{"id":"https://openalex.org/W2610736935","doi":"https://doi.org/10.1093/bib/bbx053","title":"Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling","display_name":"Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling","publication_year":2017,"publication_date":"2017-04-24","ids":{"openalex":"https://openalex.org/W2610736935","doi":"https://doi.org/10.1093/bib/bbx053","mag":"2610736935","pmid":"https://pubmed.ncbi.nlm.nih.gov/28575143"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbx053","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbx053","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://research.tees.ac.uk/en/publications/cfd26c64-5bfd-4b54-ac5b-61c0c305a11d","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000221575","display_name":"Supreeta Vijayakumar","orcid":"https://orcid.org/0000-0001-6357-0439"},"institutions":[{"id":"https://openalex.org/I874055015","display_name":"Teesside University","ror":"https://ror.org/03z28gk75","country_code":"GB","type":"education","lineage":["https://openalex.org/I874055015"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Supreeta Vijayakumar","raw_affiliation_strings":["Department of Computer Science and Information Systems, Teesside University, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Systems, Teesside University, UK","institution_ids":["https://openalex.org/I874055015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009674962","display_name":"Max Conway","orcid":"https://orcid.org/0000-0001-8913-0909"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Max Conway","raw_affiliation_strings":["Computer Laboratory, University of Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"Computer Laboratory, University of Cambridge, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056748708","display_name":"P\u00edetro Li\u00f3","orcid":"https://orcid.org/0000-0002-0540-5053"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Pietro Li\u00f3","raw_affiliation_strings":["Computer Laboratory, University of Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"Computer Laboratory, University of Cambridge, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021786062","display_name":"Claudio Angione","orcid":"https://orcid.org/0000-0002-3140-7909"},"institutions":[{"id":"https://openalex.org/I874055015","display_name":"Teesside University","ror":"https://ror.org/03z28gk75","country_code":"GB","type":"education","lineage":["https://openalex.org/I874055015"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Claudio Angione","raw_affiliation_strings":["Department of Computer Science and Information Systems, Teesside University, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Systems, Teesside University, UK","institution_ids":["https://openalex.org/I874055015"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5021786062"],"corresponding_institution_ids":["https://openalex.org/I874055015"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.582,"has_fulltext":false,"cited_by_count":49,"citation_normalized_percentile":{"value":0.90255584,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"19","issue":"6","first_page":"1218","last_page":"1235"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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":1.0,"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":0.9940000176429749,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9887999892234802,"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":0.5069401264190674},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3355964422225952}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5069401264190674},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3355964422225952}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1093/bib/bbx053","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbx053","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28575143","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28575143","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:https://research.tees.ac.uk/ws/oai:openaire/cfd26c64-5bfd-4b54-ac5b-61c0c305a11d","is_oa":true,"landing_page_url":"https://research.tees.ac.uk/en/publications/cfd26c64-5bfd-4b54-ac5b-61c0c305a11d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401198","display_name":"TeesRep (Teesside University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I874055015","host_organization_name":"Teesside University","host_organization_lineage":["https://openalex.org/I874055015"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Vijayakumar, S, Conway, M, Li\u00f3, P & Angione, C 2017, 'Seeing the wood for the trees: a forest of methods for optimisation and omic-network integration in metabolic modelling', Briefings in Bioinformatics, vol. 19, no. 6, pp. 1218\u20131235. https://doi.org/10.1093/bib/bbx053","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:arXiv.org:1809.09475","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1809.09475","pdf_url":"https://arxiv.org/pdf/1809.09475","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:eprints.lancs.ac.uk:162350","is_oa":false,"landing_page_url":"https://eprints.lancs.ac.uk/id/eprint/162350/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401916","display_name":"Lancaster EPrints (Lancaster University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67415387","host_organization_name":"Lancaster University","host_organization_lineage":["https://openalex.org/I67415387"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:tees.openrepository.com:10149/621070","is_oa":false,"landing_page_url":"http://hdl.handle.net/10149/621070","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/293226","is_oa":false,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/293226","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"doi:10.17863/cam.40376","is_oa":true,"landing_page_url":"https://doi.org/10.17863/cam.40376","pdf_url":null,"source":{"id":"https://openalex.org/S7407050737","display_name":"Apollo","issn_l":null,"issn":[],"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:https://research.tees.ac.uk/ws/oai:openaire/cfd26c64-5bfd-4b54-ac5b-61c0c305a11d","is_oa":true,"landing_page_url":"https://research.tees.ac.uk/en/publications/cfd26c64-5bfd-4b54-ac5b-61c0c305a11d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401198","display_name":"TeesRep (Teesside University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I874055015","host_organization_name":"Teesside University","host_organization_lineage":["https://openalex.org/I874055015"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Vijayakumar, S, Conway, M, Li\u00f3, P & Angione, C 2017, 'Seeing the wood for the trees: a forest of methods for optimisation and omic-network integration in metabolic modelling', Briefings in Bioinformatics, vol. 19, no. 6, pp. 1218\u20131235. https://doi.org/10.1093/bib/bbx053","raw_type":"info:eu-repo/semantics/publishedVersion"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":219,"referenced_works":["https://openalex.org/W97076651","https://openalex.org/W225977925","https://openalex.org/W598785207","https://openalex.org/W644442692","https://openalex.org/W1158629448","https://openalex.org/W1550614472","https://openalex.org/W1595498733","https://openalex.org/W1823460074","https://openalex.org/W1944909517","https://openalex.org/W1952732684","https://openalex.org/W1964232618","https://openalex.org/W1964904043","https://openalex.org/W1966497610","https://openalex.org/W1967035429","https://openalex.org/W1970556744","https://openalex.org/W1974662378","https://openalex.org/W1976742040","https://openalex.org/W1977675219","https://openalex.org/W1977688694","https://openalex.org/W1977918192","https://openalex.org/W1977927025","https://openalex.org/W1980875662","https://openalex.org/W1981849943","https://openalex.org/W1982013068","https://openalex.org/W1984378303","https://openalex.org/W1984445372","https://openalex.org/W1984577552","https://openalex.org/W1986656046","https://openalex.org/W1987219048","https://openalex.org/W1987607959","https://openalex.org/W1988250170","https://openalex.org/W1990812533","https://openalex.org/W1992170087","https://openalex.org/W1992382363","https://openalex.org/W1993410245","https://openalex.org/W1994134392","https://openalex.org/W1996893186","https://openalex.org/W1998633945","https://openalex.org/W2001673920","https://openalex.org/W2001963002","https://openalex.org/W2004788588","https://openalex.org/W2006672203","https://openalex.org/W2007057676","https://openalex.org/W2009282793","https://