{"id":"https://openalex.org/W4400140674","doi":"https://doi.org/10.1093/bioinformatics/btae261","title":"CODEX: COunterfactual Deep learning for the <i>in silico</i> EXploration of cancer cell line perturbations","display_name":"CODEX: COunterfactual Deep learning for the <i>in silico</i> EXploration of cancer cell line perturbations","publication_year":2024,"publication_date":"2024-06-28","ids":{"openalex":"https://openalex.org/W4400140674","doi":"https://doi.org/10.1093/bioinformatics/btae261","pmid":"https://pubmed.ncbi.nlm.nih.gov/38940173"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae261","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae261","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i91/58355071/btae261.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/article-pdf/40/Supplement_1/i91/58355071/btae261.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029302354","display_name":"Stefan Schrod","orcid":"https://orcid.org/0000-0001-9936-3984"},"institutions":[{"id":"https://openalex.org/I4210116730","display_name":"Universit\u00e4tsmedizin G\u00f6ttingen","ror":"https://ror.org/021ft0n22","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210116730"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Stefan Schrod","raw_affiliation_strings":["Department of Medical Bioinformatics, University Medical Center G\u00f6ttingen , 37077 Niedersachsen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Bioinformatics, University Medical Center G\u00f6ttingen , 37077 Niedersachsen, Germany","institution_ids":["https://openalex.org/I4210116730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091597117","display_name":"Helena U. Zacharias","orcid":"https://orcid.org/0000-0003-3633-1330"},"institutions":[{"id":"https://openalex.org/I34809795","display_name":"Medizinische Hochschule Hannover","ror":"https://ror.org/00f2yqf98","country_code":"DE","type":"education","lineage":["https://openalex.org/I34809795"]},{"id":"https://openalex.org/I94509681","display_name":"Technische Universit\u00e4t Braunschweig","ror":"https://ror.org/010nsgg66","country_code":"DE","type":"education","lineage":["https://openalex.org/I94509681"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Helena U Zacharias","raw_affiliation_strings":["Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Hannover Medical School , 30625 Hannover, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Hannover Medical School , 30625 Hannover, Germany","institution_ids":["https://openalex.org/I34809795","https://openalex.org/I94509681"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017944645","display_name":"Tim Bei\u00dfbarth","orcid":"https://orcid.org/0000-0001-6509-2143"},"institutions":[{"id":"https://openalex.org/I4210116730","display_name":"Universit\u00e4tsmedizin G\u00f6ttingen","ror":"https://ror.org/021ft0n22","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210116730"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tim Bei\u00dfbarth","raw_affiliation_strings":["Department of Medical Bioinformatics, University Medical Center G\u00f6ttingen , 37077 Niedersachsen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Bioinformatics, University Medical Center G\u00f6ttingen , 37077 Niedersachsen, Germany","institution_ids":["https://openalex.org/I4210116730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087041634","display_name":"Anne-Christin Hauschild","orcid":"https://orcid.org/0000-0002-7499-4373"},"institutions":[{"id":"https://openalex.org/I4210116730","display_name":"Universit\u00e4tsmedizin G\u00f6ttingen","ror":"https://ror.org/021ft0n22","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210116730"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Anne-Christin Hauschild","raw_affiliation_strings":["Department of Medical Informatics, University Medical Center G\u00f6ttingen , 37075 Niedersachsen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Informatics, University Medical Center G\u00f6ttingen , 37075 Niedersachsen, Germany","institution_ids":["https://openalex.org/I4210116730"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041687654","display_name":"Michael Altenbuchinger","orcid":"https://orcid.org/0000-0003-1102-6532"},"institutions":[{"id":"https://openalex.org/I4210116730","display_name":"Universit\u00e4tsmedizin G\u00f6ttingen","ror":"https://ror.org/021ft0n22","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210116730"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Michael Altenbuchinger","raw_affiliation_strings":["Department of Medical Bioinformatics, University Medical Center G\u00f6ttingen , 37077 Niedersachsen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Bioinformatics, University Medical Center G\u00f6ttingen , 37077 Niedersachsen, Germany","institution_ids":["https://openalex.org/I4210116730"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1197,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.76622178,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"40","issue":"Supplement_1","first_page":"i91","last_page":"i99"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.5529000163078308,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.5529000163078308,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.25360000133514404,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.038600001484155655,"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/in-silico","display_name":"In