{"id":"https://openalex.org/W2014272261","doi":"https://doi.org/10.1371/journal.pcbi.1002060","title":"Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis","display_name":"Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis","publication_year":2011,"publication_date":"2011-06-30","ids":{"openalex":"https://openalex.org/W2014272261","doi":"https://doi.org/10.1371/journal.pcbi.1002060","mag":"2014272261","pmid":"https://pubmed.ncbi.nlm.nih.gov/21738454"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1002060","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002060","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002060&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002060&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055430707","display_name":"Bhushan Bonde","orcid":"https://orcid.org/0000-0001-6651-6462"},"institutions":[{"id":"https://openalex.org/I28290843","display_name":"University of Surrey","ror":"https://ror.org/00ks66431","country_code":"GB","type":"education","lineage":["https://openalex.org/I28290843"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Bhushan K. Bonde","raw_affiliation_strings":["Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom","institution_ids":["https://openalex.org/I28290843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041730736","display_name":"Dany J. V. Beste","orcid":"https://orcid.org/0000-0001-6579-1366"},"institutions":[{"id":"https://openalex.org/I28290843","display_name":"University of Surrey","ror":"https://ror.org/00ks66431","country_code":"GB","type":"education","lineage":["https://openalex.org/I28290843"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Dany J. V. Beste","raw_affiliation_strings":["Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom","institution_ids":["https://openalex.org/I28290843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040416265","display_name":"Emma Laing","orcid":"https://orcid.org/0000-0002-2095-2442"},"institutions":[{"id":"https://openalex.org/I28290843","display_name":"University of Surrey","ror":"https://ror.org/00ks66431","country_code":"GB","type":"education","lineage":["https://openalex.org/I28290843"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Emma Laing","raw_affiliation_strings":["Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom","institution_ids":["https://openalex.org/I28290843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015589509","display_name":"Andrzej Kierzek","orcid":"https://orcid.org/0000-0002-2605-9057"},"institutions":[{"id":"https://openalex.org/I28290843","display_name":"University of Surrey","ror":"https://ror.org/00ks66431","country_code":"GB","type":"education","lineage":["https://openalex.org/I28290843"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Andrzej M. Kierzek","raw_affiliation_strings":["Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom","institution_ids":["https://openalex.org/I28290843"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028497882","display_name":"Johnjoe McFadden","orcid":"https://orcid.org/0000-0003-2145-0046"},"institutions":[{"id":"https://openalex.org/I28290843","display_name":"University of Surrey","ror":"https://ror.org/00ks66431","country_code":"GB","type":"education","lineage":["https://openalex.org/I28290843"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Johnjoe McFadden","raw_affiliation_strings":["Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom","institution_ids":["https://openalex.org/I28290843"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5028497882"],"corresponding_institution_ids":["https://openalex.org/I28290843"],"apc_list":{"value":3043,"currency":"USD","value_usd":3043},"apc_paid":{"value":3043,"currency":"USD","value_usd":3043},"fwci":1.7843,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.84207859,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"7","issue":"6","first_page":"e1002060","last_page":"e1002060"},"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/T10038","display_name":"Tuberculosis Research and Epidemiology","score":0.9912999868392944,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9821000099182129,"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/transcriptome","display_name":"Transcriptome","score":0.5802737474441528},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.470279723405838},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.45573246479034424},{"id":"https://openalex.org/keywords/tuberculosis","display_name":"Tuberculosis","score":0.4552757143974304},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40419942140579224},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3862139582633972},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.36906546354293823},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.3001062273979187},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.155083566904068},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14761406183242798},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.1444406509399414},{"id":"https://openalex.org/keywords/metabolism","display_name":"Metabolism","score":0.133296400308609},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08537036180496216},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06651398539543152}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5802737474441528},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.470279723405838},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.45573246479034424},{"id":"https://openalex.org/