{"id":"https://openalex.org/W4391743298","doi":"https://doi.org/10.1371/journal.pcbi.1011865","title":"StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses","display_name":"StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses","publication_year":2024,"publication_date":"2024-02-12","ids":{"openalex":"https://openalex.org/W4391743298","doi":"https://doi.org/10.1371/journal.pcbi.1011865","pmid":"https://pubmed.ncbi.nlm.nih.gov/38346086"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011865","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011865","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011865&type=printable","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://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011865&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011490727","display_name":"Jiao Zhao","orcid":"https://orcid.org/0000-0001-5446-1388"},"institutions":[{"id":"https://openalex.org/I204722609","display_name":"Queen's University","ror":"https://ror.org/02y72wh86","country_code":"CA","type":"education","lineage":["https://openalex.org/I204722609"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Jiao Zhao","raw_affiliation_strings":["Department of Chemical Engineering, Queen's University, Kingston, Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Queen's University, Kingston, Ontario, Canada","institution_ids":["https://openalex.org/I204722609"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100451980","display_name":"Ke Chen","orcid":"https://orcid.org/0000-0001-8357-3741"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ke Chen","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051097609","display_name":"Bernhard \u00d8. Palsson","orcid":"https://orcid.org/0000-0003-2357-6785"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bernhard O. Palsson","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-2357-6785","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101734149","display_name":"Laurence Yang","orcid":"https://orcid.org/0000-0002-2393-5189"},"institutions":[{"id":"https://openalex.org/I204722609","display_name":"Queen's University","ror":"https://ror.org/02y72wh86","country_code":"CA","type":"education","lineage":["https://openalex.org/I204722609"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Laurence Yang","raw_affiliation_strings":["Department of Chemical Engineering, Queen's University, Kingston, Ontario, Canada"],"raw_orcid":"https://orcid.org/0000-0002-2393-5189","affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Queen's University, Kingston, Ontario, Canada","institution_ids":["https://openalex.org/I204722609"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5011490727","https://openalex.org/A5051097609","https://openalex.org/A5100451980","https://openalex.org/A5101734149"],"corresponding_institution_ids":["https://openalex.org/I204722609","https://openalex.org/I36258959"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.1725,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.92198991,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"20","issue":"2","first_page":"e1011865","last_page":"e1011865"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9997000098228455,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9997000098228455,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9991000294685364,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.6811475157737732},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5388495922088623},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.5274931192398071},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5119441747665405},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.47475507855415344},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.442269504070282},{"id":"https://openalex.org/keywords/oxidative-stress","display_name":"Oxidative stress","score":0.4323100745677948},{"id":"https://openalex.org/keywords/stress","display_name":"Stress (linguistics)","score":0.41375356912612915},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3663526177406311},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3453128933906555},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.33227360248565674},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3300052285194397}],"concepts":[{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.6811475157737732},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5388495922088623},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.5274931192398071},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5119441747665405},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.47475507855415344},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.442269504070282},{"id":"https://openalex.org/C2776151105","wikidata":"https://www.wikidata.org/wiki/Q898814","display_name":"Oxidative stress","level":2,"score":0.4323100745677948},{"id":"https://openalex.org/C21036866","wikidata":"https://www.wikidata.org/wiki/Q181767","display_name":"Stress (linguistics)","level":2,"score":0.41375356912612915},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3663526177406311},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3453128933906555},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.33227360248565674},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3300052285194397},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000143","descriptor_name":"Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000143","descriptor_name":"Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000143","descriptor_name":"Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D006360","descriptor_name":"Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006360","descriptor_name":"Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006360","descriptor_name":"Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010084","descriptor_name":"Oxidation-Reduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010084","descriptor_name":"Oxidation-Reduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010084","descriptor_name":"Oxidation-Reduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013312","descriptor_name":"Stress, Physiological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013312","descriptor_name":"Stress, Physiological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013312","descriptor_name":"Stress, Physiological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1011865","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011865","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011865&type=printable","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:38346086","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38346086","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:escholarship.org:ark:/13030/qt1vb3f03q","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/1vb3f03q","pdf_url":"https://escholarship.org/content/qt1vb3f03q/qt1vb3f03q.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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 Computational Biology, vol 20, iss 2","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10890762","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10890762","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10890762/pdf/pcbi.1011865.