{"id":"https://openalex.org/W2129724487","doi":"https://doi.org/10.1093/bioinformatics/btu733","title":"TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm","display_name":"TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm","publication_year":2014,"publication_date":"2014-11-06","ids":{"openalex":"https://openalex.org/W2129724487","doi":"https://doi.org/10.1093/bioinformatics/btu733","mag":"2129724487","pmid":"https://pubmed.ncbi.nlm.nih.gov/25380956"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu733","doi":"https://doi.org/10.1093/bioinformatics/btu733","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu733","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/6/897/49011241/bioinformatics_31_6_897.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/6/897/49011241/bioinformatics_31_6_897.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046646488","display_name":"Jon Pey","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I170828890","display_name":"Centro de Estudios e Investigaciones T\u00e9cnicas de Gipuzkoa","ror":"https://ror.org/022wqqf69","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I170828890"]},{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]},{"id":"https://openalex.org/I80180929","display_name":"Universidad de Murcia","ror":"https://ror.org/03p3aeb86","country_code":"ES","type":"education","lineage":["https://openalex.org/I80180929"]},{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Jon Pey","raw_affiliation_strings":["1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK","institution_ids":["https://openalex.org/I170828890","https://openalex.org/I59433898","https://openalex.org/I80180929","https://openalex.org/I88155538"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Juan A. Villar","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I170828890","display_name":"Centro de Estudios e Investigaciones T\u00e9cnicas de Gipuzkoa","ror":"https://ror.org/022wqqf69","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I170828890"]},{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]},{"id":"https://openalex.org/I80180929","display_name":"Universidad de Murcia","ror":"https://ror.org/03p3aeb86","country_code":"ES","type":"education","lineage":["https://openalex.org/I80180929"]},{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Juan A. Villar","raw_affiliation_strings":["1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK","institution_ids":["https://openalex.org/I170828890","https://openalex.org/I59433898","https://openalex.org/I80180929","https://openalex.org/I88155538"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070151783","display_name":"Luis Tobalina","orcid":"https://orcid.org/0000-0002-1947-8309","observed_orcids":["https://orcid.org/0000-0002-1947-8309"]},"institutions":[{"id":"https://openalex.org/I170828890","display_name":"Centro de Estudios e Investigaciones T\u00e9cnicas de Gipuzkoa","ror":"https://ror.org/022wqqf69","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I170828890"]},{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]},{"id":"https://openalex.org/I80180929","display_name":"Universidad de Murcia","ror":"https://ror.org/03p3aeb86","country_code":"ES","type":"education","lineage":["https://openalex.org/I80180929"]},{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Luis Tobalina","raw_affiliation_strings":["1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK","institution_ids":["https://openalex.org/I170828890","https://openalex.org/I59433898","https://openalex.org/I80180929","https://openalex.org/I88155538"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062088195","display_name":"Alberto Rezola","orcid":"https://orcid.org/0000-0001-9942-5487","observed_orcids":["https://orcid.org/0000-0001-9942-5487"]},"institutions":[{"id":"https://openalex.org/I170828890","display_name":"Centro de Estudios e Investigaciones T\u00e9cnicas de Gipuzkoa","ror":"https://ror.org/022wqqf69","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I170828890"]},{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]},{"id":"https://openalex.org/I80180929","display_name":"Universidad de Murcia","ror":"https://ror.org/03p3aeb86","country_code":"ES","type":"education","lineage":["https://openalex.org/I80180929"]},{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Alberto Rezola","raw_affiliation_strings":["1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK","institution_ids":["https://openalex.org/I170828890","https://openalex.org/I59433898","https://openalex.org/I80180929","https://openalex.org/I88155538"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070286319","display_name":"Jos\u00e9 Manuel Garc\u00eda","orcid":"https://orcid.org/0000-0002-6388-2835","observed_orcids":["https://orcid.org/0000-0002-6388-2835","https://orcid.org/0000-0003-1235-3578"]},"institutions":[{"id":"https://openalex.org/I170828890","display_name":"Centro de Estudios e Investigaciones T\u00e9cnicas de Gipuzkoa","ror":"https://ror.org/022wqqf69","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I170828890"]},{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]},{"id":"https://openalex.org/I80180929","display_name":"Universidad de Murcia","ror":"https://ror.org/03p3aeb86","country_code":"ES","type":"education","lineage":["https://openalex.org/I80180929"]},{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Manuel