{"id":"https://openalex.org/W4395683097","doi":"https://doi.org/10.1371/journal.pcbi.1012031","title":"Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment","display_name":"Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment","publication_year":2024,"publication_date":"2024-04-26","ids":{"openalex":"https://openalex.org/W4395683097","doi":"https://doi.org/10.1371/journal.pcbi.1012031","pmid":"https://pubmed.ncbi.nlm.nih.gov/38669236"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012031","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012031","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.1012031","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082401021","display_name":"Tracy Kuper","orcid":"https://orcid.org/0000-0003-2491-1557"},"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":false,"raw_author_name":"Tracy J. Kuper","raw_affiliation_strings":["Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-2491-1557","affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101854712","display_name":"Mohammad Mazharul Islam","orcid":"https://orcid.org/0000-0002-9745-0344"},"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":false,"raw_author_name":"Mohammad Mazharul Islam","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":null,"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/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":false,"raw_author_name":"Shayn M. Peirce-Cottler","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":null,"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/A5000119406","display_name":"Jason A. Papin","orcid":"https://orcid.org/0000-0002-2769-5805"},"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":false,"raw_author_name":"Jason A. Papin","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":null,"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":"last","author":{"id":"https://openalex.org/A5049501343","display_name":"Roseanne M. Ford","orcid":"https://orcid.org/0000-0001-6763-3927"},"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":false,"raw_author_name":"Roseanne M Ford","raw_affiliation_strings":["Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-6763-3927","affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.0411,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.86474279,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"20","issue":"4","first_page":"e1012031","last_page":"e1012031"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998000264167786,"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":0.9998000264167786,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9994000196456909,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9930999875068665,"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/biofilm","display_name":"Biofilm","score":0.7184433937072754},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.5630293488502502},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.5379285216331482},{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.47798675298690796},{"id":"https://openalex.org/keywords/denitrification","display_name":"Denitrification","score":0.44682541489601135},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.44344037771224976},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.43223702907562256},{"id":"https://openalex.org/keywords/oxidative-stress","display_name":"Oxidative stress","score":0.427154004573822},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4156531095504761},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3935029208660126},{"id":"https://openalex.org/keywords/metabolism","display_name":"Metabolism","score":0.34419625997543335},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3285069465637207},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32304489612579346},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2655121088027954},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.20305195450782776},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.13953319191932678},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09020218253135681}],"concepts":[{"id":"https://openalex.org/C58123911","wikidata":"https://www.wikidata.org/wiki/Q467410","display_name":"Biofilm","level":3,"score":0.7184433937072754},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.5630293488502502},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.5379285216331482},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.47798675298690796},{"id":"https://openalex.org/C73593433","wikidata":"https://www.wikidata.org/wiki/Q742637","display_name":"Denitrification","level":3,"score":0.44682541489601135},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.44344037771224976},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.43223702907562256},{"id":"https://openalex.org/C2776151105","wikidata":"https://www.wikidata.org/wiki/Q898814","display_name":"Oxidative stress","level":2,"score":0.427154004573822},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4156531095504761},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3935029208660126},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.34419625997543335},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3285069465637207},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32304489612579346},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2655121088027954},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.20305195450782776},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.13953319191932678},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09020218253135681},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C537208039","wikidata":"https://www.wikidata.org/wiki/Q627","display_name":"Nitrogen","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009569","descriptor_name":"Nitric Oxide","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009569","descriptor_name":"Nitric Oxide","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009569","descriptor_name":"Nitric Oxide","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009569","descriptor_name":"Nitric Oxide","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":true},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":true},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":true},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058440","descriptor_name":"Denitrification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058440","descriptor_name":"Denitrification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058440","descriptor_name":"Denitrification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058440","descriptor_name":"Denitrification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1012031","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012031","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:38669236","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38669236","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:11051585","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11051585","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11051585/pdf/pcbi.1012031.