{"id":"https://openalex.org/W2108814382","doi":"https://doi.org/10.1093/bioinformatics/btu517","title":"P<scp>epper</scp>: cytoscape app for protein complex expansion using protein\u2013protein interaction networks","display_name":"P<scp>epper</scp>: cytoscape app for protein complex expansion using protein\u2013protein interaction networks","publication_year":2014,"publication_date":"2014-08-18","ids":{"openalex":"https://openalex.org/W2108814382","doi":"https://doi.org/10.1093/bioinformatics/btu517","mag":"2108814382","pmid":"https://pubmed.ncbi.nlm.nih.gov/25138169"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu517","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu517","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/23/3419/17144768/btu517.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/23/3419/17144768/btu517.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049381995","display_name":"Charles Winterhalter","orcid":"https://orcid.org/0000-0001-9673-1227"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210128926","display_name":"Genopole (France)","ror":"https://ror.org/0380k9k47","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210128926"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]},{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"C. Winterhalter","raw_affiliation_strings":["1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210128926","https://openalex.org/I80043","https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030107635","display_name":"R\u00e9my Nicolle","orcid":"https://orcid.org/0000-0001-8084-1173"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210128926","display_name":"Genopole (France)","ror":"https://ror.org/0380k9k47","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210128926"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]},{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"R. Nicolle","raw_affiliation_strings":["1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210128926","https://openalex.org/I80043","https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112136402","display_name":"Annie Louis","orcid":"https://orcid.org/0000-0003-4226-252X"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210128926","display_name":"Genopole (France)","ror":"https://ror.org/0380k9k47","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210128926"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]},{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"A. Louis","raw_affiliation_strings":["1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210128926","https://openalex.org/I80043","https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011504531","display_name":"Cuong To","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210128926","display_name":"Genopole (France)","ror":"https://ror.org/0380k9k47","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210128926"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]},{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"C. To","raw_affiliation_strings":["1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210128926","https://openalex.org/I80043","https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088103291","display_name":"Fran\u00e7ois Radvanyi","orcid":"https://orcid.org/0000-0002-5696-6424"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210128926","display_name":"Genopole (France)","ror":"https://ror.org/0380k9k47","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210128926"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]},{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"F. Radvanyi","raw_affiliation_strings":["1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210128926","https://openalex.org/I80043","https://openalex.org/I84884186"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091867750","display_name":"Mohamed Elati","orcid":"https://orcid.org/0000-0002-4440-2904"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210128926","display_name":"Genopole (France)","ror":"https://ror.org/0380k9k47","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210128926"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]},{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["FR","GB"],"is_corresponding":true,"raw_author_name":"M. Elati","raw_affiliation_strings":["1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210128926","https://openalex.org/I80043","https://openalex.org/I84884186"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5091867750"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210128926","https://openalex.org/I80043","https://openalex.org/I84884186"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.3899,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.61276663,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"30","issue":"23","first_page":"3419","last_page":"3420"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8392000198364258,"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":0.8392000198364258,"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/T13127","display_name":"Biotin and Related Studies","score":0.03550000116229057,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T10044","display_name":"Protein Structure and