C2781069245","wikidata":"https://www.wikidata.org/wiki/Q12204","display_name":"Tuberculosis","level":2,"score":0.4552757143974304},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40419942140579224},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3862139582633972},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.36906546354293823},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3001062273979187},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.155083566904068},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14761406183242798},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.1444406509399414},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.133296400308609},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08537036180496216},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06651398539543152},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000693","descriptor_name":"Anaerobiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000693","descriptor_name":"Anaerobiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000693","descriptor_name":"Anaerobiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008264","descriptor_name":"Macrophages","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D008264","descriptor_name":"Macrophages","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D008264","descriptor_name":"Macrophages","qualifier_ui":"Q000382","qualifier_name":"microbiology","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":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D013183","descriptor_name":"Sputum","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D013183","descriptor_name":"Sputum","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D013183","descriptor_name":"Sputum","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D014376","descriptor_name":"Tuberculosis","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D014376","descriptor_name":"Tuberculosis","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D014376","descriptor_name":"Tuberculosis","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"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":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1002060","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002060","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002060&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:21738454","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21738454","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":"Journal Article"},{"id":"pmh:oai:alma.44SUR_INST:11139476810002346","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4210197018","display_name":"Open Research (University of Surrey)","issn_l":"2688-268X","issn":["2688-268X","2688-3988"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:epubs.surrey.ac.uk:184902","is_oa":false,"landing_page_url":"http://epubs.surrey.ac.uk/184902/2/bonde.pdf","pdf_url":"http://epubs.surrey.ac.uk/184902/2/bonde.pdf","source":{"id":"https://openalex.org/S4306400680","display_name":"Surrey Research Insight Open Access (The University of Surrey)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28290843","host_organization_name":"University of Surrey","host_organization_lineage":["https://openalex.org/I28290843"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3127818","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3127818","pdf_url":null,"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:CiteSeerX.psu:10.1.1.290.2373","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.290.2373","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/d1/04/PLoS_Comput_Biol_2011_Jun_30_7(6)_e1002060.tar.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.693.1322","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.693.1322","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://epubs.surrey.ac.uk/184902/2/bonde.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:6cbd9098100d49cd88addc85a45977e2","is_oa":false,"landing_page_url":"https://doaj.org/article/6cbd9098100d49cd88addc85a45977e2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 7, Iss 6, p e1002060 (2011)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/135497","is_oa":true,"landing_page_url":"https://figshare.com/articles/Differential_Producibility_Analysis_DPA_of_Transcriptomic_Data_with_Metabolic_Networks_Deconstructing_the_Metabolic_Response_of_M_tuberculosis_/135497","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.1002060","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002060","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002060&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3621418010","display_name":"Construction of a genome scale metabolic model of Mycobacterium tuberculosis to investigate growth-regulated modulation of metabolism.","funder_award_id":"BB/D007208/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4651107819","display_name":null,"funder_award_id":"BB/D007208/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7659524568","display_name":"Investigation of metabolism and substrate utilization of Mycobacterium tuberculosis.","funder_award_id":"088677","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2014272261.pdf","grobid_xml":"https://content.openalex.org/works/W2014272261.