{"id":"https://openalex.org/W2143721634","doi":"https://doi.org/10.1093/bioinformatics/bts126","title":"Proteus: a web-based, context-specific modelling tool for molecular networks","display_name":"Proteus: a web-based, context-specific modelling tool for molecular networks","publication_year":2012,"publication_date":"2012-03-15","ids":{"openalex":"https://openalex.org/W2143721634","doi":"https://doi.org/10.1093/bioinformatics/bts126","mag":"2143721634","pmid":"https://pubmed.ncbi.nlm.nih.gov/22426344"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts126","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/9/1284/48874801/bioinformatics_28_9_1284.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/9/1284/48874801/bioinformatics_28_9_1284.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014672294","display_name":"Florian Gnad","orcid":"https://orcid.org/0000-0002-2287-2251"},"institutions":[{"id":"https://openalex.org/I63634437","display_name":"Universidad Aut\u00f3noma de Madrid","ror":"https://ror.org/01cby8j38","country_code":"ES","type":"education","lineage":["https://openalex.org/I63634437"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Florian Gnad","raw_affiliation_strings":["1 Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA and 2Condensed Matter Physics Department & Material Science Institute Nicol\u00e1s Cabrera, Universidad Aut\u00f3noma de Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"1 Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA and 2Condensed Matter Physics Department & Material Science Institute Nicol\u00e1s Cabrera, Universidad Aut\u00f3noma de Madrid, Spain","institution_ids":["https://openalex.org/I63634437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040589528","display_name":"Javier Estrada","orcid":"https://orcid.org/0000-0003-3646-204X"},"institutions":[{"id":"https://openalex.org/I63634437","display_name":"Universidad Aut\u00f3noma de Madrid","ror":"https://ror.org/01cby8j38","country_code":"ES","type":"education","lineage":["https://openalex.org/I63634437"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Javier Estrada","raw_affiliation_strings":["1 Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA and 2Condensed Matter Physics Department & Material Science Institute Nicol\u00e1s Cabrera, Universidad Aut\u00f3noma de Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"1 Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA and 2Condensed Matter Physics Department & Material Science Institute Nicol\u00e1s Cabrera, Universidad Aut\u00f3noma de Madrid, Spain","institution_ids":["https://openalex.org/I63634437"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056777354","display_name":"Jeremy Gunawardena","orcid":"https://orcid.org/0000-0002-7280-1152"},"institutions":[{"id":"https://openalex.org/I63634437","display_name":"Universidad Aut\u00f3noma de Madrid","ror":"https://ror.org/01cby8j38","country_code":"ES","type":"education","lineage":["https://openalex.org/I63634437"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jeremy Gunawardena","raw_affiliation_strings":["1 Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA and 2Condensed Matter Physics Department & Material Science Institute Nicol\u00e1s Cabrera, Universidad Aut\u00f3noma de Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"1 Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA and 2Condensed Matter Physics Department & Material Science Institute Nicol\u00e1s Cabrera, Universidad Aut\u00f3noma de Madrid, Spain","institution_ids":["https://openalex.org/I63634437"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014672294"],"corresponding_institution_ids":["https://openalex.org/I63634437"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1345,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.53796242,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"28","issue":"9","first_page":"1284","last_page":"1286"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9954000115394592,"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":0.9954000115394592,"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":0.9898999929428101,"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":0.9883000254631042,"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/context","display_name":"Context (archaeology)","score":0.6766895651817322},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6048167943954468},{"id":"https://openalex.org/keywords/proteus","display_name":"Proteus","score":0.5063964128494263},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4547540247440338},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4510195255279541},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.40093719959259033},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3550386428833008},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25450047850608826},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11096999049186707}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6766895651817322},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6048167943954468},{"id":"https://openalex.org/C2779464495","wikidata":"https://www.wikidata.org/wiki/Q132229","display_name":"Proteus","level":4,"score":0.5063964128494263},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4547540247440338},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4510195255279541},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.40093719959259033},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3550386428833008},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25450047850608826},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11096999049186707},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"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":"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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts126","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/9/1284/48874801/bioinformatics_28_9_1284.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22426344","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22426344","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.893.3227","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.893.3227","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2012/03/15/bioinformatics.bts126.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:2637794","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3338017","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts126","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/9/1284/48874801/bioinformatics_28_9_1284.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2143721634.pdf","grobid_xml":"https://content.openalex.org/works/W2143721634.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1485297825","https://openalex.org/W1598957092","https://openalex.org/W2028469352","https://openalex.org/W2069941324","https://openalex.org/W2100525485","https://openalex.org/W2105038431","https://openalex.org/W2107062718","https://openalex.org/W2134050761","https://openalex.org/W2175715045","https://openalex.org/W6667917037"],"related_works":["https://openalex.org/W2419441924","https://openalex.org/W2369533376","https://openalex.org/W2357348897","https://openalex.org/W2235158164","https://openalex.org/W4241042207","https://openalex.org/W2343585654","https://openalex.org/W4306825251","https://openalex.org/W2323047482","https://openalex.org/W2381293867","https://openalex.org/W2380290243"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}