{"id":"https://openalex.org/W2098983518","doi":"https://doi.org/10.1093/nar/gkq404","title":"BioMet Toolbox: genome-wide analysis of metabolism","display_name":"BioMet Toolbox: genome-wide analysis of metabolism","publication_year":2010,"publication_date":"2010-05-18","ids":{"openalex":"https://openalex.org/W2098983518","doi":"https://doi.org/10.1093/nar/gkq404","mag":"2098983518","pmid":"https://pubmed.ncbi.nlm.nih.gov/20483918"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkq404","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq404","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W144/3868639/gkq404.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W144/3868639/gkq404.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026743647","display_name":"Marija Cvijovi\u0107","orcid":"https://orcid.org/0000-0002-5142-5100"},"institutions":[{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"M. Cvijovic","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00f6teborg, Sweden","Department of Chemical and Biological Engineering, Chalmers University of Technology  G\u00f6teborg Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00f6teborg, Sweden","institution_ids":["https://openalex.org/I66862912"]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Chalmers University of Technology  G\u00f6teborg Sweden","institution_ids":["https://openalex.org/I66862912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070201382","display_name":"Roberto Olivares\u2010Hern\u00e1ndez","orcid":"https://orcid.org/0000-0002-8431-4052"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]},{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["DK","SE"],"is_corresponding":false,"raw_author_name":"R. Olivares-Hernandez","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099","https://openalex.org/I66862912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065184465","display_name":"Rasmus \u00c5gren","orcid":"https://orcid.org/0000-0002-9814-2191"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]},{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["DK","SE"],"is_corresponding":false,"raw_author_name":"R. Agren","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099","https://openalex.org/I66862912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5098504586","display_name":"N. Dahr","orcid":null},"institutions":[{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK","SE"],"is_corresponding":false,"raw_author_name":"N. Dahr","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099","https://openalex.org/I66862912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024111731","display_name":"Wanwipa Vongsangnak","orcid":"https://orcid.org/0000-0003-3805-0719"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]},{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["DK","SE"],"is_corresponding":false,"raw_author_name":"W. Vongsangnak","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099","https://openalex.org/I66862912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008739880","display_name":"Intawat Nookaew","orcid":"https://orcid.org/0000-0001-8901-1088"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]},{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["DK","SE"],"is_corresponding":false,"raw_author_name":"I. Nookaew","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099","https://openalex.org/I66862912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020329649","display_name":"Kiran Raosaheb Patil","orcid":"https://orcid.org/0000-0002-6166-8640"},"institutions":[{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK","SE"],"is_corresponding":false,"raw_author_name":"K. R. Patil","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099","https://openalex.org/I66862912"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083238115","display_name":"Jens Nielsen","orcid":"https://orcid.org/0000-0002-9955-6003"},"institutions":[{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK","SE"],"is_corresponding":false,"raw_author_name":"J. Nielsen","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Chalmers University of Technology, G\u00ef\u00bf\u00bdteborg, Sweden and 2Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099","https://openalex.org/I66862912"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5026743647"],"corresponding_institution_ids":["https://openalex.org/I66862912"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":7.4547,"has_fulltext":true,"cited_by_count":102,"citation_normalized_percentile":{"value":0.98062125,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"38","issue":"Web Server","first_page":"W144","last_page":"W149"},"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":0.9977999925613403,"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":0.9970999956130981,"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/biology","display_name":"Biology","score":0.6715872883796692},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6680418252944946},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5995987057685852},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.5845773816108704},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.522917628288269},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5010433197021484},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4774492383003235},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4235667586326599},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41079622507095337},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24836662411689758},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20987457036972046},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.08338785171508789}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6715872883796692},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6680418252944946},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5995987057685852},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.5845773816108704},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.522917628288269},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5010433197021484},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4774492383003235},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4235667586326599},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41079622507095337},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24836662411689758},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20987457036972046},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08338785171508789},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000431","descriptor_name":"Ethanol","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000431","descriptor_name":"Ethanol","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000431","descriptor_name":"Ethanol","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005947","descriptor_name":"Glucose","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005947","descriptor_name":"Glucose","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005947","descriptor_name":"Glucose","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/nar/gkq404","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq404","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W144/3868639/gkq404.