{"id":"https://openalex.org/W4413257452","doi":"https://doi.org/10.1093/bib/bbaf419","title":"Design of function-regulating RNA via deep learning and AlphaFold 3","display_name":"Design of function-regulating RNA via deep learning and AlphaFold 3","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4413257452","doi":"https://doi.org/10.1093/bib/bbaf419","pmid":"https://pubmed.ncbi.nlm.nih.gov/40817912"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf419","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf419","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf419/64068047/bbaf419.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf419/64068047/bbaf419.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100760201","display_name":"Yan Xia","orcid":"https://orcid.org/0000-0003-4509-0137"},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4210100255","display_name":"Beijing Academy of Artificial Intelligence","ror":"https://ror.org/016a74861","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210100255"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Xia","raw_affiliation_strings":["Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","Zhongguancun Artificial Intelligence Research Institute , Building 5, Yard 17, Daniu\u00adfang Second Ring Road, Haidian District, Beijing 100080 ,","Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China","Zhongguancun Artificial Intelligence Research Institute, Building 5, Yard 17, Daniu-fang Second Ring Road, Haidian District, Beijing 100080, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Zhongguancun Artificial Intelligence Research Institute , Building 5, Yard 17, Daniu\u00adfang Second Ring Road, Haidian District, Beijing 100080 ,","institution_ids":["https://openalex.org/I4210100255"]},{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China","institution_ids":["https://openalex.org/I125839683"]},{"raw_affiliation_string":"Zhongguancun Artificial Intelligence Research Institute, Building 5, Yard 17, Daniu-fang Second Ring Road, Haidian District, Beijing 100080, China","institution_ids":["https://openalex.org/I4210100255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077966478","display_name":"Zeyu Liang","orcid":"https://orcid.org/0000-0002-6441-0928"},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zeyu Liang","raw_affiliation_strings":["Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China","institution_ids":["https://openalex.org/I125839683"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102679938","display_name":"Xiaowen Du","orcid":null},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaowen Du","raw_affiliation_strings":["Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China","institution_ids":["https://openalex.org/I125839683"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113235533","display_name":"Dengtian Cao","orcid":null},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dengtian Cao","raw_affiliation_strings":["Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China","institution_ids":["https://openalex.org/I125839683"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100337139","display_name":"Jing Li","orcid":"https://orcid.org/0000-0003-4733-9100"},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Li","raw_affiliation_strings":["Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China","institution_ids":["https://openalex.org/I125839683"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086995810","display_name":"Lichao Sun","orcid":"https://orcid.org/0000-0002-3621-5252"},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I154341788","display_name":"Tangshan College","ror":"https://ror.org/00rfn0469","country_code":"CN","type":"education","lineage":["https://openalex.org/I154341788"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lichao Sun","raw_affiliation_strings":["Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","Tangshan Research Institute, Beijing Institute of Technology , No. 57, South Jianshe Road, Lubei District, Tangshan, Hebei 063000 ,","Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China","Tangshan Research Institute, Beijing Institute of Technology, No. 57, South Jianshe Road, Lubei District, Tangshan, Hebei 063000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Tangshan Research Institute, Beijing Institute of Technology , No. 57, South Jianshe Road, Lubei District, Tangshan, Hebei 063000 ,","institution_ids":["https://openalex.org/I154341788"]},{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China","institution_ids":["https://openalex.org/I125839683"]},{"raw_affiliation_string":"Tangshan Research Institute, Beijing Institute of Technology, No. 57, South Jianshe Road, Lubei District, Tangshan, Hebei 063000, China","institution_ids":["https://openalex.org/I154341788"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072246677","display_name":"Yi\u2010Xin