{"id":"https://openalex.org/W3012450467","doi":"https://doi.org/10.1186/s12859-020-3377-1","title":"MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering","display_name":"MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering","publication_year":2020,"publication_date":"2020-02-24","ids":{"openalex":"https://openalex.org/W3012450467","doi":"https://doi.org/10.1186/s12859-020-3377-1","mag":"3012450467","pmid":"https://pubmed.ncbi.nlm.nih.gov/32093622"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-3377-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3377-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3377-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3377-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032595661","display_name":"Ricardo Andrade","orcid":"https://orcid.org/0000-0002-3969-7840"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]},{"id":"https://openalex.org/I3019322962","display_name":"Universidade Brasil","ror":"https://ror.org/04031z735","country_code":"BR","type":"education","lineage":["https://openalex.org/I3019322962"]},{"id":"https://openalex.org/I4210094622","display_name":"Physiologie, Environnement et G\u00e9n\u00e9tique pour l'Animal et les Syst\u00e8mes d'Elevage","ror":"https://ror.org/00mg8nf58","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210094622","https://openalex.org/I4210117091","https://openalex.org/I4399657933"]},{"id":"https://openalex.org/I4210131883","display_name":"Brazilian Society of Computational and Applied Mathematics","ror":"https://ror.org/03kcw4w74","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210131883"]},{"id":"https://openalex.org/I4210135640","display_name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive","ror":"https://ror.org/03skt0t88","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I203339264","https://openalex.org/I4210100596","https://openalex.org/I4210104684","https://openalex.org/I4210107625","https://openalex.org/I4210135640"]}],"countries":["BR","FR"],"is_corresponding":false,"raw_author_name":"Ricardo Andrade","raw_affiliation_strings":["ERABLE European Team, INRIA, Rh\u00f4ne-Alpes, France","Institute of Mathematics and Statistics, Universidade de S\u00e3o Paulo, Sao Paulo, Brazil","Universit\u00e9 de Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie Evolutive UMR 5558, Villeurbanne, F-69622, France","ERABLE - Equipe de recherche europ\u00e9enne en algorithmique et biologie formelle et exp\u00e9rimentale (Universit\u00e9 Claude Bernard (Lyon 1), \r\nCampus DOUA\r\n43, Boulevard du 11 Novembre 1918\r\n69622 Villeurbanne cedex - France)","IME - Instituto de Matem\u00e1tica e Estat\u00edstica (Rua do Mat\u00e3o, 1010 - Cidade Universit\u00e1ria CEP 05508-090 S\u00e3o Paulo - SP - Brazil)","PEGASE - D\u00e9partement PEGASE [LBBE] (LBBE \r\n43 Bld du 11 Novembre 1918 69622 VILLEURBANNE CEDEX - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ERABLE European Team, INRIA, Rh\u00f4ne-Alpes, France","institution_ids":["https://openalex.org/I1326498283"]},{"raw_affiliation_string":"Institute of Mathematics and Statistics, Universidade de S\u00e3o Paulo, Sao Paulo, Brazil","institution_ids":["https://openalex.org/I17974374","https://openalex.org/I3019322962"]},{"raw_affiliation_string":"Universit\u00e9 de Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie Evolutive UMR 5558, Villeurbanne, F-69622, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I4210135640"]},{"raw_affiliation_string":"ERABLE - Equipe de recherche europ\u00e9enne en algorithmique et biologie formelle et exp\u00e9rimentale (Universit\u00e9 Claude Bernard (Lyon 1), \r\nCampus DOUA\r\n43, Boulevard du 11 Novembre 1918\r\n69622 Villeurbanne cedex - France)","institution_ids":["https://openalex.org/I100532134"]},{"raw_affiliation_string":"IME - Instituto de Matem\u00e1tica e Estat\u00edstica (Rua do Mat\u00e3o, 1010 - Cidade Universit\u00e1ria CEP 05508-090 S\u00e3o Paulo - SP - Brazil)","institution_ids":["https://openalex.org/I4210131883"]},{"raw_affiliation_string":"PEGASE - D\u00e9partement PEGASE [LBBE] (LBBE \r\n43 Bld du 11 Novembre 1918 69622 VILLEURBANNE CEDEX - France)","institution_ids":["https://openalex.org/I4210094622","https://openalex.org/I4210135640"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006612069","display_name":"Mahdi Doostmohammadi","orcid":"https://orcid.org/0000-0002-6865-8058"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]},{"id":"https://openalex.org/I181647926","display_name":"University of Strathclyde","ror":"https://ror.org/00n3w3b69","country_code":"GB","type":"education","lineage":["https://openalex.org/I181647926"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB","PT"],"is_corresponding":false,"raw_author_name":"Mahdi Doostmohammadi","raw_affiliation_strings":["Department of Management