Garc\u00eda","raw_affiliation_strings":["1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK","institution_ids":["https://openalex.org/I170828890","https://openalex.org/I59433898","https://openalex.org/I80180929","https://openalex.org/I88155538"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079112547","display_name":"J. E. Beasley","orcid":"https://orcid.org/0000-0002-4758-9970","observed_orcids":["https://orcid.org/0000-0002-4758-9970"]},"institutions":[{"id":"https://openalex.org/I170828890","display_name":"Centro de Estudios e Investigaciones T\u00e9cnicas de Gipuzkoa","ror":"https://ror.org/022wqqf69","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I170828890"]},{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]},{"id":"https://openalex.org/I80180929","display_name":"Universidad de Murcia","ror":"https://ror.org/03p3aeb86","country_code":"ES","type":"education","lineage":["https://openalex.org/I80180929"]},{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"John E. Beasley","raw_affiliation_strings":["1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK","institution_ids":["https://openalex.org/I170828890","https://openalex.org/I59433898","https://openalex.org/I80180929","https://openalex.org/I88155538"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010754980","display_name":"Francisco J. Planes","orcid":"https://orcid.org/0000-0003-1155-3105","observed_orcids":["https://orcid.org/0000-0003-1155-3105"]},"institutions":[{"id":"https://openalex.org/I170828890","display_name":"Centro de Estudios e Investigaciones T\u00e9cnicas de Gipuzkoa","ror":"https://ror.org/022wqqf69","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I170828890"]},{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]},{"id":"https://openalex.org/I80180929","display_name":"Universidad de Murcia","ror":"https://ror.org/03p3aeb86","country_code":"ES","type":"education","lineage":["https://openalex.org/I80180929"]},{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES","GB"],"is_corresponding":true,"raw_author_name":"Francisco J. Planes","raw_affiliation_strings":["1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Computer Engineering Department, School of Computer Science, POB 30100 University of Murcia, Spain and 3Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH Uxbridge, UK","institution_ids":["https://openalex.org/I170828890","https://openalex.org/I59433898","https://openalex.org/I80180929","https://openalex.org/I88155538"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5010754980"],"corresponding_institution_ids":["https://openalex.org/I170828890","https://openalex.org/I59433898","https://openalex.org/I80180929","https://openalex.org/I88155538"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.7709,"has_fulltext":true,"cited_by_count":34,"citation_normalized_percentile":{"value":0.65842277,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"31","issue":"6","first_page":"897","last_page":"904"},"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":0.0005000000237487257,"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":0.00019999999494757503,"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/elementary-flux-modes","display_name":"elementary flux modes","score":1.0},{"id":"https://openalex.org/keywords/genome-scale-metabolic-networks","display_name":"genome-scale metabolic networks","score":0.8949999809265137},{"id":"https://openalex.org/keywords/tree-search","display_name":"tree search","score":0.7519999742507935},{"id":"https://openalex.org/keywords/linear-programming","display_name":"linear programming","score":0.9599999785423279},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.9890000224113464},{"id":"https://openalex.org/keywords/gene-expression-data","display_name":"gene expression data","score":0.6840000152587891}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7351697087287903},{"id":"https://openalex.org/C2778770139","wikidata":"https://www.wikidata.org/wiki/Q1966904","display_name":"Solver","level":2,"score":0.7207396030426025},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6495434045791626},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.6277987957000732},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6236947774887085},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5959856510162354},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.537512481212616},{"id":"https://openalex.org/C6980683","wikidata":"https://www.wikidata.org/wiki/Q5531551","display_name":"Gene expression programming","level":2,"score":0.5344860553741455},{"id":"https://openalex.org/C41045048","wikidata":"https://www.wikidata.org/wiki/Q202843","display_name":"Linear programming","level":2,"score":0.5210351943969727},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.41088372468948364},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13618937134742737},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10552337765693665},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0984731912612915},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.09578779339790344},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000085","descriptor_name":"Acetates","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","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":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"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":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btu733","doi":"https://doi.org/10.1093/bioinformatics/btu733","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu733","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/6/897/49011241/bioinformatics_31_6_897.