{"id":"https://openalex.org/W4379599440","doi":"https://doi.org/10.1093/bib/bbad214","title":"TRAmHap: accurate prediction of transcriptional activity from DNA methylation haplotypes in bisulfite-sequencing data","display_name":"TRAmHap: accurate prediction of transcriptional activity from DNA methylation haplotypes in bisulfite-sequencing data","publication_year":2023,"publication_date":"2023-06-02","ids":{"openalex":"https://openalex.org/W4379599440","doi":"https://doi.org/10.1093/bib/bbad214","pmid":"https://pubmed.ncbi.nlm.nih.gov/37279467"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad214","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad214","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5111071013","display_name":"Siqi Gao","orcid":"https://orcid.org/0009-0007-7149-4772"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210121447","display_name":"Center for Excellence in Molecular Cell Science","ror":"https://ror.org/02rrdvm96","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210121447"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Siqi Gao","raw_affiliation_strings":["State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences , Shanghai 200031 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences , Shanghai 200031 , China","institution_ids":["https://openalex.org/I4210121447","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102713614","display_name":"Hanwen Zhu","orcid":"https://orcid.org/0000-0002-6172-0189"},"institutions":[{"id":"https://openalex.org/I21945476","display_name":"Shanghai Normal University","ror":"https://ror.org/01cxqmw89","country_code":"CN","type":"education","lineage":["https://openalex.org/I21945476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hanwen Zhu","raw_affiliation_strings":["Department of Mathematics, Shanghai Normal University , Shanghai, 200234 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Shanghai Normal University , Shanghai, 200234 , China","institution_ids":["https://openalex.org/I21945476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089136612","display_name":"Kangwen Cai","orcid":null},"institutions":[{"id":"https://openalex.org/I21945476","display_name":"Shanghai Normal University","ror":"https://ror.org/01cxqmw89","country_code":"CN","type":"education","lineage":["https://openalex.org/I21945476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kangwen Cai","raw_affiliation_strings":["Department of Mathematics, Shanghai Normal University , Shanghai, 200234 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Shanghai Normal University , Shanghai, 200234 , China","institution_ids":["https://openalex.org/I21945476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048947486","display_name":"Leiqin Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210121447","display_name":"Center for Excellence in Molecular Cell Science","ror":"https://ror.org/02rrdvm96","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210121447"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Leiqin Liu","raw_affiliation_strings":["State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences , Shanghai 200031 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences , Shanghai 200031 , China","institution_ids":["https://openalex.org/I4210121447","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100346715","display_name":"Zhiqiang Zhang","orcid":"https://orcid.org/0000-0002-6907-3481"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210121447","display_name":"Center for Excellence in Molecular Cell Science","ror":"https://ror.org/02rrdvm96","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210121447"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiqiang Zhang","raw_affiliation_strings":["State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences , Shanghai 200031 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences , Shanghai 200031 , China","institution_ids":["https://openalex.org/I4210121447","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005325306","display_name":"Yi Ding","orcid":"https://orcid.org/0000-0001-9294-8760"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210121447","display_name":"Center for Excellence in Molecular Cell Science","ror":"https://ror.org/02rrdvm96","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210121447"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Ding","raw_affiliation_strings":["State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences , Shanghai 200031 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences , Shanghai 200031 , China","institution_ids":["https://openalex.org/I4210121447","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006218098","display_name":"Yaochen Xu","orcid":"https://orcid.org/0000-0002-5039-2781"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210121447","display_name":"Center for Excellence in Molecular Cell Science","ror":"https://ror.org/02rrdvm96","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210121447"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaochen Xu","raw_affiliation_strings":["State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences , Shanghai 200031 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences , Shanghai 200031 , China","institution_ids":["https://openalex.org/I4210121447","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021047181","display_name":"Xiaoqi Zheng","orcid":"https://orcid.org/0000-0002-1832-4404"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210156766","display_name":"Shanghai Cell Therapy Research Institute","ror":"https://ror.org/044ef5h76","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I4210156766"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaoqi Zheng","raw_affiliation_strings":["Center for Single-Cell Omics , School of Public Health, , Shanghai 200025 , China","Shanghai Jiao Tong University School of Medicine , School of Public Health, , Shanghai 200025 , China","Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Single-Cell Omics , School of Public Health, , Shanghai 200025 , China","institution_ids":["https://openalex.org/I4210156766"]},{"raw_affiliation_string":"Shanghai Jiao Tong University School of Medicine , School of Public Health, , Shanghai 200025 , China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040409553","display_name":"Jiantao Shi","orcid":"https://orcid.org/0000-0002-0039-8800"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210121447","display_name":"Center for Excellence in Molecular Cell Science","ror":"https://ror.org/02rrdvm96","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210121447"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jiantao Shi","raw_affiliation_strings":["State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences , Shanghai 200031 , China"],"raw_orcid":"https://orcid.org/0000-0002-0039-8800","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences , Shanghai 200031 , China","institution_ids":["https://openalex.org/I4210121447","https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5021047181","https://openalex.org/A5040409553"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I19820366","https://openalex.org/I4210121447","https://openalex.org/I4210156766"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.4036,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.64665397,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"24","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":1.0,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":1.0,"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/T11482","display_name":"RNA