{"id":"https://openalex.org/W4367047626","doi":"https://doi.org/10.1371/journal.pcbi.1011076","title":"Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies","display_name":"Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies","publication_year":2023,"publication_date":"2023-04-26","ids":{"openalex":"https://openalex.org/W4367047626","doi":"https://doi.org/10.1371/journal.pcbi.1011076","pmid":"https://pubmed.ncbi.nlm.nih.gov/37099624"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011076","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011076","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.1011076","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110806148","display_name":"Deborah Powers","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":"Deborah A. Powers","raw_affiliation_strings":["Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053077805","display_name":"Matthew L. Jenior","orcid":"https://orcid.org/0000-0003-1884-3543"},"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":"Matthew L. Jenior","raw_affiliation_strings":["Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058436904","display_name":"Glynis L. Kolling","orcid":"https://orcid.org/0000-0001-8871-8129"},"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":"Glynis L. Kolling","raw_affiliation_strings":["Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","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":true,"raw_author_name":"Jason A. Papin","raw_affiliation_strings":["Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America","Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-2769-5805","affiliations":[{"raw_affiliation_string":"Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5000119406","https://openalex.org/A5053077805","https://openalex.org/A5058436904","https://openalex.org/A5110806148"],"corresponding_institution_ids":["https://openalex.org/I51556381"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.1923,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.87401226,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"19","issue":"4","first_page":"e1011076","last_page":"e1011076"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11288","display_name":"Clostridium difficile and Clostridium perfringens research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11288","display_name":"Clostridium difficile and Clostridium perfringens research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9771999716758728,"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/T12817","display_name":"Pharmacological Effects of Natural Compounds","score":0.9713000059127808,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/toxin","display_name":"Toxin","score":0.7812516093254089},{"id":"https://openalex.org/keywords/clostridium-difficile-toxin-a","display_name":"Clostridium difficile toxin A","score":0.6675348877906799},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.5647851824760437},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5384777188301086},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.5317408442497253},{"id":"https://openalex.org/keywords/intracellular","display_name":"Intracellular","score":0.4914783239364624},{"id":"https://openalex.org/keywords/metabolite","display_name":"Metabolite","score":0.4827834665775299},{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.469819575548172},{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.453494668006897},{"id":"https://openalex.org/keywords/arginine","display_name":"Arginine","score":0.4161511957645416},{"id":"https://openalex.org/keywords/microbiology","display_name":"Microbiology","score":0.41464027762413025},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3773271143436432},{"id":"https://openalex.org/keywords/metabolism","display_name":"Metabolism","score":0.3097738027572632},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2562388777732849},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.21259373426437378},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.1584392786026001},{"id":"https://openalex.org/keywords/antibiotics","display_name":"Antibiotics","score":0.1324298083782196}],"concepts":[{"id":"https://openalex.org/C2777367657","wikidata":"https://www.wikidata.org/wiki/Q184651","display_name":"Toxin","level":2,"score":0.7812516093254089},{"id":"https://openalex.org/C97505648","wikidata":"https://www.wikidata.org/wiki/Q5135488","display_name":"Clostridium difficile toxin A","level":4,"score":0.6675348877906799},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.5647851824760437},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5384777188301086},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.5317408442497253},{"id":"https://openalex.org/C79879829","wikidata":"https://www.wikidata.org/wiki/Q5571762","display_name":"Intracellular","level":2,"score":0.4914783239364624},{"id":"https://openalex.org/C2777477808","wikidata":"https://www.wikidata.org/wiki/Q407595","display_name":"Metabolite","level":2,"score":0.4827834665775299},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.469819575548172},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.453494668006897},{"id":"https://openalex.org/C2777468819","wikidata":"https://www.wikidata.org/wiki/Q173670","display_name":"Arginine","level":3,"score":0.4161511957645416},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.41464027762413025},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3773271143436432},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.3097738027572632},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2562388777732849},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21259373426437378},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.1584392786026001},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.1324298083782196},{"id":"https://openalex.org/C2994496256","wikidata":"https://www.wikidata.org/wiki/Q27031090","display_name":"Clostridium difficile","level":3,"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":"D000082682","descriptor_name":"Clostridioides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000082682","descriptor_name":"Clostridioides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000082682","descriptor_name":"Clostridioides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000082682","descriptor_name":"Clostridioides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001427","descriptor_name":"Bacterial Toxins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001427","descriptor_name":"Bacterial Toxins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001427","descriptor_name":"Bacterial Toxins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001427","descriptor_name":"Bacterial