{"id":"https://openalex.org/W1510568883","doi":null,"title":"Minimal Cut Sets and Their Use in Modelling Flavonoid Metabolism","display_name":"Minimal Cut Sets and Their Use in Modelling Flavonoid Metabolism","publication_year":2014,"publication_date":"2014-10-30","ids":{"openalex":"https://openalex.org/W1510568883","mag":"1510568883"},"language":"en","primary_location":{"id":"pmh:oai:researcharchive.lincoln.ac.nz:10182/5498","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/10182/5498","pdf_url":"https://hdl.handle.net/10182/5498","source":{"id":"https://openalex.org/S4306400204","display_name":"Lincoln University Research Archive (Lincoln University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I184746854","host_organization_name":"Lincoln University","host_organization_lineage":["https://openalex.org/I184746854"],"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":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hdl.handle.net/10182/5498","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065121099","display_name":"Sangaalofa Tooki Clark","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Sangaalofa Tooki Clark","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5065121099"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9726999998092651,"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":0.9726999998092651,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.016899999231100082,"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":0.004100000020116568,"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/minimal-cut-sets","display_name":"minimal cut sets","score":0.8180000185966492},{"id":"https://openalex.org/keywords/flavonoid-metabolism","display_name":"flavonoid metabolism","score":0.9710000157356262},{"id":"https://openalex.org/keywords/anthocyanin-biosynthesis","display_name":"anthocyanin biosynthesis","score":0.8700000047683716},{"id":"https://openalex.org/keywords/elementary-modes","display_name":"elementary modes","score":0.7879999876022339},{"id":"https://openalex.org/keywords/arabidopsis-thaliana","display_name":"Arabidopsis thaliana","score":0.8809999823570251},{"id":"https://openalex.org/keywords/genome-scale-metabolic-networks","display_name":"genome-scale metabolic networks","score":0.718999981880188},{"id":"https://openalex.org/keywords/subnetwork-extraction","display_name":"subnetwork extraction","score":0.7450000047683716},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"flux balance analysis","score":0.6919999718666077},{"id":"https://openalex.org/keywords/gene-connectivity","display_name":"gene connectivity","score":0.4659999907016754},{"id":"https://openalex.org/keywords/pleiotropy","display_name":"pleiotropy","score":0.6840000152587891},{"id":"https://openalex.org/keywords/gene-elimination","display_name":"gene elimination","score":0.36399999260902405},{"id":"https://openalex.org/keywords/plant-pigmentation","display_name":"plant pigmentation","score":0.47200000286102295},{"id":"https://openalex.org/keywords/metabolic-pathway-analysis","display_name":"metabolic pathway analysis","score":0.703000009059906}],"concepts":[{"id":"https://openalex.org/C2779054382","wikidata":"https://www.wikidata.org/wiki/Q72185287","display_name":"Flavonoid","level":3,"score":0.697723388671875},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.35494670271873474},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34047192335128784},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.25566965341567993},{"id":"https://openalex.org/C2778004101","wikidata":"https://www.wikidata.org/wiki/Q133948","display_name":"Antioxidant","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:researcharchive.lincoln.ac.nz:10182/5498","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/10182/5498","pdf_url":"https://hdl.handle.net/10182/5498","source":{"id":"https://openalex.org/S4306400204","display_name":"Lincoln University Research Archive (Lincoln University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I184746854","host_organization_name":"Lincoln University","host_organization_lineage":["https://openalex.org/I184746854"],"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":"Thesis"},{"id":"mag:1510568883","doi":null,"is_oa":false,"landing_page_url":"https://researcharchive.lincoln.ac.nz/bitstream/10182/5498/3/Clark_phd.