{"id":"https://openalex.org/W2409916035","doi":null,"title":"Metabolic Pathway Analysis : from small to genome-scale networks","display_name":"Metabolic Pathway Analysis : from small to genome-scale networks","publication_year":2011,"publication_date":"2011-01-01","ids":{"openalex":"https://openalex.org/W2409916035","mag":"2409916035"},"language":"en","primary_location":{"id":"pmh:oai:www.db-thueringen.de:dbt_mods_00018280","doi":null,"is_oa":true,"landing_page_url":"https://nbn-resolving.org/urn:nbn:de:gbv:27-20110511-141605-6","pdf_url":"https://www.db-thueringen.de/receive/dbt_mods_00018280","source":{"id":"https://openalex.org/S4306400120","display_name":"Common Library Network (Der Gemeinsame Bibliotheksverbund)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210149878","host_organization_name":"Verbundzentrale des GBV","host_organization_lineage":["https://openalex.org/I4210149878"],"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":"dissertation"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.db-thueringen.de/receive/dbt_mods_00018280","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073501856","display_name":"ret. nat. Figueiredo","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"ret. nat. Figueiredo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5088468753","display_name":"Luis F. D. P. de","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Luis F. D. P. de","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"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":0.9990000128746033,"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":0.9990000128746033,"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":0.0006000000284984708,"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":0.0006000000284984708,"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/metabolic-pathway-analysis","display_name":"metabolic pathway analysis","score":0.7739999890327454},{"id":"https://openalex.org/keywords/elementary-flux-modes","display_name":"elementary flux modes","score":0.9240000247955322},{"id":"https://openalex.org/keywords/constraint-based-modeling","display_name":"constraint-based modeling","score":0.7409999966621399},{"id":"https://openalex.org/keywords/metabolic-network-reconstruction","display_name":"metabolic network reconstruction","score":0.7289999723434448},{"id":"https://openalex.org/keywords/stoichiometric-analysis","display_name":"stoichiometric analysis","score":0.6589999794960022},{"id":"https://openalex.org/keywords/convex-analysis","display_name":"convex analysis","score":0.8600000143051147},{"id":"https://openalex.org/keywords/genome-scale-metabolic-networks","display_name":"genome-scale metabolic networks","score":0.878000020980835},{"id":"https://openalex.org/keywords/systems-biology","display_name":"systems biology","score":0.6970000267028809},{"id":"https://openalex.org/keywords/biotechnology-applications","display_name":"biotechnology applications","score":0.6460000276565552}],"concepts":[{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.6392418146133423},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.6335572600364685},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.6275565028190613},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5865647196769714},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.4956763982772827},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.48802343010902405},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.4756074547767639},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4703412652015686},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4569362699985504},{"id":"https://openalex.org/C160941953","wikidata":"https://www.wikidata.org/wiki/Q6822342","display_name":"Metabolic flux analysis","level":3,"score":0.4447310268878937},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.44297486543655396},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.4408493638038635},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4192141592502594},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.41413623094558716},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32555073499679565},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20614171028137207},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20392033457756042},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.19632917642593384},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.11203739047050476},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C134018914","wikidata":"https://www.wikidata.org/wiki/Q162606","display_name":"Endocrinology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:www.db-thueringen.de:dbt_mods_00018280","doi":null,"is_oa":true,"landing_page_url":"https://nbn-resolving.org/urn:nbn:de:gbv:27-20110511-141605-6","pdf_url":"https://www.db-thueringen.de/receive/dbt_mods_00018280","source":{"id":"https://openalex.org/S4306400120","display_name":"Common Library Network (Der Gemeinsame Bibliotheksverbund)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210149878","host_organization_name":"Verbundzentrale des