{"id":"https://openalex.org/W2157689062","doi":"https://doi.org/10.1371/journal.pcbi.1003371","title":"Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei","display_name":"Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei","publication_year":2013,"publication_date":"2013-12-05","ids":{"openalex":"https://openalex.org/W2157689062","doi":"https://doi.org/10.1371/journal.pcbi.1003371","mag":"2157689062","pmid":"https://pubmed.ncbi.nlm.nih.gov/24339766"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003371","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003371","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003371&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.1003371&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059167313","display_name":"Eduard J. Kerkhoven","orcid":"https://orcid.org/0000-0002-3593-5792"},"institutions":[{"id":"https://openalex.org/I4210094430","display_name":"Wellcome Centre for Molecular Parasitology","ror":"https://ror.org/00m7w8s72","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210094430","https://openalex.org/I7882870","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]},{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB","SE"],"is_corresponding":false,"raw_author_name":"Eduard J. Kerkhoven","raw_affiliation_strings":["Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom ; Systems and Synthetic Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden","Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom","Systems and Synthetic Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom ; Systems and Synthetic Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden","institution_ids":[]},{"raw_affiliation_string":"Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom","institution_ids":["https://openalex.org/I4210094430","https://openalex.org/I87048295","https://openalex.org/I7882870"]},{"raw_affiliation_string":"Systems and Synthetic Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden","institution_ids":["https://openalex.org/I66862912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071406353","display_name":"Fiona Achcar","orcid":"https://orcid.org/0000-0001-8792-7615"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["GB","NL"],"is_corresponding":false,"raw_author_name":"Fiona Achcar","raw_affiliation_strings":["Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands","Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009814086","display_name":"Vincent Pius Alibu","orcid":null},"institutions":[{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210094430","display_name":"Wellcome Centre for Molecular Parasitology","ror":"https://ror.org/00m7w8s72","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210094430","https://openalex.org/I7882870","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Vincent P. Alibu","raw_affiliation_strings":["Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom","institution_ids":["https://openalex.org/I4210094430","https://openalex.org/I87048295","https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062218408","display_name":"Richard Burchmore","orcid":"https://orcid.org/0000-0003-1663-9004"},"institutions":[{"id":"https://openalex.org/I4210094430","display_name":"Wellcome Centre for Molecular Parasitology","ror":"https://ror.org/00m7w8s72","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210094430","https://openalex.org/I7882870","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]},{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard J. Burchmore","raw_affiliation_strings":["Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom","institution_ids":["https://openalex.org/I4210094430","https://openalex.org/I87048295","https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033358436","display_name":"Ian H. Gilbert","orcid":"https://orcid.org/0000-0002-5238-1314"},"institutions":[{"id":"https://openalex.org/I177639307","display_name":"University of Dundee","ror":"https://ror.org/03h2bxq36","country_code":"GB","type":"education","lineage":["https://openalex.org/I177639307"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ian H. Gilbert","raw_affiliation_strings":["Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom","institution_ids":["https://openalex.org/I177639307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077432234","display_name":"Maciej Trybi\u0142o","orcid":null},"institutions":[{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Maciej Trybi\u0142o","raw_affiliation_strings":["School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge, United Kingdom","institution_ids":["https://openalex.org/I59433898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055626311","display_name":"Nicole N. Driessen","orcid":null},"institutions":[{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Nicole