{"id":"https://openalex.org/W4417279129","doi":"https://doi.org/10.1186/s12859-025-06332-9","title":"Pairwise ratio transformation of gene expression data leads to improved checkpoint response prediction in lung cancer patients","display_name":"Pairwise ratio transformation of gene expression data leads to improved checkpoint response prediction in lung cancer patients","publication_year":2025,"publication_date":"2025-12-12","ids":{"openalex":"https://openalex.org/W4417279129","doi":"https://doi.org/10.1186/s12859-025-06332-9","pmid":"https://pubmed.ncbi.nlm.nih.gov/41388366"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06332-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06332-9","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-025-06332-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067945000","display_name":"Jacob Pfeil","orcid":"https://orcid.org/0000-0002-8773-8520"},"institutions":[{"id":"https://openalex.org/I2948539688","display_name":"AbbVie (United States)","ror":"https://ror.org/02g5p4n58","country_code":"US","type":"company","lineage":["https://openalex.org/I2948539688"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jacob Pfeil","raw_affiliation_strings":["GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA. jacob.pfeil@abbvie.com","GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA"],"affiliations":[{"raw_affiliation_string":"GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA. jacob.pfeil@abbvie.com","institution_ids":["https://openalex.org/I2948539688"]},{"raw_affiliation_string":"GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061663604","display_name":"Liqian Ma","orcid":"https://orcid.org/0000-0002-0264-9263"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liqian Ma","raw_affiliation_strings":["GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA"],"affiliations":[{"raw_affiliation_string":"GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112349727","display_name":"Hin Ching Lo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hin Ching Lo","raw_affiliation_strings":["GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA"],"affiliations":[{"raw_affiliation_string":"GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060406962","display_name":"Tolga Turan","orcid":"https://orcid.org/0000-0002-3333-3851"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tolga Turan","raw_affiliation_strings":["GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA"],"affiliations":[{"raw_affiliation_string":"GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003946882","display_name":"Robert T. McLaughlin","orcid":"https://orcid.org/0000-0002-1650-3847"},"institutions":[{"id":"https://openalex.org/I2799285752","display_name":"Bay Institute","ror":"https://ror.org/02bgarq81","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799285752"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. Tyler McLaughlin","raw_affiliation_strings":["GRC Methods Development, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA"],"affiliations":[{"raw_affiliation_string":"GRC Methods Development, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA","institution_ids":["https://openalex.org/I2799285752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101501935","display_name":"Xu Shi","orcid":"https://orcid.org/0000-0003-3076-0134"},"institutions":[{"id":"https://openalex.org/I2799285752","display_name":"Bay Institute","ror":"https://ror.org/02bgarq81","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799285752"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xu Shi","raw_affiliation_strings":["GRC Methods Development, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA"],"affiliations":[{"raw_affiliation_string":"GRC Methods Development, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA","institution_ids":["https://openalex.org/I2799285752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100030446","display_name":"Severiano Villarruel","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Severiano Villarruel","raw_affiliation_strings":["GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA"],"affiliations":[{"raw_affiliation_string":"GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047050204","display_name":"Stephen J. Wilson","orcid":"https://orcid.org/0000-0002-2936-1315"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stephen Wilson","raw_affiliation_strings":["GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA"],"affiliations":[{"raw_affiliation_string":"GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084237969","display_name":"Xi Zhao","orcid":"https://orcid.org/0000-0002-9513-6263"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xi Zhao","raw_affiliation_strings":["GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA"],"affiliations":[{"raw_affiliation_string":"GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014321941","display_name":"Josue Samayoa","orcid":"https://orcid.org/0000-0003-3609-8954"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Josue Samayoa","raw_affiliation_strings":["GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA"],"affiliations":[{"raw_affiliation_string":"GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044737538","display_name":"Kyle Halliwill","orcid":"https://orcid.org/0000-0001-5513-4725"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kyle