{"id":"https://openalex.org/W7221567024","doi":"https://doi.org/10.64898/2026.10.11.758300","title":"Unsupervised decomposition of massively parallel TraDIS-Xpress fitness data from Escherichia coli identifies distinct functional and expression modules of antimicrobial resistance determinants","display_name":"Unsupervised decomposition of massively parallel TraDIS-Xpress fitness data from Escherichia coli identifies distinct functional and expression modules of antimicrobial resistance determinants","publication_year":2026,"publication_date":"2026-10-12","ids":{"openalex":"https://openalex.org/W7221567024","doi":"https://doi.org/10.64898/2026.10.11.758300"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.11.758300","doi":"https://doi.org/10.64898/2026.10.11.758300","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.11.758300","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/12/2026.10.11.758300.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/12/2026.10.11.758300.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048273697","display_name":"Muhammad Yasir","orcid":"https://orcid.org/0000-0001-9437-2996","observed_orcids":["https://orcid.org/0000-0001-9437-2996"]},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I3018370718","display_name":"Quadram Institute","ror":"https://ror.org/04td3ys19","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2799693246","https://openalex.org/I3018370718","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Muhammad Yasir","raw_affiliation_strings":["Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","Quadram Institute Bioscience, Norwich Research Park, Norwich, UK"],"raw_orcid":"https://orcid.org/0000-0001-9437-2996","affiliations":[{"raw_affiliation_string":"Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731"]},{"raw_affiliation_string":"Quadram Institute Bioscience, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I3018370718"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077121860","display_name":"A. Keith Turner","orcid":"https://orcid.org/0000-0002-3680-6343","observed_orcids":["https://orcid.org/0000-0002-3680-6343"]},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I3018370718","display_name":"Quadram Institute","ror":"https://ror.org/04td3ys19","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2799693246","https://openalex.org/I3018370718","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"A. Keith Turner","raw_affiliation_strings":["Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","Quadram Institute Bioscience, Norwich Research Park, Norwich, UK"],"raw_orcid":"https://orcid.org/0000-0002-3680-6343","affiliations":[{"raw_affiliation_string":"Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731"]},{"raw_affiliation_string":"Quadram Institute Bioscience, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I3018370718"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015285575","display_name":"Andrea Telatin","orcid":"https://orcid.org/0000-0001-7619-281X","observed_orcids":["https://orcid.org/0000-0001-7619-281X"]},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I3018370718","display_name":"Quadram Institute","ror":"https://ror.org/04td3ys19","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2799693246","https://openalex.org/I3018370718","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Andrea Telatin","raw_affiliation_strings":["Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","Quadram Institute Bioscience, Norwich Research Park, Norwich, UK"],"raw_orcid":"https://orcid.org/0000-0001-7619-281X","affiliations":[{"raw_affiliation_string":"Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731"]},{"raw_affiliation_string":"Quadram Institute Bioscience, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I3018370718"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069830575","display_name":"Sarah Bastkowski","orcid":"https://orcid.org/0000-0001-9002-1822","observed_orcids":["https://orcid.org/0000-0001-9002-1822"]},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I3018370718","display_name":"Quadram Institute","ror":"https://ror.org/04td3ys19","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2799693246","https://openalex.org/I3018370718","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sarah Bastkowski","raw_affiliation_strings":["Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","Quadram Institute Bioscience, Norwich Research Park, Norwich, UK"],"raw_orcid":"https://orcid.org/0000-0001-9002-1822","affiliations":[{"raw_affiliation_string":"Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731"]},{"raw_affiliation_string":"Quadram