{"id":"https://openalex.org/W2010026173","doi":"https://doi.org/10.4018/jkdb.2010100202","title":"Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets","display_name":"Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets","publication_year":2010,"publication_date":"2010-01-01","ids":{"openalex":"https://openalex.org/W2010026173","doi":"https://doi.org/10.4018/jkdb.2010100202","mag":"2010026173"},"language":"en","primary_location":{"id":"doi:10.4018/jkdb.2010100202","is_oa":false,"landing_page_url":"https://doi.org/10.4018/jkdb.2010100202","pdf_url":null,"source":{"id":"https://openalex.org/S113982356","display_name":"International Journal of Knowledge Discovery in Bioinformatics","issn_l":"1947-9115","issn":["1947-9115","1947-9123"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320424","host_organization_name":"IGI Global","host_organization_lineage":["https://openalex.org/P4310320424"],"host_organization_lineage_names":["IGI Global"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Knowledge Discovery in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041203895","display_name":"Takeyuki Tamura","orcid":"https://orcid.org/0000-0003-1596-901X"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Takeyuki Tamura","raw_affiliation_strings":["Kyoto University, Japan"],"affiliations":[{"raw_affiliation_string":"Kyoto University, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013426338","display_name":"Kazuhiro Takemoto","orcid":"https://orcid.org/0000-0002-6355-1366"},"institutions":[{"id":"https://openalex.org/I3133035077","display_name":"Ube Frontier University","ror":"https://ror.org/03sgcr744","country_code":"JP","type":"education","lineage":["https://openalex.org/I3133035077"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kazuhiro Takemoto","raw_affiliation_strings":["Graduate School of Frontier Sciences, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Frontier Sciences, Japan","institution_ids":["https://openalex.org/I3133035077"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016330265","display_name":"Tatsuya Akutsu","orcid":"https://orcid.org/0000-0001-9763-797X"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tatsuya Akutsu","raw_affiliation_strings":["Kyoto University, Japan"],"affiliations":[{"raw_affiliation_string":"Kyoto University, Japan","institution_ids":["https://openalex.org/I22299242"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5041203895"],"corresponding_institution_ids":["https://openalex.org/I22299242"],"apc_list":null,"apc_paid":null,"fwci":0.9443,"has_fulltext":false,"cited_by_count":49,"citation_normalized_percentile":{"value":0.73299197,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"1","issue":"1","first_page":"14","last_page":"31"},"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/T10404","display_name":"Enzyme Catalysis and Immobilization","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"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9947999715805054,"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/integer-programming","display_name":"Integer programming","score":0.633877158164978},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.6085531711578369},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6045872569084167},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5702729225158691},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.5519459247589111},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4575966000556946},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.4475991725921631},{"id":"https://openalex.org/keywords/pentose-phosphate-pathway","display_name":"Pentose phosphate pathway","score":0.436023473739624},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.42381569743156433},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.34825414419174194},{"id":"https://openalex.org/keywords/glycolysis","display_name":"Glycolysis","score":0.3147459924221039},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3002983331680298},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2046845257282257},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.18179866671562195},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.14047974348068237},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12004706263542175},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11545222997665405},{"id":"https://openalex.org/keywords/metabolism","display_name":"Metabolism","score":0.09220173954963684},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.08543607592582703}],"concepts":[{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.633877158164978},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.6085531711578369},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6045872569084167},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5702729225158691},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.5519459247589111},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4575966000556946},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.4475991725921631},{"id":"https://openalex.org/C3409486","wikidata":"https://www.wikidata.org/wiki/Q827489","display_name":"Pentose