openalex.org/W2011728117","https://openalex.org/W2012600591","https://openalex.org/W2012996629","https://openalex.org/W2020104452","https://openalex.org/W2022027915","https://openalex.org/W2024963167","https://openalex.org/W2025536812","https://openalex.org/W2029403511","https://openalex.org/W2030776070","https://openalex.org/W2034836368","https://openalex.org/W2034961255","https://openalex.org/W2035146557","https://openalex.org/W2037614307","https://openalex.org/W2037935034","https://openalex.org/W2038281408","https://openalex.org/W2039252507","https://openalex.org/W2042839452","https://openalex.org/W2045921664","https://openalex.org/W2045953361","https://openalex.org/W2046359382","https://openalex.org/W2048596643","https://openalex.org/W2057858265","https://openalex.org/W2058730913","https://openalex.org/W2058993911","https://openalex.org/W2059312042","https://openalex.org/W2062819025","https://openalex.org/W2063168697","https://openalex.org/W2064034649","https://openalex.org/W2065104071","https://openalex.org/W2067469807","https://openalex.org/W2070020713","https://openalex.org/W2071254403","https://openalex.org/W2073837631","https://openalex.org/W2075283200","https://openalex.org/W2076262841","https://openalex.org/W2077833923","https://openalex.org/W2078355959","https://openalex.org/W2082382448","https://openalex.org/W2082734758","https://openalex.org/W2082948758","https://openalex.org/W2085789144","https://openalex.org/W2089121522","https://openalex.org/W2089449076","https://openalex.org/W2091317547","https://openalex.org/W2093470004","https://openalex.org/W2098450614","https://openalex.org/W2099529347","https://openalex.org/W2099892456","https://openalex.org/W2100084634","https://openalex.org/W2102164505","https://openalex.org/W2102461551","https://openalex.org/W2103795997","https://openalex.org/W2103950919","https://openalex.org/W2104619491","https://openalex.org/W2105112252","https://openalex.org/W2105717378","https://openalex.org/W2107007801","https://openalex.org/W2107409961","https://openalex.org/W2107459209","https://openalex.org/W2107628565","https://openalex.org/W2109563298","https://openalex.org/W2112361359","https://openalex.org/W2112933558","https://openalex.org/W2115098117","https://openalex.org/W2115159982","https://openalex.org/W2115435945","https://openalex.org/W2116324021","https://openalex.org/W2117474489","https://openalex.org/W2118258530","https://openalex.org/W2119781196","https://openalex.org/W2121020192","https://openalex.org/W2122093325","https://openalex.org/W2124653577","https://openalex.org/W2126105956","https://openalex.org/W2126176298","https://openalex.org/W2127844534","https://openalex.org/W2128746754","https://openalex.org/W2129906961","https://openalex.org/W2129918713","https://openalex.org/W2130364940","https://openalex.org/W2131178894","https://openalex.org/W2131255911","https://openalex.org/W2132092950","https://openalex.org/W2132105963","https://openalex.org/W2134469465","https://openalex.org/W2137266088","https://openalex.org/W2138127621","https://openalex.org/W2139967559","https://openalex.org/W2141360045","https://openalex.org/W2142747156","https://openalex.org/W2144589197","https://openalex.org/W2145436499","https://openalex.org/W2146749911","https://openalex.org/W2148044817","https://openalex.org/W2148590574","https://openalex.org/W2148750928","https://openalex.org/W2149001103","https://openalex.org/W2154061034","https://openalex.org/W2155331065","https://openalex.org/W2156476088","https://openalex.org/W2158497698","https://openalex.org/W2159091719","https://openalex.org/W2159482845","https://openalex.org/W2159923578","https://openalex.org/W2160306591","https://openalex.org/W2160541874","https://openalex.org/W2161876024","https://openalex.org/W2162666840","https://openalex.org/W2163110179","https://openalex.org/W2163871517","https://openalex.org/W2165387703","https://openalex.org/W2165409758","https://openalex.org/W2167239001","https://openalex.org/W2168244801","https://openalex.org/W2168910023","https://openalex.org/W2169527381","https://openalex.org/W2169683678","https://openalex.org/W2169991570","https://openalex.org/W2170974939","https://openalex.org/W2171560951","https://openalex.org/W2172129062","https://openalex.org/W2207096656","https://openalex.org/W2208000532","