{"id":"https://openalex.org/W2158190097","doi":"https://doi.org/10.1186/1471-2105-15-201","title":"eXamine: Exploring annotated modules in networks","display_name":"eXamine: Exploring annotated modules in networks","publication_year":2014,"publication_date":"2014-07-07","ids":{"openalex":"https://openalex.org/W2158190097","doi":"https://doi.org/10.1186/1471-2105-15-201","mag":"2158190097","pmid":"https://pubmed.ncbi.nlm.nih.gov/25002203"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-201","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-201","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-201","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":null,"license_id":null,"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/counter/pdf/10.1186/1471-2105-15-201","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022287420","display_name":"Kasper Dinkla","orcid":"https://orcid.org/0000-0003-2092-166X"},"institutions":[{"id":"https://openalex.org/I83019370","display_name":"Eindhoven University of Technology","ror":"https://ror.org/02c2kyt77","country_code":"NL","type":"education","lineage":["https://openalex.org/I83019370"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Kasper Dinkla","raw_affiliation_strings":["Eindhoven University of Technology, Den Dolech 2, 5600 MB, Eindhoven, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Eindhoven University of Technology, Den Dolech 2, 5600 MB, Eindhoven, The Netherlands","institution_ids":["https://openalex.org/I83019370"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089040838","display_name":"Mohammed El-Kebir","orcid":"https://orcid.org/0000-0002-1468-2407"},"institutions":[{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832","https://openalex.org/I4405262988"]},{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Mohammed El-Kebir","raw_affiliation_strings":["Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098 XG, Amsterdam, The Netherlands","VU University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands","Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098, XG, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098 XG, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1341640284"]},{"raw_affiliation_string":"VU University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]},{"raw_affiliation_string":"Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098, XG, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1341640284"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028749027","display_name":"Cristina-Iulia Bucur","orcid":"https://orcid.org/0000-0002-7114-6459"},"institutions":[{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832","https://openalex.org/I4405262988"]},{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Cristina-Iulia Bucur","raw_affiliation_strings":["Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098 XG, Amsterdam, The Netherlands","VU University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands","Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098, XG, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098 XG, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1341640284"]},{"raw_affiliation_string":"VU University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]},{"raw_affiliation_string":"Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098, XG, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1341640284"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003446622","display_name":"Marco Siderius","orcid":"https://orcid.org/0000-0003-3630-4228"},"institutions":[{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Marco Siderius","raw_affiliation_strings":["VU University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands","VU University Amsterdam, De Boelelaan 1105, 1081, HV, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"VU University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]},{"raw_affiliation_string":"VU University Amsterdam, De Boelelaan 1105, 1081, HV, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016107952","display_name":"Martine J. Smit","orcid":"https://orcid.org/0000-0003-2713-0238"},"institutions":[{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Martine J Smit","raw_affiliation_strings":["VU University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands","VU University Amsterdam, De Boelelaan 1105, 1081, HV, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"VU University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]},{"raw_affiliation_string":"VU University Amsterdam, De Boelelaan 1105, 1081, HV, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039489539","display_name":"Michel A. Westenberg","orcid":"https://orcid.org/0000-0003-4355-7805"},"institutions":[{"id":"https://openalex.org/I83019370","display_name":"Eindhoven University of Technology","ror":"https://ror.org/02c2kyt77","country_code":"NL","type":"education","lineage":["https://openalex.org/I83019370"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Michel A Westenberg","raw_affiliation_strings":["Eindhoven University of Technology, Den Dolech 2, 5600 MB, Eindhoven, The Netherlands. m.a.westenberg@tue.nl","Eindhoven University of Technology, Den Dolech 2, 5600 MB, Eindhoven, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Eindhoven University of Technology, Den Dolech 2, 5600 MB, Eindhoven, The Netherlands. m.a.westenberg@tue.nl","institution_ids":["https://openalex.org/I83019370"]},{"raw_affiliation_string":"Eindhoven University of Technology, Den Dolech 2, 5600 MB, Eindhoven, The Netherlands","institution_ids":["https://openalex.org/I83019370"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029642674","display_name":"Gunnar W. Klau","orcid":"https://orcid.org/0000-0002-6340-0090"},"institutions":[{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832","https://openalex.org/I4405262988"]},{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Gunnar W Klau","raw_affiliation_strings":["Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098 