{"id":"https://openalex.org/W2153903044","doi":"https://doi.org/10.1093/bioinformatics/btm215","title":"Inferring protein\u2013DNA dependencies using motif alignments and mutual information","display_name":"Inferring protein\u2013DNA dependencies using motif alignments and mutual information","publication_year":2007,"publication_date":"2007-07-01","ids":{"openalex":"https://openalex.org/W2153903044","doi":"https://doi.org/10.1093/bioinformatics/btm215","mag":"2153903044","pmid":"https://pubmed.ncbi.nlm.nih.gov/17646310"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm215","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm215","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/13/i297/23707329/btm215.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/23/13/i297/23707329/btm215.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077269033","display_name":"Shaun Mahony","orcid":"https://orcid.org/0000-0002-2641-1807"},"institutions":[{"id":"https://openalex.org/I165102784","display_name":"Duquesne University","ror":"https://ror.org/02336z538","country_code":"US","type":"education","lineage":["https://openalex.org/I165102784"]},{"id":"https://openalex.org/I4210128526","display_name":"UPMC Hillman Cancer Center","ror":"https://ror.org/03bw34a45","country_code":"US","type":"facility","lineage":["https://openalex.org/I170201317","https://openalex.org/I4210128526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shaun Mahony","raw_affiliation_strings":["1 Department of Computational Biology, 2Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, 3Department of Biological Sciences, Duquesne University, 4Department of Human Genetics, Graduate School of Public Health and 5University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computational Biology, 2Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, 3Department of Biological Sciences, Duquesne University, 4Department of Human Genetics, Graduate School of Public Health and 5University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, USA","institution_ids":["https://openalex.org/I165102784","https://openalex.org/I4210128526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078347043","display_name":"Philip E. Auron","orcid":"https://orcid.org/0000-0001-5749-2622"},"institutions":[{"id":"https://openalex.org/I165102784","display_name":"Duquesne University","ror":"https://ror.org/02336z538","country_code":"US","type":"education","lineage":["https://openalex.org/I165102784"]},{"id":"https://openalex.org/I4210128526","display_name":"UPMC Hillman Cancer Center","ror":"https://ror.org/03bw34a45","country_code":"US","type":"facility","lineage":["https://openalex.org/I170201317","https://openalex.org/I4210128526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip E. Auron","raw_affiliation_strings":["1 Department of Computational Biology, 2Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, 3Department of Biological Sciences, Duquesne University, 4Department of Human Genetics, Graduate School of Public Health and 5University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computational Biology, 2Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, 3Department of Biological Sciences, Duquesne University, 4Department of Human Genetics, Graduate School of Public Health and 5University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, USA","institution_ids":["https://openalex.org/I165102784","https://openalex.org/I4210128526"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042618575","display_name":"Panayiotis V. Benos","orcid":"https://orcid.org/0000-0003-3172-3132"},"institutions":[{"id":"https://openalex.org/I165102784","display_name":"Duquesne University","ror":"https://ror.org/02336z538","country_code":"US","type":"education","lineage":["https://openalex.org/I165102784"]},{"id":"https://openalex.org/I4210128526","display_name":"UPMC Hillman Cancer Center","ror":"https://ror.org/03bw34a45","country_code":"US","type":"facility","lineage":["https://openalex.org/I170201317","https://openalex.org/I4210128526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Panayiotis V. Benos","raw_affiliation_strings":["1 Department of Computational Biology, 2Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, 3Department of Biological Sciences, Duquesne University, 4Department of Human Genetics, Graduate School of Public Health and 5University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computational Biology, 2Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, 3Department of Biological Sciences, Duquesne University, 4Department of Human Genetics, Graduate School of Public Health and 5University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, USA","institution_ids":["https://openalex.org/I165102784","https://openalex.org/I4210128526"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.0057,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.74778574,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"23","issue":"13","first_page":"i297","last_page":"i304"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9994999766349792,"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/T10604","display_name":"RNA Research and Splicing","score":0.993399977684021,"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/zinc-finger","display_name":"Zinc finger","score":0.6730493903160095},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.6477403044700623},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6298261880874634},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5389116406440735},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5279525518417358},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5138816833496094},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.505500078201294},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.49749186635017395},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.4912363886833191},{"id":"https://openalex.org/keywords/consensus-sequence","display_name":"Consensus sequence","score":0.470193475484848},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.46929627656936646},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4607558846473694},{"id":"https://openalex.org/keywords/sequence-logo","display_name":"Sequence logo","score":0.4465644955635071},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.4316827058792114},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.42159879207611084},{"id":"https://openalex.org/keywords/nucleotide","display_name":"Nucleotide","score":0.4135722219944},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3173527121543884},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.20401200652122498},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14200004935264587},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.13174062967300415},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.0993109941482544}],"concepts":[{"id":"https://openalex.org/C24284526","wikidata":"https://www.wikidata.org/wiki/Q204785","display_name":"Zinc