Science, University of Strathclyde, Glasgow, UK","IDMEC, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Lisbon, Portugal","IDMEC - Instituto de Engenharia Mec\u00e2nica [Lisboa] (Av. Rovisco Pais, 1\r\n1049-001 LISBOA - Portugal)","School of Mathematics - University of Edinburgh (University of Edinburgh Edinburgh EH9 3JZ, UK - United Kingdom)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Management Science, University of Strathclyde, Glasgow, UK","institution_ids":["https://openalex.org/I181647926"]},{"raw_affiliation_string":"IDMEC, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Lisbon, Portugal","institution_ids":["https://openalex.org/I141596103"]},{"raw_affiliation_string":"IDMEC - Instituto de Engenharia Mec\u00e2nica [Lisboa] (Av. Rovisco Pais, 1\r\n1049-001 LISBOA - Portugal)","institution_ids":[]},{"raw_affiliation_string":"School of Mathematics - University of Edinburgh (University of Edinburgh Edinburgh EH9 3JZ, UK - United Kingdom)","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077883313","display_name":"Jo\u00e3o Santos","orcid":"https://orcid.org/0000-0001-5123-8244"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]},{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I4387152517","display_name":"Instituto Superior T\u00e9cnico","ror":"https://ror.org/03db2by73","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103","https://openalex.org/I4387152517"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o L. Santos","raw_affiliation_strings":["Institute for Bioengineering and Biosciences, Instituto Superior T\u00e9cnico, Department of Bioengineering, Universidade de Lisboa, Lisbon, Portugal","Institute for Bioengineering and Bioscience, Instituto Superior T\u00e9cnico (Portugal)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Bioengineering and Biosciences, Instituto Superior T\u00e9cnico, Department of Bioengineering, Universidade de Lisboa, Lisbon, Portugal","institution_ids":["https://openalex.org/I141596103","https://openalex.org/I4210167387"]},{"raw_affiliation_string":"Institute for Bioengineering and Bioscience, Instituto Superior T\u00e9cnico (Portugal)","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I4387152517"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044540605","display_name":"Marie\u2010France Sagot","orcid":null},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"id":"https://openalex.org/I4210135640","display_name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive","ror":"https://ror.org/03skt0t88","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I203339264","https://openalex.org/I4210100596","https://openalex.org/I4210104684","https://openalex.org/I4210107625","https://openalex.org/I4210135640"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Marie-France Sagot","raw_affiliation_strings":["ERABLE European Team, INRIA, Rh\u00f4ne-Alpes, France","Universit\u00e9 de Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie Evolutive UMR 5558, Villeurbanne, F-69622, France","Baobab (LBBE\r\n43 Bld du 11 Novembre 1918 69622 VILLEURBANNE CEDEX - France)","ERABLE - Equipe de recherche europ\u00e9enne en algorithmique et biologie formelle et exp\u00e9rimentale (Universit\u00e9 Claude Bernard (Lyon 1), \r\nCampus DOUA\r\n43, Boulevard du 11 Novembre 1918\r\n69622 Villeurbanne cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ERABLE European Team, INRIA, Rh\u00f4ne-Alpes, France","institution_ids":["https://openalex.org/I1326498283"]},{"raw_affiliation_string":"Universit\u00e9 de Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie Evolutive UMR 5558, Villeurbanne, F-69622, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I4210135640"]},{"raw_affiliation_string":"Baobab (LBBE\r\n43 Bld du 11 Novembre 1918 69622 VILLEURBANNE CEDEX - France)","institution_ids":["https://openalex.org/I4210135640"]},{"raw_affiliation_string":"ERABLE - Equipe de recherche europ\u00e9enne en algorithmique et biologie formelle et exp\u00e9rimentale (Universit\u00e9 Claude Bernard (Lyon 1), \r\nCampus DOUA\r\n43, Boulevard du 11 Novembre 1918\r\n69622 Villeurbanne cedex - France)","institution_ids":["https://openalex.org/I100532134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083137468","display_name":"Nuno P. Mira","orcid":"https://orcid.org/0000-0001-7556-0385"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I4387152517","display_name":"Instituto Superior T\u00e9cnico","ror":"https://ror.org/03db2by73","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103","https://openalex.org/I4387152517"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Nuno P. Mira","raw_affiliation_strings":["Institute for Bioengineering and Biosciences, Instituto Superior T\u00e9cnico, Department of Bioengineering, Universidade de Lisboa, Lisbon, Portugal. nuno.mira@ist.utl.pt","Institute