XG, Amsterdam, The Netherlands","VU University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands","VU University Amsterdam, De Boelelaan 1105, 1081, HV, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098 XG, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1341640284"]},{"raw_affiliation_string":"VU University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]},{"raw_affiliation_string":"VU University Amsterdam, De Boelelaan 1105, 1081, HV, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.9543,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.86435636,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"15","issue":"1","first_page":"201","last_page":"201"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6833000183105469,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6833000183105469,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.09889999777078629,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.03290000185370445,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/subnetwork","display_name":"Subnetwork","score":0.8177329301834106},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7779252529144287},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.6934630274772644},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5755057334899902},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.516539990901947},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5100834965705872},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.49268943071365356},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4925282895565033},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.4138130247592926},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37506920099258423},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3630863428115845},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.2578207850456238},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10315355658531189}],"concepts":[{"id":"https://openalex.org/C2780186347","wikidata":"https://www.wikidata.org/wiki/Q11414","display_name":"Subnetwork","level":2,"score":0.8177329301834106},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7779252529144287},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.6934630274772644},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5755057334899902},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.516539990901947},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5100834965705872},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.49268943071365356},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4925282895565033},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.4138130247592926},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37506920099258423},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3630863428115845},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2578207850456238},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10315355658531189},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"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/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","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":"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":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1186/1471-2105-15-201","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-201","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-201","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25002203","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25002203","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:pure.tue.nl:openaire/dc0260c4-282f-4da7-8c34-d77dbbe6c336","is_oa":true,"landing_page_url":"https://research.tue.nl/en/publications/dc0260c4-282f-4da7-8c34-d77dbbe6c336","pdf_url":null,"source":{"id":"https://openalex.org/S4406922641","display_name":"TU/e Research Portal","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Dinkla, K, El-Kebir, M, Bucur, C-I, Siderius, M, Smit, M J, Westenberg, M A & Klau, G W 2014, 'eXamine : exploring annotated modules in networks', BMC Bioinformatics, vol. 15, no. 6, pp. 201-1/14. https://doi.org/10.1186/1471-2105-15-201","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:research.vu.nl:publications/992d89f2-2b2a-477c-90cd-7e59fc4db53d","is_oa":true,"landing_page_url":"https://research.vu.nl/en/publications/992d89f2-2b2a-477c-90cd-7e59fc4db53d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401107","display_name":"VU Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I865915315","host_organization_name":"Vrije Universiteit Amsterdam","host_organization_lineage":["https://openalex.org/I865915315"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Dinkla, K, El-Kebir, M, Bucur, C I, Siderius, M, Smit, M J, Westenberg, M A & Klau, G W 2014, 'eXamine: Exploring annotated modules in networks', BMC Bioinformatics, vol. 15, no. 201. https://doi.org/10.1186/1471-2105-15-201","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:cwi.nl:22981","is_oa":true,"landing_page_url":"https://ir.cwi.nl/pub/22981","pdf_url":"https://ir.cwi.nl/pub/22981/22981D.pdf","source":{"id":"https://openalex.org/S7407055335","display_name":"Centrum Wiskunde & Informatica (CWI), the national research institute for mathematics and computer science in the Netherlands","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":"BMC Bioinformatics vol. 15 no. 201","raw_type":"info:eu-repo/semantics/conferenceObject"},{"id":"pmh:tue:oai:pure.tue.nl:publications/dc0260c4-282f-4da7-8c34-d77dbbe6c336","is_oa":true,"landing_page_url":"https://research.tue.nl/nl/publications/dc0260c4-282f-4da7-8c34-d77dbbe6c336","pdf_url":"https://research.tue.nl/nl/publications/dc0260c4-282f-4da7-8c34-d77dbbe6c336","source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 15(6), 201 - 1/14. BioMed