Institute Bioscience, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I3018370718"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074734659","display_name":"Emma R. Holden","orcid":"https://orcid.org/0000-0002-0811-1675","observed_orcids":["https://orcid.org/0000-0002-0811-1675"]},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I3018370718","display_name":"Quadram Institute","ror":"https://ror.org/04td3ys19","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2799693246","https://openalex.org/I3018370718","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Emma R. Holden","raw_affiliation_strings":["Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","Quadram Institute Bioscience, Norwich Research Park, Norwich, UK"],"raw_orcid":"https://orcid.org/0000-0002-0811-1675","affiliations":[{"raw_affiliation_string":"Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731"]},{"raw_affiliation_string":"Quadram Institute Bioscience, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I3018370718"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054595285","display_name":"Ian G. Charles","orcid":"https://orcid.org/0000-0002-2423-1167","observed_orcids":["https://orcid.org/0000-0002-2423-1167"]},"institutions":[{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]},{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I3018370718","display_name":"Quadram Institute","ror":"https://ror.org/04td3ys19","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2799693246","https://openalex.org/I3018370718","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ian G. Charles","raw_affiliation_strings":["Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","Norwich Medical School, University of East Anglia, Norwich, UK","Quadram Institute Bioscience, Norwich Research Park, Norwich, UK"],"raw_orcid":"https://orcid.org/0000-0002-2423-1167","affiliations":[{"raw_affiliation_string":"Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731"]},{"raw_affiliation_string":"Norwich Medical School, University of East Anglia, Norwich, UK","institution_ids":["https://openalex.org/I1118541"]},{"raw_affiliation_string":"Quadram Institute Bioscience, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I3018370718"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061850489","display_name":"Mark Alexander Webber","orcid":"https://orcid.org/0000-0001-9169-7592","observed_orcids":["https://orcid.org/0000-0001-9169-7592"]},"institutions":[{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]},{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I3018370718","display_name":"Quadram Institute","ror":"https://ror.org/04td3ys19","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2799693246","https://openalex.org/I3018370718","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark A. Webber","raw_affiliation_strings":["Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","Norwich Medical School, University of East Anglia, Norwich, UK","Quadram Institute Bioscience, Norwich Research Park, Norwich, UK"],"raw_orcid":"https://orcid.org/0000-0001-9169-7592","affiliations":[{"raw_affiliation_string":"Centre for Microbial Interactions, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731"]},{"raw_affiliation_string":"Norwich Medical School, University of East Anglia, Norwich, UK","institution_ids":["https://openalex.org/I1118541"]},{"raw_affiliation_string":"Quadram Institute Bioscience, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I3018370718"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5048273697"],"corresponding_institution_ids":["https://openalex.org/I2799300731","https://openalex.org/I3018370718"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9243000149726868,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9243000149726868,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.043699998408555984,"subfield":{"id":"https://openalex.org/subfields/2726","display_name":"Microbiology (medical)"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0031999999191612005,"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/transposon-sequencing","display_name":"transposon sequencing","score":0.8600000143051147},{"id":"https://openalex.org/keywords/independent-component-analysis","display_name":"independent component analysis","score":0.8270000219345093},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.843999981880188},{"id":"https://openalex.org/keywords/antibiotic-resistance","display_name":"antibiotic