{"id":"https://openalex.org/W2159724748","doi":"https://doi.org/10.1186/1752-0509-4-49","title":"Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design","display_name":"Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design","publication_year":2010,"publication_date":"2010-04-23","ids":{"openalex":"https://openalex.org/W2159724748","doi":"https://doi.org/10.1186/1752-0509-4-49","mag":"2159724748","pmid":"https://pubmed.ncbi.nlm.nih.gov/20416071"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-4-49","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-49","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-49","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-49","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076791162","display_name":"Brett A. Boghigian","orcid":null},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brett A Boghigian","raw_affiliation_strings":["Tufts University, Department of Chemical & Biological Engineering, Science & Technology Center, 4 Colby Street, Medford, MA 02155, USA","Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, 4 Colby Street, Medford, MA, 02155, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tufts University, Department of Chemical & Biological Engineering, Science & Technology Center, 4 Colby Street, Medford, MA 02155, USA","institution_ids":["https://openalex.org/I121934306"]},{"raw_affiliation_string":"Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, 4 Colby Street, Medford, MA, 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045370658","display_name":"Hai Shi","orcid":null},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hai Shi","raw_affiliation_strings":["Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, 4 Colby Street, Medford, MA, 02155, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, 4 Colby Street, Medford, MA, 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087420269","display_name":"Kyongbum Lee","orcid":"https://orcid.org/0000-0002-0699-8057"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyongbum Lee","raw_affiliation_strings":["Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, 4 Colby Street, Medford, MA, 02155, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, 4 Colby Street, Medford, MA, 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079480513","display_name":"Blaine A. Pfeifer","orcid":null},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Blaine A Pfeifer","raw_affiliation_strings":["Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, 4 Colby Street, Medford, MA, 02155, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, 4 Colby Street, Medford, MA, 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5076791162"],"corresponding_institution_ids":["https://openalex.org/I121934306"],"apc_list":null,"apc_paid":null,"fwci":2.0349,"has_fulltext":true,"cited_by_count":39,"citation_normalized_percentile":{"value":0.86617012,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"4","issue":"1","first_page":"49","last_page":"49"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9934999942779541,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9934999942779541,"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/T13539","display_name":"thermodynamics and calorimetric analyses","score":0.0008999999845400453,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11053","display_name":"Process Optimization and Integration","score":0.0007999999797903001,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.5425664782524109},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5315840840339661},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5244922041893005},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.504827082157135},{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.4791266620159149},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.46818435192108154},{"id":"https://openalex.org/keywords/metabolic-engineering","display_name":"Metabolic engineering","score":0.45749104022979736},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.4519387185573578},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.4429014325141907},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4398627281188965},{"id":"https://openalex.org/keywords/production","display_name":"Production (economics)","score":0.4265287518501282},{"id":"https://openalex.org/keywords/product","display_name":"Product (mathematics)","score":0.421254426240921},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3849261701107025},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3721076250076294},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.368497371673584},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2726699709892273},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2554267346858978},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25109386444091797},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.21782001852989197},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.19192630052566528},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.14956432580947876},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1446005403995514}],"concepts":[{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.5425664782524109},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5315840840339661},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5244922041893005},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.504827082157135},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.4791266620159149},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.46818435192108154},{"id":"https://openalex.org/C6350086","wikidata":"https://www.wikidata.org/wiki/Q6822347","display_name":"Metabolic