Central","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:3071333","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4084410","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:research.vu.nl:openaire/992d89f2-2b2a-477c-90cd-7e59fc4db53d","is_oa":true,"landing_page_url":"https://hdl.handle.net/1871.1/992d89f2-2b2a-477c-90cd-7e59fc4db53d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401107","display_name":"VU Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I865915315","host_organization_name":"Vrije Universiteit Amsterdam","host_organization_lineage":["https://openalex.org/I865915315"],"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":"Dinkla, K, El-Kebir, M, Bucur, C I, Siderius, M, Smit, M J, Westenberg, M A & Klau, G W 2014, 'eXamine: Exploring annotated modules in networks', BMC Bioinformatics, vol. 15, no. 201. https://doi.org/10.1186/1471-2105-15-201","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-201","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-201","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-201","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2008074812","display_name":null,"funder_award_id":"612.001.004","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2158190097.pdf","grobid_xml":"https://content.openalex.org/works/W2158190097.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W48047229","https://openalex.org/W286056710","https://openalex.org/W1546952499","https://openalex.org/W1970594207","https://openalex.org/W1990517717","https://openalex.org/W1992214889","https://openalex.org/W1992613028","https://openalex.org/W1994637853","https://openalex.org/W2008116181","https://openalex.org/W2008808301","https://openalex.org/W2014592511","https://openalex.org/W2023098599","https://openalex.org/W2031005807","https://openalex.org/W2039156817","https://openalex.org/W2040847667","https://openalex.org/W2057385062","https://openalex.org/W2071584957","https://openalex.org/W2084897870","https://openalex.org/W2085995966","https://openalex.org/W2086928685","https://openalex.org/W2088709281","https://openalex.org/W2089621285","https://openalex.org/W2098816998","https://openalex.org/W2100112610","https://openalex.org/W2100714130","https://openalex.org/W2102664288","https://openalex.org/W2103017472","https://openalex.org/W2103212167","https://openalex.org/W2108639779","https://openalex.org/W2109363337","https://openalex.org/W2110687686","https://openalex.org/W2112811019","https://openalex.org/W2114566476","https://openalex.org/W2114741940","https://openalex.org/W2116634113","https://openalex.org/W2117006370","https://openalex.org/W2120024428","https://openalex.org/W2146055051","https://openalex.org/W2147246240","https://openalex.org/W2147468287","https://openalex.org/W2149906774","https://openalex.org/W2150617763","https://openalex.org/W2152301738","https://openalex.org/W2152621157","https://openalex.org/W2153620197","https://openalex.org/W2153885599","https://openalex.org/W2154560913","https://openalex.org/W2155142785","https://openalex.org/W2157348185","https://openalex.org/W2158453355","https://openalex.org/W2159205441","https://openalex.org/W2159482845","https://openalex.org/W2160450758","https://openalex.org/W2167306162","https://openalex.org/W2167482691","https://openalex.org/W2171662214","https://openalex.org/W2407343877","https://openalex.org/W4231755703","https://openalex.org/W4251391716","https://openalex.org/W4285719527","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2060724872","https://openalex.org/W2082094785","https://openalex.org/W15348386","https://openalex.org/W2099991711","https://openalex.org/W2478888221","https://openalex.org/W2095452756","https://openalex.org/W2521885831","https://openalex.org/W2494457055","https://openalex.org/W1979360205","https://openalex.org/W1986505750"],"abstract_inverted_index":{"BACKGROUND:":[0],"Biological":[1],"networks":[2],"have":[3],"a":[4,62,69,89,111,129,174,183],"growing":[5],"importance":[6],"for":[7],"the":[8,35,53,104,141,166,188],"interpretation":[9,167],"of":[10,19,71,79,110,118,134,154,157,168],"high-throughput":[11],"\"omics\"":[12],"data.":[13],"Integrative":[14],"network":[15,55,77,170],"analysis":[16,32,91,171],"makes":[17],"use":[18],"statistical":[20],"and":[21,29,57,82,101,126,150,159],"combinatorial":[22],"methods":[23],"to":[24,33,121],"extract":[25],"smaller":[26],"subnetwork":[27],"modules,":[28],"performs":[30],"enrichment":[31,59],"annotate":[34],"modules":[36,81,96,152],"with":[37,97],"ontology":[38],"terms":[39],"or":[40],"other":[41],"available":[42,139],"knowledge.":[43],"This":[44,86,178],"process":[45],"results":[46,172],"in":[47,128,173,182],"an":[48,116],"annotated":[49,151],"module,":[50],"which":[51,102],"retains":[52],"original":[54],"structure":[56,78],"includes":[58],"information":[60],"as":[61,106,140],"set":[63],"system.":[64],"A":[65],"major":[66],"bottleneck":[67],"is":[68,137],"lack":[70],"tools":[72],"that":[73,93,163],"allow":[74],"exploring":[75],"both":[76],"extracted":[80],"its":[83],"annotations.":[84,160],"RESULTS:":[85],"paper":[87],"presents":[88],"visual":[90],"approach":[92,136],"targets":[94],"small":[95,149],"many":[98],"set-based":[99],"annotations,":[100],"displays":[103],"annotations":[105],"contours":[107,127],"on":[108],"top":[109],"node-link":[112],"diagram.":[113],"We":[114,161],"introduce":[115],"extension":[117],"self-organizing":[119],"maps":[120],"lay":[122],"out":[123],"nodes,":[124],"links,":[125],"unified":[130],"way.":[131],"An":[132],"implementation":[133],"this":[135],"freely":[138],"Cytoscape":[142],"app":[143],"eXamine":[144,146,164],"CONCLUSIONS:":[145],"accurately":[147],"conveys":[148],"consisting":[153],"several":[155],"dozens":[156],"proteins":[158],"demonstrate":[162],"facilitates":[165],"integrative":[169],"guided":[175],"case":[176],"study.":[177],"study":[179],"has":[180],"resulted":[181],"novel":[184],"biological":[185],"insight":[186],"regarding":[187],"virally-encoded":[189],"G-protein":[190],"coupled":[191],"receptor":[192],"US28.":[193]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":9}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
