{"id":"https://openalex.org/W4401001949","doi":"https://doi.org/10.1016/j.isci.2024.110584","title":"Deep learning-enhanced R-loop prediction provides mechanistic implications for repeat expansion diseases","display_name":"Deep learning-enhanced R-loop prediction provides mechanistic implications for repeat expansion diseases","publication_year":2024,"publication_date":"2024-07-25","ids":{"openalex":"https://openalex.org/W4401001949","doi":"https://doi.org/10.1016/j.isci.2024.110584","pmid":"https://pubmed.ncbi.nlm.nih.gov/39188986","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/11345597"},"language":"en","primary_location":{"id":"doi:10.1016/j.isci.2024.110584","doi":"https://doi.org/10.1016/j.isci.2024.110584","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.isci.2024.110584","pdf_url":null,"source":{"id":"https://openalex.org/S2898358376","display_name":"iScience","issn_l":"2589-0042","issn":["2589-0042"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-1","ki-jl-1","norway-1","oarl","poland-20","vabb-shw"],"host_organization":"https://openalex.org/P4310315673","host_organization_name":"Cell Press","host_organization_lineage":["https://openalex.org/P4310315673","https://openalex.org/P4310320990"],"host_organization_lineage_names":["Cell Press","Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"iScience","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/j.isci.2024.110584","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Jiyun Hu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210111013","display_name":"Nanjing Drum Tower Hospital","ror":"https://ror.org/026axqv54","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210111013"]},{"id":"https://openalex.org/I4391768045","display_name":"State Key Laboratory of Pharmaceutical Biotechnology","ror":"https://ror.org/043ea4m21","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4391768045","https://openalex.org/I881766915"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiyun Hu","raw_affiliation_strings":["State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China","institution_ids":["https://openalex.org/I4210111013","https://openalex.org/I4391768045","https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113305548","display_name":"Zetong Xing","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210111013","display_name":"Nanjing Drum Tower Hospital","ror":"https://ror.org/026axqv54","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210111013"]},{"id":"https://openalex.org/I4391768045","display_name":"State Key Laboratory of Pharmaceutical Biotechnology","ror":"https://ror.org/043ea4m21","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4391768045","https://openalex.org/I881766915"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zetong Xing","raw_affiliation_strings":["State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China","institution_ids":["https://openalex.org/I4210111013","https://openalex.org/I4391768045","https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hongbing Yang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210111013","display_name":"Nanjing Drum Tower Hospital","ror":"https://ror.org/026axqv54","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210111013"]},{"id":"https://openalex.org/I4391768045","display_name":"State Key Laboratory of Pharmaceutical Biotechnology","ror":"https://ror.org/043ea4m21","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4391768045","https://openalex.org/I881766915"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongbing Yang","raw_affiliation_strings":["State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China","institution_ids":["https://openalex.org/I4210111013","https://openalex.org/I4391768045","https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025504111","display_name":"Yongli Zhou","orcid":"https://orcid.org/0000-0003-1387-2783","observed_orcids":["https://orcid.org/0000-0003-1387-2783"]},"institutions":[{"id":"https://openalex.org/I4210111013","display_name":"Nanjing Drum Tower Hospital","ror":"https://ror.org/026axqv54","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210111013"]},{"id":"https://openalex.org/I4391768045","display_name":"State Key Laboratory of Pharmaceutical Biotechnology","ror":"https://ror.org/043ea4m21","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4391768045","https://openalex.org/I881766915"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongli Zhou","raw_affiliation_strings":["State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China","institution_ids":["https://openalex.org/I4210111013","https://openalex.org/I4391768045","https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025626137","display_name":"Liufei Guo","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210136859","display_name":"Xi\u2019an University of Posts and