{"id":"https://openalex.org/W4394014672","doi":"https://doi.org/10.1093/bib/bbae143","title":"DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding","display_name":"DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding","publication_year":2024,"publication_date":"2024-03-27","ids":{"openalex":"https://openalex.org/W4394014672","doi":"https://doi.org/10.1093/bib/bbae143","pmid":"https://pubmed.ncbi.nlm.nih.gov/38581416"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae143","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae143","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae143/57160265/bbae143.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","license_id":"https://openalex.org/licenses/cc-by","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/25/3/bbae143/57160265/bbae143.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068590943","display_name":"Zhen Gao","orcid":"https://orcid.org/0000-0001-7427-6032"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Gao","raw_affiliation_strings":["Anhui University , School of Computer Science and Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Computer Science and Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China"],"raw_orcid":"https://orcid.org/0000-0001-7427-6032","affiliations":[{"raw_affiliation_string":"Anhui University , School of Computer Science and Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Computer Science and Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071754273","display_name":"Yansen Su","orcid":"https://orcid.org/0000-0002-3855-7133"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yansen Su","raw_affiliation_strings":["Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei, 230601, Anhui , China","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei, 230601, Anhui , China","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065943710","display_name":"Junfeng Xia","orcid":"https://orcid.org/0000-0003-3024-1705"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junfeng Xia","raw_affiliation_strings":["Anhui University , Institute of Physical Science and Information Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","Information Materials and Intelligent Sensing Laboratory of Anhui Province , Institute of Physical Science and Information Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Anhui University , Institute of Physical Science and Information Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province , Institute of Physical Science and Information Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101959312","display_name":"Ruifen Cao","orcid":"https://orcid.org/0000-0002-4223-3422"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui-Fen Cao","raw_affiliation_strings":["Anhui University , School of Computer Science and Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Computer Science and Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Anhui University , School of Computer Science and Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Computer Science and Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044032571","display_name":"Yun Ding","orcid":"https://orcid.org/0000-0002-2749-7710"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yun Ding","raw_affiliation_strings":["Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei, 230601, Anhui , China","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei, 230601, Anhui , China","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064185915","display_name":"Chun-Hou Zheng","orcid":"https://orcid.org/0000-0002-2695-1926"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chun-Hou Zheng","raw_affiliation_strings":["Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei, 230601, Anhui , China","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei, 230601, Anhui , China","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085214222","display_name":"Pi-Jing Wei","orcid":"https://orcid.org/0000-0003-2770-8781"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Pi-Jing Wei","raw_affiliation_strings":["Anhui University , Institute of Physical Science and Information Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","Information Materials and Intelligent Sensing Laboratory of Anhui Province , Institute of Physical Science and Information Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Anhui University , Institute of Physical Science and Information Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province , Institute of Physical Science and Information Technology, , 111 Jiulong Road, Hefei, 230601, Anhui , China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5064185915","https://openalex.org/A5085214222"],"corresponding_institution_ids":["https://openalex.org/I143868143"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":4.1562,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.95212328,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"25","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9988999962806702,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9962000250816345,"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":0.9937000274658203,"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/inference","display_name":"Inference","score":0.7968339920043945},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.7122598886489868},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6558721661567688},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5835493803024292},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5132598876953125},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5011880397796631},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.473471075296402},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4647236466407776},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.44568008184432983},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.43632954359054565},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41469213366508484},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3485994338989258},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32323676347732544},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.288632333278656},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.269258975982666},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2544516324996948},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10517582297325134}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7968339920043945},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.7122598886489868},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6558721661567688},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5835493803024292},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5132598876953125},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5011880397796631},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.473471075296402},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4647236466407776},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.44568008184432983},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.43632954359054565},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41469213366508484},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3485994338989258},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32323676347732544},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.288632333278656},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.269258975982666},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2544516324996948},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10517582297325134},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae143","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae143","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae143/57160265/bbae143.