modifications and cancer","score":0.9983999729156494,"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/T13157","display_name":"Cancer-related gene regulation","score":0.9983999729156494,"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/dnam","display_name":"dNaM","score":0.8602808117866516},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.7580116987228394},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.7307119369506836},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.7282444834709167},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6325056552886963},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.6159123182296753},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.5523449182510376},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5392118692398071},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.5233078002929688},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5058926939964294},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.4757520854473114},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.47565123438835144},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43879905343055725},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"Transcriptional regulation","score":0.42025521397590637}],"concepts":[{"id":"https://openalex.org/C2775921022","wikidata":"https://www.wikidata.org/wiki/Q25104749","display_name":"dNaM","level":5,"score":0.8602808117866516},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.7580116987228394},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.7307119369506836},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.7282444834709167},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6325056552886963},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.6159123182296753},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.5523449182510376},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5392118692398071},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.5233078002929688},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5058926939964294},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.4757520854473114},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.47565123438835144},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43879905343055725},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.42025521397590637}],"mesh":[{"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":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","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":"D013447","descriptor_name":"Sulfites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad214","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad214","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37279467","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37279467","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4752324478","display_name":null,"funder_award_id":"32270691","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G864299621","display_name":"\u878d\u5408\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u6570\u636e\u7684\u80bf\u7624\u5f02\u8d28\u6027\u5206\u6790\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61972257","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation 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/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1965722916","https://openalex.org/W1987557775","https://openalex.org/W2002698073","https://openalex.org/W2016015848","https://openalex.org/W2024819383","https://openalex.org/W2038235796","https://openalex.org/W2040875973","https://openalex.org/W2059099579","https://openalex.org/W2084203180","https://openalex.org/W2108797218","https://openalex.org/W2121417064","https://openalex.org/W2128505445","https://openalex.org/W2152656267","https://openalex.org/W2164327622","https://openalex.org/W2171783560","https://openalex.org/W2259938310","https://openalex.org/W2327450572","https://openalex.org/W2514270659","https://openalex.org/W2593934358","https://openalex.org/W2602050433","https://openalex.org/W2754109996","https://openalex.org/W2900423390","https://openalex.org/W2920879405","https://openalex.org/W2983759518","https://openalex.org/W2994655911","https://openalex.org/W3009004192","https://openalex.org/W3044496248","https://openalex.org/W3121258881","https://openalex.org/W3124489492","https://openalex.org/W3166379906","https://openalex.org/W3177334356","https://openalex.org/W3198532939","https://openalex.org/W4298326521","https://openalex.org/W4307845770","https://openalex.org/W6770120275"],"related_works":["https://openalex.org/W3204969836","https://openalex.org/W2167996825","https://openalex.org/W3161439184","https://openalex.org/W2033874367","https://openalex.org/W2769193000","https://openalex.org/W2029110662","https://openalex.org/W2980158117","https://openalex.org/W2124167740","https://openalex.org/W2094569740","https://openalex.org/W4379599440"],"abstract_inverted_index":{"Deoxyribonucleic":[0],"acid":[1],"(DNA)":[2],"methylation":[3,54,89],"(DNAm)":[4],"is":[5,28,42,74],"an":[6],"important":[7],"epigenetic":[8],"mechanism":[9],"that":[10,99,114,166],"plays":[11],"a":[12,110],"role":[13,35],"in":[14,36,56,76,125,176,192],"chromatin":[15,197],"structure":[16],"and":[17,25,72,82,128,136,160,178],"transcriptional":[18,37,83],"regulation.":[19,38],"Elucidating":[20],"the":[21,78,94,120,193],"relationship":[22,79],"between":[23,80],"DNAm":[24,81,104,123,174],"gene":[26,49,69,116,154,167],"expression":[27,50,70,117,155,168],"of":[29,62,68,96,122,134,153,195],"great":[30],"importance":[31],"for":[32],"understanding":[33],"its":[34],"The":[39],"conventional":[40],"approach":[41],"to":[43,47],"construct":[44],"machine-learning-based":[45],"methods":[46],"predict":[48],"based":[51,148],"on":[52],"mean":[53,88],"signals":[55],"promoter":[57],"regions.":[58],"However,":[59],"this":[60],"type":[61],"strategy":[63],"only":[64],"explains":[65],"about":[66],"25%":[67],"variation,":[71],"hence":[73],"inadequate":[75],"elucidating":[77],"activity.":[84],"In":[85],"addition,":[86],"using":[87],"as":[90,181,183],"input":[91],"features":[92],"neglects":[93],"heterogeneity":[95],"cell":[97],"populations":[98],"can":[100,169],"be":[101,170],"reflected":[102],"by":[103,118,150,173],"haplotypes.":[105],"We":[106],"here":[107],"developed":[108],"TRAmaHap,":[109],"novel":[111],"deep-learning":[112],"framework":[113],"predicts":[115],"utilizing":[119],"characteristics":[121],"haplotypes":[124],"proximal":[126],"promoters":[127,177],"distal":[129],"enhancers.":[130],"Using":[131],"benchmark":[132],"data":[133],"human":[135],"mouse":[137],"normal":[138],"tissues,":[139],"TRAmHap":[140],"shows":[141],"much":[142],"higher":[143],"accuracy":[144],"than":[145],"existing":[146],"machine-learning":[147],"methods,":[149],"explaining":[151],"60~80%":[152],"variation":[156],"across":[157],"tissue":[158],"types":[159],"disease":[161],"conditions.":[162],"Our":[163],"model":[164],"demonstrated":[165],"accurately":[171],"predicted":[172],"patterns":[175],"long-range":[179],"enhancers":[180],"far":[182],"25":[184],"kb":[185],"away":[186],"from":[187],"transcription":[188],"start":[189],"site,":[190],"especially":[191],"presence":[194],"intra-gene":[196],"interactions.":[198]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}