{"id":"https://openalex.org/W4310944086","doi":"https://doi.org/10.1093/bioinformatics/btac798","title":"Computational prediction and characterization of cell-type-specific and shared binding sites","display_name":"Computational prediction and characterization of cell-type-specific and shared binding sites","publication_year":2022,"publication_date":"2022-12-09","ids":{"openalex":"https://openalex.org/W4310944086","doi":"https://doi.org/10.1093/bioinformatics/btac798","pmid":"https://pubmed.ncbi.nlm.nih.gov/36484687"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac798","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac798","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac798/48520710/btac798.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","license_id":"https://openalex.org/licenses/cc-by","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/39/1/btac798/48520710/btac798.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062540383","display_name":"Qinhu Zhang","orcid":"https://orcid.org/0000-0002-4232-7736"},"institutions":[{"id":"https://openalex.org/I4210128175","display_name":"Shanghai East Hospital","ror":"https://ror.org/038xmzj21","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128175"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qinhu Zhang","raw_affiliation_strings":["Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University , Shanghai 200092, China"],"raw_orcid":"https://orcid.org/0000-0002-4232-7736","affiliations":[{"raw_affiliation_string":"Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University , Shanghai 200092, China","institution_ids":["https://openalex.org/I4210128175"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091041832","display_name":"Pengrui Teng","orcid":"https://orcid.org/0009-0005-1292-6227"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengrui Teng","raw_affiliation_strings":["School of Information and Control Engineering, China University of Mining and Technology , Xuzhou 221116, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Control Engineering, China University of Mining and Technology , Xuzhou 221116, China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054096753","display_name":"Siguo Wang","orcid":"https://orcid.org/0000-0002-3244-3629"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Siguo Wang","raw_affiliation_strings":["Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University , Shanghai 201804, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University , Shanghai 201804, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086358231","display_name":"Ying He","orcid":"https://orcid.org/0000-0002-9592-7727"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying He","raw_affiliation_strings":["Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University , Shanghai 201804, China"],"raw_orcid":"https://orcid.org/0000-0002-9592-7727","affiliations":[{"raw_affiliation_string":"Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University , Shanghai 201804, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058029547","display_name":"Zhen Cui","orcid":"https://orcid.org/0000-0001-5522-6750"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Cui","raw_affiliation_strings":["Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University , Shanghai 201804, China"],"raw_orcid":"https://orcid.org/0000-0001-5522-6750","affiliations":[{"raw_affiliation_string":"Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University , Shanghai 201804, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069781656","display_name":"Zhenghao Guo","orcid":null},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenghao Guo","raw_affiliation_strings":["Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University , Shanghai 201804, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University , Shanghai 201804, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100386691","display_name":"Yixin Liu","orcid":"https://orcid.org/0000-0003-4401-9291"},"institutions":[{"id":"https://openalex.org/I148128674","display_name":"University of Shanghai for Science and Technology","ror":"https://ror.org/00ay9v204","country_code":"CN","type":"education","lineage":["https://openalex.org/I148128674"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yixin Liu","raw_affiliation_strings":["School of Health Science and Engineering, University of Shanghai for Science and Technology , Shanghai 200093, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Health Science and Engineering, University of Shanghai for Science and Technology , Shanghai 200093, China","institution_ids":["https://openalex.org/I148128674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007724310","display_name":"Changan Yuan","orcid":"https://orcid.org/0000-0001-6912-718X"},"institutions":[{"id":"https://openalex.org/I4210165264","display_name":"Guangxi Academy of Sciences","ror":"https://ror.org/054x1kd82","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210165264"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Changan Yuan","raw_affiliation_strings":["Big Data and Intelligent Computing Research Center, Guangxi Academy of Science , Nanning 530007, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Big Data and Intelligent Computing Research Center, Guangxi Academy of Science , Nanning 