{"id":"https://openalex.org/W4396770878","doi":"https://doi.org/10.1021/acs.jcim.4c00047","title":"Prediction of Transcription Factor Binding Sites on Cell-Free DNA Based on Deep Learning","display_name":"Prediction of Transcription Factor Binding Sites on Cell-Free DNA Based on Deep Learning","publication_year":2024,"publication_date":"2024-05-09","ids":{"openalex":"https://openalex.org/W4396770878","doi":"https://doi.org/10.1021/acs.jcim.4c00047","pmid":"https://pubmed.ncbi.nlm.nih.gov/38798191"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c00047","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00047","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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/A5055475164","display_name":"Ting Qi","orcid":"https://orcid.org/0000-0003-1347-2608"},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ting Qi","raw_affiliation_strings":["State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]},{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046274878","display_name":"Ying Zhou","orcid":"https://orcid.org/0000-0002-0295-8736"},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Zhou","raw_affiliation_strings":["State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]},{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024246888","display_name":"Yuqi Sheng","orcid":null},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuqi Sheng","raw_affiliation_strings":["State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]},{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100461830","display_name":"Zhihui Li","orcid":"https://orcid.org/0000-0003-1586-5894"},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhihui Li","raw_affiliation_strings":["State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]},{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086080778","display_name":"Yuwei Yang","orcid":"https://orcid.org/0000-0003-4698-1855"},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuwei Yang","raw_affiliation_strings":["State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]},{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101661423","display_name":"Quanjun Liu","orcid":"https://orcid.org/0000-0002-9414-7892"},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Quanjun Liu","raw_affiliation_strings":["State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]},{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080758719","display_name":"Qinyu Ge","orcid":"https://orcid.org/0000-0002-1708-1949"},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qinyu Ge","raw_affiliation_strings":["State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China"],"raw_orcid":"https://orcid.org/0000-0002-1708-1949","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People\u2019s Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]},{"raw_affiliation_string":"State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5080758719"],"corresponding_institution_ids":["https://openalex.org/I4387154005","https://openalex.org/I76569877"],"apc_list":null,"apc_paid":null,"fwci":0.542,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.65481729,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"64","issue":"10","first_page":"4002","last_page":"4008"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.9994000196456909,"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":0.9991000294685364,"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/dna-binding-site","display_name":"DNA binding site","score":0.766686201095581},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.6567070484161377},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5869415998458862},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.4730219841003418},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4576389789581299},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.43682146072387695},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.40044069290161133},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3742520809173584},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36912721395492554},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.2519795298576355},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24086526036262512},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.19109082221984863}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.766686201095581},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6567070484161377},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5869415998458862},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.4730219841003418},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4576389789581299},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.43682146072387695},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.40044069290161133},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3742520809173584},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36912721395492554},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.2519795298576355},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24086526036262512},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.19109082221984863},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000073888","descriptor_name":"Cell-Free Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c00047","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00047","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:38798191","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38798191","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Zero