{"id":"https://openalex.org/W2115198483","doi":"https://doi.org/10.1093/bioinformatics/bti573","title":"Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells","display_name":"Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells","publication_year":2005,"publication_date":"2005-07-07","ids":{"openalex":"https://openalex.org/W2115198483","doi":"https://doi.org/10.1093/bioinformatics/bti573","mag":"2115198483","pmid":"https://pubmed.ncbi.nlm.nih.gov/16002431"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/17/3558/563306/bti573.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/17/3558/563306/bti573.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009596579","display_name":"Vitaly A. Selivanov","orcid":"https://orcid.org/0000-0002-7937-9249"},"institutions":[{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"V. A. Selivanov","raw_affiliation_strings":["Departamento de Bioquimica i Biologia Molecular, Facultat de Quimica and CERQT at Parc Cientic de Barcelona, Barcelona, Catalunya, Spain","Departamento de Bioquimica i Biologia Molecular, Facultat de Quimica and CERQT at Parc Cientic de Barcelona Barcelona, Catalunya, Spain#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Bioquimica i Biologia Molecular, Facultat de Quimica and CERQT at Parc Cientic de Barcelona, Barcelona, Catalunya, Spain","institution_ids":["https://openalex.org/I71999127"]},{"raw_affiliation_string":"Departamento de Bioquimica i Biologia Molecular, Facultat de Quimica and CERQT at Parc Cientic de Barcelona Barcelona, Catalunya, Spain#TAB#","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109268013","display_name":"L. E. Meshalkina","orcid":null},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"L. E. Meshalkina","raw_affiliation_strings":["A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, 199899 Moscow, Russia,","A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University  199899 Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, 199899 Moscow, Russia,","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University  199899 Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028264139","display_name":"Olga N. Solovjeva","orcid":"https://orcid.org/0000-0001-5530-5934"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"O. N. Solovjeva","raw_affiliation_strings":["A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, 199899 Moscow, Russia,","A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University  199899 Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, 199899 Moscow, Russia,","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University  199899 Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081563103","display_name":"Philip W. Kuchel","orcid":"https://orcid.org/0000-0003-4100-7332"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"P. W. Kuchel","raw_affiliation_strings":["School of Molecular and Microbial Biosciences, University of Sydney, NSW, Australia and","School of Molecular and Microbial Biosciences, University of Sydney NSW, Australia#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Molecular and Microbial Biosciences, University of Sydney, NSW, Australia and","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Molecular and Microbial Biosciences, University of Sydney NSW, Australia#TAB#","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040662322","display_name":"Antonio Ramos\u2010Montoya","orcid":"https://orcid.org/0000-0001-7573-4066"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Ramos-Montoya","raw_affiliation_strings":["Departamento de Bioquimica i Biologia Molecular, Facultat de Quimica and CERQT at Parc Cientic de Barcelona, Barcelona, Catalunya, Spain,","Departamento de Bioquimica i Biologia Molecular, Facultat de Quimica and CERQT at Parc Cientic de Barcelona Barcelona, Catalunya, Spain#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Bioquimica i Biologia Molecular, Facultat de Quimica and CERQT at Parc Cientic de Barcelona, Barcelona, Catalunya, Spain,","institution_ids":[]},{"raw_affiliation_string":"Departamento de Bioquimica i Biologia Molecular, Facultat de Quimica and CERQT at Parc Cientic de Barcelona Barcelona, Catalunya, Spain#TAB#","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110149036","display_name":"G.A. Kochetov","orcid":null},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"G. A. Kochetov","raw_affiliation_strings":["A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, 199899 Moscow, Russia,","A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University  199899 Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, 199899 Moscow, Russia,","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University  199899 Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062483693","display_name":"Paul W. N. Lee","orcid":null},"institutions":[{"id":"https://openalex.org/I2801403999","display_name":"UCLA