{"id":"https://openalex.org/W2110355460","doi":"https://doi.org/10.1093/bioinformatics/btn401","title":"Large-scale computation of elementary flux modes with bit pattern trees","display_name":"Large-scale computation of elementary flux modes with bit pattern trees","publication_year":2008,"publication_date":"2008-08-01","ids":{"openalex":"https://openalex.org/W2110355460","doi":"https://doi.org/10.1093/bioinformatics/btn401","mag":"2110355460"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn401","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn401","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/19/2229/49050673/bioinformatics_24_19_2229.pdf","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","datacite","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/19/2229/49050673/bioinformatics_24_19_2229.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007942499","display_name":"Marco Terzer","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Marco Terzer","raw_affiliation_strings":["Institute of Computational Science and Swiss Institute of Bioinformatics, ETH Zurich, 8092 Zurich, Switzerland","Institute of Computational Science and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Institute of Computational Science and Swiss Institute of Bioinformatics, ETH Zurich, 8092 Zurich, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I35440088"]},{"raw_affiliation_string":"Institute of Computational Science and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113879544","display_name":"J\u00f6rg Stelling","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"J\u00f6rg Stelling","raw_affiliation_strings":["Institute of Computational Science and Swiss Institute of Bioinformatics, ETH Zurich, 8092 Zurich, Switzerland","Institute of Computational Science and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Institute of Computational Science and Swiss Institute of Bioinformatics, ETH Zurich, 8092 Zurich, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I35440088"]},{"raw_affiliation_string":"Institute of Computational Science and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5007942499"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I35440088"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":7.8834,"has_fulltext":false,"cited_by_count":327,"citation_normalized_percentile":{"value":0.98155444,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"24","issue":"19","first_page":"2229","last_page":"2235"},"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9969000220298767,"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"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9944999814033508,"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/computation","display_name":"Computation","score":0.7448031902313232},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.5738195180892944},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5682978630065918},{"id":"https://openalex.org/keywords/enumeration","display_name":"Enumeration","score":0.5261587500572205},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5170679688453674},{"id":"https://openalex.org/keywords/rank","display_name":"Rank (graph theory)","score":0.4853898286819458},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3303598165512085},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.29951682686805725},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.21784377098083496},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.14346802234649658},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.12846413254737854},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09629964828491211}],"concepts":[{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.7448031902313232},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.5738195180892944},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5682978630065918},{"id":"https://openalex.org/C156340839","wikidata":"https://www.wikidata.org/wiki/Q2704791","display_name":"Enumeration","level":2,"score":0.5261587500572205},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5170679688453674},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.4853898286819458},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3303598165512085},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.29951682686805725},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.21784377098083496},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.14346802234649658},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.12846413254737854},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09629964828491211}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btn401","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn401","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/19/2229/49050673/bioinformatics_24_19_2229.pdf","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":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/413523","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/413523","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics, 24 (19)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:doc.rero.ch:289970","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400148","display_name":"reroDoc Digital Library","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"doi:10.3929/ethz-b-000413523","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000413523","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn401","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn401","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/19/2229/49050673/bioinformatics_24_19_2229.pdf","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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2110355460.pdf","grobid_xml":"https://content.openalex.org/works/W2110355460.