{"id":"https://openalex.org/W2890911678","doi":"https://doi.org/10.1093/bioinformatics/bty573","title":"Predicting protein\u2013protein interactions through sequence-based deep learning","display_name":"Predicting protein\u2013protein interactions through sequence-based deep learning","publication_year":2018,"publication_date":"2018-07-06","ids":{"openalex":"https://openalex.org/W2890911678","doi":"https://doi.org/10.1093/bioinformatics/bty573","mag":"2890911678","pmid":"https://pubmed.ncbi.nlm.nih.gov/30423091"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i802/25702563/bty573.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i802/25702563/bty573.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003431320","display_name":"Somaye Hashemifar","orcid":"https://orcid.org/0000-0001-9554-8519"},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Somaye Hashemifar","raw_affiliation_strings":["Toyota Technological Institute at Chicago, Chicago, IL, USA"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I160992636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035369215","display_name":"Behnam Neyshabur","orcid":null},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Behnam Neyshabur","raw_affiliation_strings":["Toyota Technological Institute at Chicago, Chicago, IL, USA"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I160992636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006360401","display_name":"Aly A. Khan","orcid":"https://orcid.org/0000-0003-3933-8538"},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aly A Khan","raw_affiliation_strings":["Toyota Technological Institute at Chicago, Chicago, IL, USA"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I160992636"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019398608","display_name":"Jinbo Xu","orcid":"https://orcid.org/0000-0001-7111-4839"},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jinbo Xu","raw_affiliation_strings":["Toyota Technological Institute at Chicago, Chicago, IL, USA"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I160992636"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5019398608"],"corresponding_institution_ids":["https://openalex.org/I160992636"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":13.3614,"has_fulltext":true,"cited_by_count":389,"citation_normalized_percentile":{"value":0.99341746,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"34","issue":"17","first_page":"i802","last_page":"i810"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9930999875068665,"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":0.7786509394645691},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6097104549407959},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5618436336517334},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5351992845535278},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5333749055862427},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.48445963859558105},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43971046805381775},{"id":"https://openalex.org/keywords/projection","display_name":"Projection (relational algebra)","score":0.43768033385276794},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.1669497787952423},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10573074221611023}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7786509394645691},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6097104549407959},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5618436336517334},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5351992845535278},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5333749055862427},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.48445963859558105},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43971046805381775},{"id":"https://openalex.org/C57493831","wikidata":"https://www.wikidata.org/wiki/Q3134666","display_name":"Projection (relational algebra)","level":2,"score":0.43768033385276794},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.1669497787952423},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10573074221611023},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i802/25702563/bty573.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30423091","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30423091","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:europepmc.org:5675860","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6129267","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i802/25702563/bty573.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2229035017","display_name":null,"funder_award_id":"R01GM089753","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3749801296","display_name":"AF:III: small: Convex optimization for protein-protein interaction network alignment","funder_award_id":"1618648","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7430159341","display_name":null,"funder_award_id":"AF-1618648","funder_id":"https://openalex.org/F4320337387","funder_display_name":"Division of Computing and Communication Foundations"},{"id":"https://openalex.org/G8288036582","display_name":null,"funder_award_id":"NIH R01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337387","display_name":"Division of Computing and Communication Foundations","ror":"https://ror.org/01mng8331"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2890911678.pdf","grobid_xml":"https://content.openalex.org/works/W2890911678.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W76924599","https://openalex.org/W104184427","https://openalex.org/W1576278180","https://openalex.org/W1806891645","https://openalex.org/W1836465849","https://openalex.org/W1886978693","https://openalex.org/W1982267716","https://openalex.org/W1985919127","https://openalex.org/W1995918845","https://openalex.org/W2011340259","https://openalex.org/W2025768430","https://openalex.org/W2031772330","https://openalex.org/W2053330214","https://openalex.org/W2070665556","https://openalex.org/W2075582876","https://openalex.org/W2079818352","https://openalex.org/W2084949662","https://openalex.org/W2095691234","https://openalex.org/W2099862356","https://openalex.org/W2107867854","https://openalex.org/W2119583098","https://openalex.org/W2120836664","https://openalex.org/W2127589108","https://openalex.org/W2127637605","https://openalex.org/W2130687290","https://openalex.org/W2140883620","https://openalex.org/W2150452800","https://openalex.org/W2152705149","https://openalex.org/W2161922860","https://openalex.org/W2162392441","https://openalex.org/W2171590421","https://openalex.org/W2178832778","https://openalex.org/W2405065882","https://openalex.org/W2558534012","https://openalex.org/W2616246685","https://openalex.org/W2618265628","https://openalex.org/W2952371400","https://openalex.org/W2963304263","https://openalex.org/W4302375066","https://openalex.org/W6604254268","https://openalex.org/W6638667902","https://openalex.org/W6639204139","https://openalex.org/W6639512201","https://openalex.org/W6679208599","https://openalex.org/W6701650085","https://openalex.org/W6713638429","https://openalex.org/W6729642067"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W2611989081","https://openalex.org/W4321487865","https://openalex.org/W4313906399","https://openalex.org/W4239306820","https://openalex.org/W4226493464","https://openalex.org/W3133861977","https://openalex.org/W2951211570","https://openalex.org/W3103566983","https://openalex.org/W4380075502"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":59},{"year":2024,"cited_by_count":62},{"year":2023,"cited_by_count":54},{"year":2022,"cited_by_count":62},{"year":2021,"cited_by_count":68},{"year":2020,"cited_by_count":46},{"year":2019,"cited_by_count":29},{"year":2018,"cited_by_count":1}],"updated_date":"2026-03-22T08:09:32.410652","created_date":"2025-10-10T00:00:00"}