for Bioengineering and Bioscience, Instituto Superior T\u00e9cnico (Portugal)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Bioengineering and Biosciences, Instituto Superior T\u00e9cnico, Department of Bioengineering, Universidade de Lisboa, Lisbon, Portugal. nuno.mira@ist.utl.pt","institution_ids":["https://openalex.org/I4210167387"]},{"raw_affiliation_string":"Institute for Bioengineering and Bioscience, Instituto Superior T\u00e9cnico (Portugal)","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I4387152517"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005271169","display_name":"Susana Vinga","orcid":"https://orcid.org/0000-0002-1954-5487"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Susana Vinga","raw_affiliation_strings":["IDMEC, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Lisbon, Portugal. susanavinga@tecnico.ulisboa.pt","INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Lisbon, Portugal. susanavinga@tecnico.ulisboa.pt","IDMEC - Instituto de Engenharia Mec\u00e2nica [Lisboa] (Av. Rovisco Pais, 1\r\n1049-001 LISBOA - Portugal)","INESC-ID - Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento em Lisboa (Rua Alves Redol 9 - Apartado 13069 - 1000-029 Lisboa - Portugal)"],"raw_orcid":"https://orcid.org/0000-0002-1954-5487","affiliations":[{"raw_affiliation_string":"IDMEC, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Lisbon, Portugal. susanavinga@tecnico.ulisboa.pt","institution_ids":["https://openalex.org/I121345201"]},{"raw_affiliation_string":"INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Lisbon, Portugal. susanavinga@tecnico.ulisboa.pt","institution_ids":["https://openalex.org/I121345201"]},{"raw_affiliation_string":"IDMEC - Instituto de Engenharia Mec\u00e2nica [Lisboa] (Av. Rovisco Pais, 1\r\n1049-001 LISBOA - Portugal)","institution_ids":[]},{"raw_affiliation_string":"INESC-ID - Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento em Lisboa (Rua Alves Redol 9 - Apartado 13069 - 1000-029 Lisboa - Portugal)","institution_ids":["https://openalex.org/I121345201"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":14,"corresponding_author_ids":["https://openalex.org/A5005271169","https://openalex.org/A5083137468"],"corresponding_institution_ids":["https://openalex.org/I121345201","https://openalex.org/I4210167387","https://openalex.org/I4387152517"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.5993,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.63002407,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"21","issue":"1","first_page":"69","last_page":"69"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998999834060669,"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":0.9998999834060669,"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5921438932418823},{"id":"https://openalex.org/keywords/maximization","display_name":"Maximization","score":0.5764970183372498},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.5568512082099915},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.5415300726890564},{"id":"https://openalex.org/keywords/solver","display_name":"Solver","score":0.5146166086196899},{"id":"https://openalex.org/keywords/metabolic-engineering","display_name":"Metabolic engineering","score":0.5134626030921936},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.4926450848579407},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.4571222960948944},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4249069094657898},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29223382472991943},{"id":"https://openalex.org/keywords/yeast","display_name":"Yeast","score":0.2836008071899414},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19950881600379944},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.18707260489463806},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14063772559165955},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.13408079743385315},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08024865388870239}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5921438932418823},{"id":"https://openalex.org/C2776330181","wikidata":"https://www.wikidata.org/wiki/Q18358244","display_name":"Maximization","level":2,"score":0.5764970183372498},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.5568512082099915},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.5415300726890564},{"id":"https://openalex.org/C2778770139","wikidata":"https://www.wikidata.org/wiki/Q1966904","display_name":"Solver","level":2,"score":0.5146166086196899},{"id":"https://openalex.org/C6350086","wikidata":"https://www.wikidata.org/wiki/Q6822347","display_name":"Metabolic