{"id":"https://openalex.org/W4390743551","doi":"https://doi.org/10.1093/bioinformatics/btae012","title":"Pitfalls of machine learning models for protein\u2013protein interaction networks","display_name":"Pitfalls of machine learning models for protein\u2013protein interaction networks","publication_year":2024,"publication_date":"2024-01-10","ids":{"openalex":"https://openalex.org/W4390743551","doi":"https://doi.org/10.1093/bioinformatics/btae012","pmid":"https://pubmed.ncbi.nlm.nih.gov/38200587"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae012","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae012","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae012/55399607/btae012.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae012/55399607/btae012.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059324690","display_name":"Lo\u00efc Lannelongue","orcid":"https://orcid.org/0000-0002-9135-1345"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I32003884","display_name":"British Heart Foundation","ror":"https://ror.org/02wdwnk04","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I32003884"]},{"id":"https://openalex.org/I4210142469","display_name":"Health Data Research UK","ror":"https://ror.org/04rtjaj74","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210142469"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Lo\u00efc Lannelongue","raw_affiliation_strings":["British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge , CB2 0BB Cambridge, United Kingdom","Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge , CB2 0BB Cambridge, United Kingdom","Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge , Cambridge, United Kingdom","Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge , CB2 0BB Cambridge, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-9135-1345","affiliations":[{"raw_affiliation_string":"British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge , CB2 0BB Cambridge, United Kingdom","institution_ids":["https://openalex.org/I32003884","https://openalex.org/I241749"]},{"raw_affiliation_string":"Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge , CB2 0BB Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge , Cambridge, United Kingdom","institution_ids":["https://openalex.org/I4210142469","https://openalex.org/I241749"]},{"raw_affiliation_string":"Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge , CB2 0BB Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056977453","display_name":"Michael Inouye","orcid":"https://orcid.org/0000-0001-9413-6520"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I32003884","display_name":"British Heart Foundation","ror":"https://ror.org/02wdwnk04","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I32003884"]},{"id":"https://openalex.org/I4210142469","display_name":"Health Data Research UK","ror":"https://ror.org/04rtjaj74","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210142469"]}],"countries":["AU","GB"],"is_corresponding":true,"raw_author_name":"Michael Inouye","raw_affiliation_strings":["British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge , CB2 0BB Cambridge, United Kingdom","British Heart Foundation Centre of Research Excellence, University of Cambridge , CB2 0BB Cambridge, United Kingdom","Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute , Melbourne, 3004 Victoria, Australia","Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge , CB2 0BB Cambridge, United Kingdom","Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge , Cambridge, United Kingdom","Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge , CB2 0BB Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge , CB2 0BB Cambridge, United Kingdom","institution_ids":["https://openalex.org/I32003884","https://openalex.org/I241749"]},{"raw_affiliation_string":"British Heart Foundation Centre of Research Excellence, University of Cambridge , CB2 0BB Cambridge, United Kingdom","institution_ids":["https://openalex.org/I32003884","https://openalex.org/I241749"]},{"raw_affiliation_string":"Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute , Melbourne, 3004 Victoria, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge , CB2 0BB Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge , Cambridge, United Kingdom","institution_ids":["https://openalex.org/I4210142469","https://openalex.org/I241749"]},{"raw_affiliation_string":"Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge , CB2 0BB Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5056977453","https://openalex.org/A5059324690"],"corresponding_institution_ids":["https://openalex.org/I142471025","https://openalex.org/I241749","https://openalex.org/I32003884","https://openalex.org/I4210142469"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.6126,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.89761811,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"40","issue":"2","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":0.9836000204086304,"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":0.9836000204086304,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.002400000113993883,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.002099999925121665,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7100619673728943},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5139250755310059},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.5101876258850098},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.47529304027557373},{"id":"https://openalex.org/keywords/protein-interaction-networks","display_name":"Protein