{"id":"https://openalex.org/W2292492942","doi":"https://doi.org/10.1186/s12859-016-0912-1","title":"Multiplex methods provide effective integration of multi-omic data in genome-scale models","display_name":"Multiplex methods provide effective integration of multi-omic data in genome-scale models","publication_year":2016,"publication_date":"2016-02-01","ids":{"openalex":"https://openalex.org/W2292492942","doi":"https://doi.org/10.1186/s12859-016-0912-1","mag":"2292492942","pmid":"https://pubmed.ncbi.nlm.nih.gov/26961692"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-0912-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-0912-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-0912-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-0912-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021786062","display_name":"Claudio Angione","orcid":"https://orcid.org/0000-0002-3140-7909"},"institutions":[{"id":"https://openalex.org/I874055015","display_name":"Teesside University","ror":"https://ror.org/03z28gk75","country_code":"GB","type":"education","lineage":["https://openalex.org/I874055015"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Claudio Angione","raw_affiliation_strings":["School of Computing - Teesside University, Middlesbrough, UK. c.angione@tees.ac.uk","School of Computing - Teesside University, Middlesbrough, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing - Teesside University, Middlesbrough, UK. c.angione@tees.ac.uk","institution_ids":[]},{"raw_affiliation_string":"School of Computing - Teesside University, Middlesbrough, UK","institution_ids":["https://openalex.org/I874055015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009674962","display_name":"Max Conway","orcid":"https://orcid.org/0000-0001-8913-0909"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Max Conway","raw_affiliation_strings":["Computer Laboratory - University of Cambridge, Cambridge, UK. max.conway@cl.cam.ac.uk","Computer Laboratory - University of Cambridge, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Laboratory - University of Cambridge, Cambridge, UK. max.conway@cl.cam.ac.uk","institution_ids":[]},{"raw_affiliation_string":"Computer Laboratory - University of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056748708","display_name":"P\u00edetro Li\u00f3","orcid":"https://orcid.org/0000-0002-0540-5053"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Pietro Li\u00f3","raw_affiliation_strings":["Computer Laboratory - University of Cambridge, Cambridge, UK. pietro.lio@cl.cam.ac.uk","Computer Laboratory - University of Cambridge, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Laboratory - University of Cambridge, Cambridge, UK. pietro.lio@cl.cam.ac.uk","institution_ids":[]},{"raw_affiliation_string":"Computer Laboratory - University of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5021786062"],"corresponding_institution_ids":["https://openalex.org/I874055015"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":6.6149,"has_fulltext":true,"cited_by_count":58,"citation_normalized_percentile":{"value":0.97129835,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"17","issue":"S4","first_page":"83","last_page":"83"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.7480000257492065,"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":0.7480000257492065,"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":0.1331000030040741,"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":0.02370000071823597,"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/computational-biology","display_name":"Computational biology","score":0.5914022326469421},{"id":"https://openalex.org/keywords/multiplex","display_name":"Multiplex","score":0.5109747648239136},{"id":"https://openalex.org/keywords/compendium","display_name":"Compendium","score":0.5103585124015808},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.5044118165969849},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46385738253593445},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.449358195066452},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44935253262519836},{"id":"https://openalex.org/keywords/adaptation","display_name":"Adaptation (eye)","score":0.42355769872665405},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.4125054180622101},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4006957709789276},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.26493537425994873},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22079136967658997},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18026894330978394}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5914022326469421},{"id":"https://openalex.org/C2781188995","wikidata":"https://www.wikidata.org/wiki/Q6934982","display_name":"Multiplex","level":2,"score":0.5109747648239136},{"id":"https://openalex.org/C2778473407","wikidata":"https://www.wikidata.org/wiki/Q1459574","display_name":"Compendium","level":2,"score":0.5103585124015808},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.5044118165969849},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46385738253593445},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.449358195066452},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44935253262519836},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.42355769872665405},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.4125054180622101},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4006957709789276},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26493537425994873},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22079136967658997},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18026894330978394},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000222","descriptor_name":"Adaptation, Physiological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000222","descriptor_name":"Adaptation, Physiological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000222","descriptor_name":"Adaptation, Physiological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000222","descriptor_name":"Adaptation, Physiological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"D016680","descriptor_name":"Genome, Bacterial","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":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","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":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","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":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-016-0912-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-0912-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-0912-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26961692","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26961692","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:https://research.tees.ac.uk/ws/oai:openaire_cris_publications/bc188c68-6579-4948-8bba-7a4674a7a738","is_oa":true,"landing_page_url":"https://research.tees.ac.uk/en/publications/bc188c68-6579-4948-8bba-7a4674a7a738","pdf_url":null,"source":{"id":"https://openalex.org/S4306401198","display_name":"TeesRep (Teesside University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I874055015","host_organization_name":"Teesside University","host_organization_lineage":["https://openalex.org/I874055015"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Angione , C , Conway , M & Li\u00f3 , P 2016 , ' Multiplex methods provide effective integration of multi-omic data in genome-scale models ' , BMC Bioinformatics , pp. - . https://doi.org/10.1186/s12859-016-0912-1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4896256","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4896256","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:tees.openrepository.com:10149/600706","is_oa":true,"landing_page_url":"http://hdl.handle.net/10149/600706","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/s12859-016-0912-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-0912-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-0912-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.7799999713897705}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2292492942.pdf","grobid_xml":"https://content.openalex.org/works/W2292492942.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1158629448","https://openalex.org/W1896739462","https://openalex.org/W1942714176","https://openalex.org/W1964564448","https://openalex.org/W1987219048","https://openalex.org/W1990406293","https://openalex.org/W1994124536","https://openalex.org/W2007057676","https://openalex.org/W2009556803","https://openalex.org/W2010295152","https://openalex.org/W2011545430","https://openalex.org/W2029158589","https://openalex.org/W2031487654","https://openalex.org/W2031681107","https://openalex.org/W2041670640","https://openalex.org/W2042839452","https://openalex.org/W2044525257","https://openalex.org/W2044935306","https://openalex.org/W2045921664","https://openalex.org/W2056756011","https://openalex.org/W2060787728","https://openalex.org/W2061958715","https://openalex.org/W2073348267","https://openalex.org/W2075721728","https://openalex.org/W2085648335","https://openalex.org/W2094701453","https://openalex.org/W2098005762","https://openalex.org/W2104187897","https://openalex.org/W2105717378","https://openalex.org/W2109563298","https://openalex.org/W2117760818","https://openalex.org/W2119686333","https://openalex.org/W2120845681","https://openalex.org/W2124737787","https://openalex.org/W2124962680","https://openalex.org/W2127931938","https://openalex.org/W2130871092","https://openalex.org/W2151023149","https://openalex.org/W2157084984","https://openalex.org/W2158714788","https://openalex.org/W2159614925","https://openalex.org/W2168621245","https://openalex.org/W2168910023","https://openalex.org/W2285763735","https://openalex.org/W2397343268","https://openalex.org/W3103589660","https://openalex.org/W4235508806","https://openalex.org/W4252676770"],"related_works":["https://openalex.org/W2164288075","https://openalex.org/W2384167225","https://openalex.org/W2113182373","https://openalex.org/W4255195499","https://openalex.org/W2088998312","https://openalex.org/W2119005669","https://openalex.org/W4250965783","https://openalex.org/W2481793228","https://openalex.org/W2403214044","https://openalex.org/W2379604225"],"abstract_inverted_index":{"BACKGROUND:":[0],"Genomic,":[1],"transcriptomic,":[2],"and":[3,89,92,131,155,180,193,221],"metabolic":[4],"variations":[5],"shape":[6],"the":[7,18,22,25,34,46,59,65,109,115,138,156,206,209,219],"complex":[8],"adaptation":[9],"landscape":[10],"of":[11,27,48,54,79,87,102,108,114,137,153,173,197,208,211,226],"bacteria":[12],"to":[13,99,168,191,217,222],"varying":[14],"environmental":[15,38,55],"conditions.":[16],"Elucidating":[17],"genotype-phenotype":[19],"relation":[20],"paves":[21],"way":[23],"for":[24,32,231,243],"prediction":[26],"such":[28],"effects,":[29],"but":[30],"methods":[31],"characterizing":[33],"relationship":[35],"between":[36,125],"multiple":[37,60],"factors":[39],"are":[40,123],"still":[41],"lacking.":[42],"Here,":[43],"we":[44,74,93],"tackle":[45],"problem":[47],"extracting":[49],"network-level":[50],"information":[51,204],"from":[52],"collections":[53,196],"conditions,":[56,126],"by":[57,105,129],"integrating":[58,106],"omic":[61,161],"levels":[62],"at":[63,249],"which":[64,232],"bacterial":[66],"response":[67],"is":[68,235,246],"measured.":[69],"RESULTS:":[70],"To":[71],"this":[72,165],"end,":[73],"model":[75],"a":[76,83,95,118,150],"large":[77],"compendium":[78],"growth":[80,103],"conditions":[81,104,154,198,213],"as":[82,127],"multiplex":[84,110],"network":[85,97,116,152,240],"consisting":[86],"transcriptomic":[88,132],"fluxomic":[90],"layers,":[91],"propose":[94],"multi-omic":[96,166,203],"approach":[98],"infer":[100,218],"similarity":[101],"layers":[107,136,144],"network.":[111,139],"Each":[112],"node":[113],"represents":[117],"single":[119],"condition,":[120],"while":[121],"edges":[122],"similarities":[124,158],"measured":[128],"phenotypic":[130],"properties":[133],"on":[134,205],"different":[135,195,200],"We":[140,163],"then":[141],"fuse":[142],"these":[143],"into":[145],"one":[146],"network,":[147],"therefore":[148],"capturing":[149],"global":[151],"associated":[157],"across":[159],"two":[160],"levels.":[162],"apply":[164],"fusion":[167,241],"an":[169],"updated":[170],"genome-scale":[171,244],"reconstruction":[172],"Escherichia":[174],"coli":[175],"that":[176],"includes":[177],"underground":[178],"metabolism":[179],"new":[181],"gene-protein-reaction":[182],"associations.":[183],"CONCLUSIONS:":[184],"Our":[185,238],"method":[186,242],"can":[187],"be":[188],"readily":[189],"used":[190],"evaluate":[192],"cross-compare":[194],"among":[199],"species.":[201],"Acquiring":[202],"topology":[207],"space":[210],"experimental":[212,233],"makes":[214],"it":[215],"possible":[216],"position":[220],"build":[223],"condition-specific":[224],"models":[225,245],"untested":[227],"or":[228],"incomplete":[229],"profiles":[230],"data":[234],"not":[236],"available.":[237],"weighted":[239],"freely":[247],"available":[248],"https://github.com/maxconway/SNFtool":[250],".":[251]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}