engineering","level":3,"score":0.5134626030921936},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.4926450848579407},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.4571222960948944},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4249069094657898},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29223382472991943},{"id":"https://openalex.org/C2779222958","wikidata":"https://www.wikidata.org/wiki/Q45422","display_name":"Yeast","level":2,"score":0.2836008071899414},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19950881600379944},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.18707260489463806},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14063772559165955},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.13408079743385315},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08024865388870239},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000431","descriptor_name":"Ethanol","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000431","descriptor_name":"Ethanol","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000431","descriptor_name":"Ethanol","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"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":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-020-3377-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3377-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3377-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32093622","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32093622","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 bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:HAL:hal-02490353v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-02490353","pdf_url":"https://inria.hal.science/hal-02490353/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2020, 21 (1), pp.1-13. &#x27E8;10.1186/s12859-020-3377-1&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7041195","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7041195","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 Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:e755aaa27a894d19b87011b0685cbc88","is_oa":true,"landing_page_url":"https://doaj.org/article/e755aaa27a894d19b87011b0685cbc88","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss 1, Pp 1-13 (2020)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-3377-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3377-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3377-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1355505928","display_name":null,"funder_award_id":"IF/00653/2012","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"},{"id":"https://openalex.org/G1885850072","display_name":"Laborat\u00f3rio Associado de Energia, Transportes e Aeron\u00e1utica","funder_award_id":"UIDB/50022/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G2441341484","display_name":"Instituto de Engenharia de Sistemas e Computadores, Investiga\u00e7\u00e3o e Desenvolvimento em Lisboa","funder_award_id":"UIDB/50021/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G2686230473","display_name":"Instituto de Bioengenharia e Bioci\u00eancias","funder_award_id":"UIDB/04565/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G2973767024","display_name":null,"funder_award_id":"UIDB/50022/2020","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"},{"id":"https://openalex.org/G3268105278","display_name":null,"funder_award_id":"UID/BIO/04565/2013","funder_id":"https://openalex.org/F4320329035","funder_display_name":"Institute for Bioengineering and Biosciences"},{"id":"https://openalex.org/G3441820327","display_name":"BACterial Hosts for production of Bioactive phenolics from bERRY fruits","funder_award_id":"613793","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3717214305","display_name":"Instituto de Bioengenharia e Bioci\u00eancias","funder_award_id":"UID/BIO/04565/2013","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G4048744776","display_name":null,"funder_award_id":"007317","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G4170071085","display_name":null,"funder_award_id":"UIDB/04565/2020","funder_id":"https://openalex.org/F4320329035","funder_display_name":"Institute for Bioengineering and Biosciences"},{"id":"https://openalex.org/G4777589704","display_name":null,"funder_award_id":"007317","funder_id":"https://openalex.org/F4320329035","funder_display_name":"Institute for Bioengineering and Biosciences"},{"id":"https://openalex.org/G4804359633","display_name":null,"funder_award_id":"(IF/00653/2012)","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G4841427915","display_name":null,"funder_award_id":"UIDB/50022/2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4909896919","display_name":null,"funder_award_id":"2017/05986-2","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G6023912115","display_name":"Em direc\u00e7\u00e3o \u00e0 optimiza\u00e7\u00e3o da produ\u00e7\u00e3o de \u00e1cidos