Medical Center","ror":"https://ror.org/04vq5kb54","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799798094","https://openalex.org/I2801403999"]},{"id":"https://openalex.org/I4210165985","display_name":"Harbor\u2013UCLA Medical Center","ror":"https://ror.org/05h4zj272","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1328359107","https://openalex.org/I4210165985"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. W. N. Lee","raw_affiliation_strings":["Department of Pediatrics, Harbor-UCLA Medical Center, Research and Education Institute, Torrance, CA 90502, USA","Department of Pediatrics, Harbor-UCLA Medical Center, Research and Education Institute, Torrance, CA 90502, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Harbor-UCLA Medical Center, Research and Education Institute, Torrance, CA 90502, USA","institution_ids":["https://openalex.org/I2801403999","https://openalex.org/I4210165985"]},{"raw_affiliation_string":"Department of Pediatrics, Harbor-UCLA Medical Center, Research and Education Institute, Torrance, CA 90502, USA#TAB#","institution_ids":["https://openalex.org/I2801403999","https://openalex.org/I4210165985"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089973047","display_name":"Marta Cascante","orcid":"https://orcid.org/0000-0002-2062-4633"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Cascante","raw_affiliation_strings":["Departamento de Bioquimica i Biologia Molecular, Facultat de Quimica and CERQT at Parc Cientic de Barcelona, Barcelona, Catalunya, Spain,","Departamento de Bioquimica i Biologia Molecular, Facultat de Quimica and CERQT at Parc Cientic de Barcelona Barcelona, Catalunya, Spain#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Bioquimica i Biologia Molecular, Facultat de Quimica and CERQT at Parc Cientic de Barcelona, Barcelona, Catalunya, Spain,","institution_ids":[]},{"raw_affiliation_string":"Departamento de Bioquimica i Biologia Molecular, Facultat de Quimica and CERQT at Parc Cientic de Barcelona Barcelona, Catalunya, Spain#TAB#","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5009596579"],"corresponding_institution_ids":["https://openalex.org/I71999127"],"apc_list":null,"apc_paid":null,"fwci":1.287,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.82563174,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"21","issue":"17","first_page":"3558","last_page":"3564"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10631","display_name":"Cancer, Hypoxia, and Metabolism","score":0.41130000352859497,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10631","display_name":"Cancer, Hypoxia, and Metabolism","score":0.41130000352859497,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T12915","display_name":"Biochemical Acid Research Studies","score":0.3450999855995178,"subfield":{"id":"https://openalex.org/subfields/1303","display_name":"Biochemistry"},"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/T14415","display_name":"Biomedical Research and Pathophysiology","score":0.1370999962091446,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic Medicine"},"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/isotopomers","display_name":"Isotopomers","score":0.9638251066207886},{"id":"https://openalex.org/keywords/transaldolase","display_name":"Transaldolase","score":0.8176096081733704},{"id":"https://openalex.org/keywords/transketolase","display_name":"Transketolase","score":0.673687219619751},{"id":"https://openalex.org/keywords/pentose-phosphate-pathway","display_name":"Pentose phosphate pathway","score":0.6350834369659424},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4902673065662384},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.40780752897262573},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3998604118824005},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.34535685181617737},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.19934603571891785},{"id":"https://openalex.org/keywords/glycolysis","display_name":"Glycolysis","score":0.17432954907417297},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1472003161907196},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13918644189834595}],"concepts":[{"id":"https://openalex.org/C127124265","wikidata":"https://www.wikidata.org/wiki/Q2100870","display_name":"Isotopomers","level":3,"score":0.9638251066207886},{"id":"https://openalex.org/C38706188","wikidata":"https://www.wikidata.org/wiki/Q358883","display_name":"Transaldolase","level":5,"score":0.8176096081733704},{"id":"https://openalex.org/C103432212","wikidata":"https://www.wikidata.org/wiki/Q412719","display_name":"Transketolase","level":3,"score":0.673687219619751},{"id":"https://openalex.org/C3409486","wikidata":"https://www.wikidata.org/wiki/Q827489","display_name":"Pentose phosphate