{"id":"https://openalex.org/W4412103210","doi":"https://doi.org/10.1093/bib/bbaf320","title":"Advancing edge-based clustering and graph embedding for biological network analysis: a case study in RASopathies","display_name":"Advancing edge-based clustering and graph embedding for biological network analysis: a case study in RASopathies","publication_year":2025,"publication_date":"2025-06-18","ids":{"openalex":"https://openalex.org/W4412103210","doi":"https://doi.org/10.1093/bib/bbaf320","pmid":"https://pubmed.ncbi.nlm.nih.gov/40619812"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf320","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf320","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf320/63679127/bbaf320.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf320/63679127/bbaf320.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031958805","display_name":"Federico Garc\u00eda-Criado","orcid":"https://orcid.org/0000-0002-5123-8348"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Federico Garc\u00eda-Criado","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, University of Malaga , 29010 Malaga ,"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga , 29010 Malaga ,","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038138862","display_name":"Pedro Seoane","orcid":"https://orcid.org/0000-0002-3020-1415"},"institutions":[{"id":"https://openalex.org/I2801357902","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886","country_code":"ES","type":"funder","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4387152914"]},{"id":"https://openalex.org/I4210111366","display_name":"Centre for Biomedical Network Research on Rare Diseases","ror":"https://ror.org/01ygm5w19","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210111366"]},{"id":"https://openalex.org/I4210149999","display_name":"Andalusian Centre for Nanomedicine and Biotechnology","ror":"https://ror.org/04enqja79","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210149999"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Pedro Seoane","raw_affiliation_strings":["Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII) , 28029 Madrid ,","Department of Molecular Biology and Biochemistry, University of Malaga , 29010 Malaga ,","Institute of Biomedical Research in Malaga and platform of nanomedicine, IBIMA Plataforma BIONAND , 29071 Malaga ,"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII) , 28029 Madrid ,","institution_ids":["https://openalex.org/I4210111366","https://openalex.org/I2801357902"]},{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga , 29010 Malaga ,","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Institute of Biomedical Research in Malaga and platform of nanomedicine, IBIMA Plataforma BIONAND , 29071 Malaga ,","institution_ids":["https://openalex.org/I4210149999"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038281376","display_name":"Elena Rojano","orcid":"https://orcid.org/0000-0002-2678-710X"},"institutions":[{"id":"https://openalex.org/I2801357902","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886","country_code":"ES","type":"funder","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4387152914"]},{"id":"https://openalex.org/I4210111366","display_name":"Centre for Biomedical Network Research on Rare Diseases","ror":"https://ror.org/01ygm5w19","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210111366"]},{"id":"https://openalex.org/I4210149999","display_name":"Andalusian Centre for Nanomedicine and Biotechnology","ror":"https://ror.org/04enqja79","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210149999"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Elena Rojano","raw_affiliation_strings":["Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII) , 28029 Madrid ,","Department of Molecular Biology and Biochemistry, University of Malaga , 29010 Malaga ,","Institute of Biomedical Research in Malaga and platform of nanomedicine, IBIMA Plataforma BIONAND , 29071 Malaga ,"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII) , 28029 Madrid ,","institution_ids":["https://openalex.org/I4210111366","https://openalex.org/I2801357902"]},{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga , 29010 Malaga ,","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Institute of Biomedical Research in Malaga and platform of nanomedicine, IBIMA Plataforma BIONAND , 29071 Malaga ,","institution_ids":["https://openalex.org/I4210149999"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065049632","display_name":"Juan A. G. Ranea","orcid":"https://orcid.org/0000-0003-0327-1837"},"institutions":[{"id":"https://openalex.org/I2801357902","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886","country_code":"ES","type":"funder","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4387152914"]},{"id":"https://openalex.org/I4210111366","display_name":"Centre for Biomedical Network Research on Rare