carbox\u00edlicos de aplica\u00e7\u00e3o industrial por Fungos: aspectos de toxicidade e transporte","funder_award_id":"ERA-IB-2-6/0003/2014","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6106687202","display_name":null,"funder_award_id":"007317","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6703756228","display_name":null,"funder_award_id":"Project N. 007317","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6934352886","display_name":null,"funder_award_id":"UIDB/50021/2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8547713841","display_name":null,"funder_award_id":"UIDB/04565/2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G999517088","display_name":null,"funder_award_id":"UIDB/50022/2020","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320329035","display_name":"Institute for Bioengineering and Biosciences","ror":null},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3012450467.pdf","grobid_xml":"https://content.openalex.org/works/W3012450467.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1970424517","https://openalex.org/W1977241851","https://openalex.org/W1984096521","https://openalex.org/W2003421484","https://openalex.org/W2006672203","https://openalex.org/W2014328192","https://openalex.org/W2036699485","https://openalex.org/W2062245653","https://openalex.org/W2073612090","https://openalex.org/W2078355959","https://openalex.org/W2078775934","https://openalex.org/W2084716075","https://openalex.org/W2100818174","https://openalex.org/W2101155309","https://openalex.org/W2102164505","https://openalex.org/W2102957972","https://openalex.org/W2115559271","https://openalex.org/W2123742569","https://openalex.org/W2128869726","https://openalex.org/W2130364940","https://openalex.org/W2143861551","https://openalex.org/W2149001103","https://openalex.org/W2153373497","https://openalex.org/W2165409758","https://openalex.org/W2167239001","https://openalex.org/W2170140196","https://openalex.org/W2174873063","https://openalex.org/W2288619269","https://openalex.org/W2609799200","https://openalex.org/W2762019694","https://openalex.org/W2778471341","https://openalex.org/W2801369487","https://openalex.org/W2949189298","https://openalex.org/W4238163351"],"related_works":["https://openalex.org/W4315558101","https://openalex.org/W3200271510","https://openalex.org/W63366483","https://openalex.org/W1516770101","https://openalex.org/W1897466773","https://openalex.org/W2357011584","https://openalex.org/W4380882399","https://openalex.org/W2623087137","https://openalex.org/W2168028372","https://openalex.org/W2576531695"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1,29],"this":[2,122],"paper,":[3],"we":[4,31,134,158],"explore":[5],"the":[6,12,27,57,73,91,106,109,140,150],"concept":[7],"of":[8,14,60,64,68,75,88,108,121,139],"multi-objective":[9,34,155,172],"optimization":[10],"in":[11,26,82,112,130,147],"field":[13],"metabolic":[15,84],"engineering":[16],"when":[17],"both":[18],"continuous":[19],"and":[20,63,119,133,164],"integer":[21],"decision":[22],"variables":[23],"are":[24],"involved":[25],"model.":[28],"particular,":[30],"propose":[32],"a":[33,61,69,76,101],"model":[35],"that":[36,44,116,137],"may":[37,53],"be":[38],"used":[39,93],"to":[40,104],"suggest":[41],"reaction":[42],"deletions":[43,142],"maximize":[45],"and/or":[46],"minimize":[47],"several":[48],"functions":[49],"simultaneously.":[50],"The":[51,154],"applications":[52],"include,":[54],"among":[55],"others,":[56],"concurrent":[58],"maximization":[59,67],"bioproduct":[62,70],"biomass,":[65],"or":[66],"while":[71],"minimizing":[72],"formation":[74],"given":[77],"by-product,":[78],"two":[79],"common":[80],"requirements":[81],"microbial":[83],"engineering.":[85],"RESULTS:":[86],"Production":[87],"ethanol":[89,145],"by":[90],"widely":[92],"cell":[94],"factory":[95],"Saccharomyces":[96],"cerevisiae":[97],"was":[98],"adopted":[99],"as":[100,170],"case":[102],"study":[103],"demonstrate":[105],"usefulness":[107],"proposed":[110],"approach":[111],"identifying":[113],"genetic":[114],"manipulations":[115],"improve":[117],"productivity":[118],"yield":[120],"economically":[123],"highly":[124],"relevant":[125],"bioproduct.":[126],"We":[127],"did":[128],"an":[129],"vivo":[131],"validation":[132],"could":[135],"show":[136],"some":[138],"predicted":[141],"exhibit":[143],"increased":[144],"levels":[146],"comparison":[148],"with":[149],"wild-type":[151],"strain.":[152],"CONCLUSIONS:":[153],"programming":[156],"framework":[157],"developed,":[159],"called":[160],"MOMO,":[161],"is":[162,175],"open-source":[163],"uses":[165],"POLYSCIP":[166],"(Available":[167],"at":[168,177],"http://polyscip.zib.de/).":[169],"underlying":[171],"solver.":[173],"MOMO":[174],"available":[176],"http://momo-sysbio.gforge.inria.fr.":[178]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
