{"id":"https://openalex.org/W2167821759","doi":"https://doi.org/10.1093/bioinformatics/btr514","title":"Revisiting the negative example sampling problem for predicting protein\u2013protein interactions","display_name":"Revisiting the negative example sampling problem for predicting protein\u2013protein interactions","publication_year":2011,"publication_date":"2011-09-09","ids":{"openalex":"https://openalex.org/W2167821759","doi":"https://doi.org/10.1093/bioinformatics/btr514","mag":"2167821759","pmid":"https://pubmed.ncbi.nlm.nih.gov/21908540"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr514","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr514","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/21/3024/48862842/bioinformatics_27_21_3024.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/27/21/3024/48862842/bioinformatics_27_21_3024.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029119720","display_name":"Yungki Park","orcid":null},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yungki Park","raw_affiliation_strings":["Center for Systems and Synthetic Biology, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA"],"affiliations":[{"raw_affiliation_string":"Center for Systems and Synthetic Biology, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079751395","display_name":"Edward M. Marcotte","orcid":"https://orcid.org/0000-0001-8808-180X"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward M. Marcotte","raw_affiliation_strings":["Center for Systems and Synthetic Biology, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA"],"affiliations":[{"raw_affiliation_string":"Center for Systems and Synthetic Biology, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA","institution_ids":["https://openalex.org/I86519309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5029119720"],"corresponding_institution_ids":["https://openalex.org/I86519309"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.3903,"has_fulltext":false,"cited_by_count":68,"citation_normalized_percentile":{"value":0.89235621,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"27","issue":"21","first_page":"3024","last_page":"3028"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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":0.9993000030517578,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9891999959945679,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9891999959945679,"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/sampling","display_name":"Sampling (signal processing)","score":0.6386033296585083},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6304067373275757},{"id":"https://openalex.org/keywords/confusion","display_name":"Confusion","score":0.5881054997444153},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.52321457862854},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.49294400215148926},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44393986463546753},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.43993955850601196},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.43138325214385986},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38126569986343384},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1613539159297943},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.0992216169834137},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.08736428618431091},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07679232954978943}],"concepts":[{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.6386033296585083},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6304067373275757},{"id":"https://openalex.org/C2781140086","wikidata":"https://www.wikidata.org/wiki/Q557945","display_name":"Confusion","level":2,"score":0.5881054997444153},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.52321457862854},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.49294400215148926},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44393986463546753},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.43993955850601196},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.43138325214385986},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38126569986343384},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1613539159297943},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0992216169834137},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.08736428618431091},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07679232954978943},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C11171543","wikidata":"https://www.wikidata.org/wiki/Q41630","display_name":"Psychoanalysis","level":1,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btr514","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr514","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/21/3024/48862842/bioinformatics_27_21_3024.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:21908540","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21908540","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:open-archive.highwire.org:bioinfo:27/21/3024","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/21/3024","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:3198576","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3198576","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr514","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr514","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/21/3024/48862842/bioinformatics_27_21_3024.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":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2167821759.pdf","grobid_xml":"https://content.openalex.org/works/W2167821759.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1576520375","https://openalex.org/W1604938182","https://openalex.org/W1982267716","https://openalex.org/W1985967447","https://openalex.org/W1987582651","https://openalex.org/W2006124679","https://openalex.org/W2050721857","https://openalex.org/W2065304353","https://openalex.org/W2074019887","https://openalex.org/W2080922074","https://openalex.org/W2097651291","https://openalex.org/W2099862356","https://openalex.org/W2107340752","https://openalex.org/W2109248504","https://openalex.org/W2116089841","https://openalex.org/W2116117181","https://openalex.org/W2120770540","https://openalex.org/W2122863289","https://openalex.org/W2127637605","https://openalex.org/W2130687290","https://openalex.org/W2136957665","https://openalex.org/W2137959503","https://openalex.org/W2150452800","https://openalex.org/W2152705149","https://openalex.org/W2153635508","https://openalex.org/W2156125289","https://openalex.org/W2164289561","https://openalex.org/W2167869241","https://openalex.org/W2170525533","https://openalex.org/W6634442568"],"related_works":["https://openalex.org/W4285488523","https://openalex.org/W2407837381","https://openalex.org/W2011367623","https://openalex.org/W2049289069","https://openalex.org/W2734065904","https://openalex.org/W2067843453","https://openalex.org/W4239320552","https://openalex.org/W2392692716","https://openalex.org/W2004845836","https://openalex.org/W2743639087"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":10}],"updated_date":"2026-03-09T08:58:05.943551","created_date":"2025-10-10T00:00:00"}