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38581416","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38581416","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:10998536","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10998536","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10998536/pdf/bbae143.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,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae143","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae143","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae143/57160265/bbae143.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7400000095367432,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1989873432","display_name":null,"funder_award_id":"2022AH020010","funder_id":"https://openalex.org/F4320321435","funder_display_name":"Anhui University"},{"id":"https://openalex.org/G2461069220","display_name":null,"funder_award_id":"62202004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4784360784","display_name":null,"funder_award_id":"2020YFA0908700","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5700703483","display_name":null,"funder_award_id":"62322301","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8602029459","display_name":null,"funder_award_id":"2108085QF267","funder_id":"https://openalex.org/F4320334897","funder_display_name":"Natural Science Foundation of Anhui Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321435","display_name":"Anhui University","ror":"https://ror.org/05th6yx34"},{"id":"https://openalex.org/F4320334897","display_name":"Natural Science Foundation of Anhui Province","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4394014672.pdf"},"referenced_works_count":76,"referenced_works":["https://openalex.org/W1978809975","https://openalex.org/W2062779027","https://openalex.org/W2070050178","https://openalex.org/W2076513103","https://openalex.org/W2103912979","https://openalex.org/W2109384743","https://openalex.org/W2115664087","https://openalex.org/W2126345910","https://openalex.org/W2136850043","https://openalex.org/W2142836135","https://openalex.org/W2142879323","https://openalex.org/W2152401289","https://openalex.org/W2159675211","https://openalex.org/W2165786088","https://openalex.org/W2175370850","https://openalex.org/W2232370058","https://openalex.org/W2345356016","https://openalex.org/W2737116586","https://openalex.org/W2782454362","https://openalex.org/W2803928488","https://openalex.org/W2890301877","https://openalex.org/W2899545492","https://openalex.org/W2914570111","https://openalex.org/W2916479752","https://openalex.org/W2949956784","https://openalex.org/W2998917483","https://openalex.org/W3003741176","https://openalex.org/W3024161231","https://openalex.org/W3087024869","https://openalex.org/W3090122263","https://openalex.org/W3095716988","https://openalex.org/W3096166580","https://openalex.org/W3097009024","https://openalex.org/W3101955739","https://openalex.org/W3127330229","https://openalex.org/W3128158089","https://openalex.org/W3145969289","https://openalex.org/W3159076767","https://openalex.org/W3159308014","https://openalex.org/W3172549105","https://openalex.org/W3173185686","https://openalex.org/W3176703930","https://openalex.org/W3184229885","https://openalex.org/W3193355876","https://openalex.org/W3201316265","https://openalex.org/W3202248730","https://openalex.org/W3211315472","https://openalex.org/W4200419205","https://openalex.org/W4206804332","https://openalex.org/W4207068394","https://openalex.org/W4211038303","https://openalex.org/W4211247697","https://openalex.org/W4220808568","https://openalex.org/W4223557148","https://openalex.org/W4225845169","https://openalex.org/W4230590699","https://openalex.org/W4286580811","https://openalex.org/W4288075003","https://openalex.org/W4290612160","https://openalex.org/W4308373390","https://openalex.org/W4312126395","https://openalex.org/W4313340543","https://openalex.org/W4315588221","https://openalex.org/W4318923052","https://openalex.org/W4321452549","https://openalex.org/W4324143648","https://openalex.org/W4362605796","https://openalex.org/W4378530717","https://openalex.org/W4379117479","https://openalex.org/W6677215612","https://openalex.org/W6785399799","https://openalex.org/W6803364997","https://openalex.org/W6847995554","https://openalex.org/W6848826828","https://openalex.org/W6849963647","https://openalex.org/W6851580717"],"related_works":["https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W2134575910","https://openalex.org/W4385727351","https://openalex.org/W4306798985","https://openalex.org/W2010571965","https://openalex.org/W2002709996","https://openalex.org/W3128451840","https://openalex.org/W4387092964"],"abstract_inverted_index":{"The":[0],"inference":[1],"of":[2,29,41,44,82,98,116,133,139,155,164,243],"gene":[3,8,68,184],"regulatory":[4,38,69,167],"networks":[5,70],"(GRNs)":[6],"from":[7],"expression":[9,162,185],"profiles":[10,163],"has":[11,202],"been":[12],"a":[13,60,104,140,171,203,236],"key":[14],"issue":[15],"in":[16,49],"systems":[17],"biology,":[18],"prompting":[19],"many":[20],"researchers":[21],"to":[22,109,127,149,239],"develop":[23],"diverse":[24],"computational":[25,51],"methods.":[26,52],"However,":[27],"most":[28],"these":[30],"methods":[31],"do":[32],"not":[33,180],"reconstruct":[34],"directed":[35,112],"GRNs":[36,81],"with":[37,72,89,166],"types":[39,75],"because":[40,160],"the":[42,50,80,96,111,117,120,129,134,152,161,190,232],"lack":[43],"benchmark":[45,56],"datasets":[46,57],"or":[47],"defects":[48],"Here,":[53],"we":[54],"collect":[55],"and":[58,76,91,122,136,194,209,214,224],"propose":[59],"deep":[61],"learning-based":[62],"model,":[63],"DeepFGRN,":[64],"for":[65,206,217],"reconstructing":[66],"fine":[67],"(FGRNs)":[71],"both":[73,207],"regulation":[74],"directions.":[77],"In":[78,158],"addition,":[79,159],"real":[83,153],"species":[84],"are":[85,125,169,228],"always":[86],"large":[87],"graphs":[88],"direction":[90],"high":[92],"sparsity,":[93],"which":[94],"impede":[95],"advancement":[97],"GRN":[99,208],"inference.":[100,211],"Therefore,":[101],"DeepFGRN":[102,201],"builds":[103],"node":[105],"bidirectional":[106],"representation":[107,115],"module":[108,174,179],"capture":[110],"graph":[113],"embedding":[114,132],"GRN.":[118],"Specifically,":[119,177],"source":[121,135],"target":[123,137,195],"generators":[124],"designed":[126],"learn":[128,151],"low-dimensional":[130],"dense":[131],"neighbors":[138,154],"gene,":[141],"respectively.":[142],"An":[143],"adversarial":[144],"learning":[145],"strategy":[146],"is":[147,175],"applied":[148],"iteratively":[150],"each":[156],"gene.":[157],"genes":[165],"associations":[168],"correlative,":[170],"correlation":[172,191],"analysis":[173],"designed.":[176],"this":[178],"only":[181],"fully":[182],"extracts":[183],"features,":[186],"but":[187],"also":[188],"captures":[189],"between":[192],"regulators":[193],"genes.":[196],"Experimental":[197],"results":[198],"show":[199],"that":[200],"competitive":[204],"capability":[205],"FGRN":[210],"Potential":[212],"biomarkers":[213],"therapeutic":[215],"drugs":[216],"breast":[218],"cancer,":[219,221],"liver":[220],"lung":[222],"cancer":[223],"coronavirus":[225],"disease":[226,244],"2019":[227],"identified":[229],"based":[230],"on":[231],"candidate":[233],"FGRNs,":[234],"providing":[235],"possible":[237],"opportunity":[238],"advance":[240],"our":[241],"knowledge":[242],"treatments.":[245]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-16T13:24:37.021932","created_date":"2025-10-10T00:00:00"}