530007, China","institution_ids":["https://openalex.org/I4210165264"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100453248","display_name":"Qi Liu","orcid":"https://orcid.org/0000-0003-2578-1221"},"institutions":[{"id":"https://openalex.org/I4210128175","display_name":"Shanghai East Hospital","ror":"https://ror.org/038xmzj21","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128175"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qi Liu","raw_affiliation_strings":["Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University , Shanghai 200092, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University , Shanghai 200092, China","institution_ids":["https://openalex.org/I4210128175"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060381913","display_name":"De-Shuang Huang","orcid":"https://orcid.org/0000-0002-6759-2691"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"De-Shuang Huang","raw_affiliation_strings":["EIT Institute for Advanced Study , Ningbo, Zhejiang 315201, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EIT Institute for Advanced Study , Ningbo, Zhejiang 315201, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5060381913","https://openalex.org/A5100453248"],"corresponding_institution_ids":["https://openalex.org/I4210128175"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.0969,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.76151915,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.414000004529953,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.414000004529953,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.32109999656677246,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.1014999970793724,"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/cell-type","display_name":"Cell type","score":0.6254852414131165},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.6150505542755127},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.5116453766822815},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5048995614051819},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.4804617762565613},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4699079394340515},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.4684130549430847},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.44301721453666687},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4209863543510437},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.36524462699890137},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3470243513584137},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3365669846534729},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25902771949768066},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2429850697517395},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11065781116485596}],"concepts":[{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.6254852414131165},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6150505542755127},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.5116453766822815},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5048995614051819},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.4804617762565613},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4699079394340515},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.4684130549430847},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.44301721453666687},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4209863543510437},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.36524462699890137},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3470243513584137},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3365669846534729},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25902771949768066},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2429850697517395},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11065781116485596},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac798","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac798","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac798/48520710/btac798.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36484687","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36484687","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:pubmedcentral.nih.gov:9825777","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825777","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac798","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac798","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac798/48520710/btac798.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1141093333","display_name":null,"funder_award_id":"2021JJA170199","funder_id":"https://openalex.org/F4320322768","funder_display_name":"Natural Science Foundation of Guangxi Province"},{"id":"https://openalex.org/G1307575636","display_name":"\u9762\u5411\u8111\u75be\u75c5\u7684\u4eba\u4f53\u80a0\u9053\u5fae\u751f\u7269\u7ec4\u5b66\u6570\u636e\u6316\u6398\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61932008","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1857610291","display_name":null,"funder_award_id":"62073231","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2034869948","display_name":null,"funder_award_id":"62002266","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3425444037","display_name":null,"funder_award_id":"2018AAA0100100","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7699868062","display_name":null,"funder_award_id":"2021JJA170204","funder_id":"https://openalex.org/F4320322768","funder_display_name":"Natural Science Foundation of Guangxi Province"},{"id":"https://openalex.org/G7970487852","display_name":null,"funder_award_id":"2018AAA0100100","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G994200641","display_name":null,"funder_award_id":"2018YFA0902600","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322768","display_name":"Natural Science Foundation of Guangxi Province","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4310944086.pdf","grobid_xml":"https://content.openalex.org/works/W4310944086.