{"id":"https://openalex.org/W2198332185","doi":"https://doi.org/10.1109/bibe.2015.7367691","title":"Modeling the metabolism of escherichia coli under oxygen gradients with dynamically changing flux bounds","display_name":"Modeling the metabolism of escherichia coli under oxygen gradients with dynamically changing flux bounds","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2198332185","doi":"https://doi.org/10.1109/bibe.2015.7367691","mag":"2198332185"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2015.7367691","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2015.7367691","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","raw_type":"proceedings-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/A5034718136","display_name":"Joachim von Wulffen","orcid":null},"institutions":[{"id":"https://openalex.org/I100066346","display_name":"University of Stuttgart","ror":"https://ror.org/04vnq7t77","country_code":"DE","type":"education","lineage":["https://openalex.org/I100066346"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Joachim von Wulffen","raw_affiliation_strings":["University of Stuttgart, Institute for System Dynamics, Stuttgart, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Stuttgart, Institute for System Dynamics, Stuttgart, Germany","institution_ids":["https://openalex.org/I100066346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035678514","display_name":"Patrick C. F. Buchholz","orcid":"https://orcid.org/0000-0001-5967-3777"},"institutions":[{"id":"https://openalex.org/I100066346","display_name":"University of Stuttgart","ror":"https://ror.org/04vnq7t77","country_code":"DE","type":"education","lineage":["https://openalex.org/I100066346"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Patrick Buchholz","raw_affiliation_strings":["University of Stuttgart, Institute of technical biochemistry, stuttgart, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Stuttgart, Institute of technical biochemistry, stuttgart, Germany","institution_ids":["https://openalex.org/I100066346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054507125","display_name":"Oliver Sawodny","orcid":"https://orcid.org/0000-0002-6910-2473"},"institutions":[{"id":"https://openalex.org/I100066346","display_name":"University of Stuttgart","ror":"https://ror.org/04vnq7t77","country_code":"DE","type":"education","lineage":["https://openalex.org/I100066346"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Oliver Sawodny","raw_affiliation_strings":["University of Stuttgart, Institute for System Dynamics, Stuttgart, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Stuttgart, Institute for System Dynamics, Stuttgart, Germany","institution_ids":["https://openalex.org/I100066346"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078315601","display_name":"Ronny Feuer","orcid":"https://orcid.org/0000-0002-5653-7670"},"institutions":[{"id":"https://openalex.org/I100066346","display_name":"University of Stuttgart","ror":"https://ror.org/04vnq7t77","country_code":"DE","type":"education","lineage":["https://openalex.org/I100066346"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ronny Feuer","raw_affiliation_strings":["University of Stuttgart, Institute for System Dynamics, Stuttgart, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Stuttgart, Institute for System Dynamics, Stuttgart, Germany","institution_ids":["https://openalex.org/I100066346"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.06824993,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"18","issue":null,"first_page":"1","last_page":"6"},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9961000084877014,"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":0.988099992275238,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/facultative","display_name":"Facultative","score":0.832821249961853},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.8141934871673584},{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.6931077241897583},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.6228902339935303},{"id":"https://openalex.org/keywords/chemostat","display_name":"Chemostat","score":0.5545868277549744},{"id":"https://openalex.org/keywords/anaerobic-exercise","display_name":"Anaerobic exercise","score":0.536218523979187},{"id":"https://openalex.org/keywords/oxygen-balance","display_name":"Oxygen balance","score":0.47168830037117004},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4610423743724823},{"id":"https://openalex.org/keywords/adaptation","display_name":"Adaptation (eye)","score":0.45499712228775024},{"id":"https://openalex.org/keywords/industrial-fermentation","display_name":"Industrial fermentation","score":0.4439874291419983},{"id":"https://openalex.org/keywords/oxygen","display_name":"Oxygen","score":0.39457541704177856},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.3891748785972595},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3275800943374634},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3190380930900574},{"id":"https://openalex.org/keywords/fermentation","display_name":"Fermentation","score":0.23619848489761353},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.2341914176940918},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.217928946018219},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.18817737698554993},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1121772825717926},{"id":"https://openalex.org/keywords/physiology","display_name":"Physiology","score":0.08353739976882935},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08082875609397888}],"concepts":[{"id":"https://openalex.org/C53144768","wikidata":"https://www.wikidata.org/wiki/Q5428855","display_name":"Facultative","level":2,"score":0.832821249961853},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.8141934871673584},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.6931077241897583},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.6228902339935303},{"id":"https://openalex.org/C125111812","wikidata":"https://www.wikidata.org/wiki/Q902311","display_name":"Chemostat","level":3,"score":0.5545868277549744},{"id":"https://openalex.org/C5140985","wikidata":"https://www.wikidata.org/wiki/Q483866","display_name":"Anaerobic