095901576","https://openalex.org/W2103183338","https://openalex.org/W7096189933","https://openalex.org/W2162836426","https://openalex.org/W2109314645","https://openalex.org/W2171252918","https://openalex.org/W2026074998","https://openalex.org/W2101133358"],"abstract_inverted_index":null,"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}