Huo","orcid":"https://orcid.org/0000-0003-4644-999X"},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I154341788","display_name":"Tangshan College","ror":"https://ror.org/00rfn0469","country_code":"CN","type":"education","lineage":["https://openalex.org/I154341788"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]},{"id":"https://openalex.org/I4210162556","display_name":"Shangri-la Institute","ror":"https://ror.org/05e0fad36","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I4210162556"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yi-Xin Huo","raw_affiliation_strings":["Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","Muyuan Laboratory, Center for Future Foods , Muyuan Building, No. 110 Shangding Road, Guancheng Hui District, Zhengzhou, Henan 450016 ,","Tangshan Research Institute, Beijing Institute of Technology , No. 57, South Jianshe Road, Lubei District, Tangshan, Hebei 063000 ,","Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China","Muyuan Laboratory, Center for Future Foods, Muyuan Building, No. 110 Shangding Road, Guancheng Hui District, Zhengzhou, Henan 450016, China","Tangshan Research Institute, Beijing Institute of Technology, No. 57, South Jianshe Road, Lubei District, Tangshan, Hebei 063000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Muyuan Laboratory, Center for Future Foods , Muyuan Building, No. 110 Shangding Road, Guancheng Hui District, Zhengzhou, Henan 450016 ,","institution_ids":["https://openalex.org/I4210162556"]},{"raw_affiliation_string":"Tangshan Research Institute, Beijing Institute of Technology , No. 57, South Jianshe Road, Lubei District, Tangshan, Hebei 063000 ,","institution_ids":["https://openalex.org/I154341788"]},{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China","institution_ids":["https://openalex.org/I125839683"]},{"raw_affiliation_string":"Muyuan Laboratory, Center for Future Foods, Muyuan Building, No. 110 Shangding Road, Guancheng Hui District, Zhengzhou, Henan 450016, China","institution_ids":["https://openalex.org/I4210162556"]},{"raw_affiliation_string":"Tangshan Research Institute, Beijing Institute of Technology, No. 57, South Jianshe Road, Lubei District, Tangshan, Hebei 063000, China","institution_ids":["https://openalex.org/I154341788"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101991899","display_name":"Shuyuan Guo","orcid":"https://orcid.org/0000-0001-7801-2528"},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shuyuan Guo","raw_affiliation_strings":["Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China"],"raw_orcid":"https://orcid.org/0000-0001-7801-2528","affiliations":[{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081 ,","institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, Beijing Municipality 100081, China","institution_ids":["https://openalex.org/I125839683"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5072246677","https://openalex.org/A5101991899"],"corresponding_institution_ids":["https://openalex.org/I125839683","https://openalex.org/I154341788","https://openalex.org/I4210161752","https://openalex.org/I4210162556"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":4.5193,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.95471157,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"26","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9998999834060669,"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/T12610","display_name":"RNA regulation and disease","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6056669354438782},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.602422297000885},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5576810836791992},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5544450283050537},{"id":"https://openalex.org/keywords/guide-rna","display_name":"Guide RNA","score":0.4594723582267761},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3685111403465271},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3514501750469208},{"id":"https://openalex.org/keywords/genome-editing","display_name":"Genome editing","score":0.2951585054397583},{"id":"https://openalex.org/keywords/crispr","display_name":"CRISPR","score":0.24420508742332458},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22379177808761597}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6056669354438782},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.602422297000885},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5576810836791992},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5544450283050537},{"id":"https://openalex.org/C97702854","wikidata":"https://www.wikidata.org/wiki/Q4039747","display_name":"Guide RNA","level":5,"score":0.4594723582267761},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3685111403465271},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3514501750469208},{"id":"https://openalex.org/C144501496","wikidata":"https://www.wikidata.org/wiki/Q5533489","display_name":"Genome editing","level":4,"score":0.2951585054397583},{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.24420508742332458},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22379177808761597}],"mesh":[{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf419","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf419","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf419/64068047/bbaf419.