hunger","score":0.46000000834465027,"id":"https://metadata.un.org/sdg/2"}],"awards":[{"id":"https://openalex.org/G2147793897","display_name":null,"funder_award_id":"JCYJ20230807114612024","funder_id":"https://openalex.org/F4320336569","funder_display_name":"Shenzhen Science and Technology Innovation Program"},{"id":"https://openalex.org/G2955086088","display_name":null,"funder_award_id":"2022YFF0710800","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320336569","display_name":"Shenzhen Science and Technology Innovation Program","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1980825481","https://openalex.org/W1993470489","https://openalex.org/W2002262418","https://openalex.org/W2023230646","https://openalex.org/W2035653659","https://openalex.org/W2036131961","https://openalex.org/W2045362835","https://openalex.org/W2102904139","https://openalex.org/W2110583812","https://openalex.org/W2137465688","https://openalex.org/W2157009395","https://openalex.org/W2162778212","https://openalex.org/W2185560378","https://openalex.org/W2202820153","https://openalex.org/W2239118478","https://openalex.org/W2331147307","https://openalex.org/W2345512687","https://openalex.org/W2567008309","https://openalex.org/W2767749844","https://openalex.org/W2785792383","https://openalex.org/W2966369432","https://openalex.org/W2979766772","https://openalex.org/W3108737349","https://openalex.org/W3175931262","https://openalex.org/W3202330825","https://openalex.org/W3213107985","https://openalex.org/W3215596355","https://openalex.org/W4200479098","https://openalex.org/W4293101932","https://openalex.org/W4300862723"],"related_works":["https://openalex.org/W2036927633","https://openalex.org/W2152664145","https://openalex.org/W2153561273","https://openalex.org/W2079197459","https://openalex.org/W2379997263","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W2367493320","https://openalex.org/W2131580913","https://openalex.org/W2090848290"],"abstract_inverted_index":{"Transcription":[0],"factors":[1],"(TFs)":[2],"are":[3,56,62],"important":[4],"regulatory":[5,25,196],"elements":[6],"for":[7,206],"vital":[8],"cellular":[9],"activities,":[10],"and":[11,51,133,138,174,202],"the":[12,43,67,103,115,155,159,190,194],"identification":[13,69],"of":[14,54,70,89,105,117,140,158,184,209],"transcription":[15],"factor":[16],"binding":[17,156],"sites":[18,157],"(TFBS)":[19],"can":[20,85],"help":[21],"to":[22,42,123,192],"explore":[23],"gene":[24],"mechanisms.":[26],"Research":[27],"studies":[28],"have":[29],"proved":[30],"that":[31,84,154],"cfDNA":[32,55,90,131,142,173],"(cell-free":[33],"DNA)":[34],"shows":[35],"relatively":[36],"higher":[37],"coverage":[38,135],"at":[39],"TFBS":[40],"due":[41],"protection":[44],"by":[45,49,91],"TF":[46,161],"from":[47,72,95,172,187,198],"degradation":[48],"nucleases":[50],"short":[52],"fragments":[53,132],"enriched":[57,176],"in":[58,66,130,163,177,211],"TFBS.":[59],"However,":[60],"there":[61],"still":[63],"great":[64],"difficulties":[65],"noninvasive":[68,200],"TFBSs":[71,88,97,186],"experimental":[73],"techniques.":[74],"In":[75,180],"this":[76,121],"study,":[77],"we":[78,126],"propose":[79],"a":[80,148,199],"deep":[81],"learning-based":[82],"approach":[83],"noninvasively":[86],"predict":[87,124],"learning":[92],"sequence":[93],"information":[94],"known":[96],"through":[98],"convolutional":[99],"neural":[100],"networks.":[101],"Under":[102],"addition":[104],"long":[106],"short-term":[107],"memory,":[108],"our":[109,182],"model":[110,122],"achieved":[111],"an":[112],"area":[113],"under":[114],"curve":[116],"84%.":[118],"Based":[119],"on":[120],"cfDNA,":[125],"found":[127,153],"consistent":[128,146],"motifs":[129],"lower":[134],"occurred":[136],"upstream":[137],"downstream":[139],"these":[141],"fragments,":[143],"which":[144],"is":[145],"with":[147],"previous":[149],"study.":[150],"We":[151],"also":[152],"same":[160],"differ":[162],"different":[164],"cell":[165],"lines.":[166],"TF-specific":[167],"target":[168],"genes":[169],"were":[170,175],"detected":[171],"cancer-related":[178],"pathways.":[179],"summary,":[181],"method":[183],"locating":[185],"plasma":[188],"has":[189],"potential":[191],"reflect":[193],"intrinsic":[195],"mechanism":[197],"perspective":[201],"provide":[203],"technical":[204],"guidance":[205],"dynamic":[207],"monitoring":[208],"disease":[210],"clinical":[212],"practice.":[213]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