Halliwill","raw_affiliation_strings":["GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA"],"affiliations":[{"raw_affiliation_string":"GRC Computational Oncology, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA, 94080, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5067945000"],"corresponding_institution_ids":["https://openalex.org/I2948539688"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.34541177,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":"15","last_page":"15"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.3010999858379364,"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/T10885","display_name":"Gene expression and cancer classification","score":0.3010999858379364,"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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.28999999165534973,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.06809999793767929,"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/lung-cancer","display_name":"Lung cancer","score":0.5701000094413757},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4650999903678894},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.4569000005722046},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4374000132083893},{"id":"https://openalex.org/keywords/feature-engineering","display_name":"Feature engineering","score":0.4327000081539154},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.42480000853538513},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.3926999866962433},{"id":"https://openalex.org/keywords/predictive-modelling","display_name":"Predictive modelling","score":0.35580000281333923},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.3544999957084656}],"concepts":[{"id":"https://openalex.org/C2776256026","wikidata":"https://www.wikidata.org/wiki/Q47912","display_name":"Lung cancer","level":2,"score":0.5701000094413757},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4984000027179718},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47699999809265137},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4650999903678894},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46050000190734863},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.4569000005722046},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4374000132083893},{"id":"https://openalex.org/C2778827112","wikidata":"https://www.wikidata.org/wiki/Q22245680","display_name":"Feature engineering","level":3,"score":0.4327000081539154},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.42480000853538513},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.3926999866962433},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3630000054836273},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.35580000281333923},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.3544999957084656},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3472000062465668},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.33880001306533813},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3352000117301941},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.3212999999523163},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.3118000030517578},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.31130000948905945},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30660000443458557},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.3046000003814697},{"id":"https://openalex.org/C114851261","wikidata":"https://www.wikidata.org/wiki/Q12147416","display_name":"Drug resistance","level":2,"score":0.30070000886917114},{"id":"https://openalex.org/C2779733811","wikidata":"https://www.wikidata.org/wiki/Q5531562","display_name":"Gene signature","level":4,"score":0.2831999957561493},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.2678999900817871},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2619999945163727},{"id":"https://openalex.org/C2994119904","wikidata":"https://www.wikidata.org/wiki/Q1251001","display_name":"Drug response","level":3,"score":0.2558000087738037},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.2517000138759613},{"id":"https://openalex.org/C2780521871","wikidata":"https://www.wikidata.org/wiki/Q7239671","display_name":"Predictive marker","level":3,"score":0.2515000104904175}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06332-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06332-9","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41388366","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41388366","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:5efef71f4a094ffa9ed36f717c99225e","is_oa":true,"landing_page_url":"https://doaj.org/article/5efef71f4a094ffa9ed36f717c99225e","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 27, Iss 1, Pp 1-16 