https://openalex.org/W2216418212","https://openalex.org/W2233061896","https://openalex.org/W2266907177","https://openalex.org/W2285763735","https://openalex.org/W2291465340","https://openalex.org/W2292492942","https://openalex.org/W2294248145","https://openalex.org/W2295663140","https://openalex.org/W2309801799","https://openalex.org/W2337188110","https://openalex.org/W2338467621","https://openalex.org/W2343646511","https://openalex.org/W2410299130","https://openalex.org/W2412400897","https://openalex.org/W2416789956","https://openalex.org/W2468889898","https://openalex.org/W2470538762","https://openalex.org/W2472163094","https://openalex.org/W2489304830","https://openalex.org/W2529551304","https://openalex.org/W2529595296","https://openalex.org/W2537645142","https://openalex.org/W2545099144","https://openalex.org/W2551372307","https://openalex.org/W2554210752","https://openalex.org/W2554842798","https://openalex.org/W2558711935","https://openalex.org/W2564204660","https://openalex.org/W2567080747","https://openalex.org/W2568731166","https://openalex.org/W2573803309","https://openalex.org/W2580505401","https://openalex.org/W2587982688","https://openalex.org/W2596399348","https://openalex.org/W2597312917","https://openalex.org/W2911964244","https://openalex.org/W2915391685","https://openalex.org/W2917411498","https://openalex.org/W2949144734","https://openalex.org/W2949454481","https://openalex.org/W2963281023","https://openalex.org/W2963408405","https://openalex.org/W2982266667","https://openalex.org/W3100644055","https://openalex.org/W3133193159","https://openalex.org/W3195881304","https://openalex.org/W4230040882","https://openalex.org/W4244529959","https://openalex.org/W4246662151","https://openalex.org/W4252676770","https://openalex.org/W4294216483","https://openalex.org/W4298084175"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829"],"abstract_inverted_index":{"Metabolic":[0],"modelling":[1,56],"has":[2],"entered":[3],"a":[4,26,48,62,115,169,184,186,193],"mature":[5],"phase":[6],"with":[7,84,110,168],"dozens":[8],"of":[9,50,65,90,97,117,137,147,162,183,199],"methods":[10,52,66,86,99,120],"and":[11,18,100,123,192,205],"software":[12],"implementations":[13],"available":[14,67,72],"to":[15,28,31,68,113],"the":[16,19,33,36,39,88,91,103,107,111,130,145,160,181,203,206],"practitioner":[17],"theoretician.":[20],"It":[21],"is":[22],"not":[23],"easy":[24],"for":[25,38,54,134,201],"modeller":[27],"be":[29,81,198],"able":[30],"see":[32],"wood":[34],"(or":[35],"forest)":[37],"trees.":[40],"Driven":[41],"by":[42],"this":[43,156],"analogy,":[44],"we":[45,158],"here":[46],"present":[47,92],"'forest'":[49],"principal":[51],"used":[53],"constraint-based":[55],"in":[57,73,106,140,152],"systems":[58],"biology.":[59],"This":[60],"provides":[61],"tree-based":[63],"view":[64],"prospective":[69],"modellers,":[70],"also":[71],"interactive":[74],"version":[75],"at":[76],"http://modellingmetabolism.net,":[77],"where":[78],"it":[79],"will":[80],"kept":[82],"updated":[83,95],"new":[85],"after":[87],"publication":[89],"manuscript.":[93],"Our":[94],"classification":[96],"existing":[98,119],"tools":[101],"highlights":[102],"most":[104],"promising":[105],"different":[108],"branches,":[109],"aim":[112],"develop":[114],"vision":[116],"how":[118],"could":[121],"hybridize":[122],"become":[124],"more":[125],"complex.":[126],"We":[127,142,178],"then":[128],"provide":[129],"first":[131],"hands-on":[132],"tutorial":[133,196],"multi-objective":[135],"optimization":[136,161],"metabolic":[138,166],"models":[139],"R.":[141],"finally":[143],"discuss":[144],"implementation":[146],"multi-view":[148,189],"machine":[149,176,190],"learning":[150,191],"approaches":[151],"poly-omic":[153],"integration.":[154],"Throughout":[155],"work,":[157],"demonstrate":[159],"trade-offs":[163],"between":[164],"multiple":[165],"objectives,":[167],"focus":[170],"on":[171,188],"omic":[172],"data":[173],"integration":[174],"through":[175],"learning.":[177],"anticipate":[179],"that":[180],"combination":[182],"survey,":[185],"perspective":[187],"step-by-step":[194],"R":[195],"should":[197],"interest":[200],"both":[202],"beginner":[204],"advanced":[207],"user.":[208]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":4}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
