{"id":"https://openalex.org/W4401214322","doi":"https://doi.org/10.3390/a17080336","title":"Pitfalls in Metaheuristics Solving Stoichiometric-Based Optimization Models for Metabolic Networks","display_name":"Pitfalls in Metaheuristics Solving Stoichiometric-Based Optimization Models for Metabolic Networks","publication_year":2024,"publication_date":"2024-08-01","ids":{"openalex":"https://openalex.org/W4401214322","doi":"https://doi.org/10.3390/a17080336"},"language":"en","primary_location":{"id":"doi:10.3390/a17080336","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a17080336","pdf_url":null,"source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3390/a17080336","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086207307","display_name":"M\u00f3nica Fabiola Briones-B\u00e1ez","orcid":"https://orcid.org/0000-0002-9405-9999"},"institutions":[{"id":"https://openalex.org/I177400693","display_name":"Instituto Tecnol\u00f3gico de Ciudad Madero","ror":"https://ror.org/04cymm537","country_code":"MX","type":"education","lineage":["https://openalex.org/I1302736544","https://openalex.org/I177400693","https://openalex.org/I4210090124","https://openalex.org/I4405258672"]}],"countries":["MX"],"is_corresponding":true,"raw_author_name":"M\u00f3nica Fabiola Briones-B\u00e1ez","raw_affiliation_strings":["Divisi\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Instituto Tecnol\u00f3gico de Ciudad Madero (TECNM), Los Mangos 89440, Mexico"],"affiliations":[{"raw_affiliation_string":"Divisi\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Instituto Tecnol\u00f3gico de Ciudad Madero (TECNM), Los Mangos 89440, Mexico","institution_ids":["https://openalex.org/I177400693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043494745","display_name":"Luciano Aguilera\u2010V\u00e1zquez","orcid":"https://orcid.org/0000-0001-8095-6528"},"institutions":[{"id":"https://openalex.org/I177400693","display_name":"Instituto Tecnol\u00f3gico de Ciudad Madero","ror":"https://ror.org/04cymm537","country_code":"MX","type":"education","lineage":["https://openalex.org/I1302736544","https://openalex.org/I177400693","https://openalex.org/I4210090124","https://openalex.org/I4405258672"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Luciano Aguilera-V\u00e1zquez","raw_affiliation_strings":["Divisi\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Instituto Tecnol\u00f3gico de Ciudad Madero (TECNM), Los Mangos 89440, Mexico"],"affiliations":[{"raw_affiliation_string":"Divisi\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Instituto Tecnol\u00f3gico de Ciudad Madero (TECNM), Los Mangos 89440, Mexico","institution_ids":["https://openalex.org/I177400693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064414262","display_name":"Nelson Rangel-Valdez","orcid":"https://orcid.org/0000-0002-4745-2325"},"institutions":[{"id":"https://openalex.org/I177400693","display_name":"Instituto Tecnol\u00f3gico de Ciudad Madero","ror":"https://ror.org/04cymm537","country_code":"MX","type":"education","lineage":["https://openalex.org/I1302736544","https://openalex.org/I177400693","https://openalex.org/I4210090124","https://openalex.org/I4405258672"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Nelson Rangel-Valdez","raw_affiliation_strings":["Divisi\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Instituto Tecnol\u00f3gico de Ciudad Madero (TECNM), Los Mangos 89440, Mexico"],"affiliations":[{"raw_affiliation_string":"Divisi\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Instituto Tecnol\u00f3gico de Ciudad Madero (TECNM), Los Mangos 89440, Mexico","institution_ids":["https://openalex.org/I177400693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084064381","display_name":"Cristal Z\u00fa\u00f1iga","orcid":"https://orcid.org/0000-0002-0135-7429"},"institutions":[{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Cristal Zu\u00f1iga","raw_affiliation_strings":["Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA","institution_ids":["https://openalex.org/I26538001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081687910","display_name":"A.L. Mart\u00ednez-Salazar","orcid":"https://orcid.org/0000-0002-2802-830X"},"institutions":[{"id":"https://openalex.org/I177400693","display_name":"Instituto Tecnol\u00f3gico de Ciudad Madero","ror":"https://ror.org/04cymm537","country_code":"MX","type":"education","lineage":["https://openalex.org/I1302736544","https://openalex.org/I177400693","https://openalex.org/I4210090124","https://openalex.org/I4405258672"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Ana Lidia Mart\u00ednez-Salazar","raw_affiliation_strings":["Divisi\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Instituto Tecnol\u00f3gico de Ciudad Madero (TECNM), Los Mangos 89440, Mexico"],"affiliations":[{"raw_affiliation_string":"Divisi\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Instituto Tecnol\u00f3gico de Ciudad Madero (TECNM), Los Mangos 