{"id":"https://openalex.org/W1903655941","doi":"https://doi.org/10.1186/s12859-015-0666-1","title":"Reliable scaling of position weight matrices for binding strength comparisons between transcription factors","display_name":"Reliable scaling of position weight matrices for binding strength comparisons between transcription factors","publication_year":2015,"publication_date":"2015-08-19","ids":{"openalex":"https://openalex.org/W1903655941","doi":"https://doi.org/10.1186/s12859-015-0666-1","mag":"1903655941","pmid":"https://pubmed.ncbi.nlm.nih.gov/26289072"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0666-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0666-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0666-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0666-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101453685","display_name":"Xiaoyan Ma","orcid":"https://orcid.org/0000-0003-1943-9809"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Xiaoyan Ma","raw_affiliation_strings":["Cambridge Systems Biology Center, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK. xm227@cam.ac.uk","Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK. xm227@cam.ac.uk","Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cambridge Systems Biology Center, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK. xm227@cam.ac.uk","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK. xm227@cam.ac.uk","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008944055","display_name":"Daphne Ezer","orcid":"https://orcid.org/0000-0002-1685-6909"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Daphne Ezer","raw_affiliation_strings":["Cambridge Systems Biology Center, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK. de276@cam.ac.uk","Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK. de276@cam.ac.uk","Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cambridge Systems Biology Center, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK. de276@cam.ac.uk","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK. de276@cam.ac.uk","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101861735","display_name":"Carmen Navarro","orcid":"https://orcid.org/0000-0001-5438-9654"},"institutions":[{"id":"https://openalex.org/I173304897","display_name":"Universidad de Granada","ror":"https://ror.org/04njjy449","country_code":"ES","type":"education","lineage":["https://openalex.org/I173304897"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Carmen Navarro","raw_affiliation_strings":["Cambridge Systems Biology Center, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK. cnluzon@decsai.ugr.es","Department of Computer Science and Artificial Intelligence, University of Granada, Periodista Daniel Saucedo Aranda, Granada, Spain. cnluzon@decsai.ugr.es","Cambridge Systems Biology Center, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cambridge Systems Biology Center, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK. cnluzon@decsai.ugr.es","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Computer Science and Artificial Intelligence, University of Granada, Periodista Daniel Saucedo Aranda, Granada, Spain. cnluzon@decsai.ugr.es","institution_ids":["https://openalex.org/I173304897"]},{"raw_affiliation_string":"Cambridge Systems Biology Center, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055348125","display_name":"Boris Adryan","orcid":"https://orcid.org/0000-0003-4588-7867"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Boris Adryan","raw_affiliation_strings":["Cambridge Systems Biology Center, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK. ba255@cam.ac.uk","Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK. ba255@cam.ac.uk","Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cambridge Systems Biology Center, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK. ba255@cam.ac.uk","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK. ba255@cam.ac.uk","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK","institution_ids":["https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5055348125"],"corresponding_institution_ids":["https://openalex.org/I241749"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5912,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.67900918,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"16","issue":"1","first_page":"265","last_page":"265"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9970999956130981,"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":0.9970999956130981,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.00039999998989515007,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.0003000000142492354,"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","display_name":"Transcription factor","score":0.7511259913444519},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5926624536514282},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.581186056137085},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49975109100341797},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.48506322503089905},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.4758027493953705},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.455879807472229},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4525739550590515},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.41375264525413513},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3590368628501892},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3432905673980713},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.2574719786643982},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19777575135231018},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.10938376188278198}],"concepts":[{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.7511259913444519},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5926624536514282},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.581186056137085},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49975109100341797},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.48506322503089905},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4758027493953705},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.455879807472229},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4525739550590515},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41375264525413513},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3590368628501892},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3432905673980713},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.2574719786643982},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19777575135231018},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10938376188278198},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-015-0666-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0666-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0666-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26289072","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26289072","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:digibug.ugr.es:10481/77971","is_oa":true,"landing_page_url":"https://hdl.handle.net/10481/77971","pdf_url":null,"source":{"id":"https://openalex.org/S4306400567","display_name":"Institutional