{"id":"https://openalex.org/W7225337288","doi":"https://doi.org/10.1021/acssynbio.6c00191","title":"Virtual Knockout in the Era of Generative AI: From Intracellular Networks to Spatial and Cross-Modal Functional Simulations","display_name":"Virtual Knockout in the Era of Generative AI: From Intracellular Networks to Spatial and Cross-Modal Functional Simulations","publication_year":2026,"publication_date":"2026-11-05","ids":{"openalex":"https://openalex.org/W7225337288","doi":"https://doi.org/10.1021/acssynbio.6c00191"},"language":"en","primary_location":{"id":"doi:10.1021/acssynbio.6c00191","doi":"https://doi.org/10.1021/acssynbio.6c00191","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acssynbio.6c00191","pdf_url":null,"source":{"id":"https://openalex.org/S54167817","display_name":"ACS Synthetic Biology","issn_l":"2161-5063","issn":["2161-5063"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","doyens","jufo-2","ki-jl-1","medline","norway-1","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACS Synthetic Biology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref"],"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/A5091274333","display_name":"Zhuo Zuo","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhuo Zuo","raw_affiliation_strings":["Northwestern Polytechnical University , , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northwestern Polytechnical University , , , ,","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5143564706","display_name":"Xiaofeng Ma","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaofeng Ma","raw_affiliation_strings":["Northwestern Polytechnical University , , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northwestern Polytechnical University , , , ,","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100652596","display_name":"Wei Shi","orcid":"https://orcid.org/0000-0002-6146-5894","observed_orcids":["https://orcid.org/0000-0002-6146-5894"]},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Shi","raw_affiliation_strings":["Northwestern Polytechnical University , , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northwestern Polytechnical University , , , ,","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101607197","display_name":"Yulong Sun","orcid":"https://orcid.org/0000-0002-6811-5926","observed_orcids":["https://orcid.org/0000-0002-6811-5926"]},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yulong Sun","raw_affiliation_strings":["Northwestern Polytechnical University , , , ,"],"raw_orcid":"https://orcid.org/0000-0002-6811-5926","affiliations":[{"raw_affiliation_string":"Northwestern Polytechnical University , , , ,","institution_ids":["https://openalex.org/I17145004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5101607197"],"corresponding_institution_ids":["https://openalex.org/I17145004"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.9843999743461609,"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":0.9843999743461609,"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":0.011300000362098217,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.0017000000225380063,"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/virtual-knockout","display_name":"virtual knockout","score":0.9890000224113464},{"id":"https://openalex.org/keywords/single-cell-perturbation","display_name":"single-cell perturbation","score":0.8600000143051147},{"id":"https://openalex.org/keywords/optimal-transport","display_name":"optimal transport","score":0.746999979019165},{"id":"https://openalex.org/keywords/graph-models","display_name":"graph-based modeling","score":0.550000011920929},{"id":"https://openalex.org/keywords/foundation-models","display_name":"foundation models","score":0.8949999809265137},{"id":"https://openalex.org/keywords/spatial-modeling","display_name":"spatial modeling","score":0.5490000247955322},{"id":"https://openalex.org/keywords/intervention-prediction","display_name":"intervention prediction","score":0.5920000076293945},{"id":"https://openalex.org/keywords/uncertainty-calibration","display_name":"uncertainty calibration","score":0.7519999742507935},{"id":"https://openalex.org/keywords/design-build-test-learn","display_name":"design-build-test-learn","score":0.8130000233650208},{"id":"https://openalex.org/keywords/generative-ai","display_name":"generative AI","score":0.7120000123977661}],"concepts":[{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.6924999952316284},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5859000086784363},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5846999883651733},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43140000104904175},{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.4269999861717224},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3953000009059906},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.34470000863075256},{"id":"https://openalex.org/C194969405","wikidata":"https://www.wikidata.org/wiki/Q170519","display_name":"Virtual reality","level":2,"score":0.3402999937534332},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.33799999952316284},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.3174000084400177},{"id":"https://openalex.org/C187590223","wikidata":"https://www.wikidata.org/wiki/Q527628","display_name":"Holography","level":2,"score":0.29350000619888306},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.29249998927116394},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.29109999537467957},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.29100000858306885},{"id":"https://openalex.org/C79379906","wikidata":"https://www.wikidata.org/wiki/Q3174497","display_name":"Dynamical