N. Driessen","raw_affiliation_strings":["Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, the Netherlands"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, the Netherlands","institution_ids":["https://openalex.org/I865915315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102913036","display_name":"David Gilbert","orcid":"https://orcid.org/0000-0002-8872-4294"},"institutions":[{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David Gilbert","raw_affiliation_strings":["School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge, United Kingdom","institution_ids":["https://openalex.org/I59433898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070145336","display_name":"Rainer Breitling","orcid":"https://orcid.org/0000-0001-7173-0922"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Rainer Breitling","raw_affiliation_strings":["Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064034989","display_name":"Barbara M. Bakker","orcid":"https://orcid.org/0000-0001-6274-3633"},"institutions":[{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]},{"id":"https://openalex.org/I1334415907","display_name":"University Medical Center Groningen","ror":"https://ror.org/03cv38k47","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I1334415907"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Barbara M. Bakker","raw_affiliation_strings":["Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, the Netherlands","Department of Pediatrics and Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, the Netherlands","institution_ids":["https://openalex.org/I865915315"]},{"raw_affiliation_string":"Department of Pediatrics and Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands","institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073175338","display_name":"Michael P. Barrett","orcid":"https://orcid.org/0000-0001-9447-3519"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210094430","display_name":"Wellcome Centre for Molecular Parasitology","ror":"https://ror.org/00m7w8s72","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210094430","https://openalex.org/I7882870","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Michael P. Barrett","raw_affiliation_strings":["Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom","institution_ids":["https://openalex.org/I4210094430","https://openalex.org/I87048295","https://openalex.org/I7882870"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5064034989","https://openalex.org/A5070145336","https://openalex.org/A5073175338"],"corresponding_institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384","https://openalex.org/I28407311","https://openalex.org/I4210094430","https://openalex.org/I7882870","https://openalex.org/I865915315","https://openalex.org/I87048295"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2106,"currency":"EUR","value_usd":2271},"fwci":3.8704,"has_fulltext":true,"cited_by_count":51,"citation_normalized_percentile":{"value":0.93937262,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"9","issue":"12","first_page":"e1003371","last_page":"e1003371"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10890","display_name":"Trypanosoma species research and implications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10890","display_name":"Trypanosoma species research and implications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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/T12827","display_name":"Biochemical and Molecular Research","score":0.9926000237464905,"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/T10945","display_name":"Lysosomal Storage Disorders Research","score":0.9889000058174133,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/trypanosoma-brucei","display_name":"Trypanosoma brucei","score":0.9520745277404785},{"id":"https://openalex.org/keywords/pentose-phosphate-pathway","display_name":"Pentose phosphate pathway","score":0.6913032531738281},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.6505357623100281},{"id":"https://openalex.org/keywords/glycolysis","display_name":"Glycolysis","score":0.629607617855072},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5571771264076233},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.4263796806335449},{"id":"https://openalex.org/keywords/hexokinase","display_name":"Hexokinase","score":0.42467200756073},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.4202956557273865},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3266153335571289},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22870880365371704}],"concepts":[{"id":"https://openalex.org/C2779502636","wikidata":"https://www.wikidata.org/wiki/Q33244","display_name":"Trypanosoma brucei","level":3,"score":0.9520745277404785},{"id":"https://openalex.org/C3409486","wikidata":"https://www.wikidata.org/wiki/Q827489","display_name":"Pentose