Repository of the University of Granada (University of Granada)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173304897","host_organization_name":"Universidad de Granada","host_organization_lineage":["https://openalex.org/I173304897"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:3520908","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4545934","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:www.repository.cam.ac.uk:1810/260460","is_oa":true,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/260460","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"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":"Article"},{"id":"doi:10.17863/cam.4694","is_oa":true,"landing_page_url":"https://doi.org/10.17863/cam.4694","pdf_url":null,"source":{"id":"https://openalex.org/S7407050737","display_name":"Apollo","issn_l":null,"issn":null,"is_oa":false,"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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"JournalArticle"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0666-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0666-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0666-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8700000047683716,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G8596770582","display_name":null,"funder_award_id":"ID0EN6AE545","funder_id":"https://openalex.org/F4320320006","funder_display_name":"Royal Society"}],"funders":[{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320335160","display_name":"Direcci\u00f3n General de Investigaci\u00f3n Cient\u00edfica y T\u00e9cnica","ror":"https://ror.org/034900433"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1903655941.pdf","grobid_xml":"https://content.openalex.org/works/W1903655941.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1498410508","https://openalex.org/W1562374859","https://openalex.org/W1964733653","https://openalex.org/W1971617105","https://openalex.org/W1975036436","https://openalex.org/W1975992663","https://openalex.org/W1976169445","https://openalex.org/W1980825481","https://openalex.org/W1987122345","https://openalex.org/W1989800873","https://openalex.org/W2008051478","https://openalex.org/W2008226163","https://openalex.org/W2026690931","https://openalex.org/W2028200156","https://openalex.org/W2038282326","https://openalex.org/W2042556311","https://openalex.org/W2055228856","https://openalex.org/W2056707311","https://openalex.org/W2079450159","https://openalex.org/W2094814523","https://openalex.org/W2099035403","https://openalex.org/W2101623680","https://openalex.org/W2116696234","https://openalex.org/W2118215072","https://openalex.org/W2127021450","https://openalex.org/W2133335149","https://openalex.org/W2135030836","https://openalex.org/W2140754446","https://openalex.org/W2142410561","https://openalex.org/W2146393977","https://openalex.org/W2149769193","https://openalex.org/W2149827510","https://openalex.org/W2154447604","https://openalex.org/W2157424463","https://openalex.org/W2160838409","https://openalex.org/W2165102934","https://openalex.org/W4251165697"],"related_works":["https://openalex.org/W2036927633","https://openalex.org/W2153561273","https://openalex.org/W2152664145","https://openalex.org/W2079197459","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W4233525429","https://openalex.org/W2090848290","https://openalex.org/W2146393977","https://openalex.org/W2146884677"],"abstract_inverted_index":{"BACKGROUND:":[0],"Scoring":[1],"DNA":[2,169],"sequences":[3],"against":[4],"Position":[5],"Weight":[6],"Matrices":[7],"(PWMs)":[8],"is":[9,96],"a":[10,34,130,137,149],"widely":[11],"adopted":[12],"method":[13,174],"to":[14,78,88,116,125,145,156,190,208],"identify":[15,79],"putative":[16],"transcription":[17,36,49,102,151,163,185,217],"factor":[18,37,103,164,218],"binding":[19,31,81,93,104,127,170,219,225],"sites.":[20],"While":[21],"common":[22],"bioinformatics":[23],"tools":[24],"produce":[25],"scores":[26,42,211],"that":[27,122,158,194],"can":[28,175],"reflect":[29],"the":[30,39,99,118,183,214],"strength":[32,215],"between":[33,47,179],"specific":[35,150],"and":[38,62,106,139,212,234],"DNA,":[40],"these":[41],"are":[43,86,229],"not":[44],"directly":[45,191],"comparable":[46],"different":[48,114,162,180,198],"factors.":[50],"Other":[51],"methods,":[52],"including":[53],"p-value":[54,64],"associated":[55],"approaches":[56,203],"(Touzet":[57],"H,":[58],"Varr\u00e9":[59],"J-S.":[60],"Efficient":[61],"accurate":[63],"computation":[65],"for":[66,98,148,161],"position":[67],"weight":[68],"matrices.":[69],"Algorithms":[70],"Mol":[71],"Biol.":[72],"2007;2(1510.1186):1748-7188),":[73],"provide":[74,112,204],"more":[75],"rigorous":[76],"ways":[77,115,207],"potential":[80],"sites,":[82],"but":[83],"their":[84,168],"results":[85,228],"difficult":[87],"interpret":[89],"in":[90,221,237],"terms":[91],"of":[92,101,182,216,224,239],"energy,":[94],"which":[95,153,187],"essential":[97],"modeling":[100],"dynamics":[105],"enhancer":[107],"activities.":[108],"RESULTS:":[109],"Here,":[110],"we":[111,154],"two":[113,202],"find":[117],"scaling":[119],"parameter":[120],"\u03bb":[121,147,159,178],"allows":[123,188],"us":[124,189],"infer":[126],"energy":[128],"from":[129],"PWM":[131,138,210],"score.":[132],"The":[133],"first":[134],"approach":[135],"uses":[136],"background":[140],"genomic":[141],"sequence":[142],"as":[143],"input":[144],"estimate":[146,213],"factor,":[152,186],"applied":[155],"show":[157],"distributions":[160],"families":[165],"correspond":[166],"with":[167,231],"properties.":[171],"Our":[172],"second":[173],"reliably":[176],"convert":[177],"PWMs":[181,193],"same":[184],"compare":[192],"were":[195],"generated":[196],"by":[197],"approaches.":[199],"CONCLUSION:":[200],"These":[201],"computationally":[205],"efficient":[206],"scale":[209],"sites":[220],"quantitative":[222],"studies":[223],"dynamics.":[226],"Their":[227],"consistent":[230],"each":[232],"other":[233],"previous":[235],"reports":[236],"most":[238],"cases.":[240]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}