{"id":"https://openalex.org/W2513890216","doi":"https://doi.org/10.1093/bioinformatics/btw555","title":"Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models","display_name":"Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models","publication_year":2016,"publication_date":"2016-08-24","ids":{"openalex":"https://openalex.org/W2513890216","doi":"https://doi.org/10.1093/bioinformatics/btw555","mag":"2513890216"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw555","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw555","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/24/3807/16921239/btw555.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","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/24/3807/16921239/btw555.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067817255","display_name":"Pedro A. Saa","orcid":"https://orcid.org/0000-0002-1659-9041"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Pedro A. Saa","raw_affiliation_strings":["Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Rds (Bldg 75), Australia"],"affiliations":[{"raw_affiliation_string":"Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Rds (Bldg 75), Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061172047","display_name":"Lars K. Nielsen","orcid":"https://orcid.org/0000-0001-8191-3511"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Lars K. Nielsen","raw_affiliation_strings":["Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Rds (Bldg 75), Australia"],"affiliations":[{"raw_affiliation_string":"Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Rds (Bldg 75), Australia","institution_ids":["https://openalex.org/I165143802"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5061172047"],"corresponding_institution_ids":["https://openalex.org/I165143802"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.8644,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.85867006,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"32","issue":"24","first_page":"3807","last_page":"3814"},"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":0.992900013923645,"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/T11053","display_name":"Process Optimization and Integration","score":0.9911999702453613,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems 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/algorithm","display_name":"Algorithm","score":0.6612453460693359},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6131930947303772},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.49718764424324036},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.34151965379714966},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.12296754121780396}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6612453460693359},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6131930947303772},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.49718764424324036},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.34151965379714966},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.12296754121780396},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw555","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw555","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/24/3807/16921239/btw555.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:open-archive.highwire.org:bioinfo:32/24/3807","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/24/3807","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:5167067","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5167067","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw555","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw555","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/24/3807/16921239/btw555.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":[{"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions","score":0.5699999928474426}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2513890216.pdf","grobid_xml":"https://content.openalex.org/works/W2513890216.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1484664627","https://openalex.org/W1616556810","https://openalex.org/W1758395617","https://openalex.org/W1966497610","https://openalex.org/W1967717294","https://openalex.org/W1988136571","https://openalex.org/W1994134392","https://openalex.org/W2003495172","https://openalex.org/W2008115217","https://openalex.org/W2008875008","https://openalex.org/W2041715023","https://openalex.org/W2044935306","https://openalex.org/W2059546521","https://openalex.org/W2076262841","https://openalex.org/W2077149408","https://openalex.org/W2078355959","https://openalex.org/W2082382448","https://openalex.org/W2104108767","https://openalex.org/W2105657635","https://openalex.org/W2106106289","https://openalex.org/W2111381495","https://openalex.org/W2115159982","https://openalex.org/W2117474489","https://openalex.org/W2117509624","https://openalex.org/W2124737787","https://openalex.org/W2128014041","https://openalex.org/W2128572161","https://openalex.org/W2128776645","https://openalex.org/W2133510724","https://openalex.org/W2133556195","https://openalex.org/W2141776893","https://openalex.org/W2141916481","https://openalex.org/W2148174909","https://openalex.org/W2152456759","https://openalex.org/W2153373497","https://openalex.org/W2157635835","https://openalex.org/W2162673839","https://openalex.org/W2165178932","https://openalex.org/W2169527381","https://openalex.org/W2202347610","https://openalex.org/W2345887956","https://openalex.org/W3104005457","https://openalex.org/W6636604668","https://openalex.org/W6682349039"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829"],"abstract_inverted_index":{"Motivation:":[0],"Computation":[1],"of":[2,31,38,81,139,150,159,177],"steady-state":[3],"flux":[4,14,33,50,182],"solutions":[5],"in":[6,128,143,162],"large":[7,67,189],"metabolic":[8,68,130],"models":[9,131],"is":[10,35,52,63,168,200,217],"routinely":[11],"performed":[12],"using":[13,44],"balance":[15],"analysis":[16,138],"based":[17],"on":[18,109],"a":[19,53,73,97,113],"simple":[20,172],"LP":[21],"(Linear":[22],"Programming)":[23,60],"formulation.":[24],"A":[25],"minimal":[26],"requirement":[27],"for":[28,66,154,174,196,203],"thermodynamic":[29],"feasibility":[30],"the":[32,36,79,82,125,140,144,155,163,220],"solution":[34],"absence":[37],"internal":[39],"loops,":[40],"which":[41,62],"are":[42,228],"enforced":[43],"\u2018loopless":[45],"constraints\u2019.":[46],"The":[47,93],"resulting":[48],"loopless":[49,84,134,181],"problem":[51,85],"substantially":[54],"harder":[55],"MILP":[56,91],"(Mixed":[57],"Integer":[58],"Linear":[59],"problem,":[61],"computationally":[64],"expensive":[65],"models.":[69],"Results:":[70],"We":[71],"developed":[72],"pre-processing":[74,94],"algorithm":[75,173],"that":[76],"significantly":[77],"reduces":[78],"size":[80],"original":[83],"into":[86],"an":[87,169],"easier":[88],"and":[89,171,185,192],"equivalent":[90],"problem.":[92],"step":[95],"employs":[96],"fast":[98],"matrix":[99,117,147],"sparsification":[100],"algorithm\u2014Fast-":[101],"sparse":[102],"null-space":[103],"pursuit":[104],"(SNP)\u2014inspired":[105],"by":[106],"recent":[107],"results":[108],"SNP.":[110],"By":[111],"finding":[112],"reduced":[114,145],"feasible":[115,184],"\u2018loop-law\u2019":[116],"subject":[118],"to":[119],"known":[120],"directionalities,":[121],"Fast-SNP":[122,167],"considerably":[123],"improves":[124],"computational":[126],"efficiency":[127],"several":[129],"running":[132],"different":[133],"optimization":[135,183],"problems.":[136],"Furthermore,":[137],"topology":[141],"encoded":[142],"loop":[146],"enabled":[148],"identification":[149],"key":[151],"directional":[152],"constraints":[153],"potential":[156],"permanent":[157],"elimination":[158],"infeasible":[160],"loops":[161],"underlying":[164],"model.":[165],"Overall,":[166],"effective":[170],"efficient":[175],"formulation":[176],"loop-law":[178],"constraints,":[179],"making":[180],"numerically":[186],"tractable":[187],"at":[188,205,230],"scale.":[190],"Availability":[191],"Implementation:":[193],"Source":[194],"code":[195],"MATLAB":[197],"including":[198],"examples":[199],"freely":[201],"available":[202,229],"download":[204],"http://www.aibn.uq.edu.au/cssb-resources":[206],"under":[207],"Software.":[208],"Optimization":[209],"uses":[210],"Gurobi,":[211],"CPLEX":[212],"or":[213],"GLPK":[214],"(the":[215],"latter":[216],"included":[218],"with":[219],"algorithm).":[221],"Contact:":[222],"lars.nielsen@uq.edu.au":[223],"Supplementary":[224,226],"information:":[225],"data":[227],"Bioinformatics":[231],"online.":[232]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}