{"id":"https://openalex.org/W4380988061","doi":"https://doi.org/10.1371/journal.pcbi.1011232","title":"Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses","display_name":"Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses","publication_year":2023,"publication_date":"2023-06-16","ids":{"openalex":"https://openalex.org/W4380988061","doi":"https://doi.org/10.1371/journal.pcbi.1011232","pmid":"https://pubmed.ncbi.nlm.nih.gov/37327241"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011232","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011232","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1011232","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058145895","display_name":"Christopher J. Skalnik","orcid":"https://orcid.org/0000-0002-6344-7331"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christopher J. Skalnik","raw_affiliation_strings":["Department of Bioengineering, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092188288","display_name":"Sean Cheah","orcid":"https://orcid.org/0000-0001-7433-1601"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sean Y. Cheah","raw_affiliation_strings":["Department of Bioengineering, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109614958","display_name":"Mica Y. Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mica Y. Yang","raw_affiliation_strings":["Department of Bioengineering, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111160306","display_name":"Mattheus Wolff","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mattheus B. Wolff","raw_affiliation_strings":["Department of Bioengineering, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053713841","display_name":"Ryan K. Spangler","orcid":"https://orcid.org/0000-0002-6080-3142"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ryan K. Spangler","raw_affiliation_strings":["Department of Bioengineering, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058950659","display_name":"Lee Talman","orcid":null},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lee Talman","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052776560","display_name":"Jerry H. Morrison","orcid":"https://orcid.org/0000-0001-9414-6999"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jerry H. Morrison","raw_affiliation_strings":["Department of Bioengineering, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017480661","display_name":"Shayn M. Peirce","orcid":"https://orcid.org/0000-0001-5857-5606"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shayn M. Peirce","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036760070","display_name":"Eran Agmon","orcid":"https://orcid.org/0000-0003-1279-2474"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eran Agmon","raw_affiliation_strings":["Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, Connecticut, United States of America","Department of Bioengineering, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064086976","display_name":"Markus W. Covert","orcid":"https://orcid.org/0000-0002-5993-8912"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Markus W. Covert","raw_affiliation_strings":["Department of Bioengineering, Stanford University, Stanford, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5017480661","https://openalex.org/A5036760070","https://openalex.org/A5052776560","https://openalex.org/A5053713841","https://openalex.org/A5058145895","https://openalex.org/A5058950659","https://openalex.org/A5064086976","https://openalex.org/A5092188288","https://openalex.org/A5109614958","https://openalex.org/A5111160306"],"corresponding_institution_ids":["https://openalex.org/I140172145","https://openalex.org/I51556381","https://openalex.org/I97018004"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.7175,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.93420555,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"19","issue":"6","first_page":"e1011232","last_page":"e1011232"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9997000098228455,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9997000098228455,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9966999888420105,"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":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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/antibiotics","display_name":"Antibiotics","score":0.6405701637268066},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6326313018798828},{"id":"https://openalex.org/keywords/antibiotic-resistance","display_name":"Antibiotic