phosphate pathway","level":4,"score":0.436023473739624},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.42381569743156433},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.34825414419174194},{"id":"https://openalex.org/C20251656","wikidata":"https://www.wikidata.org/wiki/Q162643","display_name":"Glycolysis","level":3,"score":0.3147459924221039},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3002983331680298},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2046845257282257},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.18179866671562195},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.14047974348068237},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12004706263542175},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11545222997665405},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.09220173954963684},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.08543607592582703},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.4018/jkdb.2010100202","is_oa":false,"landing_page_url":"https://doi.org/10.4018/jkdb.2010100202","pdf_url":null,"source":{"id":"https://openalex.org/S113982356","display_name":"International Journal of Knowledge Discovery in Bioinformatics","issn_l":"1947-9115","issn":["1947-9115","1947-9123"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320424","host_organization_name":"IGI Global","host_organization_lineage":["https://openalex.org/P4310320424"],"host_organization_lineage_names":["IGI Global"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Knowledge Discovery in Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:RePEc:igg:jkdb00:v:1:y:2010:i:1:p:14-31","is_oa":false,"landing_page_url":"http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/jkdb.2010100202","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1487827847","https://openalex.org/W1541316156","https://openalex.org/W1966589279","https://openalex.org/W1977199071","https://openalex.org/W1978802080","https://openalex.org/W1983202741","https://openalex.org/W1987546980","https://openalex.org/W2034993111","https://openalex.org/W2039281572","https://openalex.org/W2043093337","https://openalex.org/W2057389251","https://openalex.org/W2070745908","https://openalex.org/W2075846943","https://openalex.org/W2081880478","https://openalex.org/W2094097101","https://openalex.org/W2094399313","https://openalex.org/W2099039198","https://openalex.org/W2101414248","https://openalex.org/W2101641168","https://openalex.org/W2117486132","https://openalex.org/W2123060905","https://openalex.org/W2129110097","https://openalex.org/W2130364940","https://openalex.org/W2144885342","https://openalex.org/W2153624566","https://openalex.org/W2158069895","https://openalex.org/W2167065750","https://openalex.org/W3103786587"],"related_works":["https://openalex.org/W2083413061","https://openalex.org/W2075919068","https://openalex.org/W2133150343","https://openalex.org/W2895086873","https://openalex.org/W2136892294","https://openalex.org/W3093251697","https://openalex.org/W2323425524","https://openalex.org/W2101414248","https://openalex.org/W2010026173","https://openalex.org/W4238429262"],"abstract_inverted_index":{"In":[0,70],"this":[1,67],"paper,":[2],"the":[3,6,116,160],"authors":[4,146],"consider":[5],"problem":[7,43],"of,":[8],"given":[9],"a":[10,13,19,25,31,37,82,90,132,141],"metabolic":[11,40,53,101],"network,":[12],"set":[14,20,93,123],"of":[15,21,39,49,52,57,104,124,163],"source":[16],"compounds":[17],"and":[18,55,76,108,136,158],"target":[22],"compounds,":[23],"finding":[24],"minimum":[26],"size":[27],"reaction":[28],"cut,":[29],"where":[30],"Boolean":[32],"model":[33,38],"is":[34],"used":[35],"as":[36],"networks.":[41],"The":[42,145],"has":[44],"potential":[45],"applications":[46],"to":[47,72,97,126],"measurement":[48],"structural":[50],"robustness":[51],"networks":[54,157],"detection":[56],"drug":[58],"targets.":[59],"They":[60],"develop":[61,81],"an":[62,98,121],"integer":[63,84],"programming-based":[64],"method":[65,88,118,135,152],"for":[66,155],"optimization":[68],"problem.":[69],"order":[71],"cope":[73],"with":[74],"cycles":[75],"reversible":[77],"reactions,":[78],"they":[79],"further":[80],"novel":[83],"programming":[85],"(IP)":[86],"formalization":[87],"using":[89],"feedback":[91],"vertex":[92],"(FVS).":[94],"When":[95],"applied":[96],"E.":[99],"coli":[100],"network":[102],"consisting":[103],"Glycolysis/Glyconeogenesis,":[105],"Citrate":[106],"cycle":[107],"Pentose":[109],"phosphate":[110],"pathway":[111],"obtained":[112],"from":[113],"KEGG":[114],"database,":[115],"FVS-based":[117],"can":[119],"find":[120],"optimal":[122],"reactions":[125],"be":[127],"inactivated":[128],"much":[129],"faster":[130,139],"than":[131,140],"naive":[133],"IP-based":[134],"several":[137],"times":[138],"flux":[142],"balance-based":[143],"method.":[144],"also":[147],"confirm":[148],"that":[149],"our":[150,164],"proposed":[151],"works":[153],"even":[154],"large":[156],"discuss":[159],"biological":[161],"meaning":[162],"results.":[165]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":31},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-10T00:00:00"}