pathway","level":4,"score":0.6350834369659424},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4902673065662384},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.40780752897262573},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3998604118824005},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.34535685181617737},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.19934603571891785},{"id":"https://openalex.org/C20251656","wikidata":"https://www.wikidata.org/wiki/Q162643","display_name":"Glycolysis","level":3,"score":0.17432954907417297},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1472003161907196},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13918644189834595},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002250","descriptor_name":"Carbon Radioisotopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002250","descriptor_name":"Carbon Radioisotopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002250","descriptor_name":"Carbon Radioisotopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004789","descriptor_name":"Enzyme Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004789","descriptor_name":"Enzyme Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004789","descriptor_name":"Enzyme Activation","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":"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":"D007553","descriptor_name":"Isotope Labeling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007553","descriptor_name":"Isotope Labeling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007553","descriptor_name":"Isotope Labeling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","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":"D009097","descriptor_name":"Multienzyme Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009097","descriptor_name":"Multienzyme Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009097","descriptor_name":"Multienzyme Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010427","descriptor_name":"Pentose Phosphate Pathway","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D010427","descriptor_name":"Pentose Phosphate Pathway","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D010427","descriptor_name":"Pentose Phosphate Pathway","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014153","descriptor_name":"Transaldolase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014153","descriptor_name":"Transaldolase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014153","descriptor_name":"Transaldolase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014174","descriptor_name":"Transketolase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014174","descriptor_name":"Transketolase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014174","descriptor_name":"Transketolase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019073","descriptor_name":"HT29 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019073","descriptor_name":"HT29 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019073","descriptor_name":"HT29 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/17/3558/563306/bti573.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16002431","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16002431","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/17/3558/563306/bti573.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2857178708","display_name":null,"funder_award_id":"CA42710","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5780022460","display_name":null,"funder_award_id":"P01-CA42710","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G666329143","display_name":null,"funder_award_id":"P01-CA42710","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7313253759","display_name":null,"funder_award_id":"RR00425","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G899064110","display_name":null,"funder_award_id":"M01-RR00425","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G939135972","display_name":null,"funder_award_id":"M01-RR00425","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"}],"funders":[{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"},{"id":"https://openalex.org/F4320321505","display_name":"Generalitat de Catalunya","ror":"https://ror.org/01bg62x04"},{"id":"https://openalex.org/F4320323737","display_name":"Ministerio de Ciencia y Tecnolog\u00eda","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2115198483.pdf","grobid_xml":"https://content.openalex.org/works/W2115198483.