engineering","level":3,"score":0.45749104022979736},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.4519387185573578},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.4429014325141907},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4398627281188965},{"id":"https://openalex.org/C2778348673","wikidata":"https://www.wikidata.org/wiki/Q739302","display_name":"Production (economics)","level":2,"score":0.4265287518501282},{"id":"https://openalex.org/C90673727","wikidata":"https://www.wikidata.org/wiki/Q901718","display_name":"Product (mathematics)","level":2,"score":0.421254426240921},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3849261701107025},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3721076250076294},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.368497371673584},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2726699709892273},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2554267346858978},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25109386444091797},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.21782001852989197},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.19192630052566528},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.14956432580947876},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1446005403995514},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C139719470","wikidata":"https://www.wikidata.org/wiki/Q39680","display_name":"Macroeconomics","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000077276","descriptor_name":"Lycopene","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077276","descriptor_name":"Lycopene","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077276","descriptor_name":"Lycopene","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000431","descriptor_name":"Ethanol","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000431","descriptor_name":"Ethanol","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000431","descriptor_name":"Ethanol","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002338","descriptor_name":"Carotenoids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002338","descriptor_name":"Carotenoids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002338","descriptor_name":"Carotenoids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002338","descriptor_name":"Carotenoids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002338","descriptor_name":"Carotenoids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002338","descriptor_name":"Carotenoids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018533","descriptor_name":"Biomass","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018533","descriptor_name":"Biomass","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018533","descriptor_name":"Biomass","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1752-0509-4-49","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-49","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-49","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:20416071","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20416071","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2880971","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2880971","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-4-49","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-49","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-49","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Responsible consumption and production","id":"https://metadata.un.org/sdg/12","score":0.4699999988079071}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2159724748.pdf","grobid_xml":"https://content.openalex.org/works/W2159724748.grobid-xml"},"referenced_works_count":94,"referenced_works":["https://openalex.org/W60648455","https://openalex.org/W1501815954","https://openalex.org/W1502529406","https://openalex.org/W1504423416","https://openalex.org/W1504523189","https://openalex.org/W1536226251","https://openalex.org/W1581582023","https://openalex.org/W1597762351","https://openalex.org/W1606784130","https://openalex.org/W1621975707","https://openalex.org/W1680030081","https://openalex.org/W1758395617","https://openalex.org/W1969983517","https://openalex.org/W1970556744","https://openalex.org/W1978119727","https://openalex.org/W1978802080","https://openalex.org/W1981668065","https://openalex.org/W1982309495","https://openalex.org/W1982346730","https://openalex.org/W1983120620","https://openalex.org/W1992306474","https://openalex.org/W1994134392","https://openalex.org/W2006672203","https://openalex.org/W2009570758","https://openalex.org/W2009990638","https://openalex.org/W2011728117","https://openalex.org/W2016577330","https://openalex.org/W2018994057","https://openalex.org/W2023158791","https://openalex.org/W2025729416","https://openalex.org/W2027955923","https://openalex.org/W2028681077","https://openalex.org/W2039679384","https://openalex.org/W2041631919","https://openalex.org/W2042067428","https://openalex.org/W2044783595","https://openalex.org/W2045167474","https://openalex.org/W2049322319","https://openalex.org/W2054201845","https://openalex.org/W2055088522","https://openalex.org/W2056305771","https://openalex.org/W2056568341","https://openalex.org/W2058867396","https://openalex.org/W2062042850","https://openalex.org/W2063533285","https://openalex.org/W2064876011","https://openalex.org/W2065163714","https://openalex.org/W2066089342","https://openalex.org/W2067278945","https://openalex.org/W2068490496","https://