silico","score":0.8530629873275757},{"id":"https://openalex.org/keywords/counterfactual-thinking","display_name":"Counterfactual thinking","score":0.8258244395256042},{"id":"https://openalex.org/keywords/crispr","display_name":"CRISPR","score":0.7058951258659363},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6999937295913696},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5554152131080627},{"id":"https://openalex.org/keywords/decipher","display_name":"DECIPHER","score":0.5428822040557861},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.421932578086853},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3943544626235962},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.39366114139556885},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2700192332267761},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2642630338668823},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1276760995388031},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.09980940818786621}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.8530629873275757},{"id":"https://openalex.org/C108650721","wikidata":"https://www.wikidata.org/wiki/Q1783253","display_name":"Counterfactual thinking","level":2,"score":0.8258244395256042},{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.7058951258659363},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6999937295913696},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5554152131080627},{"id":"https://openalex.org/C164614171","wikidata":"https://www.wikidata.org/wiki/Q5204775","display_name":"DECIPHER","level":2,"score":0.5428822040557861},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.421932578086853},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3943544626235962},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39366114139556885},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2700192332267761},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2642630338668823},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1276760995388031},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.09980940818786621},{"id":"https://openalex.org/C77805123","wikidata":"https://www.wikidata.org/wiki/Q161272","display_name":"Social psychology","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"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":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"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":"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":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btae261","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae261","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i91/58355071/btae261.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38940173","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38940173","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11211812","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11211812","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11211812/pdf/btae261.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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:publications.goettingen-research-online.de:2/143861","is_oa":true,"landing_page_url":"https://resolver.sub.uni-goettingen.de/purl?gro-2/143861","pdf_url":null,"source":{"id":"https://openalex.org/S4306401634","display_name":"GoeScholar  The Publication Server of the Georg-August-Universit\u00e4t G\u00f6ttingen (Georg-August-Universit\u00e4t G\u00f6ttingen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210122495","host_organization_name":"Asklepios Klinik St. Georg","host_organization_lineage":["https://openalex.org/I4210122495"],"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":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae261","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae261","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i91/58355071/btae261.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1409212932","display_name":null,"funder_award_id":"01KD2101C","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G1878973998","display_name":null,"funder_award_id":"AL 2355/1\u20131","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G3573233656","display_name":null,"funder_award_id":"01ZX1912A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G4117827834","display_name":null,"funder_award_id":"TRR274","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G4301671841","display_name":null,"funder_award_id":"01ZX1912C","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G4360394998","display_name":null,"funder_award_id":"KFO5002","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G4473214921","display_name":"KFO 5002: Charakterisierung und Targeting der Genomdynamik f\u00fcr eine Subtypspezifische Therapie