phosphate pathway","level":4,"score":0.6913032531738281},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.6505357623100281},{"id":"https://openalex.org/C20251656","wikidata":"https://www.wikidata.org/wiki/Q162643","display_name":"Glycolysis","level":3,"score":0.629607617855072},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5571771264076233},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.4263796806335449},{"id":"https://openalex.org/C2779826832","wikidata":"https://www.wikidata.org/wiki/Q982914","display_name":"Hexokinase","level":4,"score":0.42467200756073},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.4202956557273865},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3266153335571289},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22870880365371704}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005947","descriptor_name":"Glucose","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005947","descriptor_name":"Glucose","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005947","descriptor_name":"Glucose","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005947","descriptor_name":"Glucose","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006019","descriptor_name":"Glycolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006019","descriptor_name":"Glycolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006019","descriptor_name":"Glycolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006019","descriptor_name":"Glycolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010427","descriptor_name":"Pentose Phosphate Pathway","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010427","descriptor_name":"Pentose Phosphate Pathway","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010427","descriptor_name":"Pentose Phosphate Pathway","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010427","descriptor_name":"Pentose Phosphate Pathway","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014346","descriptor_name":"Trypanosoma brucei brucei","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014346","descriptor_name":"Trypanosoma brucei brucei","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014346","descriptor_name":"Trypanosoma brucei brucei","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014346","descriptor_name":"Trypanosoma brucei brucei","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":11,"locations":[{"id":"doi:10.1371/journal.pcbi.1003371","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003371","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003371&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:24339766","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24339766","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/ae6f8790-0665-420e-8770-6bbaff46771d","is_oa":false,"landing_page_url":"https://research.manchester.ac.uk/en/publications/ae6f8790-0665-420e-8770-6bbaff46771d","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Kerkhoven, E J, Achcar, F, Alibu, V P, Burchmore, R J, Gilbert, I H, Trybi\u0142o, M, Driessen, N N, Gilbert, D, Breitling, R, Bakker, B M & Barrett, M P 2013, 'Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei', PL o S Computational Biology, vol. 9, no. 12, e1003371. https://doi.org/10.1371/journal.pcbi.1003371","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:eprints.gla.ac.uk:87022","is_oa":true,"landing_page_url":"https://eprints.gla.ac.uk/view/journal_volume/PLoS_Computational_Biology.html>,","pdf_url":"http://eprints.gla.ac.uk/87022/1/87022.pdf","source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":false,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:pure.rug.nl:publications/3a0a9bec-421e-4545-95ad-7ef17e8dad7e","is_oa":true,"landing_page_url":"https://research.rug.nl/en/publications/3a0a9bec-421e-4545-95ad-7ef17e8dad7e","pdf_url":"https://pure.rug.nl/ws/files/56058351/journal.pcbi.1003371.PDF","source":{"id":"https://openalex.org/S4306400420","display_name":"University of Groningen research database (University of Groningen / Centre for Information Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I169381384","host_organization_name":"University of Groningen","host_organization_lineage":["https://openalex.org/I169381384"],"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":"Kerkhoven, E J, Achcar, F, Alibu, V P, Burchmore, R J, Gilbert, I H, Trybilo, M, Driessen, N N, Gilbert, D, Breitling, R, Bakker, B M & Barrett, M P 2013, 'Handling Uncertainty in Dynamic Models : The Pentose Phosphate Pathway in Trypanosoma brucei', PLoS Computational Biology, vol. 9, no. 12, 1003371. https://doi.org/10.1371/journal.pcbi.1003371","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:europepmc.org:2843608","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3854711","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/869017","is_oa":true,"landing_page_url":"https://figshare.com/articles/Handling_Uncertainty_in_Dynamic_Models_The_Pentose_Phosphate_Pathway_in_Trypanosoma_brucei_/869017","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"},{"id":"pmh:oai:pure.atira.dk:publications/ae6f8790-0665-420e-8770-6bbaff46771d","is_oa":false,"landing_page_url":"https://www.research.manchester.ac.uk/portal/en/publications/handling-uncertainty-in-dynamic-models-the-pentose-phosphate-pathway-in-trypanosoma-brucei(ae6f8790-0665-420e-8770-6bbaff46771d).