resistance","score":0.6460000276565552},{"id":"https://openalex.org/keywords/antimicrobial-resistance-determinants","display_name":"antimicrobial resistance determinants","score":0.8159999847412109},{"id":"https://openalex.org/keywords/genotype-phenotype-correlation","display_name":"genotype-phenotype correlation","score":0.7839999794960022},{"id":"https://openalex.org/keywords/gene-modules","display_name":"gene modules","score":0.5580000281333923},{"id":"https://openalex.org/keywords/fosfomycin","display_name":"fosfomycin","score":0.6650000214576721},{"id":"https://openalex.org/keywords/gentamicin","display_name":"gentamicin","score":0.9929999709129333},{"id":"https://openalex.org/keywords/oxidative-phosphorylation","display_name":"oxidative phosphorylation","score":0.8510000109672546},{"id":"https://openalex.org/keywords/promoter","display_name":"promoter","score":0.40299999713897705},{"id":"https://openalex.org/keywords/stress-response","display_name":"stress response","score":0.4169999957084656}],"concepts":[{"id":"https://openalex.org/C2778473407","wikidata":"https://www.wikidata.org/wiki/Q1459574","display_name":"Compendium","level":2,"score":0.6333000063896179},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6287999749183655},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5978999733924866},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5922999978065491},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5375000238418579},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.49549999833106995},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.44519999623298645},{"id":"https://openalex.org/C2780852648","wikidata":"https://www.wikidata.org/wiki/Q143584","display_name":"SOS response","level":4,"score":0.43059998750686646},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.39879998564720154},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.36899998784065247},{"id":"https://openalex.org/C2778897966","wikidata":"https://www.wikidata.org/wiki/Q183554","display_name":"Fosfomycin","level":3,"score":0.3012000024318695},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.2971999943256378},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.2939000129699707},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.27399998903274536},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2732999920845032},{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.26739999651908875},{"id":"https://openalex.org/C2910387474","wikidata":"https://www.wikidata.org/wiki/Q331710","display_name":"Genetic Fitness","level":3,"score":0.2660999894142151},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.2646999955177307},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2630999982357025},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.26260000467300415},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.250900000333786}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.11.758300","doi":"https://doi.org/10.64898/2026.10.11.758300","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.11.758300","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/12/2026.10.11.758300.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.11.758300","doi":"https://doi.org/10.64898/2026.10.11.758300","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.11.758300","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/12/2026.10.11.758300.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7221567024.pdf","grobid_xml":"https://content.openalex.org/works/W7221567024.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4391600487","https://openalex.org/W2526467570","https://openalex.org/W3043085355","https://openalex.org/W6999637702","https://openalex.org/W7202261455","https://openalex.org/W3128033315","https://openalex.org/W1497450746","https://openalex.org/W3047156727","https://openalex.org/W2078202582","https://openalex.org/W7098340332"],"abstract_inverted_index":{"Abstract":[0],"Linking":[1],"genotype":[2],"to":[3,13,81,103,111,196,212,233,244,253,263,275,305,345,351,404,422],"phenotype":[4],"is":[5,16,101],"a":[6,29,51,91,125,241,393,396],"central":[7],"goal":[8],"in":[9,33,45,266,383,390,431,435,446],"biology,":[10],"one":[11],"way":[12],"do":[14],"this":[15,117,306],"using":[17],"transposon":[18,475],"insertion":[19],"sequencing":[20],"(TIS)":[21],"where":[22],"the":[23,67,141,147,173,183,187,214,227,230,269,298,337,349,358,436,455,469],"fitness":[24],"impacts":[25,430],"of":[26,40,53,55,60,93,204,216,226,246,268,300,315,332,339,357,425,442,450,463,471,474],"mutations":[27],"across":[28,172,281],"genome":[30],"are":[31,261],"assessed":[32],"different":[34,286