{"id":"https://openalex.org/W2734327806","doi":"https://doi.org/10.1093/bioinformatics/btx250","title":"Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data","display_name":"Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data","publication_year":2017,"publication_date":"2017-04-20","ids":{"openalex":"https://openalex.org/W2734327806","doi":"https://doi.org/10.1093/bioinformatics/btx250","mag":"2734327806","pmid":"https://pubmed.ncbi.nlm.nih.gov/28881984"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx250","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx250","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i301/25156912/btx250.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i301/25156912/btx250.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010375183","display_name":"Eugenio Cinquemani","orcid":"https://orcid.org/0000-0003-3353-6525"},"institutions":[{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Eugenio Cinquemani","raw_affiliation_strings":["Inria, Centre de Recherche Grenoble \u2013 Rh\u00f4ne-Alpes, Montbonnot, France","IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)"],"affiliations":[{"raw_affiliation_string":"Inria, Centre de Recherche Grenoble \u2013 Rh\u00f4ne-Alpes, Montbonnot, France","institution_ids":["https://openalex.org/I4210101348","https://openalex.org/I899635006"]},{"raw_affiliation_string":"IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089697453","display_name":"Val\u00e9rie Laroute","orcid":"https://orcid.org/0000-0003-1108-7714"},"institutions":[{"id":"https://openalex.org/I196454796","display_name":"Institut National des Sciences Appliqu\u00e9es de Toulouse","ror":"https://ror.org/01h8pf755","country_code":"FR","type":"education","lineage":["https://openalex.org/I196454796","https://openalex.org/I4405258862"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210110888","display_name":"Laboratoire d'Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s","ror":"https://ror.org/01yypjb30","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I196454796","https://openalex.org/I4210088668","https://openalex.org/I4210095849","https://openalex.org/I4210110888","https://openalex.org/I4405258862"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Val\u00e9rie Laroute","raw_affiliation_strings":["LISBP, Universit\u00e9 de Toulouse, CNRS, INRA, INSA, Toulouse, France"],"affiliations":[{"raw_affiliation_string":"LISBP, Universit\u00e9 de Toulouse, CNRS, INRA, INSA, Toulouse, France","institution_ids":["https://openalex.org/I196454796","https://openalex.org/I4210110888","https://openalex.org/I17866349","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035294360","display_name":"Muriel Cocaign\u2010Bousquet","orcid":"https://orcid.org/0000-0003-2033-9901"},"institutions":[{"id":"https://openalex.org/I196454796","display_name":"Institut National des Sciences Appliqu\u00e9es de Toulouse","ror":"https://ror.org/01h8pf755","country_code":"FR","type":"education","lineage":["https://openalex.org/I196454796","https://openalex.org/I4405258862"]},{"id":"https://openalex.org/I4210110888","display_name":"Laboratoire d'Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s","ror":"https://ror.org/01yypjb30","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I196454796","https://openalex.org/I4210088668","https://openalex.org/I4210095849","https://openalex.org/I4210110888","https://openalex.org/I4405258862"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Muriel Cocaign-Bousquet","raw_affiliation_strings":["LISBP, Universit\u00e9 de Toulouse, CNRS, INRA, INSA, Toulouse, France"],"affiliations":[{"raw_affiliation_string":"LISBP, Universit\u00e9 de Toulouse, CNRS, INRA, INSA, Toulouse, France","institution_ids":["https://openalex.org/I196454796","https://openalex.org/I4210110888","https://openalex.org/I17866349","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054406248","display_name":"Hidde de Jong","orcid":"https://orcid.org/0000-0002-2226-650X"},"institutions":[{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Hidde de Jong","raw_affiliation_strings":["Inria, Centre de Recherche Grenoble \u2013 Rh\u00f4ne-Alpes, Montbonnot, France","IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)"],"affiliations":[{"raw_affiliation_string":"Inria, Centre de Recherche Grenoble \u2013 Rh\u00f4ne-Alpes, Montbonnot, France","institution_ids":["https://openalex.org/I4210101348","https://openalex.org/I899635006"]},{"raw_affiliation_string":"IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062022864","display_name":"Delphine Ropers","orcid":"https://orcid.org/0000-0003-2659-3003"},"institutions":[{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Delphine Ropers","raw_affiliation_strings":["Inria, Centre de Recherche Grenoble \u2013 Rh\u00f4ne-Alpes, Montbonnot, France","IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)"],"affiliations":[{"raw_affiliation_string":"Inria, Centre de Recherche Grenoble \u2013 Rh\u00f4ne-Alpes, Montbonnot, France","institution_ids":["https://openalex.org/I4210101348","https://openalex.org/I899635006"]},{"raw_affiliation_string":"IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5010375183"],"corresponding_institution_ids":["https://openalex.org/I4210101348","https://openalex.org/I899635006"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5317,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.64415438,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"33","issue":"14","first_page":"i301","last_page":"i310"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9955000281333923,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9696999788284302,"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/smoothing","display_name":"Smoothing","score":0.5916342735290527},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5456815361976624},{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.447682648897171},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26122382283210754},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1830279529094696}],"concepts":[{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.5916342735290527},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5456815361976624},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.447682648897171},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26122382283210754},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1830279529094696},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013294","descriptor_name":"Lactococcus lactis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013294","descriptor_name":"Lactococcus lactis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013294","descriptor_name":"Lactococcus lactis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx250","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx250","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i301/25156912/btx250.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28881984","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28881984","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:hal-01607919v1","is_oa":false,"landing_page_url":"https://hal.science/hal-01607919","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2017, 33 (14), pp.i301-i310. ⟨10.1093/bioinformatics/btx250⟩","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:5870603","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5870603","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx250","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx250","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i301/25156912/btx250.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2734327806.pdf","grobid_xml":"https://content.openalex.org/works/W2734327806.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W30303522","https://openalex.org/W1483307070","https://openalex.org/W1574470162","https://openalex.org/W1704449870","https://openalex.org/W1746819321","https://openalex.org/W1953599462","https://openalex.org/W1971167763","https://openalex.org/W1988950044","https://openalex.org/W1997062226","https://openalex.org/W2016180374","https://openalex.org/W2016862626","https://openalex.org/W2021629366","https://openalex.org/W2023825654","https://openalex.org/W2029451415","https://openalex.org/W2030776070","https://openalex.org/W2041174099","https://openalex.org/W2047334633","https://openalex.org/W2048596643","https://openalex.org/W2063486355","https://openalex.org/W2071790069","https://openalex.org/W2092608614","https://openalex.org/W2117572180","https://openalex.org/W2122512809","https://openalex.org/W2123487311","https://openalex.org/W2128457724","https://openalex.org/W2131223372","https://openalex.org/W2133257834","https://openalex.org/W2140132803","https://openalex.org/W2146766088","https://openalex.org/W2148097176","https://openalex.org/W2152875113","https://openalex.org/W2164842504","https://openalex.org/W2170427655","https://openalex.org/W2197186749","https://openalex.org/W2296852683","https://openalex.org/W2389935477","https://openalex.org/W2480349439","https://openalex.org/W4211049957","https://openalex.org/W4298876635","https://openalex.org/W4301667260","https://openalex.org/W6601214623"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W42525420","https://openalex.org/W4283390424","https://openalex.org/W2137270828","https://openalex.org/W1976072307","https://openalex.org/W4205440119","https://openalex.org/W2383807498","https://openalex.org/W1978572805","https://openalex.org/W4210616727","https://openalex.org/W4292104203"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}