{"id":"https://openalex.org/W2152071686","doi":"https://doi.org/10.1093/bioinformatics/btp434","title":"Motif discovery and motif finding from genome-mapped DNase footprint data","display_name":"Motif discovery and motif finding from genome-mapped DNase footprint data","publication_year":2009,"publication_date":"2009-07-15","ids":{"openalex":"https://openalex.org/W2152071686","doi":"https://doi.org/10.1093/bioinformatics/btp434","mag":"2152071686","pmid":"https://pubmed.ncbi.nlm.nih.gov/19605419"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp434","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp434","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062435496","display_name":"Ivan V. Kulakovskiy","orcid":"https://orcid.org/0000-0002-6554-8128"},"institutions":[{"id":"https://openalex.org/I4210164401","display_name":"Sidney Kimmel Comprehensive Cancer Center","ror":"https://ror.org/05m5b8x20","country_code":"US","type":"facility","lineage":["https://openalex.org/I2799853436","https://openalex.org/I4210164401"]},{"id":"https://openalex.org/I100098275","display_name":"Engelhardt Institute of Molecular Biology","ror":"https://ror.org/027hwkg23","country_code":"RU","type":"facility","lineage":["https://openalex.org/I100098275","https://openalex.org/I1313323035","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I1313323035","display_name":"Russian Academy of Sciences","ror":"https://ror.org/05qrfxd25","country_code":"RU","type":"funder","lineage":["https://openalex.org/I1313323035"]}],"countries":["RU","US"],"is_corresponding":true,"raw_author_name":"Ivan V. Kulakovskiy","raw_affiliation_strings":["1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, 2State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, 1st Dorozhny proezd, 1, Moscow 117545, Russia and 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA"],"affiliations":[{"raw_affiliation_string":"1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, 2State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, 1st Dorozhny proezd, 1, Moscow 117545, Russia and 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA","institution_ids":["https://openalex.org/I1313323035","https://openalex.org/I4210164401","https://openalex.org/I100098275"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080546333","display_name":"Alexander V. Favorov","orcid":"https://orcid.org/0000-0003-2595-1091"},"institutions":[{"id":"https://openalex.org/I4210164401","display_name":"Sidney Kimmel Comprehensive Cancer Center","ror":"https://ror.org/05m5b8x20","country_code":"US","type":"facility","lineage":["https://openalex.org/I2799853436","https://openalex.org/I4210164401"]},{"id":"https://openalex.org/I100098275","display_name":"Engelhardt Institute of Molecular Biology","ror":"https://ror.org/027hwkg23","country_code":"RU","type":"facility","lineage":["https://openalex.org/I100098275","https://openalex.org/I1313323035","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I1313323035","display_name":"Russian Academy of Sciences","ror":"https://ror.org/05qrfxd25","country_code":"RU","type":"funder","lineage":["https://openalex.org/I1313323035"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Alexander V. Favorov","raw_affiliation_strings":["1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, 2State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, 1st Dorozhny proezd, 1, Moscow 117545, Russia and 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA"],"affiliations":[{"raw_affiliation_string":"1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, 2State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, 1st Dorozhny proezd, 1, Moscow 117545, Russia and 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA","institution_ids":["https://openalex.org/I1313323035","https://openalex.org/I4210164401","https://openalex.org/I100098275"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004606374","display_name":"Vsevolod J. Makeev","orcid":"https://orcid.org/0000-0001-9405-9748"},"institutions":[{"id":"https://openalex.org/I1313323035","display_name":"Russian Academy of Sciences","ror":"https://ror.org/05qrfxd25","country_code":"RU","type":"funder","lineage":["https://openalex.org/I1313323035"]},{"id":"https://openalex.org/I100098275","display_name":"Engelhardt Institute of Molecular Biology","ror":"https://ror.org/027hwkg23","country_code":"RU","type":"facility","lineage":["https://openalex.org/I100098275","https://openalex.org/I1313323035","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I4210164401","display_name":"Sidney Kimmel Comprehensive Cancer Center","ror":"https://ror.org/05m5b8x20","country_code":"US","type":"facility","lineage":["https://openalex.org/I2799853436","https://openalex.org/I4210164401"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Vsevolod J. Makeev","raw_affiliation_strings":["1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, 2State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, 1st Dorozhny proezd, 1, Moscow 117545, Russia and 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA"],"affiliations":[{"raw_affiliation_string":"1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, 2State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, 1st Dorozhny proezd, 1, Moscow 117545, Russia and 