des Pankreaskarzinoms","funder_award_id":"426671079","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5529525317","display_name":null,"funder_award_id":"01KD2208A","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6422587778","display_name":null,"funder_award_id":"01ZX1912C","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6667096975","display_name":null,"funder_award_id":"AL 2355/1-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G687434273","display_name":null,"funder_award_id":"01KD2209D","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G6928371558","display_name":null,"funder_award_id":"01ZX1912A","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7601528459","display_name":null,"funder_award_id":"01KU1910A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7695462251","display_name":null,"funder_award_id":"01KD2208A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8310403920","display_name":"TRR 274: Kontrollpunkte der ZNS Reparatur","funder_award_id":"408885537","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4400140674.pdf"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1527927437","https://openalex.org/W1696775091","https://openalex.org/W2060737851","https://openalex.org/W2061061337","https://openalex.org/W2103196126","https://openalex.org/W2108933868","https://openalex.org/W2132917208","https://openalex.org/W2140239055","https://openalex.org/W2335854816","https://openalex.org/W2461427403","https://openalex.org/W2612467560","https://openalex.org/W2734350874","https://openalex.org/W2775061087","https://openalex.org/W2810948010","https://openalex.org/W2889676056","https://openalex.org/W2896822135","https://openalex.org/W2950860419","https://openalex.org/W2969093152","https://openalex.org/W2993905360","https://openalex.org/W3164087725","https://openalex.org/W3212461952","https://openalex.org/W4206377455","https://openalex.org/W4281716291","https://openalex.org/W4283645503","https://openalex.org/W4306412305","https://openalex.org/W4362657842","https://openalex.org/W4375955255","https://openalex.org/W4385955324","https://openalex.org/W4387130479","https://openalex.org/W4388217091","https://openalex.org/W6703221619","https://openalex.org/W6754197187","https://openalex.org/W6855843166"],"related_works":["https://openalex.org/W3201448254","https://openalex.org/W4286970243","https://openalex.org/W2115350162","https://openalex.org/W2066431708","https://openalex.org/W2330145053","https://openalex.org/W4384133558","https://openalex.org/W4249875204","https://openalex.org/W3025615835","https://openalex.org/W173210993","https://openalex.org/W2390660599"],"abstract_inverted_index":{"MOTIVATION:":[0],"High-throughput":[1],"screens":[2],"(HTS)":[3],"provide":[4],"a":[5,26,62,95,114,160],"powerful":[6],"tool":[7],"to":[8,24,34,107,162],"decipher":[9],"the":[10,48,55,85,99,138],"causal":[11,100,116],"effects":[12],"of":[13,29,50,58,74,89,102,142,179],"chemical":[14],"and":[15,38,133,136,151],"genetic":[16,165],"perturbations":[17,106],"on":[18,113,120],"cancer":[19,90],"cell":[20,91,131],"lines.":[21],"Their":[22],"ability":[23],"evaluate":[25],"wide":[27],"spectrum":[28],"interventions,":[30],"from":[31,167],"single":[32,172],"drugs":[33],"intricate":[35],"drug":[36,143],"combinations":[37],"CRISPR-interference,":[39],"has":[40],"established":[41],"them":[42],"as":[43,94],"an":[44],"invaluable":[45],"resource":[46],"for":[47,69,84,98,148],"development":[49],"novel":[51],"therapeutic":[52],"approaches.":[53],"Nevertheless,":[54],"combinatorial":[56],"complexity":[57],"potential":[59],"interventions":[60,68],"makes":[61],"comprehensive":[63],"exploration":[64,141],"intractable.":[65],"Hence,":[66],"prioritizing":[67],"further":[70,155],"experimental":[71],"investigation":[72],"becomes":[73],"utmost":[75],"importance.":[76],"RESULTS:":[77],"We":[78,154],"propose":[79],"CODEX":[80,111,125,158,180],"(COunterfactual":[81],"Deep":[82],"learning":[83],"in":[86,139,169,171,189],"silico":[87,140,170],"EXploration":[88],"line":[92],"perturbations)":[93],"general":[96],"framework":[97],"modeling":[101,117],"HTS":[103],"data,":[104],"linking":[105],"their":[108],"downstream":[109],"consequences.":[110],"relies":[112],"stringent":[115],"strategy":[118],"based":[119],"counterfactual":[121],"reasoning.":[122],"As":[123],"such,":[124],"predicts":[126],"drug-specific":[127],"cellular":[128],"responses,":[129],"comprising":[130],"survival":[132],"molecular":[134],"alterations,":[135],"facilitates":[137],"combinations.":[144],"This":[145],"is":[146,181],"achieved":[147],"both":[149],"bulk":[150],"single-cell":[152],"HTS.":[153],"show":[156],"that":[157],"provides":[159],"rationale":[161],"explore":[163],"complex":[164],"modifications":[166],"CRISPR-interference":[168],"cells.":[173],"AVAILABILITY":[174],"AND":[175],"IMPLEMENTATION:":[176],"Our":[177],"implementation":[178],"publicly":[182,193],"available":[183],"at":[184],"https://github.com/sschrod/CODEX.":[185],"All":[186],"data":[187],"used":[188],"this":[190],"article":[191],"are":[192],"available.":[194]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2024-06-29T00:00:00"}
