{"id":"https://openalex.org/W2114066176","doi":"https://doi.org/10.1093/bioinformatics/bti1043","title":"Mining ChIP-chip data for transcription factor and cofactor binding sites","display_name":"Mining ChIP-chip data for transcription factor and cofactor binding sites","publication_year":2005,"publication_date":"2005-06-01","ids":{"openalex":"https://openalex.org/W2114066176","doi":"https://doi.org/10.1093/bioinformatics/bti1043","mag":"2114066176","pmid":"https://pubmed.ncbi.nlm.nih.gov/15961485"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti1043","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti1043","pdf_url":null,"source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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","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/A5065682481","display_name":"Andrew D. Smith","orcid":"https://orcid.org/0000-0002-3337-1970"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"A. D. Smith","raw_affiliation_strings":["Cold Spring Harbor Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. asmith@cshl.edu","Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA"],"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. asmith@cshl.edu","institution_ids":["https://openalex.org/I2750212522"]},{"raw_affiliation_string":"Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003039585","display_name":"Pavel Sumazin","orcid":"https://orcid.org/0000-0002-1215-4977"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. Sumazin","raw_affiliation_strings":["Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA"],"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054884920","display_name":"Debodipta Das","orcid":"https://orcid.org/0000-0001-7698-0736"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Das","raw_affiliation_strings":["Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA"],"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058814283","display_name":"Michael Q. Zhang","orcid":"https://orcid.org/0000-0002-7022-6115"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Q. Zhang","raw_affiliation_strings":["Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA"],"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5065682481"],"corresponding_institution_ids":["https://openalex.org/I2750212522"],"apc_list":null,"apc_paid":null,"fwci":4.0612,"has_fulltext":false,"cited_by_count":87,"citation_normalized_percentile":{"value":0.94572098,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"21","issue":"Suppl 1","first_page":"i403","last_page":"i412"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9948999881744385,"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":0.7870527505874634},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6616803407669067},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.6398606300354004},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.6115097403526306},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5353228449821472},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.4783610701560974},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.4621805250644684},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.44568973779678345},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.43866589665412903},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4223610758781433},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3947718143463135},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39055779576301575},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3678429126739502},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32618027925491333},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.1306995451450348}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7870527505874634},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6616803407669067},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.6398606300354004},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6115097403526306},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5353228449821472},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.4783610701560974},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.4621805250644684},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.44568973779678345},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43866589665412903},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4223610758781433},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3947718143463135},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39055779576301575},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3678429126739502},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32618027925491333},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.1306995451450348},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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":"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":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","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},{"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},{"descriptor_ui":"D040081","descriptor_name":"Protein Array Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040081","descriptor_name":"Protein Array Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040081","descriptor_name":"Protein Array Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti1043","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti1043","pdf_url":null,"source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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:15961485","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15961485","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:repository.cshl.edu:22707","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1480376833","https://openalex.org/W1570481371","https://openalex.org/W1578840628","https://openalex.org/W1580213736","https://openalex.org/W1586970933","https://openalex.org/W1965555277","https://openalex.org/W1988538980","https://openalex.org/W2008491350","https://openalex.org/W2025325736","https://openalex.org/W2028904582","https://openalex.org/W2043789254","https://openalex.org/W2048523814","https://openalex.org/W2050471060","https://openalex.org/W2053477045","https://openalex.org/W2055050002","https://openalex.org/W2068011423","https://openalex.org/W2070340804","https://openalex.org/W2073850887","https://openalex.org/W2077013196","https://openalex.org/W2078935819","https://openalex.org/W2083193728","https://openalex.org/W2092659658","https://openalex.org/W2096139934","https://openalex.org/W2102201073","https://openalex.org/W2103727292","https://openalex.org/W2110618077","https://openalex.org/W2113712263","https://openalex.org/W2120966823","https://openalex.org/W2126558916","https://openalex.org/W2138717237","https://openalex.org/W2139025111","https://openalex.org/W2144710927","https://openalex.org/W2144791796","https://openalex.org/W2149436483","https://openalex.org/W2149769193","https://openalex.org/W2154514071","https://openalex.org/W2162111678","https://openalex.org/W2164683872","https://openalex.org/W2166898290"],"related_works":["https://openalex.org/W2073661767","https://openalex.org/W2380185347","https://openalex.org/W2368410102","https://openalex.org/W2044328609","https://openalex.org/W2370034659","https://openalex.org/W3021477453","https://openalex.org/W2012993128","https://openalex.org/W566414894","https://openalex.org/W2364249514","https://openalex.org/W2610941444"],"abstract_inverted_index":{"Motif":[0],"discovery":[1],"programs":[2],"and":[3],"analysis":[4],"tools":[5],"are":[6],"available":[7],"on":[8],"request":[9],"from":[10],"the":[11],"authors.":[12]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":7}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}