Interaction Networks","score":0.4629223346710205},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36179405450820923},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1995217502117157},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15742680430412292},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11049473285675049}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7100619673728943},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5139250755310059},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5101876258850098},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.47529304027557373},{"id":"https://openalex.org/C2909613950","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Protein Interaction Networks","level":3,"score":0.4629223346710205},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36179405450820923},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1995217502117157},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15742680430412292},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11049473285675049}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"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":"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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"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":"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":"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":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btae012","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae012","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae012/55399607/btae012.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38200587","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38200587","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:10868344","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10868344","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10868344/pdf/btae012.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/364498","is_oa":true,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/364498","pdf_url":"https://www.repository.cam.ac.uk/bitstreams/b72f2f0c-94dc-4c2b-9dd1-873f0ad90e79/download","source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"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":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae012","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae012","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae012/55399607/btae012.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1671907826","display_name":null,"funder_award_id":"RG/13/13/30194","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G1895122974","display_name":null,"funder_award_id":"BRC-1215-20014","funder_id":"https://openalex.org/F4320319990","funder_display_name":"National Institute for Health and Care Research"},{"id":"https://openalex.org/G2424152919","display_name":"Large-scale integrative genomic studies of high-dimensional traits in cardiovascular diseases (renewal)","funder_award_id":"RG/18/13/33946","funder_id":"https://openalex.org/F4320319992","funder_display_name":"British Heart Foundation"},{"id":"https://openalex.org/G3244234731","display_name":null,"funder_award_id":"BRC-1215\u201320014","funder_id":"https://openalex.org/F4320336709","funder_display_name":"NIHR Cambridge Biomedical Research Centre"},{"id":"https://openalex.org/G5309236915","display_name":null,"funder_award_id":"BRC-1215-20014","funder_id":"https://openalex.org/F4320336709","funder_display_name":"NIHR Cambridge Biomedical Research Centre"},{"id":"https://openalex.org/G6635873859","display_name":"Artificial intelligence to create equitable multi-ethnic polygenic risk scores that improve clinical care","funder_award_id":"ES/T013192/1","funder_id":"https://openalex.org/F4320334630","funder_display_name":"Economic and Social Research Council"},{"id":"https://openalex.org/G6641991021","display_name":null,"funder_award_id":"BRC-1215-20014","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7595091512","display_name":"Large-scale integrative studies of risk factors in coronary heart disease: from discovery to application (renewal). (Joint funding with MRC)","funder_award_id":"RG/13/13/30194","funder_id":"https://openalex.org/F4320319992","funder_display_name":"British Heart Foundation"},{"id":"https://openalex.org/G8880254197","display_name":"Industrial Strategy PhD studentships Application from University of Cambridge","funder_award_id":"MR/S502443/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320309229","display_name":"National Institute on Handicapped Research","ror":null},{"id":"https://openalex.org/F4320313269","display_name":"Scottish