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:research.chalmers.se:188507","is_oa":false,"landing_page_url":"https://research.chalmers.se/en/publication/188507","pdf_url":null,"source":{"id":"https://openalex.org/S4306402469","display_name":"Chalmers Research (Chalmers University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66862912","host_organization_name":"Chalmers University of Technology","host_organization_lineage":["https://openalex.org/I66862912"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:research.vu.nl:openaire_cris_publications/d985975d-2947-4228-b67b-e5222964e7ff","is_oa":true,"landing_page_url":"https://hdl.handle.net/1871.1/d985975d-2947-4228-b67b-e5222964e7ff","pdf_url":null,"source":{"id":"https://openalex.org/S4306401107","display_name":"VU Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I865915315","host_organization_name":"Vrije Universiteit Amsterdam","host_organization_lineage":["https://openalex.org/I865915315"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Kerkhoven, E J, Achcar, R, Alibu, V P, Burchmore, R J, Gilbert, I H, Trybito, M, Driessen, N N, Gilbert, D, Breitling, R, Bakker, B M & Barrett, M P 2013, 'Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei.', PLoS Computational Biology, vol. 9, e1003371. https://doi.org/10.1371/journal.pcbi.1003371","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:vu:oai:research.vu.nl:publications/d985975d-2947-4228-b67b-e5222964e7ff","is_oa":true,"landing_page_url":"https://research.vu.nl/en/publications/d985975d-2947-4228-b67b-e5222964e7ff","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, 9:e1003371. Public Library of Science","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003371","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003371","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003371&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":[{"score":0.41999998688697815,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1940269619","display_name":null,"funder_award_id":"085349","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G2626217064","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320307874","funder_display_name":"Wellcome"},{"id":"https://openalex.org/G4623480208","display_name":null,"funder_award_id":"NWO Vidi","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G5455436254","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G5996571452","display_name":null,"funder_award_id":"085349","funder_id":"https://openalex.org/F4320307874","funder_display_name":"Wellcome"},{"id":"https://openalex.org/G6009445997","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G6606129312","display_name":null,"funder_award_id":"BB/I004599/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7703678402","display_name":null,"funder_award_id":"www.nwo.nl","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G8193949165","display_name":null,"funder_award_id":"SULSA","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320307874","display_name":"Wellcome","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2157689062.pdf","grobid_xml":"https://content.openalex.org/works/W2157689062.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W1489501628","https://openalex.org/W1633214403","https://openalex.org/W1648569894","https://openalex.org/W1853891491","https://openalex.org/W1912109328","https://openalex.org/W1963617455","https://openalex.org/W1964318956","https://openalex.org/W1964491374","https://openalex.org/W1968243869","https://openalex.org/W1970851578","https://openalex.org/W1975858959","https://openalex.org/W1976482941","https://openalex.org/W1979015967","https://openalex.org/W1979080877","https://openalex.org/W1979141662","https://openalex.org/W1979720390","https://openalex.org/W1980119632","https://openalex.org/W1986401343","https://openalex.org/W1986867603","https://openalex.org/W1987735269","https://openalex.org/W1991265914","https://openalex.org/W1992890375","https://openalex.org/W1994844474","https://openalex.org/W1996689433","https://openalex.org/W2009523353","https://openalex.org/W2010313380","https://openalex.org/W2013132097","https://openalex.org/W2016238670","https://openalex.org/W2017976110","https