Diseases","ror":"https://ror.org/01ygm5w19","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210111366"]},{"id":"https://openalex.org/I4210149999","display_name":"Andalusian Centre for Nanomedicine and Biotechnology","ror":"https://ror.org/04enqja79","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210149999"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Juan A G Ranea","raw_affiliation_strings":["Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII) , 28029 Madrid ,","Department of Molecular Biology and Biochemistry, University of Malaga , 29010 Malaga ,","Institute of Biomedical Research in Malaga and platform of nanomedicine, IBIMA Plataforma BIONAND , 29071 Malaga ,","Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Instituto de Salud Carlos III (ISCIII) , 28020 Madrid ,"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII) , 28029 Madrid ,","institution_ids":["https://openalex.org/I4210111366","https://openalex.org/I2801357902"]},{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga , 29010 Malaga ,","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Institute of Biomedical Research in Malaga and platform of nanomedicine, IBIMA Plataforma BIONAND , 29071 Malaga ,","institution_ids":["https://openalex.org/I4210149999"]},{"raw_affiliation_string":"Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Instituto de Salud Carlos III (ISCIII) , 28020 Madrid ,","institution_ids":["https://openalex.org/I2801357902"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032959797","display_name":"James R. Perkins","orcid":"https://orcid.org/0000-0003-4108-096X"},"institutions":[{"id":"https://openalex.org/I2801357902","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886","country_code":"ES","type":"funder","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4387152914"]},{"id":"https://openalex.org/I4210111366","display_name":"Centre for Biomedical Network Research on Rare Diseases","ror":"https://ror.org/01ygm5w19","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210111366"]},{"id":"https://openalex.org/I4210149999","display_name":"Andalusian Centre for Nanomedicine and Biotechnology","ror":"https://ror.org/04enqja79","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210149999"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"James R Perkins","raw_affiliation_strings":["Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII) , 28029 Madrid ,","Department of Molecular Biology and Biochemistry, University of Malaga , 29010 Malaga ,","Institute of Biomedical Research in Malaga and platform of nanomedicine, IBIMA Plataforma BIONAND , 29071 Malaga ,"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII) , 28029 Madrid ,","institution_ids":["https://openalex.org/I4210111366","https://openalex.org/I2801357902"]},{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga , 29010 Malaga ,","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Institute of Biomedical Research in Malaga and platform of nanomedicine, IBIMA Plataforma BIONAND , 29071 Malaga ,","institution_ids":["https://openalex.org/I4210149999"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5031958805"],"corresponding_institution_ids":["https://openalex.org/I82767444"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.2876,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.88334465,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"26","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994000196456909,"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":0.9994000196456909,"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/T12104","display_name":"Protein Tyrosine Phosphatases","score":0.9952999949455261,"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/T10587","display_name":"Autophagy in Disease and Therapy","score":0.9872999787330627,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7470270395278931},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6854103207588196},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.6497741937637329},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.639268159866333},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.569253146648407},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.525029718875885},{"id":"https://openalex.org/keywords/graph-embedding","display_name":"Graph