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W1597762351","https://openalex.org/W1642162696","https://openalex.org/W1776092349","https://openalex.org/W1864461701","https://openalex.org/W1899896176","https://openalex.org/W1919468846","https://openalex.org/W1971087365","https://openalex.org/W1981824586","https://openalex.org/W1987005877","https://openalex.org/W1987220754","https://openalex.org/W1991233072","https://openalex.org/W1996791690","https://openalex.org/W1999268553","https://openalex.org/W2004361822","https://openalex.org/W2007097682","https://openalex.org/W2028561804","https://openalex.org/W2032303370","https://openalex.org/W2039630338","https://openalex.org/W2047330514","https://openalex.org/W2053867514","https://openalex.org/W2059546521","https://openalex.org/W2059848727","https://openalex.org/W2064943876","https://openalex.org/W2065163714","https://openalex.org/W2069179741","https://openalex.org/W2075795553","https://openalex.org/W2081024768","https://openalex.org/W2082573007","https://openalex.org/W2085004267","https://openalex.org/W2090099066","https://openalex.org/W2090311177","https://openalex.org/W2090710180","https://openalex.org/W2096992728","https://openalex.org/W2099852681","https://openalex.org/W2107598685","https://openalex.org/W2114611316","https://openalex.org/W2116340114","https://openalex.org/W2123084649","https://openalex.org/W2127257007","https://openalex.org/W2129240547","https://openalex.org/W2133707124","https://openalex.org/W2136477180","https://openalex.org/W2141360045","https://openalex.org/W2142437557","https://openalex.org/W2144010669","https://openalex.org/W2147045968","https://openalex.org/W2148190806","https://openalex.org/W2154061034","https://openalex.org/W2157737997","https://openalex.org/W2162684083","https://openalex.org/W2163855763","https://openalex.org/W2164429494","https://openalex.org/W2165539745","https://openalex.org/W2170427655","https://openalex.org/W2170535863","https://openalex.org/W2171793445","https://openalex.org/W2321516796","https://openalex.org/W2339493109","https://openalex.org/W2775779729","https://openalex.org/W2892585814","https://openalex.org/W4244151339"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2806061655","https://openalex.org/W2028462563","https://openalex.org/W1955737261","https://openalex.org/W2942994004","https://openalex.org/W2775573077","https://openalex.org/W2982720988","https://openalex.org/W3150324899","https://openalex.org/W2911461202"],"abstract_inverted_index":{"A":[0],"general":[1,287],"paucity":[2],"of":[3,9,22,35,40,50,93,134,143,172,184,196,199,208,218,223,236,239,250,254,274,278],"knowledge":[4],"about":[5],"the":[6,13,36,47,91,97,104,131,144,169,176,197,203,237,240,244,272],"metabolic":[7,38,73,77,132,151,161,170,291],"state":[8,39],"Mycobacterium":[10],"tuberculosis":[11,174,201,280],"within":[12],"host":[14,264],"environment":[15,246],"is":[16,110,247],"a":[17,41,63,72,122,182,192,206,233,248],"major":[18],"factor":[19],"impeding":[20],"development":[21],"novel":[23,64,160],"drugs":[24],"against":[25],"tuberculosis.":[26],"Current":[27],"experimental":[28,156],"methods":[29],"do":[30],"not":[31],"allow":[32],"direct":[33],"determination":[34],"global":[37,146],"bacterial":[42],"pathogen":[43],"in":[44,57,103,185,212,259],"vivo,":[45],"but":[46],"transcriptional":[48,123],"activity":[49],"all":[51],"encoded":[52],"genes":[53,94,209,219],"has":[54],"been":[55],"investigated":[56],"numerous":[58],"microarray":[59],"studies.":[60],"We":[61,125,163],"describe":[62],"algorithm,":[65],"Differential":[66],"Producibility":[67],"Analysis":[68,87,109],"(DPA)":[69],"that":[70,95,153,220,232],"uses":[71],"network":[74],"to":[75,89,99,112,117,129,137,155,167,175,202,243,270],"extract":[76],"signals":[78,152,292],"from":[79,293],"transcriptome":[80],"data.":[81,296],"The":[82,189],"method":[83],"utilizes":[84],"Flux":[85],"Balance":[86],"(FBA)":[88],"identify":[90,113],"set":[92],"affect":[96],"ability":[98],"produce":[100],"each":[101],"metabolite":[102],"network.":[105],"Subsequently,":[106],"Rank":[107],"Product":[108],"used":[111,269],"those":[114],"metabolites":[115,211],"predicted":[116],"be":[118,268],"most":[119],"affected":[120],"by":[121,263],"signal.":[124],"first":[126],"apply":[127,165],"DPA":[128,148,166,230,266],"investigate":[130,168],"response":[133,171,198,238],"E.":[135],"coli":[136],"both":[138],"anaerobic":[139],"growth":[140],"and":[141,158,181,215,227,276,281,284],"inactivation":[142],"FNR":[145],"regulator.":[147],"successfully":[149],"extracts":[150],"correspond":[154],"data":[157],"provides":[159],"insights.":[162],"next":[164],"M.":[173,200,279],"macrophage":[177,204],"environment,":[178],"human":[179],"sputum":[180],"range":[183],"vitro":[186],"environmental":[187],"perturbations.":[188],"analysis":[190],"revealed":[191],"previously":[193],"unrecognized":[194],"feature":[195,235],"environment:":[205],"down-regulation":[207],"influencing":[210],"central":[213],"metabolism":[214],"concomitant":[216],"up-regulation":[217],"influence":[221],"synthesis":[222],"cell":[224,256],"wall":[225],"components":[226],"virulence":[228,275],"factors.":[229],"suggests":[231],"significant":[234],"tubercle":[241],"bacillus":[242],"intracellular":[245],"channeling":[249],"resources":[251],"towards":[252],"remodeling":[253],"its":[255],"envelope,":[257],"possibly":[258],"preparation":[260],"for":[261,289],"attack":[262],"defenses.":[265],"may":[267,285],"unravel":[271],"mechanisms":[273],"persistence":[277],"other":[282,294],"pathogens":[283],"have":[286],"application":[288],"extracting":[290],"\"-omics\"":[295]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":6}],"updated_date":"2026-09-02T18:50:13.731487","created_date":"2025-10-10T00:00:00"}