Telecommunications","ror":"https://ror.org/04jn0td46","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210136859"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liufei Guo","raw_affiliation_strings":["School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, Shaanxi 710121, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, Shaanxi 710121, China","institution_ids":["https://openalex.org/I4210136859"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065425755","display_name":"Xianhong Zhang","orcid":"https://orcid.org/0000-0003-4595-9189","observed_orcids":["https://orcid.org/0000-0003-4595-9189"]},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xianhong Zhang","raw_affiliation_strings":["RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000913831","display_name":"Longsheng Xu","orcid":"https://orcid.org/0009-0004-1959-8185","observed_orcids":["https://orcid.org/0009-0004-1959-8185"]},"institutions":[{"id":"https://openalex.org/I4210111013","display_name":"Nanjing Drum Tower Hospital","ror":"https://ror.org/026axqv54","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210111013"]},{"id":"https://openalex.org/I4391768045","display_name":"State Key Laboratory of Pharmaceutical Biotechnology","ror":"https://ror.org/043ea4m21","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4391768045","https://openalex.org/I881766915"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Longsheng Xu","raw_affiliation_strings":["State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China","institution_ids":["https://openalex.org/I4210111013","https://openalex.org/I4391768045","https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100336321","display_name":"Qiong Liu","orcid":"https://orcid.org/0000-0003-1459-448X","observed_orcids":["https://orcid.org/0000-0003-1459-448X"]},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I4210159865","display_name":"Xiangya Hospital Central South University","ror":"https://ror.org/05c1yfj14","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159865"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiong Liu","raw_affiliation_strings":["Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China","institution_ids":["https://openalex.org/I139660479","https://openalex.org/I4210159865"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100394421","display_name":"Jing Ye","orcid":"https://orcid.org/0000-0003-3507-5355","observed_orcids":["https://orcid.org/0000-0003-3507-5355","https://orcid.org/0009-0008-0848-1570"]},"institutions":[{"id":"https://openalex.org/I4210111013","display_name":"Nanjing Drum Tower Hospital","ror":"https://ror.org/026axqv54","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210111013"]},{"id":"https://openalex.org/I4391768045","display_name":"State Key Laboratory of Pharmaceutical Biotechnology","ror":"https://ror.org/043ea4m21","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4391768045","https://openalex.org/I881766915"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Ye","raw_affiliation_strings":["State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China","institution_ids":["https://openalex.org/I4210111013","https://openalex.org/I4391768045","https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101843659","display_name":"Xiaoming Zhong","orcid":"https://orcid.org/0000-0003-1415-074X","observed_orcids":["https://orcid.org/0000-0003-1415-074X"]},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoming Zhong","raw_affiliation_strings":["Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, Memphis, TN 38105, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, Memphis, TN 38105, USA","institution_ids":["https://openalex.org/I1313298211"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101965287","display_name":"Jixin Wang","orcid":"https://orcid.org/0000-0003-4085-6041","observed_orcids":["https://orcid.org/0000-0003-4085-6041"]},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":"CN","type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jixin Wang","raw_affiliation_strings":["Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China","institution_ids":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056029519","display_name":"Ruoyao Lin","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210111013","display_name":"Nanjing Drum Tower Hospital","ror":"https://ror.org/026axqv54","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210111013"]},{"id":"https://openalex.org/I4391768045","display_name":"State Key Laboratory of Pharmaceutical Biotechnology","ror":"https://ror.org/043ea4m21","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4391768045","https://openalex.org/I881766915"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruoyao Lin","raw_affiliation_strings":["State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China","institution_ids":["https://openalex.org/I4210111013","https://openalex.org/I4391768045","https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088402297","display_name":"Erping