embedding","score":0.49262768030166626},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.4791761636734009},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.47069883346557617},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34661388397216797},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33892786502838135},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.300766259431839},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1587519645690918}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7470270395278931},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6854103207588196},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6497741937637329},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.639268159866333},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.569253146648407},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.525029718875885},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.49262768030166626},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.4791761636734009},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.47069883346557617},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34661388397216797},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33892786502838135},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.300766259431839},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1587519645690918},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","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":"D009634","descriptor_name":"Noonan Syndrome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009634","descriptor_name":"Noonan Syndrome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009634","descriptor_name":"Noonan Syndrome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009634","descriptor_name":"Noonan Syndrome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009634","descriptor_name":"Noonan Syndrome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009634","descriptor_name":"Noonan Syndrome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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},{"descriptor_ui":"D018631","descriptor_name":"ras Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D018631","descriptor_name":"ras Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D018631","descriptor_name":"ras Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D018631","descriptor_name":"ras Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D018631","descriptor_name":"ras Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D018631","descriptor_name":"ras Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf320","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf320","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf320/63679127/bbaf320.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40619812","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40619812","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11038380","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12229990","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf320","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf320","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf320/63679127/bbaf320.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4000000059604645}],"awards":[{"id":"https://openalex.org/G4967548787","display_name":null,"funder_award_id":"IMP/00019","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"},{"id":"https://openalex.org/G5488295180","display_name":null,"funder_award_id":"PID2022-140047OB-C21","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"},{"id":"https://openalex.org/G5916997013","display_name":null,"funder_award_id":"BIO-267","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G6638883864","display_name":null,"funder_award_id":"PID2019-108096RB-C21","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G8326448714","display_name":null,"funder_award_id":"PID2022-140047OB-C21","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G8875107625","display_name":null,"funder_award_id":"PID2019-108096RB-C21","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"}],"funders":[{"id":"https://openalex.org/F4320311265","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28"},{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320326754","display_name":"Junta de Andaluc\u00eda","ror":"https://ror.org/01jem9c82"},{"id":"https://openalex.org/F4320332805","display_name":"Smithsonian Conservation Biology Institute","ror":"https://ror.org/04hnzva96"},{"id":"https://openalex.org/F4320334923","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412103210.pdf"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W1974903221","https://openalex.org/W1985915435","https://openalex.org/W1989277387","https://openalex.org/W1998493448","https://openalex.org/W2034246581","https://openalex.org/W2042236541","https://openalex.org/W2075939958","https://openalex.org/W2090891622","https://openalex.org/W2096578372","https://openalex.org/W2097308346","https://openalex.org/W2110620844","https://openalex.org/W2112173990","https://openalex.org/W2139451715","https://openalex.org/W2154851992","https://openalex.org/W2156151509","https://openalex.org/W2204540292","https://openalex.org/W2250539671","https://openalex.org/W2387462954","https://openalex.org/W2462226918","https://openalex.org/W2493614923","https://openalex.org/W2519890829","https://openalex.org/W2623060321","https://openalex.org/W2743104969","https://openalex.org/W2765386553","https://openalex.org/W2785951678","https://openalex.org/W2789374663","https://openalex.org/W2845798836","https://openalex.org/W2892