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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:25380956","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25380956","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,"listed_in":[],"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":"Journal Article"},{"id":"mag:2340716478","doi":null,"is_oa":false,"landing_page_url":"https://webs.um.es/jmgarcia/miwiki/lib/exe/fetch.php?id=pubs&cache=cache&media=bioinformatics.btu733.full.pdf","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":"doi:10.1093/bioinformatics/btu733","doi":"https://doi.org/10.1093/bioinformatics/btu733","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu733","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/6/897/49011241/bioinformatics_31_6_897.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G454699790","display_name":null,"funder_award_id":"TIN2012-31345","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6078012479","display_name":null,"funder_award_id":"BIO2013-48933","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321705","display_name":"Eusko Jaurlaritza","ror":"https://ror.org/00pz2fp31"},{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2129724487.pdf","grobid_xml":"https://content.openalex.org/works/W2129724487.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1487827847","https://openalex.org/W1560281752","https://openalex.org/W1758395617","https://openalex.org/W1971258090","https://openalex.org/W1988319444","https://openalex.org/W1996529795","https://openalex.org/W2022101765","https://openalex.org/W2023421878","https://openalex.org/W2025536812","https://openalex.org/W2034494369","https://openalex.org/W2054321273","https://openalex.org/W2063150195","https://openalex.org/W2076573047","https://openalex.org/W2077278144","https://openalex.org/W2085993965","https://openalex.org/W2091364465","https://openalex.org/W2091921469","https://openalex.org/W2093241068","https://openalex.org/W2094397891","https://openalex.org/W2100084634","https://openalex.org/W2108759241","https://openalex.org/W2110355460","https://openalex.org/W2113816218","https://openalex.org/W2116324021","https://openalex.org/W2125637976","https://openalex.org/W2126994347","https://openalex.org/W2127844534","https://openalex.org/W2129906961","https://openalex.org/W2132218677","https://openalex.org/W2137473984","https://openalex.org/W2147660556","https://openalex.org/W2148033653","https://openalex.org/W2154066017","https://openalex.org/W2158069895","https://openalex.org/W2163871517","https://openalex.org/W2170427655","https://openalex.org/W3195881304","https://openalex.org/W4240374930"],"related_works":["https://openalex.org/W2340716478","https://openalex.org/W3195881304","https://openalex.org/W2108759241","https://openalex.org/W3020383970","https://openalex.org/W2110355460","https://openalex.org/W2127844534","https://openalex.org/W2296033497","https://openalex.org/W2073599468","https://openalex.org/W2161711455","https://openalex.org/W2125187853"],"abstract_inverted_index":{"MOTIVATION:":[0],"Elementary":[1],"flux":[2],"modes":[3],"(EFMs)":[4],"analysis":[5],"constitutes":[6],"a":[7,26,30,35,43,59],"fundamental":[8],"tool":[9],"in":[10,19,47,62,80,153],"systems":[11],"biology.":[12],"However,":[13],"the":[14,55,68,76,81,101,114,125,134,158],"efficient":[15],"calculation":[16],"of":[17,45,70,103,136],"EFMs":[18,46,92],"genome-scale":[20],"metabolic":[21],"networks":[22],"(GSMNs)":[23],"is":[24,52,151],"still":[25],"challenge.":[27],"We":[28,65,117],"present":[29],"novel":[31],"algorithm":[32],"that":[33],"uses":[34],"linear":[36,160],"programming-based":[37],"tree":[38],"search":[39],"and":[40,98,113,124,155],"efficiently":[41],"enumerates":[42],"subset":[44],"GSMNs.":[48,143],"RESULTS:":[49],"Our":[50],"approach":[51,73,138],"compared":[53],"with":[54,157],"EFMEvolver":[56],"approach,":[57],"demonstrating":[58],"significant":[60],"improvement":[61],"computation":[63],"time.":[64],"also":[66,132],"validate":[67],"usefulness":[69],"our":[71,137],"new":[72],"by":[74],"studying":[75],"acetate":[77],"overflow":[78],"metabolism":[79],"Escherichia":[82],"coli":[83],"bacteria.":[84],"To":[85],"do":[86],"so,":[87],"we":[88,131],"computed":[89],"1":[90],"million":[91],"for":[93],"each":[94,104],"energetic":[95,105],"amino":[96,106],"acid":[97,107],"then":[99],"analysed":[100,133],"relevance":[102],"based":[108],"on":[109],"gene/protein":[110],"expression":[111],"data":[112],"obtained":[115],"EFMs.":[116,129],"found":[118],"good":[119],"agreement":[120],"between":[121],"previous":[122],"experiments":[123],"conclusions":[126],"reached":[127],"using":[128],"Finally,":[130],"performance":[135],"when":[139],"applied":[140],"to":[141],"large":[142],"AVAILABILITY":[144],"AND":[145],"IMPLEMENTATION:":[146],"The":[147],"stand-alone":[148],"software":[149],"TreeEFM":[150],"implemented":[152],"C++":[154],"interacts":[156],"open-source":[159],"solver":[161],"COIN-OR":[162],"Linear":[163],"program":[164],"Solver":[165],"(CLP).":[166]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