Long","orcid":"https://orcid.org/0000-0002-3502-5596","observed_orcids":["https://orcid.org/0000-0002-3502-5596"]},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":"CN","type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Erping Long","raw_affiliation_strings":["Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China","institution_ids":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003053955","display_name":"Jiewei Jiang","orcid":"https://orcid.org/0000-0002-4306-793X","observed_orcids":["https://orcid.org/0000-0002-4306-793X"]},"institutions":[{"id":"https://openalex.org/I4210136859","display_name":"Xi\u2019an University of Posts and Telecommunications","ror":"https://ror.org/04jn0td46","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210136859"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiewei Jiang","raw_affiliation_strings":["School of Electronic Engineering, Xi'an University of Posts and Telecommunications, Xi'an, Shaanxi 710121, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electronic Engineering, Xi'an University of Posts and Telecommunications, Xi'an, Shaanxi 710121, China","institution_ids":["https://openalex.org/I4210136859"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100334546","display_name":"Liang Chen","orcid":"https://orcid.org/0000-0001-5845-2235","observed_orcids":["https://orcid.org/0000-0001-5845-2235"]},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liang Chen","raw_affiliation_strings":["RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058026632","display_name":"Yongcheng Pan","orcid":"https://orcid.org/0000-0001-5317-3675","observed_orcids":["https://orcid.org/0000-0001-5317-3675"]},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I4210159865","display_name":"Xiangya Hospital Central South University","ror":"https://ror.org/05c1yfj14","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159865"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongcheng Pan","raw_affiliation_strings":["Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China","institution_ids":["https://openalex.org/I139660479","https://openalex.org/I4210159865"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054625077","display_name":"Lang He","orcid":"https://orcid.org/0000-0003-2515-8579","observed_orcids":["https://orcid.org/0000-0003-2515-8579"]},"institutions":[{"id":"https://openalex.org/I4210136859","display_name":"Xi\u2019an University of Posts and Telecommunications","ror":"https://ror.org/04jn0td46","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210136859"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lang He","raw_affiliation_strings":["School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, Shaanxi 710121, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, Shaanxi 710121, China","institution_ids":["https://openalex.org/I4210136859"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100380043","display_name":"Jiayu Chen","orcid":"https://orcid.org/0000-0001-9449-9321","observed_orcids":["https://orcid.org/0000-0001-9449-9321","https://orcid.org/0009-0002-6500-2835"]},"institutions":[{"id":"https://openalex.org/I4210111013","display_name":"Nanjing Drum Tower Hospital","ror":"https://ror.org/026axqv54","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210111013"]},{"id":"https://openalex.org/I4391768045","display_name":"State Key Laboratory of Pharmaceutical Biotechnology","ror":"https://ror.org/043ea4m21","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4391768045","https://openalex.org/I881766915"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jia-Yu Chen","raw_affiliation_strings":["Nanchuang (Jiangsu) Institute of Chemistry and Health, Nanjing, Jiangsu 210023, China","State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China"],"raw_orcid":"https://orcid.org/0000-0001-9449-9321","affiliations":[{"raw_affiliation_string":"Nanchuang (Jiangsu) Institute of Chemistry and Health, Nanjing, Jiangsu 210023, China","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China","institution_ids":["https://openalex.org/I4210111013","https://openalex.org/I4391768045","https://openalex.org/I881766915"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5054625077","https://openalex.org/A5100380043"],"corresponding_institution_ids":["https://openalex.org/I4210111013","https://openalex.org/I4210136859","https://openalex.org/I4391768045","https://openalex.org/I881766915"],"apc_list":{"value":3150,"currency":"USD","value_usd":3150},"apc_paid":{"value":3150,"currency":"USD","value_usd":3150},"fwci":0.8144,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.67755903,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"27","issue":"8","first_page":"110584","last_page":"110584"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.22550000250339508,"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":0.22550000250339508,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.133200004696846,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.08510000258684158,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/r-loops","display_name":"R-loops","score":0.8759999871253967},{"id":"https://openalex.org/keywords/repeat-expansion-disorders","display_name":"repeat