{"id":"https://openalex.org/W2743007869","doi":"https://doi.org/10.1186/s12859-017-1773-y","title":"Network design and analysis for multi-enzyme biocatalysis","display_name":"Network design and analysis for multi-enzyme biocatalysis","publication_year":2017,"publication_date":"2017-08-10","ids":{"openalex":"https://openalex.org/W2743007869","doi":"https://doi.org/10.1186/s12859-017-1773-y","mag":"2743007869","pmid":"https://pubmed.ncbi.nlm.nih.gov/28797226"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1773-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1773-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1773-y","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/s12859-017-1773-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005159436","display_name":"Lisa Katharina Bla\u00df","orcid":null},"institutions":[{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Lisa Katharina Bla\u00df","raw_affiliation_strings":["Biochemical Engineering Institute, Saarland University, Campus A1.5, Saarbr\u00fccken, 66123, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biochemical Engineering Institute, Saarland University, Campus A1.5, Saarbr\u00fccken, 66123, Germany","institution_ids":["https://openalex.org/I91712215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033353542","display_name":"Christian Weyler","orcid":"https://orcid.org/0000-0002-6997-0799"},"institutions":[{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christian Weyler","raw_affiliation_strings":["Biochemical Engineering Institute, Saarland University, Campus A1.5, Saarbr\u00fccken, 66123, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biochemical Engineering Institute, Saarland University, Campus A1.5, Saarbr\u00fccken, 66123, Germany","institution_ids":["https://openalex.org/I91712215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050506001","display_name":"Elmar Heinzle","orcid":"https://orcid.org/0000-0002-1689-9300"},"institutions":[{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Elmar Heinzle","raw_affiliation_strings":["Biochemical Engineering Institute, Saarland University, Campus A1.5, Saarbr\u00fccken, 66123, Germany. e.heinzle@mx.uni-saarland.de","Biochemical Engineering Institute, Saarland University, Campus A1.5, Saarbr\u00fccken, 66123, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biochemical Engineering Institute, Saarland University, Campus A1.5, Saarbr\u00fccken, 66123, Germany. e.heinzle@mx.uni-saarland.de","institution_ids":[]},{"raw_affiliation_string":"Biochemical Engineering Institute, Saarland University, Campus A1.5, Saarbr\u00fccken, 66123, Germany","institution_ids":["https://openalex.org/I91712215"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005159436"],"corresponding_institution_ids":["https://openalex.org/I91712215"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.2243,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.5645681,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"18","issue":"1","first_page":"366","last_page":"366"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9294000267982483,"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":0.9294000267982483,"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/T10404","display_name":"Enzyme Catalysis and Immobilization","score":0.01080000028014183,"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/T12915","display_name":"Biochemical Acid Research Studies","score":0.006500000134110451,"subfield":{"id":"https://openalex.org/subfields/1303","display_name":"Biochemistry"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.6652986407279968},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.5914043188095093},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5806369781494141},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5676714181900024},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.5629931688308716},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.4608108699321747},{"id":"https://openalex.org/keywords/commodity-chemicals","display_name":"Commodity chemicals","score":0.43239104747772217},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.4241471290588379},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.41377922892570496},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32171177864074707},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.23573532700538635},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18005290627479553},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15126627683639526},{"id":"https://openalex.org/keywords/catalysis","display_name":"Catalysis","score":0.11033755540847778},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10902523994445801},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.10515713691711426},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09384918212890625}],"concepts":[{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.6652986407279968},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.5914043188095093},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5806369781494141},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5676714181900024},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.5629931688308716},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.4608108699321747},{"id":"https://openalex.org/C179720865","wikidata":"https://www.wikidata.org/wiki/Q1550480","display_name":"Commodity chemicals","level":3,"score":0.43239104747772217},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.4241471290588379},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.41377922892570496},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32171177864074707},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.23573532700538635},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18005290627479553},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15126627683639526},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.11033755540847778},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10902523994445801},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.10515713691711426},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09384918212890625},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053898","descriptor_name":"Biosynthetic Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053898","descriptor_name":"Biosynthetic Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053898","descriptor_name":"Biosynthetic Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053898","descriptor_name":"Biosynthetic Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055162","descriptor_name":"Biocatalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055162","descriptor_name":"Biocatalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055162","descriptor_name":"Biocatalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055162","descriptor_name":"Biocatalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-017-1773-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1773-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1773-y","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:28797226","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28797226","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":null},{"id":"pmh:oai:doaj.org/article:c44a482881e84404a6c181c96aa7bf29","is_oa":true,"landing_page_url":"https://doaj.org/article/c44a482881e84404a6c181c96aa7bf29","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 