{"id":"https://openalex.org/W2035105875","doi":"https://doi.org/10.1109/bibe.2008.4696727","title":"A framework for the integrated analysis of metabolic and regulatory networks","display_name":"A framework for the integrated analysis of metabolic and regulatory networks","publication_year":2008,"publication_date":"2008-10-01","ids":{"openalex":"https://openalex.org/W2035105875","doi":"https://doi.org/10.1109/bibe.2008.4696727","mag":"2035105875"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2008.4696727","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2008.4696727","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 8th IEEE International Conference on BioInformatics and BioEngineering","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://repositorium.uminho.pt/bitstreams/816c8266-0990-4406-b699-542c85e7d591/download","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081140606","display_name":"Rui Mendes","orcid":"https://orcid.org/0000-0002-5321-6863"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Rui Mendes","raw_affiliation_strings":["Department of Informatics /CCTC, University of Minho, Braga, Portugal","Dept. of Inf., Univ. of Minho, Braga"],"affiliations":[{"raw_affiliation_string":"Department of Informatics /CCTC, University of Minho, Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"Dept. of Inf., Univ. of Minho, Braga","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033016354","display_name":"An\u00e1lia Louren\u00e7o","orcid":"https://orcid.org/0000-0001-8401-5362"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]},{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Analia Lourenco","raw_affiliation_strings":["IBB-Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho, Braga, Portugal","Center of Biol. Eng., Univ. of Minho, Braga"],"affiliations":[{"raw_affiliation_string":"IBB-Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho, Braga, Portugal","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]},{"raw_affiliation_string":"Center of Biol. Eng., Univ. of Minho, Braga","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054642116","display_name":"S\u00f3nia Carneiro","orcid":"https://orcid.org/0000-0001-8037-937X"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Sonia Carneiro","raw_affiliation_strings":["IBB-Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho, Braga, Portugal","Center of Biol. Eng., Univ. of Minho, Braga"],"affiliations":[{"raw_affiliation_string":"IBB-Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho, Braga, Portugal","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]},{"raw_affiliation_string":"Center of Biol. Eng., Univ. of Minho, Braga","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040524717","display_name":"Miguel Rocha","orcid":"https://orcid.org/0000-0001-8439-8172"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]},{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Miguel Rocha","raw_affiliation_strings":["IBB-Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho, Braga, Portugal","Dept. of Inf., Univ. of Minho, Braga"],"affiliations":[{"raw_affiliation_string":"IBB-Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho, Braga, Portugal","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]},{"raw_affiliation_string":"Dept. of Inf., Univ. of Minho, Braga","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079343705","display_name":"Isabel Rocha","orcid":"https://orcid.org/0000-0001-9494-3410"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Isabel Rocha","raw_affiliation_strings":["IBB-Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho, Braga, Portugal","Center of Biol. Eng., Univ. of Minho, Braga"],"affiliations":[{"raw_affiliation_string":"IBB-Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho, Braga, Portugal","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]},{"raw_affiliation_string":"Center of Biol. Eng., Univ. of Minho, Braga","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064824604","display_name":"Eug\u00e9nio C. Ferreira","orcid":"https://orcid.org/0000-0002-5400-3333"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Eugenio C. Ferreira","raw_affiliation_strings":["IBB-Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho, Braga, Portugal","Center of Biol. Eng., Univ. of Minho, Braga"],"affiliations":[{"raw_affiliation_string":"IBB-Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho, Braga, Portugal","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]},{"raw_affiliation_string":"Center of Biol. Eng., Univ. of Minho, Braga","institution_ids":["https://openalex.org/I99682543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5081140606"],"corresponding_institution_ids":["https://openalex.org/I99682543"],"apc_list":null,"apc_paid":null,"fwci":0.1383,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.54589631,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"7","issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9984999895095825,"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":0.9973000288009644,"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/computer-science","display_name":"Computer