{"id":"https://openalex.org/W2910511306","doi":"https://doi.org/10.1371/journal.pcbi.1006644","title":"A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types","display_name":"A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types","publication_year":2019,"publication_date":"2019-01-09","ids":{"openalex":"https://openalex.org/W2910511306","doi":"https://doi.org/10.1371/journal.pcbi.1006644","mag":"2910511306","pmid":"https://pubmed.ncbi.nlm.nih.gov/30625152"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006644","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006644","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.1006644","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090742414","display_name":"Yara Seif","orcid":"https://orcid.org/0000-0001-8813-5679"},"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":false,"raw_author_name":"Yara Seif","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088968927","display_name":"Jonathan M. Monk","orcid":"https://orcid.org/0000-0002-3895-8949"},"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":false,"raw_author_name":"Jonathan M. Monk","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023323263","display_name":"Nathan Mih","orcid":"https://orcid.org/0000-0002-4302-9052"},"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":false,"raw_author_name":"Nathan Mih","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-4302-9052","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042162895","display_name":"Hannah Tsunemoto","orcid":"https://orcid.org/0000-0002-1546-097X"},"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":false,"raw_author_name":"Hannah Tsunemoto","raw_affiliation_strings":["Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-1546-097X","affiliations":[{"raw_affiliation_string":"Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018695597","display_name":"Saugat Poudel","orcid":"https://orcid.org/0000-0002-3732-2463"},"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":false,"raw_author_name":"Saugat Poudel","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3732-2463","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084064381","display_name":"Cristal Z\u00fa\u00f1iga","orcid":"https://orcid.org/0000-0002-0135-7429"},"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":false,"raw_author_name":"Cristal Zuniga","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-0135-7429","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090688831","display_name":"Jared T. Broddrick","orcid":"https://orcid.org/0000-0003-4871-4822"},"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":false,"raw_author_name":"Jared Broddrick","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-4871-4822","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072461088","display_name":"Karsten Zengler","orcid":"https://orcid.org/0000-0002-8062-3296"},"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":false,"raw_author_name":"Karsten Zengler","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","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, CA, United States of America","Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America","Division of Biological Sciences, University of California San Diego, La Jolla, CA, 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, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5051097609"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.7352,"has_fulltext":false,"cited_by_count":61,"citation_normalized_percentile":{"value":0.91070128,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"15","issue":"1","first_page":"e1006644","last_page":"e1006644"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9995999932289124,"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":0.9995999932289124,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9983000159263611,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9980999827384949,"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/staphylococcus-aureus","display_name":"Staphylococcus aureus","score":0.7354813814163208},{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.5809876322746277},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5731432437896729},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5606318116188049},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5429319143295288},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4997599124908447},{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.47506898641586304},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.4546833038330078},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39890140295028687},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.33666324615478516},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.3268822133541107},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.24264982342720032}],"concepts":[{"id":"https://openalex.org/C2779489039","wikidata":"https://www.wikidata.org/wiki/Q188121","display_name":"Staphylococcus aureus","level":3,"score":0.7354813814163208},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.5809876322746277},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5731432437896729},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5606318116188049},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5429319143295288},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4997599124908447},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.47506898641586304},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.4546833038330078},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39890140295028687},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.33666324615478516},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.3268822133541107},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.24264982342720032}],"mesh":[{"descriptor_ui":"D003470","descriptor_name":"Culture Media","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D003470","descriptor_name":"Culture Media","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D003470","descriptor_name":"Culture Media","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D003470","descriptor_name":"Culture Media","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D003470","descriptor_name":"Culture Media","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D003470","descriptor_name":"Culture Media","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":true},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":true},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":true},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000187","qualifier_name":"drug effects","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":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1006644","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006644","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:30625152","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30625152","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:ark:/13030/qt6zg416ws","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:c6f098ce42454bc2b59f14de7f90b918","is_oa":true,"landing_page_url":"https://doaj.org/article/c6f098ce42454bc2b59f14de7f90b918","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 