systems theory","level":2,"score":0.2818000018596649},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2678000032901764},{"id":"https://openalex.org/C2775945657","wikidata":"https://www.wikidata.org/wiki/Q381442","display_name":"Structuring","level":2,"score":0.25369998812675476}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1021/acssynbio.6c00191","doi":"https://doi.org/10.1021/acssynbio.6c00191","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acssynbio.6c00191","pdf_url":null,"source":{"id":"https://openalex.org/S54167817","display_name":"ACS Synthetic Biology","issn_l":"2161-5063","issn":["2161-5063"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","doyens","jufo-2","ki-jl-1","medline","norway-1","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACS Synthetic Biology","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":69,"referenced_works":["https://openalex.org/W2081781433","https://openalex.org/W2561754210","https://openalex.org/W2562947047","https://openalex.org/W2577994754","https://openalex.org/W2806394571","https://openalex.org/W2965552103","https://openalex.org/W2969093152","https://openalex.org/W2993905360","https://openalex.org/W2997831639","https://openalex.org/W3080295962","https://openalex.org/W3117464799","https://openalex.org/W3129866267","https://openalex.org/W3133712085","https://openalex.org/W3134444564","https://openalex.org/W3164448939","https://openalex.org/W4210396037","https://openalex.org/W4220765071","https://openalex.org/W4225278475","https://openalex.org/W4225426244","https://openalex.org/W4281716291","https://openalex.org/W4281777185","https://openalex.org/W4312114042","https://openalex.org/W4319591822","https://openalex.org/W4375955255","https://openalex.org/W4378640029","https://openalex.org/W4378838672","https://openalex.org/W4385760593","https://openalex.org/W4385955324","https://openalex.org/W4386091496","https://openalex.org/W4387130479","https://openalex.org/W4388217091","https://openalex.org/W4390880427","https://openalex.org/W4391262585","https://openalex.org/W4391349656","https://openalex.org/W4392168151","https://openalex.org/W4394853345","https://openalex.org/W4396895461","https://openalex.org/W4399387478","https://openalex.org/W4400140744","https://openalex.org/W4401736259","https://openalex.org/W4402253203","https://openalex.org/W4402860131","https://openalex.org/W4403007117","https://openalex.org/W4403216706","https://openalex.org/W4403405969","https://openalex.org/W4403784877","https://openalex.org/W4403995420","https://openalex.org/W4404668596","https://openalex.org/W4407896879","https://openalex.org/W4408327225","https://openalex.org/W4408363679","https://openalex.org/W4410521040","https://openalex.org/W4411338098","https://openalex.org/W4411757935","https://openalex.org/W4411910961","https://openalex.org/W4412160990","https://openalex.org/W4412929241","https://openalex.org/W4413495491","https://openalex.org/W4413892920","https://openalex.org/W4416199263","https://openalex.org/W4416257539","https://openalex.org/W4416398238","https://openalex.org/W4416401025","https://openalex.org/W4416716586","https://openalex.org/W4417297892","https://openalex.org/W7130855811","https://openalex.org/W7133242378","https://openalex.org/W7159833008","https://openalex.org/W7171448335"],"related_works":["https://openalex.org/W7223123247","https://openalex.org/W7211936047","https://openalex.org/W4416070613","https://openalex.org/W7169825925","https://openalex.org/W4416975498","https://openalex.org/W7155362583","https://openalex.org/W7221758128","https://openalex.org/W7154357661","https://openalex.org/W7165650193","https://openalex.org/W7213862979"],"abstract_inverted_index":{"Abstract":[0],"Single-cell":[1],"perturbation":[2,60],"data":[3],"have":[4],"enabled":[5],"computational":[6],"models":[7],"that":[8],"predict":[9],"intervention-associated":[10],"cellular":[11],"responses.":[12],"This":[13],"narrative":[14],"review":[15],"organizes":[16],"explicit":[17],"gene-regulatory-network":[18],"simulations,":[19],"latent":[20],"and":[21,27,32,50,64,73,76,88,96,104],"compositional":[22],"response":[23],"models,":[24],"graph,":[25],"optimal-transport,":[26],"dynamical":[28],"approaches,":[29],"foundation-model":[30],"representations,":[31],"emerging":[33],"spatial":[34],"or":[35,58],"cross-modal":[36],"settings":[37],"through":[38],"a":[39,79],"virtual-knockout":[40],"lens.":[41],"We":[42,66],"distinguish":[43],"representation-level":[44],"ablation":[45],"from":[46],"causal":[47],"genetic":[48],"intervention":[49],"separate":[51],"held-out":[52],"regimes":[53],"for":[54],"genes,":[55],"cell":[56,83,103],"types":[57],"contexts,":[59],"combinations,":[61],"chemical":[62],"structures,":[63],"doses.":[65],"compare":[67],"representative":[68],"methods,":[69],"experimental":[70],"resources,":[71],"metrics,":[72],"benchmark":[74],"frameworks":[75],"operationally":[77],"define":[78],"prospective":[80,97],"holographic":[81,101],"virtual":[82,102],"by":[84],"its":[85],"modalities,":[86],"regulatory":[87],"physical":[89],"constraints,":[90],"intervention-conditioned":[91],"outputs":[92],"with":[93],"calibrated":[94],"uncertainty,":[95],"validation":[98],"requirements.":[99],"The":[100],"Design\u2212Build\u2212Test\u2212Learn":[105],"roadmap":[106],"are":[107],"presented":[108],"as":[109,114],"future-facing":[110],"criteria":[111],"rather":[112],"than":[113],"an":[115],"achieved":[116],"clinical":[117],"capability.":[118]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2026-11-06T00:00:00"}