expansion disorders","score":0.7670000195503235},{"id":"https://openalex.org/keywords/tandem-repeats","display_name":"tandem repeats","score":0.984000027179718},{"id":"https://openalex.org/keywords/nucleotide-composition","display_name":"nucleotide composition","score":0.8790000081062317},{"id":"https://openalex.org/keywords/web-server","display_name":"web server","score":0.7020000219345093},{"id":"https://openalex.org/keywords/deep-learning","display_name":"deep learning","score":0.6060000061988831}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6284991502761841},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.5941258668899536},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5321207642555237},{"id":"https://openalex.org/C186886427","wikidata":"https://www.wikidata.org/wiki/Q5441213","display_name":"Feedback loop","level":2,"score":0.481610506772995},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4722278118133545},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4266631007194519},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4167129695415497},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.41486042737960815},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38213539123535156},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3568534553050995},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32083335518836975},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.16809087991714478},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1016/j.isci.2024.110584","doi":"https://doi.org/10.1016/j.isci.2024.110584","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.isci.2024.110584","pdf_url":null,"source":{"id":"https://openalex.org/S2898358376","display_name":"iScience","issn_l":"2589-0042","issn":["2589-0042"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-1","ki-jl-1","norway-1","oarl","poland-20","vabb-shw"],"host_organization":"https://openalex.org/P4310315673","host_organization_name":"Cell Press","host_organization_lineage":["https://openalex.org/P4310315673","https://openalex.org/P4310320990"],"host_organization_lineage_names":["Cell Press","Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"iScience","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11345597","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11345597","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11345597/pdf/main.pdf","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,"listed_in":[],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"iScience","raw_type":"Text"},{"id":"pmid:39188986","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39188986","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,"listed_in":[],"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":"iScience","raw_type":"Journal Article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt6c1262zh","doi":null,"is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/6c1262zh","pdf_url":"https://escholarship.org/content/qt6c1262zh/qt6c1262zh.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"iScience, vol 27, iss 8","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:c714c0812b68414f9e41a158f9664b95","doi":null,"is_oa":false,"landing_page_url":"https://doaj.org/article/c714c0812b68414f9e41a158f9664b95","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"iScience, Vol 27, Iss 8, Pp 110584- (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1016/j.isci.2024.110584","doi":"https://doi.org/10.1016/j.isci.2024.110584","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.isci.2024.110584","pdf_url":null,"source":{"id":"https://openalex.org/S2898358376","display_name":"iScience","issn_l":"2589-0042","issn":["2589-0042"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-1","ki-jl-1","norway-1","oarl","poland-20","vabb-shw"],"host_organization":"https://openalex.org/P4310315673","host_organization_name":"Cell Press","host_organization_lineage":["https://openalex.org/P4310315673","https://openalex.org/P4310320990"],"host_organization_lineage_names":["Cell Press","Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"iScience","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G134330249","display_name":null,"funder_award_id":"62,376,215","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6121050021","display_name":null,"funder_award_id":"22293051","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7586881478","display_name":null,"funder_award_id":"32170653","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/F4320324207","display_name":"Jiangsu Provincial Department of