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:researcharchive.lincoln.ac.nz:10182/5498","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/10182/5498","pdf_url":"https://hdl.handle.net/10182/5498","source":{"id":"https://openalex.org/S4306400204","display_name":"Lincoln University Research Archive (Lincoln University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I184746854","host_organization_name":"Lincoln University","host_organization_lineage":["https://openalex.org/I184746854"],"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":"Thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1510568883.pdf","grobid_xml":"https://content.openalex.org/works/W1510568883.grobid-xml"},"referenced_works_count":165,"referenced_works":["https://openalex.org/W35601271","https://openalex.org/W74487828","https://openalex.org/W139760298","https://openalex.org/W317028738","https://openalex.org/W564848705","https://openalex.org/W1032551114","https://openalex.org/W1487827847","https://openalex.org/W1506654328","https://openalex.org/W1529898704","https://openalex.org/W1553833389","https://openalex.org/W1596254730","https://openalex.org/W1599969036","https://openalex.org/W1602102244","https://openalex.org/W1604021722","https://openalex.org/W1621975707","https://openalex.org/W1668115650","https://openalex.org/W1758395617","https://openalex.org/W1764115441","https://openalex.org/W1764124879","https://openalex.org/W1807981783","https://openalex.org/W1921005127","https://openalex.org/W1963948396","https://openalex.org/W1965518203","https://openalex.org/W1969918920","https://openalex.org/W1978486653","https://openalex.org/W1978802080","https://openalex.org/W1980609967","https://openalex.org/W1983352396","https://openalex.org/W1990396337","https://openalex.org/W1991721460","https://openalex.org/W1992306474","https://openalex.org/W1994656497","https://openalex.org/W2004308928","https://openalex.org/W2005287355","https://openalex.org/W2005673176","https://openalex.org/W2009940763","https://openalex.org/W2010645400","https://openalex.org/W2012139697","https://openalex.org/W2012996629","https://openalex.org/W2013310688","https://openalex.org/W2013685063","https://openalex.org/W2017023826","https://openalex.org/W2017855215","https://openalex.org/W2019653411","https://openalex.org/W2020916135","https://openalex.org/W2022347357","https://openalex.org/W2023173927","https://openalex.org/W2026089579","https://openalex.org/W2028333247","https://openalex.org/W2028681077","https://openalex.org/W2029422551","https://openalex.org/W2032074709","https://openalex.org/W2032418840","https://openalex.org/W2034085081","https://openalex.org/W2035910303","https://openalex.org/W2037614307","https://openalex.org/W2041042514","https://openalex.org/W2042605932","https://openalex.org/W2043440339","https://openalex.org/W2043912525","https://openalex.org/W2044940018","https://openalex.org/W2047632644","https://openalex.org/W2050984657","https://openalex.org/W2051283122","https://openalex.org/W2060677679","https://openalex.org/W2060806574","https://openalex.org/W2061154390","https://openalex.org/W2063475537","https://openalex.org/W2065669781","https://openalex.org/W2067775922","https://openalex.org/W2070020713","https://openalex.org/W2070074729","https://openalex.org/W2071902637","https://openalex.org/W2073612090","https://openalex.org/W2075846943","https://openalex.org/W2079619772","https://openalex.org/W2079863010","https://openalex.org/W2080018242","https://openalex.org/W2080760786","https://openalex.org/W2080947358","https://openalex.org/W2081052511","https://openalex.org/W2084716075","https://openalex.org/W2085945924","https://openalex.org/W2085993965","https://openalex.org/W2087139200","https://openalex.org/W2089026326","https://openalex.org/W2089120439","https://openalex.org/W2089499069","https://openalex.org/W2090534913","https://openalex.org/W2091793452","https://openalex.org/W2092248920","https://openalex.org/W2092401751","https://openalex.org/W2092420079","https://openalex.org/W2093241