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1988581590","https://openalex.org/W1989338936","https://openalex.org/W1994122295","https://openalex.org/W2032140335","https://openalex.org/W2045273474","https://openalex.org/W2084160423","https://openalex.org/W2092988184","https://openalex.org/W2101234009","https://openalex.org/W2102904139","https://openalex.org/W2118608526","https://openalex.org/W2145091349","https://openalex.org/W2179438025","https://openalex.org/W2195190137","https://openalex.org/W2198606573","https://openalex.org/W2259938310","https://openalex.org/W2330303612","https://openalex.org/W2336509392","https://openalex.org/W2785792383","https://openalex.org/W2888886037","https://openalex.org/W2892741787","https://openalex.org/W2904110212","https://openalex.org/W2912321349","https://openalex.org/W2951410692","https://openalex.org/W2979343233","https://openalex.org/W2980777527","https://openalex.org/W3041895828","https://openalex.org/W3107527779","https://openalex.org/W3121554924","https://openalex.org/W3137533336","https://openalex.org/W3175250943","https://openalex.org/W3215596355","https://openalex.org/W4220872625","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W4286930115","https://openalex.org/W3004891660","https://openalex.org/W2969540308","https://openalex.org/W2414971881","https://openalex.org/W4206381471","https://openalex.org/W1886874180","https://openalex.org/W42421305","https://openalex.org/W3162204513","https://openalex.org/W2400987468","https://openalex.org/W1598419885"],"abstract_inverted_index":{"MOTIVATION:":[0],"Cell-type-specific":[1],"gene":[2],"expression":[3],"is":[4,34,63,93,99,242],"maintained":[5],"in":[6,20,90,231],"large":[7],"part":[8],"by":[9,36,84,211],"transcription":[10],"factors":[11,119,230],"(TFs)":[12],"selectively":[13],"binding":[14,33,61,82,118,146,155,209,229],"to":[15,159,204,227],"distinct":[16],"sets":[17],"of":[18,57,88,110,116,134,151,200,223],"sites":[19,62,83,156,192,210],"different":[21,228],"cell":[22,131],"types.":[23],"Recent":[24],"research":[25],"works":[26],"have":[27],"provided":[28],"evidence":[29],"that":[30,169],"such":[31],"cell-type-specific":[32,45,58,79,140,189,206],"determined":[35],"TF's":[37],"intrinsic":[38],"sequence":[39],"preferences,":[40],"cooperative":[41],"interactions":[42],"with":[43],"co-factors,":[44],"chromatin":[46,50],"landscapes":[47],"and":[48,55,59,77,80,97,126,142,144,163,190,196,207],"3D":[49],"interactions.":[51],"However,":[52],"computational":[53,73],"prediction":[54],"characterization":[56],"shared":[60,81,145,191,208],"rarely":[64],"studied.":[65],"RESULTS:":[66],"In":[67],"this":[68],"article,":[69],"we":[70,183,218],"propose":[71],"two":[72],"approaches":[74,172,226],"for":[75,153,188],"predicting":[76],"characterizing":[78],"integrating":[85],"multiple":[86,149],"types":[87,150],"features,":[89],"which":[91,135],"one":[92],"based":[94,100],"on":[95,101,178],"XGBoost":[96],"another":[98],"convolutional":[102],"neural":[103],"network":[104],"(CNN).":[105],"To":[106],"validate":[107],"the":[108,123,161,198,201,220,232],"performance":[109],"our":[111,170,224],"proposed":[112,171,225],"approaches,":[113],"ChIP-seq":[114],"datasets":[115],"10":[117],"were":[120,157],"collected":[121],"from":[122],"GM12878":[124],"(lymphoblastoid)":[125],"K562":[127],"(erythroleukemic)":[128],"human":[129],"hematopoietic":[130],"lines,":[132],"each":[133],"was":[136],"further":[137],"categorized":[138],"into":[139],"(GM12878-":[141],"K562-specific)":[143],"sites.":[147],"Then,":[148],"features":[152],"these":[154],"integrated":[158],"train":[160],"XGBoost-":[162],"CNN-based":[164,202],"models.":[165],"Experimental":[166],"results":[167],"show":[168],"significantly":[173],"outperform":[174],"other":[175],"competing":[176],"methods":[177],"three":[179],"classification":[180],"tasks.":[181],"Moreover,":[182],"identified":[184],"independent":[185],"feature":[186],"contributions":[187],"through":[193],"SHAP":[194],"values":[195],"explored":[197],"ability":[199,222],"model":[203],"predict":[205],"excluding":[212],"or":[213],"including":[214],"DNase":[215],"signals.":[216],"Furthermore,":[217],"investigated":[219],"generalization":[221],"same":[233],"cellular":[234],"environment.":[235],"AVAILABILITY":[236],"AND":[237],"IMPLEMENTATION:":[238],"The":[239],"source":[240],"code":[241],"available":[243,251],"at:":[244],"https://github.com/turningpoint1988/CSSBS.":[245],"SUPPLEMENTARY":[246],"INFORMATION:":[247],"Supplementary":[248],"data":[249],"are":[250],"at":[252],"Bioinformatics":[253],"online.":[254]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}