openalex.org/W2072042166","https://openalex.org/W2072361216","https://openalex.org/W2076592452","https://openalex.org/W2076839808","https://openalex.org/W2079619772","https://openalex.org/W2083693802","https://openalex.org/W2088099835","https://openalex.org/W2092205568","https://openalex.org/W2094216282","https://openalex.org/W2100195325","https://openalex.org/W2100818174","https://openalex.org/W2102164505","https://openalex.org/W2106840138","https://openalex.org/W2107333582","https://openalex.org/W2109918485","https://openalex.org/W2110355460","https://openalex.org/W2111421616","https://openalex.org/W2115437893","https://openalex.org/W2116324021","https://openalex.org/W2120590006","https://openalex.org/W2123945540","https://openalex.org/W2124758943","https://openalex.org/W2126175129","https://openalex.org/W2126176298","https://openalex.org/W2127767489","https://openalex.org/W2127844534","https://openalex.org/W2128746754","https://openalex.org/W2130364940","https://openalex.org/W2131178894","https://openalex.org/W2134153749","https://openalex.org/W2134783465","https://openalex.org/W2134981469","https://openalex.org/W2140055375","https://openalex.org/W2140825380","https://openalex.org/W2143861551","https://openalex.org/W2153930194","https://openalex.org/W2154767435","https://openalex.org/W2154797402","https://openalex.org/W2158069895","https://openalex.org/W2160675272","https://openalex.org/W2163799837","https://openalex.org/W2167909188","https://openalex.org/W2504970287","https://openalex.org/W2980048381"],"related_works":["https://openalex.org/W2126646394","https://openalex.org/W2338895903","https://openalex.org/W1992844569","https://openalex.org/W3044523069","https://openalex.org/W2133150343","https://openalex.org/W3130044579","https://openalex.org/W2613838074","https://openalex.org/W3033588432","https://openalex.org/W2020641517","https://openalex.org/W2216418212"],"abstract_inverted_index":{"BACKGROUND:":[0],"Microbial":[1],"hosts":[2],"offer":[3],"a":[4,30,43,48,57,124,150,231,246,280],"number":[5],"of":[6,56,80,146,152,156,163,171,182,230,261,274,287,307,319],"unique":[7],"advantages":[8,21],"when":[9,93],"used":[10,200],"as":[11,114],"production":[12,50,145,193,286,318],"systems":[13],"for":[14,70,106,136,144,160,224,258,264],"both":[15,84,147],"native":[16],"and":[17,25,86,89,127,149,191,207,209,279,292,314],"heterologous":[18],"small-molecules.":[19],"These":[20],"include":[22],"high":[23],"selectivity":[24],"benign":[26],"environmental":[27],"impact;":[28],"however,":[29],"principal":[31],"drawback":[32],"is":[33,52,83,238,256],"low":[34],"yield":[35],"and/or":[36],"productivity,":[37],"which":[38],"limits":[39],"economic":[40],"viability.":[41],"Therefore":[42],"major":[44],"challenge":[45],"in":[46,194,245],"developing":[47],"microbial":[49,68],"system":[51],"to":[53,65,100,131,175,189,201,240,283,303],"maximize":[54],"formation":[55,211,267],"specific":[58],"product":[59,203,208,226,266],"while":[60],"sustaining":[61],"cell":[62],"growth.":[63],"Tools":[64],"rationally":[66],"reconfigure":[67],"metabolism":[69,167,309],"these":[71],"potentially":[72],"conflicting":[73],"objectives":[74,244],"remain":[75],"limited.":[76],"Exhaustively":[77],"exploring":[78],"combinations":[79],"genetic":[81,125,233,249,281],"modifications":[82,109],"experimentally":[85,223],"computationally":[87,253],"inefficient,":[88],"can":[90,300],"become":[91],"intractable":[92],"multiple":[94],"gene":[95,108],"deletions":[96],"or":[97],"insertions":[98],"need":[99],"be":[101,111,301],"considered.":[102],"Alternatively,":[103],"the":[104,185,242,259,285,317],"search":[105],"desirable":[107],"may":[110],"solved":[112],"heuristically":[113],"an":[115,133],"evolutionary":[116],"optimization":[117,134],"problem.":[118],"In":[119],"this":[120],"study,":[121],"we":[122],"combine":[123],"algorithm":[126,186,198,234,282,299],"elementary":[128,158,269],"mode":[129,270],"analysis":[130,271],"develop":[132],"framework":[135,255],"evolving":[137],"metabolic":[138,262],"networks":[139,263],"with":[140,173],"energetically":[141],"favorable":[142],"pathways":[143],"biomass":[148,205,210],"compound":[151],"interest.":[153],"RESULTS:":[154],"Utilization":[155],"thermodynamically-weighted":[157],"modes":[159],"flux":[161],"reconstruction":[162],"E.":[164,195,295],"coli":[165],"central":[166],"revealed":[168],"two":[169,243,288],"clusters":[170],"EMs":[172],"respect":[174],"their":[176],"Delta":[177],"Gp":[178],"degrees.":[179],"For":[180],"proof":[181],"principle":[183],"testing,":[184],"was":[187,199],"applied":[188,302,315],"ethanol":[190,291],"lycopene":[192],"coli.":[196,296],"The":[197,228,297],"optimize":[202,284],"formation,":[204,206],"simultaneously.":[212],"Predicted":[213],"knockouts":[214],"often":[215],"matched":[216],"those":[217],"that":[218,236],"have":[219],"previously":[220],"been":[221],"implemented":[222],"improved":[225],"formation.":[227],"performance":[229],"multi-objective":[232],"showed":[235],"it":[237],"better":[239],"couple":[241],"single":[247],"objective":[248],"algorithm.":[250],"CONCLUSION:":[251],"A":[252],"tractable":[254],"presented":[257],"redesign":[260],"maximal":[265],"combining":[268],"(a":[272],"form":[273],"convex":[275],"analysis),":[276],"pathway":[277],"thermodynamics,":[278],"industrially-relevant":[289],"products,":[290],"lycopene,":[293],"from":[294],"designed":[298],"any":[304,312,320],"small-scale":[305],"model":[306],"cellular":[308],"theoretically":[310],"utilizing":[311],"substrate":[313],"towards":[316],"product.":[321]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":5}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