exercise","level":2,"score":0.536218523979187},{"id":"https://openalex.org/C81626062","wikidata":"https://www.wikidata.org/wiki/Q693784","display_name":"Oxygen balance","level":3,"score":0.47168830037117004},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4610423743724823},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.45499712228775024},{"id":"https://openalex.org/C73401843","wikidata":"https://www.wikidata.org/wiki/Q845523","display_name":"Industrial fermentation","level":3,"score":0.4439874291419983},{"id":"https://openalex.org/C540031477","wikidata":"https://www.wikidata.org/wiki/Q629","display_name":"Oxygen","level":2,"score":0.39457541704177856},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.3891748785972595},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3275800943374634},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3190380930900574},{"id":"https://openalex.org/C100544194","wikidata":"https://www.wikidata.org/wiki/Q41760","display_name":"Fermentation","level":2,"score":0.23619848489761353},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.2341914176940918},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.217928946018219},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.18817737698554993},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1121772825717926},{"id":"https://openalex.org/C42407357","wikidata":"https://www.wikidata.org/wiki/Q521","display_name":"Physiology","level":1,"score":0.08353739976882935},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08082875609397888},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2015.7367691","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2015.7367691","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.44999998807907104,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1518045910","https://openalex.org/W1756209275","https://openalex.org/W1964848254","https://openalex.org/W1969690273","https://openalex.org/W1972001730","https://openalex.org/W1972863608","https://openalex.org/W1972948824","https://openalex.org/W1978915602","https://openalex.org/W1982309495","https://openalex.org/W1996144508","https://openalex.org/W2002635898","https://openalex.org/W2006512938","https://openalex.org/W2006887615","https://openalex.org/W2018591360","https://openalex.org/W2020571033","https://openalex.org/W2025630877","https://openalex.org/W2027068064","https://openalex.org/W2029403511","https://openalex.org/W2041715023","https://openalex.org/W2042125327","https://openalex.org/W2046254395","https://openalex.org/W2048596643","https://openalex.org/W2056269112","https://openalex.org/W2057731673","https://openalex.org/W2061133366","https://openalex.org/W2067031112","https://openalex.org/W2072447727","https://openalex.org/W2077060980","https://openalex.org/W2078355959","https://openalex.org/W2079269820","https://openalex.org/W2086729080","https://openalex.org/W2087459352","https://openalex.org/W2092972772","https://openalex.org/W2107333582","https://openalex.org/W2111421616","https://openalex.org/W2115606218","https://openalex.org/W2124737787","https://openalex.org/W2126176298","https://openalex.org/W2132990040","https://openalex.org/W2134440848","https://openalex.org/W2136430686","https://openalex.org/W2143861551","https://openalex.org/W2146244728","https://openalex.org/W2147472054","https://openalex.org/W2157457604","https://openalex.org/W2167563198","https://openalex.org/W2171463471","https://openalex.org/W2394767835","https://openalex.org/W4238101851","https://openalex.org/W4245225949","https://openalex.org/W7073855572"],"related_works":["https://openalex.org/W1608758340","https://openalex.org/W2123404724","https://openalex.org/W47420346","https://openalex.org/W1505019344","https://openalex.org/W4237795480","https://openalex.org/W2143478158","https://openalex.org/W2025026414","https://openalex.org/W1993528908","https://openalex.org/W2471930122","https://openalex.org/W2198332185"],"abstract_inverted_index":{"In":[0,27],"bioindustrial":[1],"large":[2],"scale":[3],"fermenters":[4,21],"microorganisms":[5],"are":[6,95,103,146,151,180],"exposed":[7],"to":[8,24,59,75,117,133,161],"conditions":[9],"of":[10,34,48,101,112,129,157,164],"unsteady":[11],"nutrient":[12],"supply":[13],"which":[14,94],"occur":[15],"only":[16],"rarely":[17],"on":[18,86],"small":[19],"lab-scale":[20],"and":[22,37,106,143,148,173,187],"lead":[23],"economic":[25],"losses.":[26],"aerobic":[28,174],"processes":[29],"cells":[30],"face":[31],"different":[32],"availabilities":[33],"oxygen,":[35],"nitrogen":[36],"carbon":[38],"sources":[39],"along":[40],"various":[41],"directions":[42],"inside":[43],"a":[44,87,127,162,183],"fermenter.":[45],"The":[46,154,178,191],"adaptation":[47],"the":[49,53,104],"central":[50,167],"metabolism":[51],"in":[52,121,131,195],"facultative":[54],"anaerobic":[55,172],"bacterium":[56],"Escherichia":[57],"coli":[58,166],"changing":[60,118],"oxygen":[61],"concentrations":[62],"will":[63],"be":[64],"investigated.":[65],"Flux":[66],"balance":[67],"analysis":[68],"(FBA)":[69],"is":[70,84,159,176],"an":[71],"often":[72],"used":[73],"method":[74,193],"calculate":[76],"reaction":[77,92],"fluxes":[78,93],"under":[79],"given":[80],"environmental":[81],"conditions.":[82],"FBA":[83,113,130,158,185,189,192],"based":[85],"stoichiometric":[88],"model":[89,163],"with":[90,182],"possible":[91,199],"limited":[96],"by":[97],"constraints.":[98],"One":[99],"sort":[100],"constraints":[102],"lower":[105],"upper":[107],"flux":[108,149],"bounds.":[109],"Existing":[110],"methods":[111],"describe":[114],"metabolic":[115],"adaptations":[116],"environments":[119],"not":[120],"sufficient":[122],"detail.":[123],"This":[124],"work":[125],"develops":[126],"variant":[128,156],"order":[132],"close":[134],"this":[135,196],"gap.":[136],"Balance":[137],"equations":[138],"for":[139,201],"important":[140],"gene":[141,144],"transcripts":[142],"products":[145],"formulated":[147],"bounds":[150],"calculated":[152],"continuously.":[153],"described":[155,194],"applied":[160],"E.":[165],"metabolism.":[168],"A":[169],"transition":[170],"between":[171],"environment":[175],"simulated.":[177],"results":[179],"compared":[181],"conventional":[184],"approach":[186],"regulatory":[188],"(rFBA).":[190],"study":[197],"shows":[198],"targets":[200],"experimental":[202],"validation.":[203]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