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:oai:doaj.org/article:c9d808f3db5e4d5bb8d1a446440efb2d","is_oa":true,"landing_page_url":"https://doaj.org/article/c9d808f3db5e4d5bb8d1a446440efb2d","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 20, Iss 4, p e1012031 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012031","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012031","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":[{"id":"https://metadata.un.org/sdg/6","score":0.6899999976158142,"display_name":"Clean water and sanitation"}],"awards":[{"id":"https://openalex.org/G1373449718","display_name":null,"funder_award_id":"R01 AI154242","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G354376238","display_name":null,"funder_award_id":"R01 AI154242","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5071331563","display_name":null,"funder_award_id":"T32GM136615","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8674629323","display_name":null,"funder_award_id":"T32GM136615","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"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/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1491234030","https://openalex.org/W1973288856","https://openalex.org/W1991190924","https://openalex.org/W1994471795","https://openalex.org/W1996064131","https://openalex.org/W2005143673","https://openalex.org/W2010417142","https://openalex.org/W2015101858","https://openalex.org/W2019347117","https://openalex.org/W2048465561","https://openalex.org/W2048596643","https://openalex.org/W2049266487","https://openalex.org/W2055975025","https://openalex.org/W2060074423","https://openalex.org/W2081904485","https://openalex.org/W2097944090","https://openalex.org/W2098824895","https://openalex.org/W2103023806","https://openalex.org/W2111020654","https://openalex.org/W2112933558","https://openalex.org/W2127351071","https://openalex.org/W2136004458","https://openalex.org/W2146260692","https://openalex.org/W2152869680","https://openalex.org/W2158709371","https://openalex.org/W2161897808","https://openalex.org/W2162666840","https://openalex.org/W2164113064","https://openalex.org/W2166976236","https://openalex.org/W2167244112","https://openalex.org/W2225908389","https://openalex.org/W2469909519","https://openalex.org/W2594824548","https://openalex.org/W2601454055","https://openalex.org/W2617261748","https://openalex.org/W2745012239","https://openalex.org/W2748965945","https://openalex.org/W2791073960","https://openalex.org/W2801535289","https://openalex.org/W2979558755","https://openalex.org/W2980763984","https://openalex.org/W2983683026","https://openalex.org/W3007876418","https://openalex.org/W3009698679","https://openalex.org/W3016499228","https://openalex.org/W3025235884","https://openalex.org/W3028922180","https://openalex.org/W3081949562","https://openalex.org/W3091964154","https://openalex.org/W3192380610","https://openalex.org/W3203505575","https://openalex.org/W3206959204","https://openalex.org/W4220948810","https://openalex.org/W4280586541","https://openalex.org/W4280630487","https://openalex.org/W4319985931","https://openalex.org/W4367668742","https://openalex.org/W4379599517"],"related_works":["https://openalex.org/W1999460937","https://openalex.org/W2083413061","https://openalex.org/W1984242440","https://openalex.org/W2799517538","https://openalex.org/W2113329733","https://openalex.org/W4288069755","https://openalex.org/W1983989854","https://openalex.org/W2070388085","https://openalex.org/W2341681417","https://openalex.org/W2158163767"],"abstract_inverted_index":{"With":[0],"the":[1,21,72,94,153,173,179,223,230,259,295],"generation":[2],"of":[3,7,34,69,105,120,146,196,252],"spatially":[4],"resolved":[5],"transcriptomics":[6],"microbial":[8,291],"biofilms,":[9],"computational":[10,43,279],"tools":[11],"can":[12,81],"be":[13],"used":[14,98],"to":[15,19,74,93,100,171,219,246,265,281,287,294],"integrate":[16],"this":[17],"data":[18,127],"elucidate":[20],"multi-scale":[22],"mechanisms":[23],"controlling":[24],"heterogeneous":[25,290],"biofilm":[26,117,124,225,296],"metabolism.":[27,241],"This":[28],"work":[29],"presents":[30],"a":[31,42,47,129,187,194,277],"Multi-scale":[32],"model":[33,61,64,138,156,190],"Metabolism":[35],"In":[36],"Cellular":[37],"Systems":[38],"(MiMICS)":[39],"which":[40,80,262],"is":[41,71,276],"framework":[44],"that":[45,86,140,166,274],"couples":[46],"genome-scale":[48],"metabolic":[49,78,84,89,137,155,189,215,285,292],"network":[50],"reconstruction":[51],"(GENRE)":[52],"with":[53],"Hybrid":[54],"Automata":[55],"Library":[56],"(HAL),":[57],"an":[58],"existing":[59],"agent-based":[60],"and":[62,107,113,149,162,199,204,212,238],"reaction-diffusion":[63,181],"platform.":[65],"A":[66],"key":[67],"feature":[68],"MiMICS":[70,99,207,227,249,275],"ability":[73],"incorporate":[75,282],"multiple":[76,283],"-omics-guided":[77,284],"models,":[79],"represent":[82],"unique":[83],"states":[85,139,157,293],"yield":[87],"different":[88,159],"parameter":[90],"values":[91],"passed":[92,168],"extracellular":[95,180,247],"models.":[96],"We":[97,272],"simulate":[101],"Pseudomonas":[102],"aeruginosa":[103,122,131],"regulation":[104],"denitrification":[106,211,260],"oxidative":[108,150,213,236],"stress":[109,151,214],"metabolism":[110],"in":[111,178,222,258],"hypoxic":[112],"nitric":[114],"oxide":[115],"(NO)":[116],"microenvironments.":[118],"Integration":[119],"P.":[121,130],"PA14":[123,132,136,188],"spatial":[125,232],"transcriptomic":[126],"into":[128,143],"GENRE":[133],"generated":[134],"four":[135,154],"were":[141,167],"input":[142],"MiMICS.":[144],"Characteristic":[145],"aerobic,":[147],"denitrification,":[148,235],"metabolism,":[152],"predicted":[158,229],"oxygen,":[160],"nitrate,":[161],"NO":[163,224,267],"exchange":[164],"fluxes":[165],"as":[169],"inputs":[170],"update":[172],"agent's":[174],"local":[175,202,220],"metabolite":[176],"concentrations":[177],"model.":[182],"Individual":[183],"bacterial":[184],"agents":[185,200],"chose":[186],"state":[191],"based":[192],"on":[193],"combination":[195],"stochastic":[197],"rules,":[198],"sensing":[201],"oxygen":[203],"NO.":[205],"Transcriptome-guided":[206],"predictions":[208],"suggested":[209],"microscale":[210],"heterogeneity":[216],"emerged":[217],"due":[218],"variability":[221],"microenvironment.":[226,297],"accurately":[228],"biofilm's":[231],"relationships":[233],"between":[234],"stress,":[237],"central":[239],"carbon":[240],"As":[242],"simulated":[243],"cells":[244],"responded":[245],"NO,":[248],"revealed":[250],"dynamics":[251],"cell":[253],"populations":[254],"heterogeneously":[255],"upregulating":[256],"reactions":[257],"pathway,":[261],"may":[263],"function":[264],"maintain":[266],"levels":[268],"within":[269],"non-toxic":[270],"ranges.":[271],"demonstrated":[273],"valuable":[278],"tool":[280],"models":[286],"mechanistically":[288],"map":[289]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}