068","https://openalex.org/W2094097101","https://openalex.org/W2094399313","https://openalex.org/W2094525983","https://openalex.org/W2096484674","https://openalex.org/W2098537586","https://openalex.org/W2098709515","https://openalex.org/W2099039198","https://openalex.org/W2099551325","https://openalex.org/W2099922550","https://openalex.org/W2101309566","https://openalex.org/W2102417623","https://openalex.org/W2102805480","https://openalex.org/W2103170157","https://openalex.org/W2104362138","https://openalex.org/W2105318887","https://openalex.org/W2106576546","https://openalex.org/W2108625374","https://openalex.org/W2110678397","https://openalex.org/W2111102591","https://openalex.org/W2113329733","https://openalex.org/W2115831900","https://openalex.org/W2116027790","https://openalex.org/W2116324021","https://openalex.org/W2117486132","https://openalex.org/W2120661262","https://openalex.org/W2125299541","https://openalex.org/W2125776280","https://openalex.org/W2126175129","https://openalex.org/W2127020923","https://openalex.org/W2127169316","https://openalex.org/W2128601422","https://openalex.org/W2130364940","https://openalex.org/W2131178894","https://openalex.org/W2131506127","https://openalex.org/W2141703917","https://openalex.org/W2143517204","https://openalex.org/W2144000913","https://openalex.org/W2144372567","https://openalex.org/W2146420365","https://openalex.org/W2149001103","https://openalex.org/W2150465569","https://openalex.org/W2150908245","https://openalex.org/W2151023149","https://openalex.org/W2152639239","https://openalex.org/W2152867500","https://openalex.org/W2153134260","https://openalex.org/W2155481116","https://openalex.org/W2157646380","https://openalex.org/W2158075343","https://openalex.org/W2158784643","https://openalex.org/W2159482845","https://openalex.org/W2160201278","https://openalex.org/W2161955420","https://openalex.org/W2162684083","https://openalex.org/W2163668513","https://openalex.org/W2163823651","https://openalex.org/W2164100233","https://openalex.org/W2164904029","https://openalex.org/W2165011536","https://openalex.org/W2165247488","https://openalex.org/W2166927282","https://openalex.org/W2170079416","https://openalex.org/W2170576111","https://openalex.org/W2240428226","https://openalex.org/W2296679604","https://openalex.org/W2891212941","https://openalex.org/W2952647989","https://openalex.org/W3137299218","https://openalex.org/W3154268888","https://openalex.org/W3213583783","https://openalex.org/W7073557482"],"related_works":["https://openalex.org/W2089120439","https://openalex.org/W6941121787","https://openalex.org/W7097029058","https://openalex.org/W2012996629","https://openalex.org/W2158075343","https://openalex.org/W2094097101","https://openalex.org/W2920336299","https://openalex.org/W3162663756","https://openalex.org/W2246313755","https://openalex.org/W2956622428"],"abstract_inverted_index":{"This":[0,47,82,456],"research":[1,101,166,341,430],"makes":[2],"use":[3],"of":[4,9,21,72,78,151,169,184,188,214,231,242,263,285,311,324,366,381,412],"the":[5,10,18,37,58,76,117,130,149,158,165,189,202,258,261,273,282,286,295,309,313,321,325,338,354,367,371,377,395,400,403,407,410,413,487,497,503,512],"genome-scale":[6],"metabolic":[7,177],"information":[8,452],"Arabidopsis":[11,51,98,498],"thaliana":[12],"(Arabidopsis)":[13],"plant":[14],"to":[15,132,156,195,236,256,279,294,333,348,391,465,491,511,530],"better":[16],"understand":[17],"systemic":[19],"behaviour":[20],"a":[22,93,105,174,210,219,224,363,433,443,463,473,536],"multicellular":[23],"cell,":[24],"using":[25,445],"mathematical":[26],"and":[27,68,90,96,145,192,289,319,329,379,384,447,461,477,485,535],"in":[28,49,57,75,113,164,205,245,272,337,442,449,472,496],"silico":[29],"methods.":[30],"To":[31,115],"avoid":[32],"combinatorial":[33],"explosion":[34],"resulting":[35],"from":[36,223,398,502],"large":[38],"network":[39,484,489],"size,":[40],"an":[41,50,459,482],"appropriate":[42],"subnetwork":[43,53,83],"is":[44,55,70,84,167,199],"first":[45,203],"extracted.":[46],"results":[48,304,504],"flavonoid":[52,73,488],"that":[54,60,128,168,260,370,409,508,519],"self-contained,":[56],"sense":[59],"all":[61],"its":[62,88,193],"exchange":[63