GBV","host_organization_lineage":["https://openalex.org/I4210149878"],"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":"dissertation"},{"id":"mag:2409916035","doi":null,"is_oa":false,"landing_page_url":"http://www.db-thueringen.de/servlets/DocumentServlet?id=18280","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:www.db-thueringen.de:dbt_mods_00018280","doi":null,"is_oa":true,"landing_page_url":"https://nbn-resolving.org/urn:nbn:de:gbv:27-20110511-141605-6","pdf_url":"https://www.db-thueringen.de/receive/dbt_mods_00018280","source":{"id":"https://openalex.org/S4306400120","display_name":"Common Library Network (Der Gemeinsame Bibliotheksverbund)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210149878","host_organization_name":"Verbundzentrale des GBV","host_organization_lineage":["https://openalex.org/I4210149878"],"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":"dissertation"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G7356386875","display_name":"CAREER: Interrogating the pathogen-host relationship with genome-scale network analysis","funder_award_id":"0643548","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320313941","display_name":"Friedrich-Schiller-Universit\u00e4t Jena","ror":"https://ror.org/05qpz1x62"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2409916035.pdf","grobid_xml":"https://content.openalex.org/works/W2409916035.grobid-xml"},"referenced_works_count":170,"referenced_works":["https://openalex.org/W140895041","https://openalex.org/W190590157","https://openalex.org/W596784770","https://openalex.org/W1482646691","https://openalex.org/W1484198052","https://openalex.org/W1487122482","https://openalex.org/W1487827847","https://openalex.org/W1490544414","https://openalex.org/W1491174923","https://openalex.org/W1511494479","https://openalex.org/W1512383952","https://openalex.org/W1516271250","https://openalex.org/W1517036688","https://openalex.org/W1561267729","https://openalex.org/W1561767438","https://openalex.org/W1575307919","https://openalex.org/W1583636709","https://openalex.org/W1590994961","https://openalex.org/W1591310699","https://openalex.org/W1595569274","https://openalex.org/W1595961914","https://openalex.org/W1600492551","https://openalex.org/W1601296974","https://openalex.org/W1604281503","https://openalex.org/W1606784130","https://openalex.org/W1621975707","https://openalex.org/W1642162696","https://openalex.org/W1668115650","https://openalex.org/W1758395617","https://openalex.org/W1780605602","https://openalex.org/W1827177018","https://openalex.org/W1841771524","https://openalex.org/W1864895841","https://openalex.org/W1963547452","https://openalex.org/W1964491374","https://openalex.org/W1965518203","https://openalex.org/W1966392395","https://openalex.org/W1969529366","https://openalex.org/W1969680556","https://openalex.org/W1969738839","https://openalex.org/W1970556744","https://openalex.org/W1971323277","https://openalex.org/W1971403296","https://openalex.org/W1973525129","https://openalex.org/W1976548998","https://openalex.org/W1976672440","https://openalex.org/W1977199071","https://openalex.org/W1979537657","https://openalex.org/W1980737779","https://openalex.org/W1981719666","https://openalex.org/W1983120620","https://openalex.org/W1983202741","https://openalex.org/W1987198680","https://openalex.org/W1988047583","https://openalex.org/W1993170943","https://openalex.org/W1996202330","https://openalex.org/W1996529795","https://openalex.org/W1996791690","https://openalex.org/W1998783652","https://openalex.org/W1999104032","https://openalex.org/W2003268506","https://openalex.org/W2006912660","https://openalex.org/W2006943154","https://openalex.org/W2008818443","https://openalex.org/W2011039300","https://openalex.org/W2013522363","https://openalex.org/W2017666959","https://openalex.org/W2017723268","https://openalex.org/W2018045523","https://openalex.org/W2020916135","https://openalex.org/W2022012525","https://openalex.org/W2022684902","https://openalex.org/W2024963167","https://openalex.org/W2025060809","https://openalex.org/W2034285024","https://openalex.org/W2034645234","https://openalex.org/W2034994407","https://openalex.org/W2037614307","https://openalex.org/W2038478640","https://openalex.org/W2044775606","https://openalex.org/W2046760236","https://openalex.org/W2047496194","https://openalex.org/W2048214825","https://openalex.org/W2049814691","https://openalex.org/W2051265576","https://openalex.org/W2053913299","https://openalex.org/W2055677741","https://openalex.org/W2059310837","https://openalex.org/W2059761552","https://openalex.org/W2061364094","https://openalex.org/W2063475537","https://openalex.org/W2065432632","https://openalex.org/W2070020713","https://openalex.org/W2075846943","https://openalex.org/W2076262841","https://openalex.org/W2077440882","https://openalex.org/W2078775934","https://openalex.org/W2083011190","https://openalex.org/W2083693802","https://openalex.org/W2083786039","https://openalex.org/W2084916894","https://openalex.org/W2085993965","https://openalex.org/W2089637700","https://openalex.org/W2090846925","https://openalex.org/W2091793452","https://openalex.org/W2092873989","https://openalex.org/W2092899907","https://openalex.org/W2094399313","https://openalex.org/W2095279025","https://openalex.org/W2096528150