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:20483918","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20483918","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:nar:38/suppl_2/W144","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/38/suppl_2/W144","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:publications.lib.chalmers.se:131217","is_oa":false,"landing_page_url":"http://publications.lib.chalmers.se/publication/131217-biomet-toolbox-genome-wide-analysis-of-metabolism","pdf_url":null,"source":{"id":"https://openalex.org/S4377196470","display_name":"Chalmers Publication Library (Chalmers University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66862912","host_organization_name":"Chalmers University of Technology","host_organization_lineage":["https://openalex.org/I66862912"],"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.Article.Journal.PeerReviewed"},{"id":"pmh:oai:pubmedcentral.nih.gov:2896146","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkq404","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:publications/937fc86a-f9c2-43e5-817b-30b3fbe09ac3","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/937fc86a-f9c2-43e5-817b-30b3fbe09ac3","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Cvijovic , M , Olivares Hernandez , R , Agren , R , Dahr , N , Vongsangnak , W , Nookaew , I , Patil , K R & Nielsen , J 2010 , ' BioMet Toolbox: genome-wide analysis of metabolism ' , Nucleic Acids Research , vol. 38 , pp. W144-W149 . https://doi.org/10.1093/nar/gkq404","raw_type":"article"},{"id":"pmh:oai:research.chalmers.se:131217","is_oa":false,"landing_page_url":"https://research.chalmers.se/en/publication/131217","pdf_url":null,"source":{"id":"https://openalex.org/S4306402469","display_name":"Chalmers Research (Chalmers University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66862912","host_organization_name":"Chalmers University of Technology","host_organization_lineage":["https://openalex.org/I66862912"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1093/nar/gkq404","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq404","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W144/3868639/gkq404.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2098983518.pdf","grobid_xml":"https://content.openalex.org/works/W2098983518.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1987622597","https://openalex.org/W1992306474","https://openalex.org/W1998777096","https://openalex.org/W2028561804","https://openalex.org/W2030028650","https://openalex.org/W2035600188","https://openalex.org/W2047632644","https://openalex.org/W2056735082","https://openalex.org/W2076611281","https://openalex.org/W2088933296","https://openalex.org/W2098824895","https://openalex.org/W2099735525","https://openalex.org/W2110384600","https://openalex.org/W2112811019","https://openalex.org/W2113329733","https://openalex.org/W2123698848","https://openalex.org/W2128572161","https://openalex.org/W2130410032","https://openalex.org/W2147472054","https://openalex.org/W2150908245","https://openalex.org/W2158069895","https://openalex.org/W2159675211","https://openalex.org/W2162471251","https://openalex.org/W2163855763","https://openalex.org/W2165554064","https://openalex.org/W2168846334","https://openalex.org/W4238101851"],"related_works":["https://openalex.org/W1504020891","https://openalex.org/W2133150343","https://openalex.org/W2072067873","https://openalex.org/W2047632644","https://openalex.org/W2031492751","https://openalex.org/W3033588432","https://openalex.org/W2147102947","https://openalex.org/W2075919068","https://openalex.org/W1989168955","https://openalex.org/W235738631"],"abstract_inverted_index":{"The":[0,100],"rapid":[1],"progress":[2],"of":[3,20,31,42,47,55,60,87,96,185],"molecular":[4],"biology":[5],"tools":[6,147],"for":[7,27,81,85,151,163,181],"directed":[8],"genetic":[9],"modifications,":[10],"accurate":[11],"quantitative":[12],"experimental":[13],"approaches,":[14],"high-throughput":[15,152],"measurements,":[16],"together":[17],"with":[18],"development":[19],"genome":[21],"sequencing":[22],"has":[23,51],"made":[24,52],"the":[25,53,75,94,173,183],"foundation":[26],"a":[28,78,178],"new":[29],"area":[30],"metabolic":[32,38,56,61,98,123,187],"engineering":[33],"that":[34],"is":[35,191],"driven":[36],"by":[37,45,126],"models.":[39,99],"Systematic":[40],"analysis":[41,83],"biological":[43],"processes":[44],"means":[46],"modelling":[48],"and":[49,58,84,89,122,132,156,168],"simulations":[50,112],"identification":[54],"networks":[57],"prediction":[59],"capabilities":[62,95,184],"under":[63],"different":[64],"conditions":[65],"possible.":[66],"For":[67],"facilitating":[68],"such":[69],"systemic":[70],"analysis,":[71],"we":[72],"have":[73],"developed":[74],"BioMet":[76,101,174,189],"Toolbox,":[77],"web-based":[79],"resource":[80,180],"stoichiometric":[82],"integration":[86],"transcriptome":[88],"interactome":[90],"data,":[91],"thereby":[92],"exploiting":[93],"genome-scale":[97],"Toolbox":[102,175,190],"provides":[103],"an":[104],"effective":[105],"user-friendly":[106],"way":[107],"to":[108],"perform":[109],"linear":[110],"programming":[111],"towards":[113],"maximized":[114],"or":[115,136],"minimized":[116],"growth":[117],"rates,":[118],"substrate":[119],"uptake":[120],"rates":[121,125],"production":[124],"detecting":[127],"relevant":[128],"fluxes,":[129],"simulate":[130],"single":[131],"double":[133],"gene":[134],"deletions":[135],"detect":[137],"metabolites":[138],"around":[139],"which":[140],"major":[141],"transcriptional":[142],"changes":[143],"are":[144,170],"concentrated.":[145],"These":[146],"can":[148],"be":[149],"used":[150],"in":[153],"silico":[154],"screening":[155],"allows":[157],"fully":[158],"standardized":[159],"simulations.":[160],"Model":[161],"files":[162],"various":[164],"model":[165],"organisms":[166],"(fungi":[167],"bacteria)":[169],"included.":[171],"Overall,":[172],"serves":[176],"as":[177],"valuable":[179],"exploring":[182],"these":[186],"networks.":[188],"freely":[192],"available":[193],"at":[194],"www.sysbio.se/BioMet/.":[195]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":19},{"year":2013,"cited_by_count":21},{"year":2012,"cited_by_count":20}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}