Toxins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004768","descriptor_name":"Enterotoxins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004768","descriptor_name":"Enterotoxins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004768","descriptor_name":"Enterotoxins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004768","descriptor_name":"Enterotoxins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016360","descriptor_name":"Clostridioides difficile","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016360","descriptor_name":"Clostridioides difficile","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016360","descriptor_name":"Clostridioides difficile","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016360","descriptor_name":"Clostridioides difficile","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1011076","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011076","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:37099624","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37099624","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:10166488","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10166488","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10166488/pdf/pcbi.1011076.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:f77febbc9d2a4d049f4d498d546b5f9e","is_oa":true,"landing_page_url":"https://doaj.org/article/f77febbc9d2a4d049f4d498d546b5f9e","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 19, Iss 4, p e1011076 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011076","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011076","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":[{"score":0.6700000166893005,"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger"}],"awards":[{"id":"https://openalex.org/G1572225543","display_name":null,"funder_award_id":"AI007046","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5797893022","display_name":null,"funder_award_id":"T32 AI007046","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8674107031","display_name":null,"funder_award_id":"R01 AT010253","funder_id":"https://openalex.org/F4320337593","funder_display_name":"National Center for Complementary and Integrative Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337593","display_name":"National Center for Complementary and Integrative Health","ror":"https://ror.org/00190t495"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1583343932","https://openalex.org/W1665355332","https://openalex.org/W1911807020","https://openalex.org/W1974327174","https://openalex.org/W1976833226","https://openalex.org/W1992720763","https://openalex.org/W1996646253","https://openalex.org/W2003877977","https://openalex.org/W2034081663","https://openalex.org/W2064276453","https://openalex.org/W2087538130","https://openalex.org/W2091003597","https://openalex.org/W2097814039","https://openalex.org/W2102459023","https://openalex.org/W2109049071","https://openalex.org/W2113976657","https://openalex.org/W2120563768","https://openalex.org/W2123641345","https://openalex.org/W2140039966","https://openalex.org/W2144511134","https://openalex.org/W2150187794","https://openalex.org/W2166128109","https://openalex.org/W2171079736","https://openalex.org/W2347869237","https://openalex.org/W2387768143","https://openalex.org/W2410295001","https://openalex.org/W2424956380","https://openalex.org/W2507162024","https://openalex.org/W2603627669","https://openalex.org/W2765868029","https://openalex.org/W2911411449","https://openalex.org/W2912671352","https://openalex.org/W3016499228","https://openalex.org/W3048946346","https://openalex.org/W3118639735","https://openalex.org/W3123374720","https://openalex.org/W3140075632","https://openalex.org/W3203478130","https://openalex.org/W4206037640","https://openalex.org/W4238901242","https://openalex.org/W4296628385","https://openalex.org/W4309411734","https://openalex.org/W4323038954","https://openalex.org/W4399976616"],"related_works":["https://openalex.org/W2799517538","https://openalex.org/W4288069755","https://openalex.org/W1854805732","https://openalex.org/W2063475537","https://openalex.org/W2341681417","https://openalex.org/W1961707331","https://openalex.org/W3180007124","https://openalex.org/W2012938657","https://openalex.org/W2332273970","https://openalex.org/W4229007988"],"abstract_inverted_index":{"Clostridioides":[0],"difficile":[1,27,80,107,207],"pathogenesis":[2],"is":[3,22,41,147,160],"mediated":[4],"through":[5],"its":[6],"two":[7],"toxin":[8,28,53,68,116,135,152,190,195,203],"proteins,":[9],"TcdA":[10],"and":[11,19,49,67,83,86,115,125,137,144,158,167,208],"TcdB,":[12],"which":[13,43],"induce":[14],"intestinal":[15],"epithelial":[16],"cell":[17],"death":[18],"inflammation.":[20],"It":[21],"possible":[23],"to":[24,63,101,129,180,192,216],"alter":[25],"C.":[26,79,106,206],"production":[29,69,204],"by":[30],"changing":[31],"various":[32],"metabolite":[33,170],"concentrations":[34],"within":[35],"the":[36,57,95,98,175],"extracellular":[37],"environment.":[38,138],"However,":[39],"it":[40],"unknown":[42],"intracellular":[44,60,164],"metabolic":[45,61,76,131,176,210],"pathways":[46,62],"are":[47],"involved":[48],"how":[50],"they":[51],"regulate":[52],"production.":[54],"To":[55],"investigate":[56],"response":[58],"of":[59,78,112,156,202],"diverse":[64],"nutritional":[65,113],"environments":[66,114],"states,":[70],"we":[71,140],"use":[72],"previously":[73],"published":[74],"genome-scale":[75],"models":[77,96,108],"strains":[81],"CD630":[82],"CDR20291":[84],"(iCdG709":[85],"iCdR703).":[87],"We":[88,118,172],"integrated":[89],"publicly":[90],"available":[91],"transcriptomic":[92],"data":[93],"with":[94,122,134],"using":[97],"RIPTiDe":[99],"algorithm":[100,178],"create":[102],"16":[103],"unique":[104],"contextualized":[105],"representing":[109],"a":[110,188,193],"range":[111],"states.":[117,153],"used":[119],"Random":[120],"Forest":[121],"flux":[123],"sampling":[124],"shadow":[126],"pricing":[127],"analyses":[128],"identify":[130,181],"patterns":[132],"correlated":[133],"states":[136],"Specifically,":[139],"found":[141],"that":[142,184,212],"arginine":[143,157],"ornithine":[145,159],"uptake":[146,155],"particularly":[148],"active":[149],"in":[150,205],"low":[151,194],"Additionally,":[154],"highly":[161],"dependent":[162],"on":[163],"fatty":[165],"acid":[166],"large":[168],"polymer":[169],"pools.":[171],"also":[173],"applied":[174],"transformation":[177],"(MTA)":[179],"model":[182],"perturbations":[183],"shift":[185],"metabolism":[186],"from":[187],"high":[189],"state":[191],"state.":[196],"This":[197],"analysis":[198],"expands":[199],"our":[200],"understanding":[201],"identifies":[209],"dependencies":[211],"could":[213],"be":[214],"leveraged":[215],"mitigate":[217],"disease":[218],"severity.":[219]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