resistance","score":0.6275542974472046},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.625405490398407},{"id":"https://openalex.org/keywords/tetracycline","display_name":"Tetracycline","score":0.6106516122817993},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.5496649146080017},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5060133337974548},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.466799795627594},{"id":"https://openalex.org/keywords/efflux","display_name":"Efflux","score":0.41034433245658875},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3994547128677368},{"id":"https://openalex.org/keywords/microbiology","display_name":"Microbiology","score":0.38411182165145874},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.37790942192077637},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.07172152400016785}],"concepts":[{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.6405701637268066},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6326313018798828},{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.6275542974472046},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.625405490398407},{"id":"https://openalex.org/C2780923616","wikidata":"https://www.wikidata.org/wiki/Q193045","display_name":"Tetracycline","level":3,"score":0.6106516122817993},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.5496649146080017},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5060133337974548},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.466799795627594},{"id":"https://openalex.org/C200082930","wikidata":"https://www.wikidata.org/wiki/Q22327148","display_name":"Efflux","level":2,"score":0.41034433245658875},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3994547128677368},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.38411182165145874},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37790942192077637},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.07172152400016785},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000667","descriptor_name":"Ampicillin","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000667","descriptor_name":"Ampicillin","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000667","descriptor_name":"Ampicillin","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000667","descriptor_name":"Ampicillin","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000667","descriptor_name":"Ampicillin","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000667","descriptor_name":"Ampicillin","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001618","descriptor_name":"beta-Lactamases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001618","descriptor_name":"beta-Lactamases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001618","descriptor_name":"beta-Lactamases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001618","descriptor_name":"beta-Lactamases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001618","descriptor_name":"beta-Lactamases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001618","descriptor_name":"beta-Lactamases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D008826","descriptor_name":"Microbial Sensitivity Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008826","descriptor_name":"Microbial Sensitivity Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008826","descriptor_name":"Microbial Sensitivity Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008826","descriptor_name":"Microbial Sensitivity Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008826","descriptor_name":"Microbial Sensitivity Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008826","descriptor_name":"Microbial Sensitivity Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013752","descriptor_name":"Tetracycline","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D013752","descriptor_name":"Tetracycline","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D013752","descriptor_name":"Tetracycline","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D013752","descriptor_name":"Tetracycline","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D013752","descriptor_name":"Tetracycline","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D013752","descriptor_name":"Tetracycline","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1011232","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011232","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37327241","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37327241","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10310025","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10310025","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10310025/pdf/pcbi.1011232.