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA","institution_ids":["https://openalex.org/I1313323035","https://openalex.org/I4210164401","https://openalex.org/I100098275"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5062435496"],"corresponding_institution_ids":["https://openalex.org/I100098275","https://openalex.org/I1313323035","https://openalex.org/I4210164401"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9186,"has_fulltext":false,"cited_by_count":38,"citation_normalized_percentile":{"value":0.74227193,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"25","issue":"18","first_page":"2318","last_page":"2325"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9976999759674072,"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/motif","display_name":"Motif (music)","score":0.7054514288902283},{"id":"https://openalex.org/keywords/overfitting","display_name":"Overfitting","score":0.682386040687561},{"id":"https://openalex.org/keywords/footprinting","display_name":"Footprinting","score":0.6499026417732239},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5617659091949463},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5320032238960266},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4736389219760895},{"id":"https://openalex.org/keywords/dna-footprinting","display_name":"DNA footprinting","score":0.44600051641464233},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44318878650665283},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41372695565223694},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.38016146421432495},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2896616458892822},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2747266888618469},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.274583637714386},{"id":"https://openalex.org/keywords/dna-binding-protein","display_name":"DNA-binding protein","score":0.11578521132469177}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7054514288902283},{"id":"https://openalex.org/C22019652","wikidata":"https://www.wikidata.org/wiki/Q331309","display_name":"Overfitting","level":3,"score":0.682386040687561},{"id":"https://openalex.org/C2778021871","wikidata":"https://www.wikidata.org/wiki/Q648006","display_name":"Footprinting","level":4,"score":0.6499026417732239},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5617659091949463},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5320032238960266},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4736389219760895},{"id":"https://openalex.org/C22427896","wikidata":"https://www.wikidata.org/wiki/Q4493748","display_name":"DNA footprinting","level":5,"score":0.44600051641464233},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44318878650665283},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41372695565223694},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38016146421432495},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2896616458892822},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2747266888618469},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.274583637714386},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.11578521132469177},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"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":"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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003851","descriptor_name":"Deoxyribonucleases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003851","descriptor_name":"Deoxyribonucleases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003851","descriptor_name":"Deoxyribonucleases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btp434","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp434","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19605419","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19605419","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W109379300","https://openalex.org/W643497748","https://openalex.org/W1483132463","https://openalex.org/W1564972078","https://openalex.org/W1967085530","https://openalex.org/W1989080074","https://openalex.org/W2005281324","https://openalex.org/W2019673480","https://openalex.org/W2021492982","https://openalex.org/W2030823670","https://openalex.org/W2034206030","https://openalex.org/W2045104360","https://openalex.org/W2046374070","https://openalex.org/W2058552632","https://openalex.org/W2059699217","https://openalex.org/W2064442647","https://openalex.org/W2069328936","https://openalex.org/W2071735418","https://openalex.org/W2074703985","https://openalex.org/W2079321730","https://openalex.org/W2079450159","https://openalex.org/W2087892194","https://openalex.org/W2095718954","https://openalex.org/W2099800150","https://openalex.org/W2101234997","https://openalex.org/W2101835893","https://openalex.org/W2102159699","https://openalex.org/W2102998538","https://openalex.org/W2120062331","https://openalex.org/W2130396264","https://openalex.org/W2135030836","https://openalex.org/W2141354959","https://openalex.org/W2153550523","https://openalex.org/W2158266834","https://openalex.org/W2161888246","https://openalex.org/W2164814636","https://openalex.org/W2170628952","https://openalex.org/W2519703809","https://openalex.org/W3016843226"],"related_works":["https://openalex.org/W2035953360","https://openalex.org/W2359735815","https://openalex.org/W1488292500","https://openalex.org/W4200378786","https://openalex.org/W2019624648","https://openalex.org/W2055124487","https://openalex.org/W588807030","https://openalex.org/W3107479402","https://openalex.org/W198962041","https://openalex.org/W1528913684"],"abstract_inverted_index":{"Software":[0],"and":[1],"the":[2],"collection":[3],"of":[4],"regulatory":[5],"motifs":[6],"are":[7],"freely":[8],"available":[9],"at":[10],"http://line.imb.ac.ru/DMMPMM.":[11]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