Government","ror":"https://ror.org/04v2xmd71"},{"id":"https://openalex.org/F4320319990","display_name":"National Institute for Health and Care Research","ror":"https://ror.org/0187kwz08"},{"id":"https://openalex.org/F4320319992","display_name":"British Heart Foundation","ror":"https://ror.org/02wdwnk04"},{"id":"https://openalex.org/F4320319994","display_name":"Department of Health and Social Care","ror":"https://ror.org/03sbpja79"},{"id":"https://openalex.org/F4320320273","display_name":"University of Cambridge","ror":"https://ror.org/013meh722"},{"id":"https://openalex.org/F4320320853","display_name":"Public Health Agency","ror":"https://ror.org/03ek62e72"},{"id":"https://openalex.org/F4320333685","display_name":"Chief Scientist Office, Scottish Government Health and Social Care Directorate","ror":"https://ror.org/01613vh25"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334630","display_name":"Economic and Social Research Council","ror":"https://ror.org/03n0ht308"},{"id":"https://openalex.org/F4320335543","display_name":"Health and Social Care Research and Development Division","ror":null},{"id":"https://openalex.org/F4320336709","display_name":"NIHR Cambridge Biomedical Research Centre","ror":null},{"id":"https://openalex.org/F7757660664","display_name":"Health Data Research UK","ror":"https://ror.org/04rtjaj74"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390743551.pdf"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W2008840001","https://openalex.org/W2039473152","https://openalex.org/W2081375228","https://openalex.org/W2099862356","https://openalex.org/W2120770540","https://openalex.org/W2136957665","https://openalex.org/W2145427519","https://openalex.org/W2149310258","https://openalex.org/W2166020074","https://openalex.org/W2167821759","https://openalex.org/W2343534129","https://openalex.org/W2771169143","https://openalex.org/W2786213090","https://openalex.org/W2980007617","https://openalex.org/W3134169372","https://openalex.org/W3157788795","https://openalex.org/W3180841033","https://openalex.org/W3199468887","https://openalex.org/W3200707343","https://openalex.org/W4200461926","https://openalex.org/W4210302214","https://openalex.org/W4220895458","https://openalex.org/W4283716699","https://openalex.org/W4311070988","https://openalex.org/W4353066697","https://openalex.org/W4392500220","https://openalex.org/W6849246577"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W1998222399"],"abstract_inverted_index":{"MOTIVATION:":[0],"Protein-protein":[1],"interactions":[2,142],"(PPIs)":[3],"are":[4,51,178,218],"essential":[5],"to":[6,47,53,97,181],"understanding":[7],"biological":[8,87],"pathways":[9],"as":[10,12,129],"well":[11],"their":[13,127],"roles":[14],"in":[15,32,141],"development":[16],"and":[17,39,55,88,106,119,167,171,192,206,216],"disease.":[18],"Computational":[19],"tools,":[20],"based":[21],"on":[22,100,122,134,154,220],"classic":[23],"machine":[24],"learning,":[25],"have":[26],"been":[27],"successful":[28],"at":[29],"predicting":[30],"PPIs":[31],"silico,":[33],"but":[34],"the":[35,66,101,130,138],"lack":[36],"of":[37,86,103,190,208],"consistent":[38],"reliable":[40],"frameworks":[41],"for":[42,79,83,202],"this":[43],"task":[44],"has":[45,151],"led":[46],"network":[48,104],"models":[49,121,174],"that":[50,59,70,81,148,173],"difficult":[52],"compare":[54],"discrepancies":[56],"between":[57,164],"algorithms":[58,109],"remain":[60],"unexplained.":[61],"RESULTS:":[62],"To":[63],"better":[64,179],"understand":[65],"underlying":[67],"inference":[68],"mechanisms":[69],"underpin":[71],"these":[72],"models,":[73],"we":[74,125],"designed":[75],"an":[76],"open-source":[77],"framework":[78],"benchmarking":[80],"accounts":[82],"a":[84,199],"range":[85],"statistical":[89],"pitfalls":[90],"while":[91,137],"facilitating":[92],"reproducibility.":[93],"We":[94,145,160],"use":[95],"it":[96],"shed":[98],"light":[99],"impact":[102,153],"topology":[105],"how":[107],"different":[108],"deal":[110],"with":[111,156],"highly":[112],"connected":[113],"proteins.":[114],"By":[115],"studying":[116],"functional":[117,157,176,193],"genomics-based":[118],"sequence-based":[120],"human":[123,166],"PPIs,":[124],"show":[126,147],"complementarity":[128],"former":[131],"performs":[132],"best":[133],"lone":[135],"proteins":[136],"latter":[139],"specializes":[140],"involving":[143],"hubs.":[144],"also":[146],"algorithm":[149],"design":[150],"little":[152],"performance":[155],"genomic":[158],"data.":[159],"replicate":[161],"our":[162,196],"results":[163],"both":[165],"S.":[168],"cerevisiae":[169],"data":[170,217],"demonstrate":[172],"using":[175],"genomics":[177,194],"suited":[180],"PPI":[182,209],"prediction":[183],"across":[184],"species.":[185],"With":[186],"rapidly":[187],"increasing":[188],"amounts":[189],"sequence":[191],"data,":[195],"study":[197],"provides":[198],"principled":[200],"foundation":[201],"future":[203],"construction,":[204],"comparison,":[205],"application":[207],"networks.":[210],"AVAILABILITY":[211],"AND":[212],"IMPLEMENTATION:":[213],"The":[214],"code":[215],"available":[219],"GitHub:":[221],"https://github.com/Llannelongue/B4PPI.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