science","score":0.7169553637504578},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.6859416365623474},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6529592275619507},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4945537745952606},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4919095039367676},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4454788863658905},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.4386412501335144},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.4245699644088745},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.4140596389770508},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3599347472190857},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33418530225753784},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.33076098561286926},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28676438331604004},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16249796748161316},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13287565112113953},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11740916967391968},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09342172741889954}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7169553637504578},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.6859416365623474},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6529592275619507},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4945537745952606},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4919095039367676},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4454788863658905},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.4386412501335144},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.4245699644088745},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.4140596389770508},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3599347472190857},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33418530225753784},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.33076098561286926},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28676438331604004},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16249796748161316},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13287565112113953},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11740916967391968},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09342172741889954},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibe.2008.4696727","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2008.4696727","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 8th IEEE International Conference on BioInformatics and BioEngineering","raw_type":"proceedings-article"},{"id":"pmh:oai:repositorium.uminho.pt:1822/16835","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/16835","pdf_url":"https://repositorium.uminho.pt/bitstreams/816c8266-0990-4406-b699-542c85e7d591/download","source":{"id":"https://openalex.org/S4306401240","display_name":"Reposit\u00f3riUM (Universidade do Minho)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99682543","host_organization_name":"University of Minho","host_organization_lineage":["https://openalex.org/I99682543"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"conferencePaper"}],"best_oa_location":{"id":"pmh:oai:repositorium.uminho.pt:1822/16835","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/16835","pdf_url":"https://repositorium.uminho.pt/bitstreams/816c8266-0990-4406-b699-542c85e7d591/download","source":{"id":"https://openalex.org/S4306401240","display_name":"Reposit\u00f3riUM (Universidade do Minho)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99682543","host_organization_name":"University of Minho","host_organization_lineage":["https://openalex.org/I99682543"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"conferencePaper"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2035105875.pdf","grobid_xml":"https://content.openalex.org/works/W2035105875.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2002880495","https://openalex.org/W2018817177","https://openalex.org/W2046254395","https://openalex.org/W2076470995","https://openalex.org/W2096245011","https://openalex.org/W2130721915","https://openalex.org/W2143838095","https://openalex.org/W2156481615","https://openalex.org/W2160319713","https://openalex.org/W2164727176","https://openalex.org/W2165392091","https://openalex.org/W2170427655","https://openalex.org/W3146956997"],"related_works":["https://openalex.org/W2560421304","https://openalex.org/W2950199998","https://openalex.org/W2951387065","https://openalex.org/W4385727351","https://openalex.org/W2072067873","https://openalex.org/W4306798985","https://openalex.org/W2949927938","https://openalex.org/W2047632644","https://openalex.org/W2031492751","https://openalex.org/W3033588432"],"abstract_inverted_index":{"The":[0,15,57],"analysis":[1,17,51],"of":[2,12,18,24,35,52,69,126],"cellular":[3,40],"behavior":[4],"and":[5,54,95,107],"functionality":[6],"is":[7,77,120],"the":[8,19,33,49,67,72,127],"most":[9],"challenging":[10],"aim":[11],"systems":[13],"biology.":[14],"extensive":[16],"interactions":[20],"between":[21],"different":[22,39],"classes":[23],"intra-cellular":[25],"molecules":[26],"reacting":[27],"to":[28,89,122],"genetic/environment":[29],"changes":[30],"can":[31],"elucidate":[32],"mechanisms":[34],"regulation":[36],"involved":[37],"on":[38,61,79],"processes.":[41],"We":[42],"propose":[43],"a":[44,86,124],"novel":[45],"framework":[46,58,119],"that":[47],"enables":[48],"integrated":[50,73],"metabolic":[53],"regulatory":[55],"networks.":[56],"takes":[59],"advantage":[60],"publicly":[62],"available":[63],"data":[64],"repositories,":[65],"sustaining":[66],"inference":[68],"knowledge":[70],"from":[71],"network.":[74],"Since":[75],"it":[76,82,100],"based":[78],"logic":[80],"programming,":[81],"provides":[83],"users":[84],"with":[85],"powerful":[87],"language":[88],"query":[90],"information":[91],"using":[92],"both":[93],"first":[94],"second":[96],"order":[97],"predicates.":[98],"Also,":[99],"supports":[101],"network":[102],"topology":[103],"analysis,":[104],"motif":[105],"finding":[106],"robustness":[108],"evaluation.":[109],"In":[110],"this":[111],"work,":[112],"as":[113],"an":[114],"illustrative":[115],"case":[116],"study,":[117],"our":[118],"used":[121],"build":[123],"model":[125],"bacterium":[128],"Escherichia":[129],"coli":[130],"K12.":[131]},"counts_by_year":[],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-10-10T00:00:00"}