{"id":"https://openalex.org/W4415971009","doi":"https://doi.org/10.1109/jbhi.2025.3629554","title":"Genetic Perturbation Modeling for Human Cell Therapy With BRNET","display_name":"Genetic Perturbation Modeling for Human Cell Therapy With BRNET","publication_year":2025,"publication_date":"2025-11-06","ids":{"openalex":"https://openalex.org/W4415971009","doi":"https://doi.org/10.1109/jbhi.2025.3629554","pmid":"https://pubmed.ncbi.nlm.nih.gov/41196787"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3629554","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3629554","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5120284313","display_name":"Luyang Cai","orcid":"https://orcid.org/0000-0002-2303-492X"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Luyang Cai","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR"],"raw_orcid":"https://orcid.org/0000-0002-2303-492X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067196905","display_name":"Jixiang Yu","orcid":"https://orcid.org/0000-0001-8163-3253"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jixang Yu","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR"],"raw_orcid":"https://orcid.org/0000-0001-8163-3253","affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066935890","display_name":"Qiuzhen Lin","orcid":"https://orcid.org/0000-0003-2415-0401"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiuzhen Lin","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0003-2415-0401","affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101436881","display_name":"Licheng Liu","orcid":"https://orcid.org/0000-0003-4891-9211"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lichen Liu","raw_affiliation_strings":["College of Electrical and Information Engineering, Hunan University, Changsha, China"],"raw_orcid":"https://orcid.org/0000-0003-4891-9211","affiliations":[{"raw_affiliation_string":"College of Electrical and Information Engineering, Hunan University, Changsha, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102718214","display_name":"Xiangtao Li","orcid":"https://orcid.org/0000-0002-8716-9823"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangtao Li","raw_affiliation_strings":["School of Artificial Intelligence, Jilin University, Changchun, China"],"raw_orcid":"https://orcid.org/0000-0002-8716-9823","affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University, Changchun, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030015771","display_name":"Ka\u2010Chun Wong","orcid":"https://orcid.org/0000-0001-6062-733X"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Ka-Chun Wong","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR"],"raw_orcid":"https://orcid.org/0000-0001-6062-733X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.24466619,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"30","issue":"5","first_page":"3971","last_page":"3980"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.13860000669956207,"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":0.13860000669956207,"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/T10505","display_name":"Pluripotent Stem Cells Research","score":0.0925000011920929,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.0406000018119812,"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/deep-learning","display_name":"Deep learning","score":0.454800009727478},{"id":"https://openalex.org/keywords/human-cell","display_name":"Human cell","score":0.42640000581741333},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.42100000381469727},{"id":"https://openalex.org/keywords/perturbation","display_name":"Perturbation (astronomy)","score":0.413100004196167},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.37070000171661377},{"id":"https://openalex.org/keywords/deep-neural-networks","display_name":"Deep neural networks","score":0.33169999718666077},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.31630000472068787},{"id":"https://openalex.org/keywords/genetic-variants","display_name":"Genetic variants","score":0.3124000132083893}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.614300012588501},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.578000009059906},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5009999871253967},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.46619999408721924},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.454800009727478},{"id":"https://openalex.org/C2993684226","wikidata":"https://www.wikidata.org/wiki/Q2662727","display_name":"Human cell","level":3,"score":0.42640000581741333},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.42100000381469727},{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.413100004196167},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.37070000171661377},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.33169999718666077},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.31630000472068787},{"id":"https://openalex.org/C2993967602","wikidata":"https://www.wikidata.org/wiki/Q5532932","display_name":"Genetic variants","level":4,"score":0.3124000132083893},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3019999861717224},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2955999970436096},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.29409998655319214},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.28220000863075256},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.2745000123977661},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.26919999718666077},{"id":"https://openalex.org/C2986949344","wikidata":"https://www.wikidata.org/wiki/Q9404","display_name":"Neural system","level":2,"score":0.2685999870300293},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26829999685287476},{"id":"https://openalex.org/C2993807623","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genetic data","level":3,"score":0.2669000029563904},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.26260000467300415},{"id":"https://openalex.org/C47042493","wikidata":"https://www.wikidata.org/wiki/Q265799","display_name":"Human genetics","level":3,"score":0.25360000133514404}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":true},{"descriptor_ui":"D064987","descriptor_name":"Cell- and Tissue-Based Therapy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2025.3629554","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3629554","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:41196787","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41196787","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":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1164128992","display_name":null,"funder_award_id":"CityU 9667265","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"},{"id":"https://openalex.org/G285707867","display_name":null,"funder_award_id":"ITB/FBL/9037/22/S","funder_id":"https://openalex.org/F4320321920","funder_display_name":"Innovation and Technology Commission"},{"id":"https://openalex.org/G4263406905","display_name":null,"funder_award_id":"CityU 7030022","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"},{"id":"https://openalex.org/G585430619","display_name":null,"funder_award_id":"C1056-24G","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"},{"id":"https://openalex.org/G6278479301","display_name":null,"funder_award_id":"32170654","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8797692665","display_name":null,"funder_award_id":"32000464","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320309893","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321920","display_name":"Innovation and Technology Commission","ror":"https://ror.org/04vf9tr09"},{"id":"https://openalex.org/F4320333998","display_name":"Shenzhen Research Institute, City University of Hong Kong","ror":"https://ror.org/00xc0ma20"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Cellular":[0],"responses":[1,76],"to":[2,16,73,77,107],"genetic":[3,82],"perturbations":[4,59],"are":[5],"prevalent":[6],"in":[7],"wide":[8],"contexts":[9],"from":[10],"the":[11,17,23,30,47,92,98],"fundamental":[12],"understandings":[13],"on":[14],"pathology":[15],"development":[18],"of":[19,25,33,100],"clinical":[20],"therapies":[21],"and":[22,42,80],"discovery":[24],"novel":[26],"drug":[27],"targets.":[28],"Nonetheless,":[29],"substantial":[31],"amount":[32],"possible":[34],"perturbation":[35],"combinations":[36],"renders":[37],"wet-lab":[38],"experiments":[39],"prohibitively":[40],"expensive":[41],"time-consuming.":[43],"To":[44],"address":[45],"it,":[46],"BRNET":[48,61,87],"model":[49],"is":[50],"proposed":[51],"for":[52],"predicting":[53],"non-linear":[54],"transcriptional":[55,75],"outcomes":[56],"where":[57],"multiple":[58,81],"exist.":[60],"integrates":[62],"prior":[63],"knowledge":[64],"with":[65],"advanced":[66],"embeddings":[67],"into":[68],"a":[69],"non-stacked":[70],"neural":[71],"structure":[72],"predict":[74],"both":[78],"individual":[79],"perturbations.":[83,94],"For":[84],"unseen":[85],"scenarios,":[86],"also":[88],"generalizes":[89],"well":[90],"under":[91],"corresponding":[93],"Experimental":[95],"results":[96],"highlight":[97],"capabilities":[99],"BRNET,":[101],"demonstrating":[102],"promising":[103],"performance":[104],"as":[105],"compared":[106],"established":[108],"deep":[109],"learning":[110],"models.":[111]},"counts_by_year":[],"updated_date":"2026-05-08T13:12:06.581006","created_date":"2025-11-06T00:00:00"}