{"id":"https://openalex.org/W4412971922","doi":"https://doi.org/10.1109/tcbbio.2025.3590141","title":"DeepGDel: Deep Learning-Based Gene Deletion Prediction Framework for Growth-Coupled Production in Genome-Scale Metabolic Models","display_name":"DeepGDel: Deep Learning-Based Gene Deletion Prediction Framework for Growth-Coupled Production in Genome-Scale Metabolic Models","publication_year":2025,"publication_date":"2025-07-17","ids":{"openalex":"https://openalex.org/W4412971922","doi":"https://doi.org/10.1109/tcbbio.2025.3590141","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811281"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3590141","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3590141","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2433/297620","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070359048","display_name":"Ziwei Yang","orcid":"https://orcid.org/0000-0001-9846-840X"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ziwei Yang","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0001-9846-840X","affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041203895","display_name":"Takeyuki Tamura","orcid":"https://orcid.org/0000-0003-1596-901X"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takeyuki Tamura","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0003-1596-901X","affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"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":0.15100498,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"5","first_page":"2252","last_page":"2266"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9980000257492065,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9980000257492065,"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9336000084877014,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.928600013256073,"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/production","display_name":"Production (economics)","score":0.5674834847450256},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5638067126274109},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5372965335845947},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5362552404403687},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5290823578834534},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4926033616065979},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.47141146659851074},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4196033477783203},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41948679089546204},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3968556821346283},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.08854043483734131},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.057116568088531494}],"concepts":[{"id":"https://openalex.org/C2778348673","wikidata":"https://www.wikidata.org/wiki/Q739302","display_name":"Production (economics)","level":2,"score":0.5674834847450256},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5638067126274109},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5372965335845947},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5362552404403687},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5290823578834534},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4926033616065979},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47141146659851074},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4196033477783203},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41948679089546204},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3968556821346283},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.08854043483734131},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.057116568088531494},{"id":"https://openalex.org/C139719470","wikidata":"https://www.wikidata.org/wiki/Q39680","display_name":"Macroeconomics","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"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":"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":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbbio.2025.3590141","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3590141","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811281","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811281","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 transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:irdb.nii.ac.jp:01221:0006996586","is_oa":true,"landing_page_url":"http://hdl.handle.net/2433/297620","pdf_url":null,"source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal article"}],"best_oa_location":{"id":"pmh:oai:irdb.nii.ac.jp:01221:0006996586","is_oa":true,"landing_page_url":"http://hdl.handle.net/2433/297620","pdf_url":null,"source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal article"},"sustainable_development_goals":[{"score":0.4399999976158142,"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2"}],"awards":[{"id":"https://openalex.org/G6446962367","display_name":"Algorithms for  metabolic network design for efficient production of  valuable substances","funder_award_id":"23K20386","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1554187497","https://openalex.org/W1969983517","https://openalex.org/W1987607959","https://openalex.org/W2030776070","https://openalex.org/W2041715023","https://openalex.org/W2046546139","https://openalex.org/W2052056715","https://openalex.org/W2078355959","https://openalex.org/W2083693802","https://openalex.org/W2130832653","https://openalex.org/W2131629152","https://openalex.org/W2147598079","https://openalex.org/W2160541874","https://openalex.org/W2274217459","https://openalex.org/W2764202526","https://openalex.org/W2806157403","https://openalex.org/W2915175970","https://openalex.org/W2919115771","https://openalex.org/W2949325692","https://openalex.org/W2949564236","https://openalex.org/W2970610255","https://openalex.org/W3029836473","https://openalex.org/W3044625502","https://openalex.org/W3087971117","https://openalex.org/W3094103901","https://openalex.org/W3110776987","https://openalex.org/W3117121284","https://openalex.org/W3194997660","https://openalex.org/W4283032119","https://openalex.org/W4318071656","https://openalex.org/W4321454199","https://openalex.org/W4384561707","https://openalex.org/W4386918905","https://openalex.org/W4404944348","https://openalex.org/W4406828533","https://openalex.org/W4409019364","https://openalex.org/W4409077023"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W2611989081","https://openalex.org/W2086525401","https://openalex.org/W2731899572","https://openalex.org/W4230611425","https://openalex.org/W2006735166","https://openalex.org/W2079327011","https://openalex.org/W2053325634","https://openalex.org/W4294635752","https://openalex.org/W2394416426"],"abstract_inverted_index":{"In":[0,78],"genome-scale":[1,105],"constraint-based":[2],"metabolic":[3,106,164],"models,":[4],"gene":[5,29,39,87,98,120,128,179],"deletion":[6,40,88,99,129,180],"strategies":[7,100],"are":[8,21],"crucial":[9],"for":[10,27,61,75,96,101],"achieving":[11],"growth-coupled":[12,102],"production,":[13],"where":[14],"cell":[15],"growth":[16],"and":[17,35,48,91,117,121,156,175],"target":[18],"metabolite":[19,122],"production":[20,103],"simultaneously":[22],"achieved.":[23],"While":[24],"computational":[25],"methods":[26],"calculating":[28],"deletions":[30],"have":[31,36,49],"been":[32],"widely":[33],"explored":[34],"contributed":[37],"to":[38,51,70,115],"strategy":[41,89,130],"databases,":[42],"current":[43],"approaches":[44],"remain":[45],"computationally":[46],"demanding":[47],"yet":[50],"fully":[52],"leverage":[53],"emerging":[54],"data-driven":[55],"paradigms,":[56],"such":[57],"as":[58],"machine":[59],"learning,":[60],"more":[62],"efficient":[63],"strain":[64],"design.":[65],"Therefore,":[66],"it":[67],"is":[68],"necessary":[69],"propose":[71,93],"a":[72,94,153],"fundamental":[73],"framework":[74,95,110,151],"this":[76,79],"objective.":[77],"study,":[80,170],"we":[81],"first":[82],"formulate":[83],"the":[84,126,136,139,149],"problem":[85],"of":[86,138,166],"prediction":[90],"then":[92],"predicting":[97,178],"in":[104,159,177],"models.":[107],"The":[108],"proposed":[109,140,150],"leverages":[111],"deep":[112],"learning":[113],"algorithms":[114],"learn":[116],"integrate":[118],"sequential":[119],"data":[123],"representation,":[124],"enabling":[125],"automatic":[127],"prediction.":[131],"Computational":[132],"experiment":[133],"results":[134],"demonstrate":[135],"feasibility":[137],"framework,":[141],"showing":[142],"substantial":[143],"improvements":[144],"over":[145],"baseline":[146],"methods.":[147],"Specifically,":[148],"achieves":[152],"14.69%,":[154],"22.52%,":[155],"13.03%":[157],"increase":[158],"overall":[160],"accuracy":[161],"across":[162],"three":[163],"models":[165],"different":[167],"scales":[168],"under":[169],"while":[171],"maintaining":[172],"balanced":[173],"precision":[174],"recall":[176],"statuses.":[181]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}