18, Iss 1, Pp 1-12 (2017)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5553788","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5553788","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"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1773-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1773-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1773-y","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/G3919691657","display_name":null,"funder_award_id":"031P7238","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7980816445","display_name":null,"funder_award_id":"FKZ 031P7238","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2743007869.pdf","grobid_xml":"https://content.openalex.org/works/W2743007869.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W152260425","https://openalex.org/W589036708","https://openalex.org/W615269938","https://openalex.org/W756199213","https://openalex.org/W1601296974","https://openalex.org/W1992043510","https://openalex.org/W1997733142","https://openalex.org/W2003268506","https://openalex.org/W2025060809","https://openalex.org/W2043185636","https://openalex.org/W2057214803","https://openalex.org/W2071646838","https://openalex.org/W2099039198","https://openalex.org/W2104619491","https://openalex.org/W2110256992","https://openalex.org/W2113816218","https://openalex.org/W2116976883","https://openalex.org/W2128746754","https://openalex.org/W2129014750","https://openalex.org/W2147472054","https://openalex.org/W2150908245","https://openalex.org/W2155142785","https://openalex.org/W2159482845","https://openalex.org/W2159675211","https://openalex.org/W2164538999","https://openalex.org/W2169517653","https://openalex.org/W2184417913","https://openalex.org/W2236604918","https://openalex.org/W2304171844","https://openalex.org/W2313385485","https://openalex.org/W2332912708","https://openalex.org/W2505971024","https://openalex.org/W2561960911","https://openalex.org/W2569419820","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2378339845","https://openalex.org/W1726300337","https://openalex.org/W1961707331","https://openalex.org/W2341681417","https://openalex.org/W2977457557","https://openalex.org/W2063475537","https://openalex.org/W4206444712","https://openalex.org/W2012938657","https://openalex.org/W2296005855","https://openalex.org/W4223538309"],"abstract_inverted_index":{"BACKGROUND:":[0],"As":[1],"more":[2,4],"and":[3,77,96,115,125,128,188,233,264,307,335],"biological":[5,235],"reaction":[6,114,116],"data":[7,118],"become":[8],"available,":[9],"the":[10,14,18,50,60,87,97,100,120,129,141,191,260,290,314,317],"full":[11,51],"exploration":[12],"of":[13,20,36,63,89,99,123,190,220,225,240,292,316],"enzymatic":[15,52],"potential":[16,265],"for":[17,59,67,104,139,166,209,274,278,289,326],"synthesis":[19,107],"valuable":[21],"products":[22],"opens":[23],"up":[24],"exciting":[25],"new":[26],"opportunities":[27],"but":[28,205],"is":[29,45,111,136,247,304,323],"becoming":[30],"increasingly":[31],"complex.":[32],"The":[33,109,133,302],"manual":[34],"design":[35,62,291],"multi-step":[37,68],"biosynthesis":[38],"routes":[39],"involving":[40],"enzymes":[41,242],"from":[42,119,149,212,298],"different":[43],"organisms":[44],"very":[46],"challenging.":[47],"To":[48],"harness":[49],"potential,":[53],"we":[54,197],"developed":[55],"a":[56,83,90,146,150,167,172,177,201,217,223,257,299],"computational":[57],"tool":[58,288],"directed":[61],"biosynthetic":[64,294],"production":[65,295],"pathways":[66,210,296],"catalysis":[69],"with":[70,161],"in":[71,286,328],"vitro":[72,329],"enzyme":[73,330],"cascades,":[74,331],"cell":[75,333],"hydrolysates":[76,334],"permeabilized":[78,337],"cells.":[79,338],"RESULTS:":[80],"We":[81,170,283],"present":[82,284],"method":[84,157,303,322],"which":[85,182],"encompasses":[86],"reconstruction":[88],"genome-scale":[91],"pan-organism":[92,134,300],"metabolic":[93],"network,":[94],"path-finding":[95,173],"ranking":[98,227],"resulting":[101],"pathway":[102,144,230,253,280],"candidates":[103],"proposing":[105],"suitable":[106,143],"pathways.":[108],"network":[110,135,163],"based":[112,175],"on":[113,176],"pair":[117],"Kyoto":[121],"Encyclopedia":[122],"Genes":[124],"Genomes":[126],"(KEGG)":[127],"thermodynamics":[130,232],"calculator":[131],"eQuilibrator.":[132],"especially":[137],"useful":[138],"finding":[140],"most":[142],"to":[145,216,249,313],"target":[147,218],"metabolite":[148],"thermodynamic":[151,258],"or":[152,243],"economic":[153],"standpoint.":[154],"However,":[155],"our":[156,206],"can":[158,310],"be":[159,311],"used":[160],"any":[162],"reconstruction,":[164],"e.g.":[165],"specific":[168],"organism.":[169],"implemented":[171],"algorithm":[174,207],"mixed-integer":[178],"linear":[179],"program":[180],"(MILP)":[181],"takes":[183],"into":[184],"account":[185],"both":[186],"topology":[187],"stoichiometry":[189],"underlying":[192],"network.":[193,301],"Unlike":[194],"other":[195,234],"methods":[196],"do":[198],"not":[199],"specify":[200],"single":[202],"starting":[203,211,297],"metabolite,":[204],"searches":[208],"arbitrary":[213],"start":[214],"metabolites":[215],"product":[219],"interest.":[221],"Using":[222],"set":[224],"biochemical":[226],"criteria":[228],"including":[229],"length,":[231],"characteristics":[236],"such":[237],"as":[238,268,270],"number":[239],"heterologous":[241],"cofactor":[244],"requirement,":[245],"it":[246],"possible":[248],"obtain":[250],"well-designed":[251],"meaningful":[252],"alternatives.":[254],"In":[255],"addition,":[256],"profile,":[259],"overall":[261],"reactant":[262],"balance":[263],"side":[266],"reactions":[267],"well":[269],"an":[271,285],"SBML":[272],"file":[273],"visualization":[275],"are":[276],"generated":[277],"each":[279,308],"alternative.":[281],"CONCLUSION:":[282],"silico":[287],"multi-enzyme":[293],"highly":[305],"customizable":[306],"module":[309],"adapted":[312],"focus":[315],"project":[318],"at":[319],"hand.":[320],"This":[321],"directly":[324],"applicable":[325],"(i)":[327],"(ii)":[332],"(iii)":[336]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