","https://openalex.org/W2097664794","https://openalex.org/W2099039198","https://openalex.org/W2100818174","https://openalex.org/W2102164505","https://openalex.org/W2102263388","https://openalex.org/W2102653059","https://openalex.org/W2104108767","https://openalex.org/W2108590631","https://openalex.org/W2110355460","https://openalex.org/W2111421616","https://openalex.org/W2112515372","https://openalex.org/W2113024448","https://openalex.org/W2115826669","https://openalex.org/W2116324021","https://openalex.org/W2119221480","https://openalex.org/W2123698848","https://openalex.org/W2126175129","https://openalex.org/W2127020923","https://openalex.org/W2127844534","https://openalex.org/W2128329041","https://openalex.org/W2129106849","https://openalex.org/W2130364940","https://openalex.org/W2131178894","https://openalex.org/W2132048431","https://openalex.org/W2133319394","https://openalex.org/W2134153749","https://openalex.org/W2136060005","https://openalex.org/W2140040278","https://openalex.org/W2141356165","https://openalex.org/W2142747156","https://openalex.org/W2142750990","https://openalex.org/W2144885342","https://openalex.org/W2152776677","https://openalex.org/W2153020710","https://openalex.org/W2153283265","https://openalex.org/W2153373497","https://openalex.org/W2154066017","https://openalex.org/W2154402996","https://openalex.org/W2155681752","https://openalex.org/W2159482845","https://openalex.org/W2159724748","https://openalex.org/W2160433236","https://openalex.org/W2164904029","https://openalex.org/W2165056588","https://openalex.org/W2165674132","https://openalex.org/W2165932090","https://openalex.org/W2166665154","https://openalex.org/W2166927282","https://openalex.org/W2169517653","https://openalex.org/W2169804422","https://openalex.org/W2170427655","https://openalex.org/W2178117785","https://openalex.org/W2192454018","https://openalex.org/W2287671349","https://openalex.org/W2342891076","https://openalex.org/W2492988171","https://openalex.org/W3023540311","https://openalex.org/W3145128584","https://openalex.org/W3195881304","https://openalex.org/W7073557482"],"related_works":["https://openalex.org/W2415355040","https://openalex.org/W2587297699","https://openalex.org/W2163871517","https://openalex.org/W2402112396","https://openalex.org/W2378289348","https://openalex.org/W2147102947","https://openalex.org/W2129106849","https://openalex.org/W2025172803","https://openalex.org/W2801106193","https://openalex.org/W7096577340"],"abstract_inverted_index":{"The":[0,182],"need":[1],"for":[2,69,228],"mathematical":[3,93,171],"modelling":[4,38,111,217],"of":[5,24,41,51,57,66,84,95,104,129,135,169,184,201,208],"biological":[6],"processes":[7],"has":[8],"grown":[9],"alongside":[10],"with":[11,232],"the":[12,15,20,54,81,99,102,126,130,136,155,160,170,198],"achievements":[13,210],"in":[14,44,114,150,194,211,239],"experimental":[16,42,230],"field":[17],"leading":[18],"to":[19,46,91,120,166,174,188],"appearance":[21],"and":[22,39,74,107,159,178,215],"development":[23],"new":[25,35,186],"fields":[26],"like":[27,113],"systems":[28],"biology.":[29],"Systems":[30],"biology":[31,177],"aims":[32],"at":[33],"generating":[34],"knowledge":[36],"through":[37],"integration":[40],"data":[43,231],"order":[45],"develop":[47],"a":[48,87],"holistic":[49],"understanding":[50],"organisms.":[52],"In":[53,125,197],"first":[55,137],"part":[56,128,200],"my":[58,202],"PhD":[59],"thesis,":[60,131,203],"I":[61,78,132,204,224],"compare":[62],"two":[63,134],"different":[64],"levels":[65],"abstraction":[67],"used":[68],"computing":[70],"metabolic":[71,96,123,148,153,212],"pathways,":[72],"constraint-based":[73,216],"graph":[75,89],"theoretical":[76],"methods.":[77],"show":[79],"that":[80,145,245],"current":[82],"representations":[83],"metabolism":[85],"as":[86,110,218,220],"simple":[88],"correspond":[90],"wrong":[92],"descriptions":[94],"pathways.":[97,124],"On":[98],"other":[100],"hand,":[101],"use":[103],"stoichiometric":[105],"information":[106],"convex":[108],"analysis":[109],"framework":[112],"elementary":[115,141,233,240],"flux":[116,142,234,241],"mode":[117,143,235,242],"analysis,":[118,144],"allows":[119],"correctly":[121],"predict":[122],"second":[127],"present":[133],"methods,":[138],"based":[139],"on":[140,244],"can":[146],"compute":[147],"pathways":[149],"such":[151],"large":[152],"networks:":[154],"K-shortest":[156],"EFMs":[157],"method":[158],"EFMEvolver":[161],"method.":[162],"These":[163],"methods":[164,187],"contribute":[165],"an":[167,206],"enrichment":[168],"tools":[172],"available":[173],"model":[175],"cell":[176],"more":[179],"precisely,":[180],"metabolism.":[181],"application":[183],"these":[185],"biotechnological":[189],"problems":[190],"is":[191],"also":[192],"explored":[193],"this":[195],"part.":[196],"last":[199],"give":[205],"overview":[207],"recent":[209],"network":[213],"reconstruction":[214],"well":[219],"open":[221],"issues.":[222],"Moreover,":[223],"discuss":[225],"possible":[226],"strategies":[227],"integrating":[229],"analysis.":[236],"Further":[237],"improvements":[238],"computation":[243],"direction":[246],"are":[247],"put":[248],"forward.":[249]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2016-06-24T00:00:00"}