,291],"conditions.":[35],"Traditional":[36],"analyses":[37],"use":[38],"comparison":[39],"each":[41,119],"gene":[42,63,121,126,151,248,391,397,448],"response":[43],"independently":[44],"control":[46,272,385],"versus":[47],"test":[48,56],"conditions,":[49],"so":[50,135],"compendium":[52,175],"hundreds":[54,59],"conditions":[57],"returns":[58],"separate":[61,198],"ranked":[62],"lists.":[64],"To":[65],"unlock":[66],"potential":[68],"information":[69],"hidden":[70,105],"within":[71,107],"large":[72],"data":[73,109,409],"sets,":[74],"we":[75,160],"applied":[76],"independent":[77,420],"component":[78],"(ICA)":[79],"analysis":[80,118,221,245],"754":[82,184],"Escherichia":[83],"coli":[84,302],"BW25113":[85],"TraDIS-Xpress":[86],"samples.":[87],"These":[88,408],"samples":[89,192],"included":[90,190],"series":[92],"antibiotic":[94,188],"and":[95,110,128,132,229,273,288,334,387,417,467],"other":[96,324],"stress":[97,185],"condition":[98,434],"exposures.":[99],"ICA":[100,412],"designed":[102],"identify":[104],"structure":[106],"complex":[108],"extract":[112],"meaningfully":[113],"linked":[114],"components.":[115],"In":[116],"annotated":[120],"was":[122],"resolved":[123,362],"into":[124],"body":[127],"198":[129],"bp":[130],"5\u2032":[131],"3\u2032":[133],"features":[134],"that":[136,395,411],"expression":[137],"effects":[138],"driven":[139],"by":[140,368,381],"transposon\u2019s":[142],"outwards":[143],"facing":[144],"promoter":[145,369],"enter":[146],"matrix":[148,399],"separately":[149],"from":[150,194],"disruption":[152],"effects.":[153],"The":[154,438],"decomposition":[155,413],"returned":[156],"99":[157],"components,":[158],"which":[159,163,260,364],"term":[161],"fxModules,":[162],"were":[164,321,365,379],"defined":[165,340],"as":[166,342],"containing":[167,258],"elements":[168],"with":[169,285,308,406,427],"similar":[170],"responses":[171],"whole":[174],"rather":[176],"than":[177],"per":[178],"any":[179,312,432],"individual":[180,234],"experiment.":[181],"Of":[182],"samples,":[186],"arm":[189],"110":[191],"derived":[193],"exposure":[195,252,274],"14":[197],"agents":[199],"at":[200,240,290],"multiple":[201,472],"concentrations.":[202,292],"Many":[203],"these":[205],"have":[206],"been":[207],"highly":[208],"studied":[209],"allowing":[210],"us":[211],"explore":[213],"accuracy":[215],"predicted":[217],"responsive":[218,232,256,344],"fxModules.":[219],"This":[220,293,458],"showed":[222],"excellent":[223],"predictive":[224],"power":[225,470],"approach":[228,421,459],"fxModules":[231,257,283,363],"drugs":[235],"typically":[236],"reproduced":[237],"known":[238,262],"mechanisms":[239],"resolution":[242],"superior":[243],"single":[247],"sets.":[249],"For":[250],"example,":[251],"fosfomycin":[254],"identified":[255,277,329,380],"genes":[259,303,333,375,426,443,452],"be":[264,402],"involved":[265],"uptake":[267],"drug,":[270],"cAMP-CRP":[271],"gentamicin":[276],"oxidative":[278],"phosphorylation":[279],"split":[280],"three":[282],"responding":[284],"magnitudes":[287],"directions":[289],"recapitulates":[294],"recent":[295],"work":[296],"studying":[297],"landscape":[299],"E.":[301],"sensitive":[304],"drug":[307],"high":[309],"precision":[310],"without":[311],"prior":[313],"knowledge":[314],"functional":[316,429,439],"annotation.":[317],"Similarly":[318],"precise":[319],"predictions":[320],"made":[322],"for":[323,371,373,377],"drugs.":[325],"Responsive":[326],"modules":[327],"also":[328,361,444],"novel":[330,464],"groups":[331],"linkages":[335],"beyond":[336],"boundaries":[338],"pathways":[341],"being":[343],"various":[346],"stresses":[347],"demonstrating":[348],"ability":[350],"predict":[352,405],"new":[353],"genotype-phenotype":[354,465],"links.":[355],"Inclusion":[356],"regulatory":[359],"regions":[360],"entirely":[366],"contributed":[367],"regions,":[370,386],"example":[372],"chloramphenicol":[374],"responsible":[376],"efflux":[378],"signals":[382],"intergenic":[384],"unidirectional":[388],"insertions":[389],"bodies,":[392],"signal":[394],"level":[398],"would":[400],"not":[401],"able":[403],"accuracy.":[407],"show":[410],"provides":[414],"an":[415],"efficient":[416],"accurate":[418],"annotation":[419],"identifying":[423],"sets":[424],"related":[428],"given":[433],"compendium.":[437],"modular":[440],"association":[441],"help":[445],"predicting":[447],"functions":[449],"unknown":[451],"based":[453],"on":[454],"group":[456],"function.":[457],"allows":[460],"rapid":[461],"identification":[462],"links":[466],"unlocks":[468],"comparisons":[473],"mutagenesis":[476],"data.":[477]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-10-13T00:00:00"}
