{"id":"https://openalex.org/W2157125182","doi":"https://doi.org/10.1093/bioinformatics/btv111","title":"tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks","display_name":"tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks","publication_year":2015,"publication_date":"2015-02-19","ids":{"openalex":"https://openalex.org/W2157125182","doi":"https://doi.org/10.1093/bioinformatics/btv111","mag":"2157125182","pmid":"https://pubmed.ncbi.nlm.nih.gov/25701571"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv111","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv111","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"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/A5015293905","display_name":"Matthias P. Gerstl","orcid":"https://orcid.org/0000-0001-5331-5776"},"institutions":[{"id":"https://openalex.org/I4210138243","display_name":"Austrian Centre of Industrial Biotechnology (Austria)","ror":"https://ror.org/03dm7dd93","country_code":"AT","type":"company","lineage":["https://openalex.org/I4210138243"]},{"id":"https://openalex.org/I92869138","display_name":"BOKU University","ror":"https://ror.org/057ff4y42","country_code":"AT","type":"education","lineage":["https://openalex.org/I92869138"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Matthias P. Gerstl","raw_affiliation_strings":["1 Austrian Centre of Industrial Biotechnology, Vienna, Austria and 2Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Austrian Centre of Industrial Biotechnology, Vienna, Austria and 2Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria","institution_ids":["https://openalex.org/I4210138243","https://openalex.org/I92869138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104351663","display_name":"Christian Jungreuthmayer","orcid":null},"institutions":[{"id":"https://openalex.org/I4210138243","display_name":"Austrian Centre of Industrial Biotechnology (Austria)","ror":"https://ror.org/03dm7dd93","country_code":"AT","type":"company","lineage":["https://openalex.org/I4210138243"]},{"id":"https://openalex.org/I92869138","display_name":"BOKU University","ror":"https://ror.org/057ff4y42","country_code":"AT","type":"education","lineage":["https://openalex.org/I92869138"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Christian Jungreuthmayer","raw_affiliation_strings":["1 Austrian Centre of Industrial Biotechnology, Vienna, Austria and 2Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Austrian Centre of Industrial Biotechnology, Vienna, Austria and 2Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria","institution_ids":["https://openalex.org/I4210138243","https://openalex.org/I92869138"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053663717","display_name":"J\u00fcrgen Zanghellini","orcid":"https://orcid.org/0000-0002-1964-2455"},"institutions":[{"id":"https://openalex.org/I4210138243","display_name":"Austrian Centre of Industrial Biotechnology (Austria)","ror":"https://ror.org/03dm7dd93","country_code":"AT","type":"company","lineage":["https://openalex.org/I4210138243"]},{"id":"https://openalex.org/I92869138","display_name":"BOKU University","ror":"https://ror.org/057ff4y42","country_code":"AT","type":"education","lineage":["https://openalex.org/I92869138"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"J\u00fcrgen Zanghellini","raw_affiliation_strings":["1 Austrian Centre of Industrial Biotechnology, Vienna, Austria and 2Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Austrian Centre of Industrial Biotechnology, Vienna, Austria and 2Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria","institution_ids":["https://openalex.org/I4210138243","https://openalex.org/I92869138"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5053663717","https://openalex.org/A5104351663"],"corresponding_institution_ids":["https://openalex.org/I4210138243","https://openalex.org/I92869138"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.8183,"has_fulltext":false,"cited_by_count":52,"citation_normalized_percentile":{"value":0.95775837,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"31","issue":"13","first_page":"2232","last_page":"2234"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9799000024795532,"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":0.9799000024795532,"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":0.00430000014603138,"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/T12643","display_name":"Sustainability and Ecological Systems Analysis","score":0.002899999963119626,"subfield":{"id":"https://openalex.org/subfields/2305","display_name":"Environmental Engineering"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.6016719341278076},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.594685971736908},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4579440951347351},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4285608232021332},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.22643664479255676},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.21177321672439575}],"concepts":[{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.6016719341278076},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.594685971736908},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4579440951347351},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4285608232021332},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.22643664479255676},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.21177321672439575},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv111","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv111","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25701571","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25701571","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/13/2232","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/13/2232","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320323033","display_name":"Bundesministerium f\u00fcr Verkehr, Innovation und Technologie","ror":"https://ror.org/04marky29"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W399385914","https://openalex.org/W1487827847","https://openalex.org/W1526262508","https://openalex.org/W1684307508","https://openalex.org/W1984378303","https://openalex.org/W1996893186","https://openalex.org/W2004235182","https://openalex.org/W2015816943","https://openalex.org/W2041715023","https://openalex.org/W2099039198","https://openalex.org/W2103795997","https://openalex.org/W2110355460","https://openalex.org/W2115038235","https://openalex.org/W2116976883","https://openalex.org/W2127844534","https://openalex.org/W2147660556","https://openalex.org/W2160259320","https://openalex.org/W2482371382","https://openalex.org/W6631643967"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2149263892"],"abstract_inverted_index":{"UNLABELLED:":[0],":":[1,113],"Elementary":[2],"flux":[3],"modes":[4],"(EFMs)":[5],"are":[6,24,29,121],"important":[7],"structural":[8],"tools":[9,28],"for":[10],"the":[11,33,44,49,69,78,87,91],"analysis":[12,40],"of":[13,51,72],"metabolic":[14,58,106],"networks.":[15,107],"It":[16],"is":[17],"known":[18],"that":[19],"many":[20],"topologically":[21],"feasible":[22,74],"EFMs":[23,75],"biologically":[25],"irrelevant.":[26],"Therefore,":[27],"needed":[30],"to":[31,47,100],"find":[32],"relevant":[34],"ones.":[35],"We":[36],"present":[37],"thermodynamic":[38],"tEFM":[39],"(tEFMA)":[41],"which":[42],"uses":[43],"cellular":[45],"metabolome":[46],"avoid":[48],"enumeration":[50],"thermodynamically":[52,73],"infeasible":[53],"EFMs.":[54],"Specifically,":[55],"given":[56],"a":[57,61,97],"network":[59],"and":[60,90],"not":[62],"necessarily":[63],"complete":[64],"metabolome,":[65],"tEFMA":[66,84,95],"efficiently":[67],"returns":[68],"full":[70],"set":[71],"consistent":[76],"with":[77,81],"metabolome.":[79],"Compared":[80],"standard":[82],"approaches,":[83],"strongly":[85],"reduces":[86],"memory":[88],"consumption":[89],"overall":[92],"runtime.":[93],"Thus":[94],"provides":[96],"new":[98],"way":[99],"analyze":[101],"unbiasedly":[102],"hitherto":[103],"inaccessible":[104],"large-scale":[105],"AVAILABILITY":[108],"AND":[109],"IMPLEMENTATION:":[110],"https://github.com/mpgerstl/tEFMA":[111],"CONTACT:":[112],"christian.jungreuthmayer@boku.ac.at":[114],"or":[115],"juergen.zanghellini@boku.ac.at":[116],"SUPPLEMENTARY":[117],"INFORMATION:":[118],"Supplementary":[119],"data":[120],"available":[122],"at":[123],"Bioinformatics":[124],"online.":[125]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":18},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