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:ark:/13030/qt1vb3f03q","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:f7e9f279146f465f87c3c595460cdbc0","is_oa":false,"landing_page_url":"https://doaj.org/article/f7e9f279146f465f87c3c595460cdbc0","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 20, Iss 2, p e1011865 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011865","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011865","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011865&type=printable","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":[{"score":0.41999998688697815,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G1108557835","display_name":null,"funder_award_id":"RGPIN-2020-06325","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1170729765","display_name":null,"funder_award_id":"OGI-207","funder_id":"https://openalex.org/F4320314024","funder_display_name":"Ontario Genomics"},{"id":"https://openalex.org/G1540404058","display_name":null,"funder_award_id":"R01 GM057089","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2113485703","display_name":null,"funder_award_id":"OGI-207","funder_id":"https://openalex.org/F4320319880","funder_display_name":"Government of Canada"},{"id":"https://openalex.org/G230793895","display_name":null,"funder_award_id":"06325","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2470632991","display_name":null,"funder_award_id":"R01GM057089","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2493954264","display_name":null,"funder_award_id":"RGPIN-2020-06325","funder_id":"https://openalex.org/F4320321832","funder_display_name":"Queen's University"},{"id":"https://openalex.org/G3508784843","display_name":null,"funder_award_id":"OGI-207","funder_id":"https://openalex.org/F4320310787","funder_display_name":"Genome Canada"},{"id":"https://openalex.org/G3525686075","display_name":null,"funder_award_id":"RGPIN-2020","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G4818650334","display_name":null,"funder_award_id":"R01GM057089","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6690747165","display_name":null,"funder_award_id":"R01GM057089","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8720209422","display_name":null,"funder_award_id":"R01GM057089","funder_id":"https://openalex.org/F4320321832","funder_display_name":"Queen's University"},{"id":"https://openalex.org/G930017303","display_name":null,"funder_award_id":"RGPIN-2020-06325","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320314024","display_name":"Ontario Genomics","ror":null},{"id":"https://openalex.org/F4320314607","display_name":"Government of Ontario","ror":"https://ror.org/015pzp858"},{"id":"https://openalex.org/F4320319880","display_name":"Government of Canada","ror":"https://ror.org/010q4q527"},{"id":"https://openalex.org/F4320321832","display_name":"Queen's University","ror":"https://ror.org/02y72wh86"},{"id":"https://openalex.org/F4320331257","display_name":"Alliance de recherche num\u00e9rique du Canada","ror":"https://ror.org/010r6td27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391743298.pdf","grobid_xml":"https://content.openalex.org/works/W4391743298.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1910268468","https://openalex.org/W1981365590","https://openalex.org/W1985053703","https://openalex.org/W1987573660","https://openalex.org/W1998546722","https://openalex.org/W2023776166","https://openalex.org/W2035250546","https://openalex.org/W2041792339","https://openalex.org/W2058582378","https://openalex.org/W2077776831","https://openalex.org/W2079308952","https://openalex.org/W2087378201","https://openalex.org/W2103133590","https://openalex.org/W2122860350","https://openalex.org/W2126696746","https://openalex.org/W2157100014","https://openalex.org/W2191824721","https://openalex.org/W2265804764","https://openalex.org/W2416065856","https://openalex.org/W2541638185","https://openalex.org/W2552860965","https://openalex.org/W2729864939","https://openalex.org/W2760895823","https://openalex.org/W2833943491","https://openalex.org/W2938882297","https://openalex.org/W2954205175","https://openalex.org/W2978188190","https://openalex.org/W2982211492","https://openalex.org/W2989622943","https://openalex.org/W2991767217","https://openalex.org/W3012078265","https://openalex.org/W3044656883","https://openalex.org/W3094512440","https://openalex.org/W3157966802","https://openalex.org/W4210529806","https://openalex.org/W4224951807","https://openalex.org/W4229903309","https://openalex.org/W4366245488"],"related_works":["https://openalex.org/W2360987025","https://openalex.org/W2387178301","https://openalex.org/W3144733943","https://openalex.org/W2785993273","https://openalex.org/W2382269147","https://openalex.org/W3184323118","https://openalex.org/W1973959357","https://openalex.org/W2799462113","https://openalex.org/W36834100","https://openalex.org/W2376819606"],"abstract_inverted_index":{"Generalist":[0],"microbes":[1],"have":[2,19],"adapted":[3],"to":[4,78,99,146,180],"a":[5],"multitude":[6],"of":[7,41,60,139,171],"environmental":[8],"stresses":[9],"through":[10],"their":[11],"integrated":[12],"stress":[13,17,47,57,71,182],"response":[14,58],"system.":[15],"Individual":[16],"responses":[18,48,152],"been":[20],"quantified":[21],"by":[22,126,184],"E.":[23,61,83],"coli":[24,62,84],"metabolism":[25],"and":[26,33,68,85,105,118,137,149,157,165],"expression":[27,138,151],"(ME)":[28],"models":[29],"under":[30,153],"thermal,":[31],"oxidative":[32,66],"acid":[34,69],"stress,":[35],"respectively.":[36],"However,":[37],"the":[38,55,75,185],"systematic":[39],"quantification":[40],"cross-stress":[42,117],"&":[43],"cross-talk":[44,119],"among":[45],"these":[46],"remains":[49],"lacking.":[50],"Here,":[51],"we":[52],"present":[53],"StressME:":[54],"unified":[56],"model":[59,81,177],"combining":[63],"thermal":[64,158],"(FoldME),":[65],"(OxidizeME)":[67],"(AcidifyME)":[70],"responses.":[72,120],"StressME":[73,108,143],"is":[74,144,161],"most":[76],"up":[77],"date":[79],"ME":[80,91],"for":[82,103,163],"it":[86,94,160],"reproduces":[87],"all":[88],"published":[89],"single-stress":[90],"models.":[92],"Additionally,":[93],"includes":[95],"refined":[96],"rate":[97],"constants":[98],"improve":[100],"prediction":[101],"accuracy":[102],"wild-type":[104],"stress-evolved":[106],"strains.":[107],"revealed":[109],"certain":[110],"optimal":[111],"proteome":[112],"allocation":[113],"strategies":[114],"associated":[115],"with":[116],"These":[121],"stress-optimal":[122],"proteomes":[123],"were":[124],"shaped":[125],"trade-offs":[127],"between":[128],"protective":[129],"vs.":[130,134],"metabolic":[131,148],"enzymes;":[132],"cytoplasmic":[133],"periplasmic":[135],"chaperones;":[136],"stress-specific":[140],"proteins.":[141],"As":[142],"tuned":[145],"compute":[147],"gene":[150],"mild":[154],"acid,":[155],"oxidative,":[156],"stresses,":[159],"useful":[162],"engineering":[164],"health":[166],"applications.":[167],"The":[168],"modular":[169],"design":[170],"our":[172],"open-source":[173],"package":[174],"also":[175],"facilitates":[176],"expansion":[178],"(e.g.,":[179],"new":[181],"mechanisms)":[183],"computational":[186],"biology":[187],"community.":[188]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