Dynamics","score":0.02500000037252903,"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/proteome","display_name":"Proteome","score":0.6336162090301514},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5855022668838501},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.557322084903717},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.5283508896827698},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.505640983581543},{"id":"https://openalex.org/keywords/pepper","display_name":"Pepper","score":0.49580463767051697},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.4744875431060791},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38718947768211365},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29132115840911865},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2763219475746155},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.146450012922287},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13787898421287537}],"concepts":[{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.6336162090301514},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5855022668838501},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.557322084903717},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5283508896827698},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.505640983581543},{"id":"https://openalex.org/C2776242653","wikidata":"https://www.wikidata.org/wiki/Q22907699","display_name":"Pepper","level":2,"score":0.49580463767051697},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.4744875431060791},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38718947768211365},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29132115840911865},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2763219475746155},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.146450012922287},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13787898421287537},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btu517","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu517","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/23/3419/17144768/btu517.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25138169","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25138169","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:pubmedcentral.nih.gov:4816032","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4816032","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:HAL:hal-05093957v1","is_oa":false,"landing_page_url":"https://hal.science/hal-05093957","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2014, 30 (23), pp.3419-3420. &#x27E8;10.1093/bioinformatics/btu517&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:eprints.ncl.ac.uk:277975","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402485","display_name":"Newcastle University ePrints (Newcastle Univesity)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I84884186","host_organization_name":"Newcastle University","host_organization_lineage":["https://openalex.org/I84884186"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu517","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu517","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/23/3419/17144768/btu517.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5430618183","display_name":"A systems biology approach to dissect cilia function and its disruption in human genetic disease","funder_award_id":"241955","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320323807","display_name":"Institut National Du Cancer","ror":"https://ror.org/03m8vkq32"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2108814382.pdf","grobid_xml":"https://content.openalex.org/works/W2108814382.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W96765779","https://openalex.org/W1585939719","https://openalex.org/W2047077861","https://openalex.org/W2048839385","https://openalex.org/W2082565035","https://openalex.org/W2136850043","https://openalex.org/W6635097213"],"related_works":["https://openalex.org/W2348255987","https://openalex.org/W216299563","https://openalex.org/W2383317600","https://openalex.org/W2374854175","https://openalex.org/W4287378204","https://openalex.org/W2981957539","https://openalex.org/W47352601","https://openalex.org/W2389892717","https://openalex.org/W2545422590","https://openalex.org/W4247002034"],"abstract_inverted_index":{"UNLABELLED:":[0],"We":[1],"introduce":[2],"Pepper":[3,31,126,142],"(Protein":[4],"complex":[5,97,124],"Expansion":[6],"using":[7,36,71],"Protein-Protein":[8],"intERactions),":[9],"a":[10,45,63,75,128],"Cytoscape":[11,147],"app":[12],"designed":[13],"to":[14,94,135],"identify":[15],"protein":[16,96],"complexes":[17],"as":[18,49,55,67,69,92],"densely":[19],"connected":[20,33,68],"subnetworks":[21],"from":[22,28,52,74,145],"seed":[23,54],"lists":[24],"of":[25,62,104,139],"proteins":[26,51,61],"derived":[27],"proteomic":[29],"studies.":[30],"identifies":[32],"subgraph":[34],"by":[35,109],"multi-objective":[37],"optimization":[38],"involving":[39],"two":[40],"functions:":[41],"(i)":[42],"the":[43,53,58,60,105,122,146],"coverage,":[44],"solution":[46,64],"must":[47,65],"contain":[48],"many":[50],"possible,":[56,70],"(ii)":[57],"density,":[59],"be":[66,133],"only":[72],"interactions":[73],"proteome-wide":[76],"interaction":[77],"network.":[78],"Comparisons":[79],"based":[80,114],"on":[81,115],"gold":[82],"standard":[83,95],"yeast":[84],"and":[85,102,118,153],"human":[86],"datasets":[87],"showed":[88],"Pepper's":[89],"integrative":[90],"approach":[91],"superior":[93],"discovery":[98],"methods.":[99],"The":[100],"visualization":[101],"interpretation":[103],"results":[106],"are":[107],"facilitated":[108],"an":[110],"automated":[111],"post-processing":[112],"pipeline":[113],"topological":[116],"analysis":[117],"data":[119],"integration":[120],"about":[121],"predicted":[123],"proteins.":[125,140],"is":[127,143],"user-friendly":[129],"tool":[130],"that":[131],"can":[132],"used":[134],"analyse":[136],"any":[137],"list":[138],"AVAILABILITY:":[141],"available":[144],"plug-in":[148],"manager":[149],"or":[150],"online":[151],"(http://apps.cytoscape.org/apps/pepper)":[152],"released":[154],"under":[155],"GNU":[156],"General":[157],"Public":[158],"License":[159],"version":[160],"3.":[161]},"counts_by_year":[{"year":2026,"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":2},{"year":2017,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2016-06-24T00:00:00"}