333522","https://openalex.org/W2946860994","https://openalex.org/W2951006102","https://openalex.org/W2962756421","https://openalex.org/W2966321063","https://openalex.org/W2981274387","https://openalex.org/W2989932024","https://openalex.org/W3021518969","https://openalex.org/W3089704999","https://openalex.org/W3093943311","https://openalex.org/W3096716703","https://openalex.org/W3104097132","https://openalex.org/W3175155243","https://openalex.org/W3177371828","https://openalex.org/W3182404821","https://openalex.org/W3186075610","https://openalex.org/W4206673825","https://openalex.org/W4213351467","https://openalex.org/W4225264853","https://openalex.org/W4233698560","https://openalex.org/W4283257049","https://openalex.org/W4285579224","https://openalex.org/W4291474301","https://openalex.org/W4294170691","https://openalex.org/W4297571622","https://openalex.org/W4308834893","https://openalex.org/W4309990752","https://openalex.org/W4379599555","https://openalex.org/W4387535095","https://openalex.org/W4389861133","https://openalex.org/W4391948933","https://openalex.org/W4392500220","https://openalex.org/W4392817525","https://openalex.org/W4396810503","https://openalex.org/W4396878042","https://openalex.org/W4399439055","https://openalex.org/W4401009475","https://openalex.org/W4403965075","https://openalex.org/W6707620307","https://openalex.org/W6748375523","https://openalex.org/W6769441996","https://openalex.org/W6777926273","https://openalex.org/W6810597844"],"related_works":["https://openalex.org/W3206528106","https://openalex.org/W3036264823","https://openalex.org/W2912814903","https://openalex.org/W2123605750","https://openalex.org/W2088740331","https://openalex.org/W3038102983","https://openalex.org/W2950907416","https://openalex.org/W1559483280","https://openalex.org/W2082479932","https://openalex.org/W2932872266"],"abstract_inverted_index":{"Understanding":[0],"and":[1,12,47,85,139,148,228,240,245],"predicting":[2],"biological":[3,31,45,106,163],"processes":[4],"from":[5,201],"protein-protein":[6],"interaction":[7],"(PPI)":[8],"networks":[9,52],"requires":[10],"accurate":[11],"efficient":[13],"representations":[14],"of":[15,30,66,105,162,187,194],"their":[16],"structure.":[17],"However,":[18,92],"many":[19],"existing":[20,143],"methods":[21,96,144],"fail":[22],"to":[23,81,155,182,211,217],"capture":[24],"the":[25,64,79,89,102,114,160,170,202,236],"complex,":[26],"overlapping":[27,103],"modular":[28],"structure":[29],"systems.":[32],"To":[33],"address":[34],"this,":[35],"we":[36,131,158],"propose":[37],"a":[38,54,71,185,191],"network":[39,72],"embedding":[40,62,74,90,122,180],"strategy":[41],"that":[42],"improves":[43],"both":[44,141],"interpretability":[46],"predictive":[48],"power.":[49],"By":[50],"transforming":[51],"into":[53,120],"low-dimensional":[55],"space":[56],"while":[57],"preserving":[58],"key":[59],"topological":[60],"properties,":[61],"enables":[63],"discovery":[65],"novel":[67,220],"functional":[68,86],"relationships.":[69],"Pre-clustering":[70],"before":[73],"enhances":[75],"representation":[76,161],"quality,":[77],"i.e.":[78],"ability":[80],"preserve":[82],"meaningful":[83],"structural":[84],"properties":[87],"in":[88,145,199,235],"space.":[91],"traditional":[93],"non-overlapping":[94],"clustering":[95,146],"can":[97],"introduce":[98,132],"bias":[99],"by":[100,112,151,197],"ignoring":[101],"nature":[104],"communities.":[107],"We":[108,174],"overcome":[109],"this":[110],"limitation":[111],"integrating":[113],"Hierarchical":[115],"Link":[116],"Clustering":[117],"(HLC)":[118],"algorithm":[119],"an":[121],"workflow":[123,181],"tailored":[124],"for":[125,137,243],"large,":[126],"weighted,":[127],"undirected":[128],"networks.":[129],"First,":[130],"two":[133],"optimized":[134],"HLC":[135,231],"implementations":[136,232],"Python":[138,244],"R,":[140,246],"outperforming":[142],"accuracy":[147],"scalability.":[149],"Then,":[150],"restricting":[152],"random":[153],"walks":[154],"HLC-defined":[156],"communities,":[157],"improve":[159],"pathways,":[164,214],"as":[165],"shown":[166],"using":[167],"Reactome":[168],"on":[169],"human":[171],"PPI":[172],"network.":[173],"also":[175,216],"apply":[176],"our":[177],"full":[178],"cluster":[179],"analyze":[183],"RASopathies,":[184,225],"group":[186],"interrelated":[188],"disorders":[189],"with":[190,224],"diverse":[192],"range":[193],"phenotypes,":[195],"caused":[196],"mutations":[198],"genes":[200],"RAS/MAPK":[203],"pathway.":[204],"This":[205],"approach":[206],"was":[207],"used":[208],"not":[209],"only":[210],"represent":[212],"known":[213],"but":[215],"identify":[218],"potential":[219],"gene":[221],"candidates":[222],"associated":[223],"including":[226],"Noonan":[227],"Costello":[229],"syndrome.":[230],"are":[233],"available":[234],"CDLIB":[237],"library":[238],"(https://github.com/GiulioRossetti/cdlib),":[239],"at":[241],"https://github.com/jimrperkins/linkcomm":[242],"respectively.":[247]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