://openalex.org/W2021123893","https://openalex.org/W2022348939","https://openalex.org/W2030317461","https://openalex.org/W2033044759","https://openalex.org/W2033848039","https://openalex.org/W2046715416","https://openalex.org/W2047141819","https://openalex.org/W2064394012","https://openalex.org/W2071921489","https://openalex.org/W2071923700","https://openalex.org/W2074955861","https://openalex.org/W2075914357","https://openalex.org/W2077737072","https://openalex.org/W2078174957","https://openalex.org/W2102653059","https://openalex.org/W2110756690","https://openalex.org/W2117110612","https://openalex.org/W2127011189","https://openalex.org/W2127877398","https://openalex.org/W2132906724","https://openalex.org/W2136056144","https://openalex.org/W2136978039","https://openalex.org/W2151877638","https://openalex.org/W2155817635","https://openalex.org/W2157236463","https://openalex.org/W2168377403","https://openalex.org/W2170032647","https://openalex.org/W2182394854","https://openalex.org/W2241181457","https://openalex.org/W2341711817","https://openalex.org/W2414201531","https://openalex.org/W2983542272","https://openalex.org/W4211252435","https://openalex.org/W4236645299","https://openalex.org/W4238108613"],"related_works":["https://openalex.org/W2007530787","https://openalex.org/W2124975218","https://openalex.org/W1966368483","https://openalex.org/W2440640039","https://openalex.org/W4285114920","https://openalex.org/W3030723589","https://openalex.org/W2067125197","https://openalex.org/W2089980899","https://openalex.org/W1982759779","https://openalex.org/W2013763665"],"abstract_inverted_index":{"Dynamic":[0],"models":[1],"of":[2,18,24,35,46,78,100,106,138,142,148,162,190,198,215,243,259,261],"metabolism":[3],"can":[4],"be":[5,90,96,113,145],"useful":[6],"in":[7,13,20,120,164,184,207,240],"identifying":[8],"potential":[9],"drug":[10],"targets,":[11],"especially":[12],"unicellular":[14],"organisms.":[15],"A":[16],"model":[17,70,94,271],"glycolysis":[19],"the":[21,33,41,50,59,62,68,79,84,93,110,121,139,146,186,191,196,208,212,241,253,256,262,270],"causative":[22],"agent":[23],"human":[25],"African":[26],"trypanosomiasis,":[27],"Trypanosoma":[28],"brucei,":[29],"has":[30],"already":[31],"shown":[32],"utility":[34],"this":[36,229,249],"approach.":[37],"Here":[38],"we":[39,231],"add":[40],"pentose":[42],"phosphate":[43,87,187],"pathway":[44],"(PPP)":[45],"T.":[47,165],"brucei":[48,166],"to":[49,57,67,75,95,109,128,152],"glycolytic":[51,69],"model.":[52],"The":[53],"PPP":[54,263],"is":[55],"localized":[56],"both":[58],"cytosol":[60,133],"and":[61,64,134,158,265],"glycosome":[63],"adding":[65,125],"it":[66,267],"without":[71],"further":[72],"adjustments":[73],"leads":[74],"a":[76,97,126,149,233],"draining":[77],"essential":[80,257],"bound-phosphate":[81],"moiety":[82],"within":[83],"glycosome.":[85,135],"This":[86],"\"leak\"":[88],"must":[89],"resolved":[91],"for":[92,175],"reasonable":[98],"representation":[99],"parasite":[101,176],"physiology.":[102],"Two":[103],"main":[104],"types":[105],"theoretical":[107],"solution":[108,143],"problem":[111],"could":[112],"identified:":[114],"(i)":[115],"including":[116],"additional":[117],"enzymatic":[118],"reactions":[119],"glycosome,":[122],"or":[123,202],"(ii)":[124],"mechanism":[127,254],"transfer":[129],"bound":[130],"phosphates":[131],"between":[132],"One":[136],"example":[137],"first":[140],"type":[141,193],"would":[144,194],"presence":[147,197],"glycosomal":[150,209],"ribokinase":[151,163],"regenerate":[153],"ATP":[154],"from":[155],"ribose":[156],"5-phosphate":[157],"ADP.":[159],"Experimental":[160],"characterization":[161],"showed":[167],"that":[168,179,236],"very":[169],"low":[170],"enzyme":[171],"levels":[172],"are":[173,182],"sufficient":[174],"survival,":[177],"indicating":[178],"other":[180],"mechanisms":[181],"required":[183],"controlling":[185],"leak.":[188],"Examples":[189],"second":[192],"involve":[195],"an":[199],"ATP:ADP":[200],"exchanger":[201],"recently":[203],"described":[204],"permeability":[205],"pores":[206],"membrane,":[210],"although":[211],"current":[213],"absence":[214],"identified":[216],"genes":[217],"encoding":[218],"such":[219],"molecules":[220],"impedes":[221],"experimental":[222],"testing":[223],"by":[224,251,268],"genetic":[225],"manipulation.":[226],"Confronted":[227],"with":[228],"uncertainty,":[230],"present":[232],"modeling":[234],"strategy":[235,250],"identifies":[237],"robust":[238],"predictions":[239,272],"context":[242],"incomplete":[244],"system":[245],"characterization.":[246],"We":[247],"illustrate":[248],"exploring":[252],"underlying":[255],"function":[258],"one":[260],"enzymes,":[264],"validate":[266],"confirming":[269],"experimentally.":[273]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":8}],"updated_date":"2026-04-06T07:47:59.780226","created_date":"2025-10-10T00:00:00"}