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:c586e70966d047e2adda5d4777ce5255","is_oa":true,"landing_page_url":"https://doaj.org/article/c586e70966d047e2adda5d4777ce5255","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":"PLoS Computational Biology, Vol 19, Iss 6, p e1011232 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011232","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011232","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1595369249","display_name":null,"funder_award_id":"F32GM137464","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1615559399","display_name":null,"funder_award_id":"T32GM136568","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G196654039","display_name":null,"funder_award_id":"F32GM137464","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2033891796","display_name":null,"funder_award_id":"T32GM136568","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2109706152","display_name":null,"funder_award_id":"R01LM013229","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G3090102801","display_name":null,"funder_award_id":"LM013229","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3175321091","display_name":null,"funder_award_id":"Matter-to-Life program","funder_id":"https://openalex.org/F4320306151","funder_display_name":"Alfred P. Sloan Foundation"},{"id":"https://openalex.org/G3426213143","display_name":null,"funder_award_id":"C-CoMP","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3509939709","display_name":null,"funder_award_id":"R01LM013229","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4359693134","display_name":null,"funder_award_id":"NIGMS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4972729266","display_name":null,"funder_award_id":"GM140008","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5921281487","display_name":null,"funder_award_id":"number","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6008524571","display_name":null,"funder_award_id":"R01GM140008","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6268941785","display_name":null,"funder_award_id":"GM137464","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6430894958","display_name":null,"funder_award_id":"R01GM140008","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6755165505","display_name":null,"funder_award_id":"award","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306151","display_name":"Alfred P. Sloan Foundation","ror":"https://ror.org/052csg198"},{"id":"https://openalex.org/F4320317068","display_name":"Paul G. Allen Frontiers Group","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":123,"referenced_works":["https://openalex.org/W1487593985","https://openalex.org/W1497758287","https://openalex.org/W1506418113","https://openalex.org/W1513439761","https://openalex.org/W1540179470","https://openalex.org/W1572693909","https://openalex.org/W1605984840","https://openalex.org/W1788555328","https://openalex.org/W1944808330","https://openalex.org/W1968723178","https://openalex.org/W1970703124","https://openalex.org/W1980111518","https://openalex.org/W1980595924","https://openalex.org/W1981100467","https://openalex.org/W1990221500","https://openalex.org/W1999055779","https://openalex.org/W2002254680","https://openalex.org/W2008892999","https://openalex.org/W2018562548","https://openalex.org/W2019130140","https://openalex.org/W2019593727","https://openalex.org/W2037731504","https://openalex.org/W2040280990","https://openalex.org/W2049242968","https://openalex.org/W2049526353","https://openalex.org/W2050952012","https://openalex.org/W2053460598","https://openalex.org/W2055571822","https://openalex.org/W2061659241","https://openalex.org/W2068179698","https://openalex.org/W2069704172","https://openalex.org/W2071905283","https://openalex.org/W2072996759","https://openalex.org/W2073824449","https://openalex.org/W2075781111","https://openalex.org/W2076279677","https://openalex.org/W2081781433","https://openalex.org/W2086064524","https://openalex.org/W2087920996","https://openalex.org/W2090453523","https://openalex.org/W2092076850","https://openalex.org/W2094420829","https://openalex.org/W2096984614","https://openalex.org/W2097645659","https://openalex.org/W2098814128","https://openalex.org/W2099303284","https://openalex.org/W2103846074","https://openalex.org/W2105389904","https://openalex.org/W2105999876","https://openalex.org/W2106024571","https://openalex.org/W2111354165","https://openalex.org/W2113007471","https://openalex.org/W2114746743","https://openalex.org/W2115069651","https://openalex.org/W2116777154","https://openalex.org/W2119711877","https://openalex.org/W2120069280","https://openalex.org/W2121924211","https://openalex.org/W2122432936","https://openalex.org/W2124514539","https://openalex.org/W2124726310","https://openalex.org/W2125823891","https://openalex.org/W2125882807","https://openalex.org/W2128537028","https://openalex.org/W2130497602","https://openalex.org/W2131614333","https://openalex.org/W2132963724","https://openalex.org/W2133894066","https://openalex.org/W2148323109","https://openalex.org/W2151003045","https://openalex.org/W2152910720","https://openalex.org/W2153280156","https://openalex.org/W2156623862","https://openalex.org/W2157523980","https://openalex.org/W2157664391","https://openalex.org/W2158789691","https://openalex.org/W2162198167","https://openalex.org/W2164856850","https://openalex.org/W2174130978","https://openalex.org/W2191824721","https://openalex.org/W2240061877","https://openalex.org/W2258657513","https://openalex.org/W2277953252","https://openalex