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1526262508","https://openalex.org/W1621975707","https://openalex.org/W1841771524","https://openalex.org/W1976672440","https://openalex.org/W1987198680","https://openalex.org/W1996529795","https://openalex.org/W2046760236","https://openalex.org/W2065432632","https://openalex.org/W2070020713","https://openalex.org/W2090846925","https://openalex.org/W2094399313","https://openalex.org/W2102164505","https://openalex.org/W2111421616","https://openalex.org/W2165558283","https://openalex.org/W2170576111","https://openalex.org/W2492353954","https://openalex.org/W2493111772","https://openalex.org/W2500724408","https://openalex.org/W2561675875","https://openalex.org/W4233442745","https://openalex.org/W6631643967","https://openalex.org/W6638758801","https://openalex.org/W6723406818"],"related_works":["https://openalex.org/W108845024","https://openalex.org/W57712237","https://openalex.org/W2578985712","https://openalex.org/W4300125793","https://openalex.org/W2406961474","https://openalex.org/W2143566611","https://openalex.org/W2013740965","https://openalex.org/W588267724","https://openalex.org/W2952598754","https://openalex.org/W2026779193"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Elementary":[2],"flux":[3,35,204],"modes":[4,29,195,238],"(EFMs)\u2014non-decomposable":[5],"minimal":[6],"pathways\u2014are":[7],"commonly":[8],"accepted":[9],"tools":[10,268],"for":[11,115,144,152,170,215,222],"metabolic":[12,73,225],"network":[13,23,182,226],"analysis":[14,71,233],"under":[15],"steady":[16],"state":[17],"conditions.":[18],"Valid":[19],"states":[20],"of":[21,27,56,72,88,101,119,126,164,183,200,218,227,237,256],"the":[22,69,102,192,201,216,235,267,274],"are":[24,176,271,284],"linear":[25],"superpositions":[26],"elementary":[28],"shaping":[30],"a":[31,39,61,106,135,148,179,223],"polyhedral":[32,57],"cone":[33],"(the":[34],"cone),":[36],"which":[37,156],"is":[38,48,60,97,122,140,206,262],"well-studied":[40],"convex":[41],"set":[42],"in":[43,187,203,248,266],"computational":[44],"geometry.":[45],"Computing":[46],"EFMs":[47,214],"thus":[49],"basically":[50],"equivalent":[51],"to":[52,178],"extreme":[53,91,120],"ray":[54],"enumeration":[55,109],"cones.":[58],"This":[59],"combinatorial":[62],"problem":[63],"with":[64,111,250],"poorly":[65],"scaling":[66],"algorithms,":[67],"preventing":[68],"large-scale":[70,86,231],"networks":[74],"so":[75],"far.":[76],"Results:":[77],"Here,":[78],"we":[79,133,210],"introduce":[80,134],"new":[81,107],"algorithmic":[82],"concepts":[83],"that":[84,139,239],"enable":[85],"computation":[87,146],"EFMs.":[89,190],"Distinguishing":[90],"rays":[92],"from":[93,273],"normal":[94],"(composite)":[95],"vectors":[96],"one":[98,124],"critical":[99],"aspect":[100],"algorithm.":[103],"We":[104],"present":[105],"recursive":[108],"strategy":[110],"bit":[112],"pattern":[113],"trees":[114],"adjacent":[116],"rays\u2014the":[117],"ancestors":[118],"rays\u2014that":[121],"roughly":[123],"order":[125],"magnitude":[127],"faster":[128],"than":[129],"previous":[130],"methods.":[131],"Additionally,":[132],"rank":[136,154],"updating":[137],"method":[138,151],"particularly":[141],"well":[142],"suited":[143],"parallel":[145],"and":[147,254],"residue":[149],"arithmetic":[150],"matrix":[153],"computations,":[155],"circumvents":[157],"potential":[158],"numerical":[159],"instability":[160],"problems.":[161],"Multi-core":[162],"architectures":[163],"modern":[165],"CPUs":[166],"can":[167],"be":[168],"exploited":[169],"further":[171],"performance":[172],"improvements.":[173],"The":[174],"methods":[175],"applied":[177],"central":[180],"metabolism":[181],"Escherichia":[184],"coli,":[185],"resulting":[186],"\u224826":[188],"Mio.":[189,213],"Within":[191],"top":[193],"2%":[194],"considering":[196],"biomass":[197],"production,":[198],"most":[199],"gain":[202],"variability":[205],"achieved.":[207],"In":[208],"addition,":[209],"compute":[211],"\u22485":[212],"production":[217],"non-essential":[219],"amino":[220,242],"acids":[221,243],"genome-scale":[224],"Helicobacter":[228],"pylori.":[229],"Only":[230],"EFM":[232],"reveals":[234],"&amp;gt;85%":[236],"generate":[240],"several":[241],"simultaneously.":[244],"Availability:":[245],"An":[246],"implementation":[247],"Java,":[249],"integration":[251],"into":[252],"MATLAB":[253],"support":[255],"various":[257],"input":[258],"formats,":[259],"including":[260],"SBML,":[261],"available":[263,272,285],"at":[264,286],"http://www.csb.ethz.ch":[265],"section;":[269],"sources":[270],"authors":[275],"upon":[276],"request.":[277],"Contact:":[278],"joerg.stelling@inf.ethz.ch":[279],"Supplementary":[280,282],"information:":[281],"data":[283],"Bioinformatics":[287],"online.":[288]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":18},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":27},{"year":2017,"cited_by_count":17},{"year":2016,"cited_by_count":20},{"year":2015,"cited_by_count":26},{"year":2014,"cited_by_count":31},{"year":2013,"cited_by_count":30},{"year":2012,"cited_by_count":27}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