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40817912","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40817912","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},{"id":"pmh:oai:pubmedcentral.nih.gov:12357492","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12357492","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf419","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf419","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf419/64068047/bbaf419.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.5299999713897705,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G4357571571","display_name":null,"funder_award_id":"32370095","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6411109246","display_name":null,"funder_award_id":"32371489","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8257678389","display_name":null,"funder_award_id":"2024YFA0917501","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320323110","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413257452.pdf","grobid_xml":"https://content.openalex.org/works/W4413257452.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W125198778","https://openalex.org/W1969189143","https://openalex.org/W1973468599","https://openalex.org/W1978942464","https://openalex.org/W2021333801","https://openalex.org/W2035687084","https://openalex.org/W2097971843","https://openalex.org/W2104820165","https://openalex.org/W2107959600","https://openalex.org/W2137721714","https://openalex.org/W2147988069","https://openalex.org/W2319766208","https://openalex.org/W2330294152","https://openalex.org/W2330361263","https://openalex.org/W2404280981","https://openalex.org/W2433523887","https://openalex.org/W2554763217","https://openalex.org/W2557904026","https://openalex.org/W2790470680","https://openalex.org/W2803245377","https://openalex.org/W2810756255","https://openalex.org/W2949223833","https://openalex.org/W2977817275","https://openalex.org/W3005061245","https://openalex.org/W3092434764","https://openalex.org/W3101525813","https://openalex.org/W3127135885","https://openalex.org/W4200232768","https://openalex.org/W4206680700","https://openalex.org/W4292779060","https://openalex.org/W4293475204","https://openalex.org/W4362062054","https://openalex.org/W4387440676","https://openalex.org/W4390975839","https://openalex.org/W4396721167","https://openalex.org/W4399202307","https://openalex.org/W4404112650","https://openalex.org/W4404595545"],"related_works":["https://openalex.org/W4402525460","https://openalex.org/W4244488511","https://openalex.org/W2013278374","https://openalex.org/W1892019602","https://openalex.org/W2127264766","https://openalex.org/W2147993839","https://openalex.org/W4407569316","https://openalex.org/W2464653720","https://openalex.org/W2898360779","https://openalex.org/W2794852126"],"abstract_inverted_index":{"RNAs":[0,122],"are":[1],"programmable":[2],"macromolecules":[3],"that":[4,33,96],"play":[5],"diverse":[6],"regulatory":[7,19,121],"roles":[8],"in":[9,133],"living":[10],"organisms.":[11],"However,":[12],"the":[13,42,73,80,88,97,128],"intricate":[14],"structure-function":[15],"relationships":[16],"underlying":[17],"their":[18],"activities":[20],"pose":[21],"significant":[22],"challenges":[23],"for":[24,58,62,68,119],"RNA":[25,135],"design.":[26,136],"Here,":[27],"we":[28,94],"introduce":[29],"a":[30],"computational":[31],"framework":[32],"integrates":[34],"deep":[35],"learning":[36],"and":[37,66,126],"energy-based":[38],"methods":[39],"to":[40,56,87],"enhance":[41],"sequence":[43],"diversity":[44],"of":[45,54,82,90,100,111,130],"sgRNAs":[46],"designs.":[47],"Our":[48],"approach":[49],"demonstrates":[50],"high":[51],"editing":[52,71],"efficiencies":[53],"up":[55],"75%":[57],"gene":[59,70],"knockouts,":[60],"100%":[61],"large":[63],"fragment":[64],"deletions,":[65],"62.5%":[67],"multiplex":[69],"using":[72],"designed":[74,91],"sgRNAs.":[75],"Molecular":[76],"dynamic":[77],"simulations":[78],"suggested":[79],"stability":[81],"DNA-RNA-protein":[83],"complex":[84,124],"is":[85],"essential":[86],"functionality":[89],"RNAs.":[92],"Moreover,":[93],"reveal":[95],"confidence":[98],"metrics":[99],"AlphaFold":[101,131],"3":[102,132],"can":[103],"effectively":[104],"distinguish":[105],"functional":[106],"sequences,":[107],"enabling":[108],"one-shot":[109],"design":[110],"crRNAs.":[112],"This":[113],"work":[114],"presents":[115],"an":[116],"efficient":[117],"strategy":[118],"designing":[120],"with":[123],"interactions":[125],"establishes":[127],"potential":[129],"advancing":[134]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":3}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}