Education","ror":"https://ror.org/059md9404"},{"id":"https://openalex.org/F4320324852","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760"},{"id":"https://openalex.org/F4320328119","display_name":"National University's Basic Research Foundation of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null},{"id":"https://openalex.org/F4320335895","display_name":"Dream Project of Ministry of Science and Technology of the People's Republic of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W146312310","https://openalex.org/W1585249222","https://openalex.org/W1709815505","https://openalex.org/W1967706132","https://openalex.org/W1968421165","https://openalex.org/W1969558292","https://openalex.org/W1978916055","https://openalex.org/W1986097552","https://openalex.org/W1996425563","https://openalex.org/W2014440367","https://openalex.org/W2034973272","https://openalex.org/W2044375974","https://openalex.org/W2065219073","https://openalex.org/W2087587381","https://openalex.org/W2100440853","https://openalex.org/W2102619694","https://openalex.org/W2134018441","https://openalex.org/W2138207763","https://openalex.org/W2149919973","https://openalex.org/W2170551349","https://openalex.org/W2171808845","https://openalex.org/W2340421620","https://openalex.org/W2463453322","https://openalex.org/W2513764101","https://openalex.org/W2555792758","https://openalex.org/W2558179461","https://openalex.org/W2612410326","https://openalex.org/W2749177415","https://openalex.org/W2765204989","https://openalex.org/W2766758135","https://openalex.org/W2783549214","https://openalex.org/W2795054998","https://openalex.org/W2894328098","https://openalex.org/W2901218091","https://openalex.org/W2913346540","https://openalex.org/W2921848211","https://openalex.org/W2933273758","https://openalex.org/W2935703330","https://openalex.org/W2936173918","https://openalex.org/W2939234892","https://openalex.org/W2952759709","https://openalex.org/W2979531443","https://openalex.org/W2982329060","https://openalex.org/W2982599603","https://openalex.org/W3004029085","https://openalex.org/W3006145935","https://openalex.org/W3007507416","https://openalex.org/W3035507786","https://openalex.org/W3045910546","https://openalex.org/W3119904643","https://openalex.org/W3122083512","https://openalex.org/W3130392918","https://openalex.org/W3130538872","https://openalex.org/W3170696603","https://openalex.org/W3184027992","https://openalex.org/W3213066457","https://openalex.org/W3217268895","https://openalex.org/W4212869955","https://openalex.org/W4224293621","https://openalex.org/W4250605189","https://openalex.org/W4283578693","https://openalex.org/W4292451571","https://openalex.org/W4293555592","https://openalex.org/W4296100759","https://openalex.org/W4310088497","https://openalex.org/W4312019771","https://openalex.org/W4380536483"],"related_works":["https://openalex.org/W3217268895","https://openalex.org/W2606776612","https://openalex.org/W4411209978","https://openalex.org/W4286210692","https://openalex.org/W4312019771","https://openalex.org/W2558179461","https://openalex.org/W2098090834","https://openalex.org/W4353096517","https://openalex.org/W6931078160","https://openalex.org/W4293555592"],"abstract_inverted_index":{"R-loops":[0,10,34,62],"play":[1],"diverse":[2],"functional":[3],"roles,":[4],"but":[5],"controversial":[6],"genomic":[7],"localization":[8],"of":[9,26,61,67,73,120,133],"have":[11,110],"emerged":[12],"from":[13],"experimental":[14],"approaches,":[15],"posing":[16],"significant":[17],"challenges":[18],"for":[19,31,96],"R-loop":[20,46,77,90,134],"research.":[21,135],"The":[22],"development":[23],"and":[24,63,70,89],"application":[25],"an":[27,36,117],"accurate":[28,58],"computational":[29],"tool":[30],"studying":[32],"human":[33],"remains":[35],"unmet":[37],"need.":[38],"Here,":[39],"we":[40,109],"introduce":[41],"DeepER,":[42],"a":[43,64,82,93,112],"deep":[44],"learning-enhanced":[45],"prediction":[47],"tool.":[48],"DeepER":[49,79,125],"showcases":[50],"outstanding":[51],"performance":[52],"compared":[53],"to":[54],"existing":[55],"tools,":[56],"facilitating":[57],"genome-wide":[59],"annotation":[60],"deeper":[65],"understanding":[66,97],"the":[68,98,131],"position-":[69],"context-dependent":[71],"effects":[72],"nucleotide":[74],"composition":[75],"on":[76],"formation.":[78],"also":[80],"unveils":[81],"strong":[83],"association":[84],"between":[85],"certain":[86],"tandem":[87],"repeats":[88],"formation,":[91],"opening":[92],"new":[94],"avenue":[95],"mechanisms":[99],"underlying":[100],"some":[101],"repeat":[102],"expansion":[103],"diseases.":[104],"To":[105],"facilitate":[106],"broader":[107],"utilization,":[108],"developed":[111],"user-friendly":[113],"web":[114],"server":[115],"as":[116],"integral":[118],"component":[119],"R-loopBase.":[121],"We":[122],"anticipate":[123],"that":[124],"will":[126],"find":[127],"extensive":[128],"applications":[129],"in":[130],"field":[132]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":2}],"updated_date":"2026-10-29T09:56:32.521200","created_date":"2024-07-26T00:00:00"}