89440, Mexico","institution_ids":["https://openalex.org/I177400693"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033236021","display_name":"Claudia G\u00f3mez-Santill\u00e1n","orcid":"https://orcid.org/0000-0002-1455-4480"},"institutions":[{"id":"https://openalex.org/I177400693","display_name":"Instituto Tecnol\u00f3gico de Ciudad Madero","ror":"https://ror.org/04cymm537","country_code":"MX","type":"education","lineage":["https://openalex.org/I1302736544","https://openalex.org/I177400693","https://openalex.org/I4210090124","https://openalex.org/I4405258672"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Claudia Gomez-Santillan","raw_affiliation_strings":["Divisi\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Instituto Tecnol\u00f3gico de Ciudad Madero (TECNM), Los Mangos 89440, Mexico"],"affiliations":[{"raw_affiliation_string":"Divisi\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Instituto Tecnol\u00f3gico de Ciudad Madero (TECNM), Los Mangos 89440, Mexico","institution_ids":["https://openalex.org/I177400693"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5084064381","https://openalex.org/A5086207307"],"corresponding_institution_ids":["https://openalex.org/I177400693","https://openalex.org/I26538001"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.4679,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.64103605,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"17","issue":"8","first_page":"336","last_page":"336"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998000264167786,"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":0.9998000264167786,"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/T10476","display_name":"Algal biology and biofuel production","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2105","display_name":"Renewable Energy, Sustainability and the Environment"},"field":{"id":"https://openalex.org/fields/21","display_name":"Energy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11053","display_name":"Process Optimization and Integration","score":0.9955999851226807,"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/flux-balance-analysis","display_name":"Flux balance analysis","score":0.7987996339797974},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.650869607925415},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.5681107044219971},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.5572218298912048},{"id":"https://openalex.org/keywords/autotroph","display_name":"Autotroph","score":0.554523229598999},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.48569950461387634},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.48247602581977844},{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.4794141948223114},{"id":"https://openalex.org/keywords/metaheuristic","display_name":"Metaheuristic","score":0.4708530306816101},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4638723134994507},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34708529710769653},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2303430736064911},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18688631057739258},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.18402713537216187},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16284817457199097},{"id":"https://openalex.org/keywords/metabolism","display_name":"Metabolism","score":0.15913036465644836},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13270705938339233},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09446108341217041}],"concepts":[{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.7987996339797974},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.650869607925415},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.5681107044219971},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.5572218298912048},{"id":"https://openalex.org/C104647666","wikidata":"https://www.wikidata.org/wiki/Q131427","display_name":"Autotroph","level":3,"score":0.554523229598999},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.48569950461387634},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.48247602581977844},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.4794141948223114},{"id":"https://openalex.org/C109718341","wikidata":"https://www.wikidata.org/wiki/Q1385229","display_name":"Metaheuristic","level":2,"score":0.4708530306816101},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4638723134994507},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34708529710769653},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2303430736064911},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18688631057739258},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.18402713537216187},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16284817457199097},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.15913036465644836},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13270705938339233},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09446108341217041},{"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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3390/a17080336","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a17080336","pdf_url":null,"source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:4dacfc521c6f47d2919d7028fdb6f3d8","is_oa":true,"landing_page_url":"https://doaj.org/article/4dacfc521c6f47d2919d7028fdb6f3d8","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms, Vol 