],"fluxes":[64,350,397],"are":[65,137,141,154,234,253,276,293,316,439,469,509],"accounted":[66],"for":[67,110,148,201,217,240,302,353,435],"it":[69,331],"representative":[71],"metabolism":[74],"context":[77],"whole":[79],"cell":[80],"metabolism.":[81],"verified":[85,97],"by":[86],"comparing":[87],"compounds":[89,153],"reactions":[91,468,493,507],"with":[92,451],"recently":[94],"reconstructed":[95],"network.":[99],"The":[100,160,340,360,429,475,524],"focusses":[102],"on":[103,269,376,481,486],"anthocyanins,":[104],"major":[106],"flavonoids":[107,383,421],"subgroup":[108],"responsible":[109,147],"colour":[111,243],"pigmentation":[112,244],"plants.":[114,246],"determine":[116,466,492],"anthocyanin":[118,152,358,414],"biosynthetic":[119],"pathway":[120,178],"(ABP),":[121],"elementary":[122],"modes":[123],"(EMs)":[124],"or":[125],"non-decomposable":[126],"pathways":[127],"allow":[129],"system":[131],"operate":[133],"at":[134,281],"steady":[135],"state,":[136],"calculated.":[138],"These":[139,297],"EMs":[140,312,446],"classified":[142],"into":[143],"groups":[144],"those":[146],"formation":[150],"taken":[155],"constitute":[157],"ABP.":[159],"central":[161],"analysis":[162,179,346],"approach":[163],"minimal":[170],"cut":[171],"sets":[172,518],"(MCSs),":[173],"fairly":[175],"new":[176],"(MPA)":[180],"concept.":[181],"A":[182],"review":[183],"various":[185],"development":[186,529],"stages":[187],"MCS":[190,401],"concept":[191],"relationship":[194],"other":[196,270,382],"similar":[197],"approaches":[198],"given":[200],"time":[204],"this":[206],"thesis.":[207],"MCSs":[208,275,356,373,448],"provide":[209,299],"mathematically":[211],"complete":[212],"list":[213],"candidate":[215],"genes":[216,239,266,288,315,328,438],"eliminating":[218,357,399],"certain":[220],"objective":[221],"function":[222],"holistic":[225],"perspective,":[226],"without":[227],"needing":[228],"prior":[229],"knowledge":[230],"genes.":[232],"They":[233],"used":[235,255,278,490],"identify":[237],"target":[238,265],"loss":[241],"Other":[247],"methods,":[248],"such":[249],"as":[250,514,516],"reaction":[251,517],"participation,":[252],"then":[254],"study":[257],"implications":[259],"elimination":[262],"these":[264],"would":[267,374,520],"have":[268,375],"processes":[271,380],"cell.":[274],"also":[277,342,431],"look":[280],"fragility":[283],"coefficient":[284],"ABP":[287,314,327],"how":[290,330],"crucial":[291],"they":[292,335],"pathway.":[296,339],"analyses":[298],"quantitative":[300,364],"support":[301,406],"experimental":[303,392],"e.g.,":[305,394],"gene":[306,522],"connectivity":[307],"determines":[308],"number":[310],"connected":[317],"to,":[318],"backs":[320],"pleiotropic":[322],"characteristics":[323],"\u201cearly\u201d":[326],"relates":[332],"where":[334],"occur":[336],"uses":[343],"flux":[344],"balance":[345],"(FBA)":[347],"simulate":[349],"(reaction":[351],"rates)":[352],"different":[355,372],"compounds.":[359,386],"FBA":[361],"provides":[362],"measure":[365],"relative":[368],"impact":[369],"production":[378],"related":[385],"Certain":[387],"simulation":[388],"outcomes":[389],"correspond":[390],"observations,":[393],"simulated":[396],"containing":[402],"CHS":[404,417],"gene,":[405],"observation":[408],"suppression":[411],"pathway,":[415],"via":[416],"silencing,":[418],"dramatically":[419],"reduces":[420],"but":[422],"does":[423],"not":[424],"affect":[425],"scent":[426],"(benzenoids)":[427],"production.":[428],"develops":[432],"method":[434],"determining":[436],"which":[437,467],"being":[440,470],"expressed":[441,471],"tissue,":[444],"conjunction":[450],"about":[453],"compound":[454],"products.":[455],"involves":[457],"developing":[458],"algorithm":[460,476],"writing":[462],"program":[464,478,525],"tissue.":[474],"worked":[479],"both":[480],"example":[483],"taking":[494],"place":[495],"flower.":[499],"Information":[500],"obtained":[501],"includes":[505],"identifying":[506],"critical":[510],"flower":[513],"well":[515],"represent":[521],"sets.":[523],"still":[526],"needs":[527],"further":[528],"incorporate":[531],"analytical":[532],"clustering":[533],"methods":[534],"user-friendly":[537],"interface.":[538]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}