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W31733398","https://openalex.org/W79437885","https://openalex.org/W1468178842","https://openalex.org/W1485030470","https://openalex.org/W1576919957","https://openalex.org/W1582190823","https://openalex.org/W1940014006","https://openalex.org/W1969560495","https://openalex.org/W2022008424","https://openalex.org/W2030708049","https://openalex.org/W2074424962","https://openalex.org/W2096767559","https://openalex.org/W2111602998","https://openalex.org/W2171749735","https://openalex.org/W2395983676"],"related_works":["https://openalex.org/W75334843","https://openalex.org/W2026448567","https://openalex.org/W2072049884","https://openalex.org/W2001340534","https://openalex.org/W190286435","https://openalex.org/W2028995352","https://openalex.org/W2289707431","https://openalex.org/W2111602998","https://openalex.org/W2115198483","https://openalex.org/W2015247318"],"abstract_inverted_index":{"MOTIVATION:":[0],"Addition":[1],"of":[2,8,12,35,47,57,62,74,119,132,237,247,300,309,326,338,351,355,364],"labeled":[3],"substrates":[4],"and":[5,77,103,113,175,190,207,268,283,311,328],"the":[6,9,13,40,60,63,67,94,97,117,123,155,164,176,182,184,188,205,214,241,287,292,295,306,324,349,362],"measurement":[7],"subsequent":[10],"distribution":[11,151,289],"labels":[14],"in":[15,17,28,81,173,187,230,240,262,286,291,316,333,343],"isotopomers":[16,172],"reaction":[18],"networks":[19],"provide":[20],"a":[21,53,129,259,271],"unique":[22],"method":[23],"for":[24,93,159,163,170,203,342],"assessing":[25],"metabolic":[26,359],"fluxes":[27,41,98,121,185,301],"whole":[29],"cells.":[30],"However,":[31],"owing":[32],"to":[33,38,69,122,258,321,357],"insufficiency":[34],"information,":[36],"attempts":[37],"quantify":[39],"often":[42,85],"yield":[43],"multiple":[44],"possible":[45],"sets":[46],"solutions":[48],"that":[49,145,201,302],"are":[50,193,211],"consistent":[51],"with":[52,128,137,149,213,305],"given":[54,130],"experimental":[55,133],"pattern":[56],"isotopomers.":[58],"In":[59,181],"study":[61],"pentose":[64,177],"phosphate":[65,178],"pathways,":[66],"need":[68],"consider":[70],"isotope":[71],"exchange":[72],"reactions":[73,192],"transketolase":[75],"(TK)":[76],"transaldolase":[78],"(TA)":[79],"(which":[80],"past":[82],"analyses":[83],"have":[84,219],"been":[86,220],"ignored)":[87],"magnifies":[88],"this":[89,233],"problem;":[90],"but":[91,135],"accounting":[92],"interrelation":[95],"between":[96,111],"known":[99],"from":[100,275,294],"biochemical":[101,139,366],"studies":[102],"kinetic":[104,112,147,165,206,282,307],"modeling":[105,148],"solves":[106,154],"it.":[107],"The":[108,199,223,251],"mathematical":[109],"relationships":[110],"equilibrium":[114,284],"constants":[115,285],"restrict":[116],"domain":[118],"estimated":[120],"ones":[124],"compatible":[125],"not":[126],"only":[127],"set":[131],"data,":[134],"also":[136,269],"other":[138],"information.":[140,367],"METHOD:":[141],"We":[142],"present":[143],"software":[144,252],"integrates":[146],"isotopomer":[150,288],"analysis.":[152],"It":[153],"ordinary":[156],"differential":[157],"equations":[158],"total":[160],"concentrations":[161],"(accounting":[162],"mechanisms)":[166],"as":[167,169,255,270,330],"well":[168],"all":[171,204],"glycolysis":[174],"pathway":[179],"(PPP).":[180],"PPP":[183],"created":[186],"TK":[189,310,327],"TA":[191,329],"expressed":[194],"through":[195],"unitary":[196],"rate":[197],"constants.":[198],"algorithms":[200],"account":[202],"equilbrium":[208],"constant":[209],"constraints":[210,279],"integrated":[212],"previously":[215],"developed":[216,254],"algorithms,":[217],"which":[218],"further":[221],"optimized.":[222],"most":[224],"time-consuming":[225],"calculations":[226],"were":[227,303],"programmed":[228],"directly":[229],"assembly":[231],"language;":[232],"gave":[234],"an":[235],"order":[236],"magnitude":[238],"decrease":[239],"computation":[242],"time,":[243],"thus":[244],"allowing":[245],"analysis":[246,290,346],"more":[248],"complex":[249],"systems.":[250],"was":[253],"C-code":[256],"linked":[257],"program":[260,273],"written":[261],"Mathematica":[263],"(Wolfram":[264],"Research,":[265],"Champaign,":[266],"IL),":[267],"C++":[272],"independent":[274],"Mathematica.":[276],"RESULTS:":[277],"Implementing":[278],"imposed":[280],"by":[281],"data":[293],"cancer":[296],"cells":[297,317],"eliminated":[298],"estimates":[299],"inconsistent":[304],"mechanisms":[308],"TA.":[312],"Fluxes":[313],"measured":[314],"experimentally":[315],"can":[318],"be":[319],"used":[320],"estimate":[322],"better":[323],"kinetics":[325],"they":[331],"operate":[332],"situ.":[334],"Thus,":[335],"our":[336],"approach":[337],"integrating":[339],"various":[340],"methods":[341],"situ":[344],"flux":[345],"opens":[347],"up":[348],"possibility":[350],"designing":[352],"new":[353],"types":[354],"experiments":[356],"probe":[358],"interrelationships,":[360],"including":[361],"incorporation":[363],"additional":[365],"AVAILABILITY:":[368],"Software":[369],"is":[370],"available":[371],"freely":[372],"at:":[373],"http://www.bq.ub.es/bioqint/selivanov.htm":[374],"CONTACT:":[375],"martacascante@ub.edu":[376]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":5}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}