.org/W2298318901","https://openalex.org/W2513958854","https://openalex.org/W2582932073","https://openalex.org/W2593536290","https://openalex.org/W2751799791","https://openalex.org/W2791402832","https://openalex.org/W2795072897","https://openalex.org/W2899699117","https://openalex.org/W2903562424","https://openalex.org/W2936521062","https://openalex.org/W2942626330","https://openalex.org/W2944579961","https://openalex.org/W2944664266","https://openalex.org/W2945959861","https://openalex.org/W2946458716","https://openalex.org/W2972545617","https://openalex.org/W3006398942","https://openalex.org/W3044339796","https://openalex.org/W3158729831","https://openalex.org/W3172704448","https://openalex.org/W3180845106","https://openalex.org/W3184479113","https://openalex.org/W3185730212","https://openalex.org/W3190916927","https://openalex.org/W3206959204","https://openalex.org/W3207520013","https://openalex.org/W3214093190","https://openalex.org/W4205956675","https://openalex.org/W4210262538","https://openalex.org/W4210560508","https://openalex.org/W4211217632","https://openalex.org/W4226188368","https://openalex.org/W4246645615","https://openalex.org/W4281293277","https://openalex.org/W4292302479","https://openalex.org/W4293567382","https://openalex.org/W4308952854","https://openalex.org/W4311883472","https://openalex.org/W4376595873","https://openalex.org/W6678609067"],"related_works":["https://openalex.org/W4294636674","https://openalex.org/W2501597952","https://openalex.org/W1994168874","https://openalex.org/W2187662771","https://openalex.org/W2036585666","https://openalex.org/W2127447560","https://openalex.org/W2384484634","https://openalex.org/W4367676407","https://openalex.org/W4367681091","https://openalex.org/W2792886283"],"abstract_inverted_index":{"Antibiotic":[0],"resistance":[1,48,63],"poses":[2],"mounting":[3],"risks":[4],"to":[5,82,112,138,151,175,211,218,231,243],"human":[6],"health,":[7],"as":[8,36,103,236],"current":[9],"antibiotics":[10,220],"are":[11,90],"losing":[12],"efficacy":[13],"against":[14],"increasingly":[15],"resistant":[16],"pathogenic":[17],"bacteria.":[18],"Of":[19],"particular":[20],"concern":[21],"is":[22,77,88],"the":[23,72,140,152,181,186,190,213,237],"emergence":[24],"of":[25,42,61,135,144,159,168,189,198,215,224],"multidrug-resistant":[26],"strains,":[27],"which":[28,54,129,240],"has":[29,44],"been":[30],"rapid":[31],"among":[32],"Gram-negative":[33],"bacteria":[34],"such":[35,68,235],"Escherichia":[37],"coli.":[38],"A":[39],"large":[40],"body":[41],"work":[43],"established":[45],"that":[46,75,94,183],"antibiotic":[47,62,85],"mechanisms":[49,223],"depend":[50],"on":[51,180],"phenotypic":[52,97],"heterogeneity,":[53,102],"may":[55],"be":[56],"mediated":[57],"by":[58,118],"stochastic":[59],"expression":[60,70],"genes.":[64],"The":[65,206],"link":[66],"between":[67],"molecular-level":[69],"and":[71,79,115,132,194,227,251],"population":[73],"levels":[74],"result":[76],"complex":[78],"multi-scale.":[80],"Therefore,":[81],"better":[83],"understand":[84],"resistance,":[86],"what":[87],"needed":[89],"new":[91],"mechanistic":[92,133],"models":[93],"reflect":[95],"single-cell":[96,114],"dynamics":[98],"together":[99],"with":[100,221],"population-level":[101],"an":[104,127],"integrated":[105],"whole.":[106],"In":[107],"this":[108],"work,":[109],"we":[110,155],"sought":[111],"bridge":[113],"population-scale":[116],"modeling":[117,150],"building":[119],"upon":[120],"our":[121],"previous":[122,191],"experience":[123],"in":[124,202,247,256],"\"whole-cell\"":[125],"modeling,":[126],"approach":[128],"integrates":[130],"mathematical":[131],"descriptions":[134],"biological":[136],"processes":[137],"recapitulate":[139],"experimentally":[141],"observed":[142],"behaviors":[143],"entire":[145],"cells.":[146],"To":[147],"extend":[148],"whole-cell":[149,161,192],"\"whole-colony\"":[153],"scale,":[154],"embedded":[156],"multiple":[157],"instances":[158],"a":[160,166,169,199,203,253],"E.":[162,216],"coli":[163,217],"model":[164,167,193],"within":[165],"dynamic":[170],"spatial":[171],"environment,":[172],"allowing":[173],"us":[174,230],"run":[176],"large,":[177],"parallelized":[178],"simulations":[179,208],"cloud":[182],"contained":[184],"all":[185],"molecular":[187],"detail":[188],"many":[195],"interactive":[196],"effects":[197],"colony":[200],"growing":[201],"shared":[204],"environment.":[205],"resulting":[207],"were":[209],"used":[210],"explore":[212],"response":[214],"two":[219],"different":[222],"action,":[225],"tetracycline":[226],"ampicillin,":[228],"enabling":[229],"identify":[232],"sub-generationally-expressed":[233],"genes,":[234],"beta-lactamase":[238],"ampC,":[239],"contributed":[241],"greatly":[242],"dramatic":[244],"cellular":[245],"differences":[246],"steady-state":[248],"periplasmic":[249],"ampicillin":[250],"was":[252],"significant":[254],"factor":[255],"determining":[257],"cell":[258],"survival.":[259]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