15, Iss 1, p e1006644 (2019)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt6zg416ws","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/6zg416ws","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS computational biology, vol 15, iss 1","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5311990","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6326480","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/7567352","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/A_computational_knowledge-base_elucidates_the_response_of_i_Staphylococcus_aureus_i_to_different_media_types/7567352","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006644","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006644","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/G2366015525","display_name":null,"funder_award_id":"1-U01-AI124316-01","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":98,"referenced_works":["https://openalex.org/W1481257824","https://openalex.org/W1543388089","https://openalex.org/W1598900371","https://openalex.org/W1823942469","https://openalex.org/W1843501261","https://openalex.org/W1873084373","https://openalex.org/W1947356700","https://openalex.org/W1974996001","https://openalex.org/W1976759652","https://openalex.org/W1979824847","https://openalex.org/W1986787331","https://openalex.org/W1987253954","https://openalex.org/W1988020173","https://openalex.org/W1991004166","https://openalex.org/W1993584543","https://openalex.org/W1997374187","https://openalex.org/W1997867228","https://openalex.org/W1997955858","https://openalex.org/W2007857508","https://openalex.org/W2008249406","https://openalex.org/W2019974881","https://openalex.org/W2027888467","https://openalex.org/W2028067981","https://openalex.org/W2029403511","https://openalex.org/W2030531577","https://openalex.org/W2041715023","https://openalex.org/W2048465561","https://openalex.org/W2052380534","https://openalex.org/W2052670782","https://openalex.org/W2057717820","https://openalex.org/W2060038413","https://openalex.org/W2078355959","https://openalex.org/W2085993965","https://openalex.org/W2092006645","https://openalex.org/W2095898564","https://openalex.org/W2097252391","https://openalex.org/W2100345001","https://openalex.org/W2101616986","https://openalex.org/W2101716379","https://openalex.org/W2109636459","https://openalex.org/W2110845902","https://openalex.org/W2113248983","https://openalex.org/W2113365252","https://openalex.org/W2113638991","https://openalex.org/W2115127793","https://openalex.org/W2120753451","https://openalex.org/W2124064813","https://openalex.org/W2124737787","https://openalex.org/W2125423423","https://openalex.org/W2127113854","https://openalex.org/W2127872845","https://openalex.org/W2131316809","https://openalex.org/W2131589156","https://openalex.org/W2135763006","https://openalex.org/W2140006321","https://openalex.org/W2143401494","https://openalex.org/W2143589202","https://openalex.org/W2145589671","https://openalex.org/W2148033653","https://openalex.org/W2148044817","https://openalex.org/W2148853951","https://openalex.org/W2149085197","https://openalex.org/W2160076370","https://openalex.org/W2162731436","https://openalex.org/W2166270451","https://openalex.org/W2168046582","https://openalex.org/W2168482920","https://openalex.org/W2202347610","https://openalex.org/W2255142656","https://openalex.org/W2403430327","https://openalex.org/W2419335772","https://openalex.org/W2460791328","https://openalex.org/W2461899760","https://openalex.org/W2474432644","https://openalex.org/W2474580351","https://openalex.org/W2476757800","https://openalex.org/W2486475734","https://openalex.org/W2517554512","https://openalex.org/W2530273761","https://openalex.org/W2541638185","https://openalex.org/W2588283941","https://openalex.org/W2596650357","https://openalex.org/W2598359550","https://openalex.org/W2605504874","https://openalex.org/W2736031041","https://openalex.org/W2737081818","https://openalex.org/W2746135285","https://openalex.org/W2764202526","https://openalex.org/W2782489043","https://openalex.org/W2786774014","https://openalex.org/W2789128799","https://openalex.org/W2794083788","https://openalex.org/W2796442704","https://openalex.org/W2950428171","https://openalex.org/W4245225949","https://openalex.org/W4253808806","https://openalex.org/W6771822510","https://openalex.org/W7073855572"],"related_works":["https://openalex.org/W2053969879","https://openalex.org/W2082641564","https://openalex.org/W2107333779","https://openalex.org/W2790772971","https://openalex.org/W3108190435","https://openalex.org/W1964419640","https://openalex.org/W4288069755","https://openalex.org/W1854805732","https://openalex.org/W3180007124","https://openalex.org/W2332273970"],"abstract_inverted_index":{"S.":[0,26,58,170],"aureus":[1,27,59],"is":[2,10],"classified":[3],"as":[4,149,164],"a":[5,11,45,138,150,165],"serious":[6],"threat":[7],"pathogen":[8],"and":[9,17,70,91,128,136],"priority":[12],"that":[13],"guides":[14],"the":[15,124],"discovery":[16],"development":[18],"of":[19,25,32,51,99,108,126,152,155],"new":[20],"antibiotics.":[21],"Despite":[22],"growing":[23],"knowledge":[24],"metabolic":[28,113,172],"capabilities,":[29],"our":[30],"understanding":[31],"its":[33,175],"systems-level":[34],"responses":[35],"to":[36,116,140,145,168,174],"different":[37],"media":[38],"types":[39],"remains":[40],"incomplete.":[41],"Here,":[42],"we":[43],"develop":[44],"manually":[46],"reconstructed":[47],"genome-scale":[48],"model":[49],"(GEM-PRO)":[50],"metabolism":[52],"with":[53,80,94,102],"3D":[54],"protein":[55,73],"structures":[56],"for":[57],"USA300":[60],"str.":[61],"JE2":[62],"containing":[63],"854":[64],"genes,":[65],"1,440":[66],"reactions,":[67],"1,327":[68],"metabolites":[69],"673":[71],"3-dimensional":[72],"structures.":[74],"Computations":[75],"were":[76],"in":[77,120,132],"85%":[78],"agreement":[79,93],"gene":[81],"essentiality":[82,125],"data":[83],"from":[84],"random":[85],"barcode":[86],"transposon":[87],"site":[88],"sequencing":[89],"(RB-TnSeq)":[90],"68%":[92],"experimental":[95,103],"physiological":[96,134],"data.":[97,158],"Comparisons":[98],"computational":[100],"predictions":[101],"observations":[104],"highlight:":[105],"1)":[106],"cases":[107],"non-essential":[109],"biomass":[110],"precursors;":[111],"2)":[112],"genes":[114],"subject":[115],"transcriptional":[117],"regulation":[118],"involved":[119],"Staphyloxanthin":[121],"biosynthesis;":[122],"3)":[123],"purine":[127],"amino":[129],"acid":[130],"biosynthesis":[131],"synthetic":[133],"media;":[135],"4)":[137],"switch":[139],"aerobic":[141],"fermentation":[142],"upon":[143],"exposure":[144],"extracellular":[146],"glucose":[147],"elucidated":[148],"result":[151],"integrating":[153],"time-course":[154],"quantitative":[156],"exo-metabolomics":[157],"An":[159],"up-to-date":[160],"GEM-PRO":[161],"thus":[162],"serves":[163],"knowledge-based":[166],"platform":[167],"elucidate":[169],"aureus'":[171],"response":[173],"environment.":[176]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":5}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}