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12809930","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12809930/","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06332-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06332-9","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W1548779692","https://openalex.org/W1570622790","https://openalex.org/W2010457001","https://openalex.org/W2011301426","https://openalex.org/W2040982194","https://openalex.org/W2093535002","https://openalex.org/W2103017472","https://openalex.org/W2110940238","https://openalex.org/W2123879591","https://openalex.org/W2130410032","https://openalex.org/W2137839234","https://openalex.org/W2143326696","https://openalex.org/W2144182447","https://openalex.org/W2146198038","https://openalex.org/W2152239989","https://openalex.org/W2159637520","https://openalex.org/W2159707944","https://openalex.org/W2180481128","https://openalex.org/W2296719434","https://openalex.org/W2299181842","https://openalex.org/W2346025119","https://openalex.org/W2540833380","https://openalex.org/W2796207838","https://openalex.org/W2805627121","https://openalex.org/W2820886885","https://openalex.org/W2897815318","https://openalex.org/W2900032527","https://openalex.org/W2921471761","https://openalex.org/W2938634307","https://openalex.org/W2949676527","https://openalex.org/W2952001873","https://openalex.org/W2963899699","https://openalex.org/W2984591067","https://openalex.org/W3013528572","https://openalex.org/W3118358720","https://openalex.org/W3136176646","https://openalex.org/W3150635270","https://openalex.org/W3173362574","https://openalex.org/W3203728929","https://openalex.org/W3211402536","https://openalex.org/W3215607492","https://openalex.org/W3216633781","https://openalex.org/W4213202429","https://openalex.org/W4214876469","https://openalex.org/W4220727783","https://openalex.org/W4242289937","https://openalex.org/W4244559366","https://openalex.org/W4284882271","https://openalex.org/W4294216483","https://openalex.org/W4311892119","https://openalex.org/W4362673605","https://openalex.org/W4376275201","https://openalex.org/W4385597052","https://openalex.org/W4386209732","https://openalex.org/W4390739342","https://openalex.org/W6950273931"],"related_works":[],"abstract_inverted_index":{"Machine":[0],"learning":[1,22,112],"algorithms":[2],"identify":[3,299],"patterns":[4,259],"that":[5,260,305,329],"would":[6],"otherwise":[7],"be":[8,76,105,170,262,282,296],"difficult":[9],"to":[10,26,75,81,99,104,114,140,172,180,190,213,251,264,281,284,298,332],"observe":[11],"in":[12,43,150,269,312,324],"high-dimensional":[13],"molecular":[14,79],"and":[15,34,56,84,119,135,178,196,249,278],"clinical":[16,32,48,51,334],"data.":[17,126],"For":[18,63],"this":[19],"reason,":[20],"machine":[21,111],"has":[23,72],"the":[24,109,121,142,166,174,187,254,275,291,317,325],"potential":[25],"have":[27],"a":[28,77,147,154,234],"profound":[29],"impact":[30],"on":[31],"decision-making":[33,323],"drug":[35,252,300,313],"target":[36],"discovery.":[37],"However,":[38],"there":[39],"are":[40],"technical":[41],"challenges":[42],"adapting":[44],"these":[45],"tools":[46],"for":[47,60,94,336],"use,":[49],"including":[50],"feature":[52,218],"engineering,":[53],"model":[54,61],"selection,":[55],"defining":[57],"optimal":[58,92],"strategies":[59,220,268],"training.":[62],"cancer":[64,224],"care,":[65],"RNA":[66],"sequencing":[67],"of":[68,124,133,157,176,290],"patient":[69],"tumor":[70],"biopsies":[71],"already":[73],"proven":[74],"powerful":[78],"assay":[80],"characterize":[82],"tumor-intrinsic":[83],"-extrinsic":[85],"phenotypes":[86],"influencing":[87],"therapeutic":[88],"response,":[89],"but":[90],"an":[91],"solution":[93],"using":[95,153,184,316],"gene":[96,116,159,225,243],"expression":[97,117,160,226,244,258],"data":[98,185],"predict":[100],"outcome":[101],"is":[102,231],"yet":[103],"established.":[106],"We":[107,145,162],"developed":[108],"tauX":[110,128,167,203,229,255,273,292,318],"framework":[113,129,168,204,230,293],"refine":[115],"features":[118],"improve":[120,265],"predictive":[122,138,151,207],"performance":[123,152,208,311],"RNA-sequencing":[125],"The":[127,197,202,228],"uses":[130],"aggregated":[131],"ratios":[132],"positively":[134],"negatively":[136],"associated":[137,246],"genes":[139,304],"simplify":[141],"prediction":[143,315],"task.":[144],"showed":[146,164],"significant":[148],"improvement":[149],"large":[155],"database":[156],"synthetic":[158],"profiles.":[161],"also":[163,295],"how":[165],"can":[169,261,294,320,330],"used":[171,223,263,283,297],"elucidate":[173],"mechanisms":[175],"response":[177,248,277,314],"resistance":[179,250,279],"checkpoint":[181],"blockade":[182],"therapy":[183],"from":[186],"Stand":[188],"Up":[189],"Cancer":[191,198],"(SU2C)":[192],"Lung":[193],"Response":[194],"Cohort":[195],"Genome":[199],"Atlas":[200],"(TCGA).":[201],"achieved":[205],"superior":[206],"(~":[209],"30%":[210],"improvement)":[211],"compared":[212],"models":[214],"built":[215],"upon":[216],"established":[217],"engineering":[219],"or":[221],"widely":[222],"signatures.":[227],"available":[232],"as":[233],"freely":[235],"deployable":[236],"docker":[237],"container":[238],"(https://hub.docker.com/r/pfeiljx/taux).":[239],"By":[240],"simultaneously":[241],"modeling":[242],"signatures":[245,280],"with":[247,308],"therapy,":[253],"approach":[256,319],"revealed":[257],"genomic":[266],"medicine":[267,327],"several":[270],"ways.":[271],"Significantly,":[272],"allows":[274],"paired":[276],"design":[285],"new":[286],"companion":[287],"diagnostics.":[288],"Application":[289],"targets":[301],"by":[302],"indicating":[303],"consistently":[306],"associate":[307],"resistance.":[309],"Improved":[310],"support":[321],"data-driven":[322],"precision":[326],"space":[328],"lead":[331],"improved":[333],"outcomes":[335],"patients.":[337]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-12-12T00:00:00"}