finger","level":4,"score":0.6730493903160095},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.6477403044700623},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6298261880874634},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5389116406440735},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5279525518417358},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5138816833496094},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.505500078201294},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.49749186635017395},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4912363886833191},{"id":"https://openalex.org/C54985914","wikidata":"https://www.wikidata.org/wiki/Q1295754","display_name":"Consensus sequence","level":4,"score":0.470193475484848},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.46929627656936646},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4607558846473694},{"id":"https://openalex.org/C105082737","wikidata":"https://www.wikidata.org/wiki/Q7452470","display_name":"Sequence logo","level":5,"score":0.4465644955635071},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.4316827058792114},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.42159879207611084},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.4135722219944},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3173527121543884},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.20401200652122498},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14200004935264587},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.13174062967300415},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0993109941482544},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","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":"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":"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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"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":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm215","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm215","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/13/i297/23707329/btm215.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17646310","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17646310","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":{"id":"doi:10.1093/bioinformatics/btm215","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm215","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/13/i297/23707329/btm215.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3029568606","display_name":null,"funder_award_id":"CA06668544","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3285567117","display_name":null,"funder_award_id":"1R01LM007994-01","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G4220837839","display_name":null,"funder_award_id":"RR014214","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G5850682332","display_name":null,"funder_award_id":"W81XWH","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7364797127","display_name":null,"funder_award_id":"N01-AI50018","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8477613290","display_name":null,"funder_award_id":"RR014214","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"},{"id":"https://openalex.org/F4320338297","display_name":"Telemedicine and Advanced Technology Research Center","ror":"https://ror.org/014pvr265"},{"id":"https://openalex.org/F4320338478","display_name":"U.S. Army Medical Research Acquisition Activity","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2153903044.pdf","grobid_xml":"https://content.openalex.org/works/W2153903044.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1527979595","https://openalex.org/W1973095653","https://openalex.org/W1986748430","https://openalex.org/W1991647220","https://openalex.org/W2026258231","https://openalex.org/W2026979173","https://openalex.org/W2027662098","https://openalex.org/W2055166643","https://openalex.org/W2065635150","https://openalex.org/W2076849893","https://openalex.org/W2084620487","https://openalex.org/W2087064593","https://openalex.org/W2097035920","https://openalex.org/W2100271852","https://openalex.org/W2103325210","https://openalex.org/W2107528836","https://openalex.org/W2119320698","https://openalex.org/W2132256310","https://openalex.org/W2132291850","https://openalex.org/W2133747691","https://openalex.org/W2141885858","https://openalex.org/W2149769193","https://openalex.org/W2151538750","https://openalex.org/W2153550523","https://openalex.org/W2155625886","https://openalex.org/W2166277117","https://openalex.org/W2166898290","https://openalex.org/W2168157737","https://openalex.org/W3028383551","https://openalex.org/W4210400672","https://openalex.org/W4376545436","https://openalex.org/W6675132646","https://openalex.org/W6682740300"],"related_works":["https://openalex.org/W2036131961","https://openalex.org/W2019019284","https://openalex.org/W2164809504","https://openalex.org/W1546667006","https://openalex.org/W3149778688","https://openalex.org/W2143172590","https://openalex.org/W2183608621","https://openalex.org/W2133328876","https://openalex.org/W2044284701","https://openalex.org/W2208708370"],"abstract_inverted_index":{"MOTIVATION:":[0],"Mutual":[1,114],"information":[2,115,137],"can":[3],"be":[4],"used":[5,20],"to":[6,21],"explore":[7],"covarying":[8,79],"positions":[9,82,111,144],"in":[10,53,90],"biological":[11],"sequences.":[12],"In":[13,31],"the":[14,37,41,119],"past,":[15],"it":[16],"has":[17],"been":[18],"successfully":[19],"infer":[22],"RNA":[23],"secondary":[24],"structure":[25],"conformations":[26],"from":[27,135],"multiple":[28],"sequence":[29,136],"alignments.":[30],"this":[32,91],"study,":[33],"we":[34,75],"show":[35],"that":[36,48,77],"same":[38],"principles":[39],"allow":[40],"discovery":[42],"of":[43,61,70,106,121,141,150],"transcription":[44,62,128],"factor":[45,63,129],"amino":[46],"acids":[47],"are":[49,112],"coevolving":[50],"with":[51],"nucleotides":[52],"their":[54,71],"DNA-binding":[55,100],"targets.":[56],"RESULTS:":[57],"Given":[58],"an":[59],"alignment":[60,69],"binding":[64],"domains,":[65],"and":[66,98],"a":[67,104],"separate":[68],"DNA":[72,151],"target":[73],"motifs,":[74],"demonstrate":[76],"mutually":[78],"base-amino":[80,108,122],"acid":[81,109,123],"may":[83,117,145],"indicate":[84],"possible":[85],"protein-DNA":[86,142],"contacts.":[87],"Examples":[88],"explored":[89],"study":[92],"include":[93],"C2H2":[94],"zinc":[95],"finger,":[96],"homeodomain":[97],"bHLH":[99],"motif":[101],"families,":[102,130],"where":[103],"number":[105],"known":[107],"contacting":[110,124,143],"identified.":[113],"analyses":[116],"aid":[118],"prediction":[120],"pairs":[125],"for":[126],"particular":[127],"thereby":[131],"yielding":[132],"structural":[133],"insights":[134],"alone.":[138],"Such":[139],"inference":[140],"guide":[146],"future":[147],"experimental":[148],"studies":[149],"recognition.":[152]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