17, Iss 8, p 336 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3390/a17080336","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a17080336","pdf_url":null,"source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4639064609","display_name":null,"funder_award_id":"2313313","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W61067137","https://openalex.org/W1522538275","https://openalex.org/W2011301426","https://openalex.org/W2033909818","https://openalex.org/W2048465561","https://openalex.org/W2078355959","https://openalex.org/W2078775934","https://openalex.org/W2082382448","https://openalex.org/W2101700211","https://openalex.org/W2114206363","https://openalex.org/W2126105956","https://openalex.org/W2134493171","https://openalex.org/W2143381319","https://openalex.org/W2145479420","https://openalex.org/W2326002501","https://openalex.org/W2465843936","https://openalex.org/W2563052820","https://openalex.org/W2883204331","https://openalex.org/W2920531146","https://openalex.org/W2978201745","https://openalex.org/W2981109800","https://openalex.org/W2987597555","https://openalex.org/W2999846266","https://openalex.org/W3011758108","https://openalex.org/W3012450467","https://openalex.org/W3047741612","https://openalex.org/W3111447193","https://openalex.org/W3187466589","https://openalex.org/W3196188174","https://openalex.org/W4200002109","https://openalex.org/W4283731095","https://openalex.org/W4323348698","https://openalex.org/W4361304224","https://openalex.org/W4391772635","https://openalex.org/W4391848793","https://openalex.org/W6631460888","https://openalex.org/W6806779962"],"related_works":["https://openalex.org/W1999460937","https://openalex.org/W2083413061","https://openalex.org/W1984242440","https://openalex.org/W2113329733","https://openalex.org/W1983989854","https://openalex.org/W2070388085","https://openalex.org/W2886446279","https://openalex.org/W832244386","https://openalex.org/W2341681417","https://openalex.org/W2158163767"],"abstract_inverted_index":{"Flux":[0],"Balance":[1],"Analysis":[2],"(FBA)":[3],"is":[4,9],"a":[5,152],"constraint-based":[6],"method":[7,39],"that":[8,18,89,101,201],"commonly":[10],"used":[11],"to":[12,68,92,116,122],"guide":[13],"metabolites":[14,57,71],"through":[15],"restricting":[16],"pathways":[17,36,54,137],"often":[19],"involve":[20],"conditions":[21,44,175],"such":[22,105],"as":[23,85,186],"anaplerotic":[24],"cycles":[25],"like":[26],"Calvin,":[27],"reversible":[28],"or":[29],"irreversible":[30],"reactions,":[31],"and":[32,119,142,145,161,178,198],"nodes":[33],"where":[34],"metabolic":[35,184],"branch.":[37],"The":[38,191],"can":[40,208],"identify":[41],"the":[42,53,81,97,102,124,130,133,136,140,158,162,168,202],"best":[43],"for":[45,182],"one":[46],"course":[47],"but":[48],"fails":[49],"when":[50],"dealing":[51],"with":[52],"of":[55,58,83,104,135,167,204],"multiple":[56,94],"interest.":[59],"Recent":[60],"studies":[61],"on":[62,132,154],"metabolism":[63,166],"consider":[64],"it":[65,112,150],"more":[66],"natural":[67],"optimize":[69],"several":[70,146],"simultaneously":[72],"rather":[73],"than":[74],"just":[75],"one;":[76],"moreover,":[77],"they":[78],"point":[79],"out":[80],"use":[82,103],"metaheuristics":[84],"an":[86,205],"attractive":[87],"alternative":[88],"extends":[90],"FBA":[91],"tackle":[93],"objectives.":[95],"However,":[96],"literature":[98],"also":[99],"warns":[100],"techniques":[106],"must":[107,113],"not":[108],"be":[109,114],"wild.":[110],"Instead,":[111],"subject":[115],"careful":[117],"fine-tuning":[118],"selection":[120,203],"processes":[121],"achieve":[123],"desired":[125],"results.":[126],"This":[127],"work":[128],"analyses":[129],"impact":[131],"quality":[134],"built":[138],"using":[139],"NSGAII":[141,197],"MOEA/D":[143],"algorithms":[144],"novel":[147],"optimization":[148,206],"models;":[149],"conducts":[151],"study":[153],"two":[155],"case":[156],"studies,":[157],"pigment":[159],"biosynthesis":[160],"node":[163],"in":[164],"glutamate":[165],"microalgae":[169],"Chlorella":[170],"vulgaris,":[171],"under":[172],"three":[173,183],"culture":[174],"(autotrophic,":[176],"heterotrophic,":[177],"mixotrophic)":[179],"while":[180],"optimizing":[181],"intermediaries":[185],"independent":[187],"objective":[188],"functions":[189],"simultaneously.":[190],"results":[192],"show":[193],"varying":[194],"performances":[195],"between":[196],"MOEA/D,":[199],"demonstrating":[200],"model":[207],"greatly":[209],"affect":[210],"predicted":[211],"phenotypes.":[212]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
