{"id":"https://openalex.org/W1576210418","doi":"https://doi.org/10.1109/csb.2004.1332435","title":"Estimating and improving protein interaction error rates","display_name":"Estimating and improving protein interaction error rates","publication_year":2004,"publication_date":"2004-11-08","ids":{"openalex":"https://openalex.org/W1576210418","doi":"https://doi.org/10.1109/csb.2004.1332435","mag":"1576210418","pmid":"https://pubmed.ncbi.nlm.nih.gov/16448015"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2004.1332435","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332435","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063057754","display_name":"Patrik D\u2019haeseleer","orcid":"https://orcid.org/0000-0003-0007-8150"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210105714","display_name":"Center for Human Genetics","ror":"https://ror.org/01gcrbc43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210105714"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. D'haeseleer","raw_affiliation_strings":["Lipper Center for Computational Genetics, Harvard Medical School, USA. patrik@genetics.med.harvard.edu","Lipper Center for Comput. Genetics, Harvard Med. Sch., Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lipper Center for Computational Genetics, Harvard Medical School, USA. patrik@genetics.med.harvard.edu","institution_ids":["https://openalex.org/I4210105714"]},{"raw_affiliation_string":"Lipper Center for Comput. Genetics, Harvard Med. Sch., Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103076360","display_name":"George M. Church","orcid":"https://orcid.org/0000-0003-3535-2076"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G.M. Church","raw_affiliation_strings":["Lipper Center for Computational Genetics, Harvard Medical School, USA","Lipper Center for Comput. Genetics, Harvard Med. Sch., Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lipper Center for Computational Genetics, Harvard Medical School, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Lipper Center for Comput. Genetics, Harvard Med. Sch., Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":45,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"403","issue":null,"first_page":"208","last_page":"215"},"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/T10497","display_name":"Fungal and yeast genetics research","score":0.9904999732971191,"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":0.9872999787330627,"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":0.6439819931983948},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6055512428283691},{"id":"https://openalex.org/keywords/reliability","display_name":"Reliability (semiconductor)","score":0.5964985489845276},{"id":"https://openalex.org/keywords/word-error-rate","display_name":"Word error rate","score":0.575268566608429},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5127211809158325},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.5048955082893372},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.488677054643631},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.4577005207538605},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4414484202861786},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4400044083595276},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3212435245513916},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24981310963630676},{"id":"https://openalex.org/keywords/power","display_name":"Power (physics)","score":0.13543227314949036}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6439819931983948},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6055512428283691},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.5964985489845276},{"id":"https://openalex.org/C40969351","wikidata":"https://www.wikidata.org/wiki/Q3516228","display_name":"Word error rate","level":2,"score":0.575268566608429},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5127211809158325},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.5048955082893372},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.488677054643631},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.4577005207538605},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4414484202861786},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4400044083595276},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3212435245513916},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24981310963630676},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.13543227314949036},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020798","descriptor_name":"Two-Hybrid System Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020798","descriptor_name":"Two-Hybrid System Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020798","descriptor_name":"Two-Hybrid System Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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}],"locations_count":2,"locations":[{"id":"doi:10.1109/csb.2004.1332435","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332435","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"},{"id":"pmid:16448015","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16448015","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":"Proceedings. IEEE Computational Systems Bioinformatics Conference","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1994191814","https://openalex.org/W2027439534","https://openalex.org/W2037036397","https://openalex.org/W2040411864","https://openalex.org/W2053906518","https://openalex.org/W2065304353","https://openalex.org/W2079007492","https://openalex.org/W2080182143","https://openalex.org/W2082367094","https://openalex.org/W2084619201","https://openalex.org/W2092568200","https://openalex.org/W2099913238","https://openalex.org/W2101803429","https://openalex.org/W2113654464","https://openalex.org/W2121507105","https://openalex.org/W2131532450","https://openalex.org/W2133894503","https://openalex.org/W2137786672","https://openalex.org/W2145753039","https://openalex.org/W2149310258","https://openalex.org/W2155436344","https://openalex.org/W2158597576","https://openalex.org/W2164021883","https://openalex.org/W2167869241","https://openalex.org/W2168702870","https://openalex.org/W2172049947","https://openalex.org/W2427191465","https://openalex.org/W4236956086"],"related_works":["https://openalex.org/W2136583354","https://openalex.org/W2111238207","https://openalex.org/W2012531322","https://openalex.org/W2402761219","https://openalex.org/W2760721665","https://openalex.org/W2785900585","https://openalex.org/W2353730437","https://openalex.org/W2490303674","https://openalex.org/W2609066826","https://openalex.org/W2810752900"],"abstract_inverted_index":{"High":[0],"throughput":[1],"protein":[2,79,110],"interaction":[3,80],"data":[4,81,91,134,138],"sets":[5,92],"have":[6],"proven":[7],"to":[8,16,161],"be":[9,53,121],"notoriously":[10],"noisy.":[11],"Although":[12],"it":[13],"is":[14],"possible":[15],"focus":[17],"on":[18],"interactions":[19,63,88,111,155],"with":[20,60,77,86],"higher":[21],"reliability":[22],"by":[23,31,55],"using":[24],"only":[25],"those":[26],"that":[27],"are":[28],"backed":[29],"up":[30],"two":[32],"or":[33],"more":[34,49],"lines":[35],"of":[36,45,109,116,132,154,159],"evidence,":[37],"this":[38],"approach":[39],"invariably":[40],"throws":[41],"out":[42],"the":[43,57,65,90,106,133,149],"majority":[44],"available":[46,62],"data.":[47],"A":[48],"optimal":[50,164],"use":[51],"could":[52],"achieved":[54],"incorporating":[56],"probabilities":[58],"associated":[59,76],"all":[61],"into":[64],"analysis.":[66],"We":[67],"present":[68],"a":[69,98,127,146],"novel":[70],"method":[71],"for":[72,105],"estimating":[73],"error":[74,167],"rates":[75],"specific":[78],"sets,":[82,139],"as":[83,85],"well":[84],"individual":[87],"given":[89],"in":[93,112,126,130],"which":[94],"they":[95],"appear.":[96],"As":[97],"bonus,":[99],"we":[100,140,143],"also":[101],"get":[102],"an":[103,163],"estimate":[104],"total":[107],"number":[108],"yeast.":[113],"Certain":[114],"types":[115],"false":[117,165],"positive":[118,166],"results":[119],"can":[120,144],"identified":[122],"and":[123,151],"removed,":[124],"resulting":[125],"significant":[128],"improvement":[129],"quality":[131],"set.":[135],"For":[136],"co-purification":[137],"show":[141],"how":[142],"reach":[145],"tradeoff":[147],"between":[148],"\"spoke\"":[150],"\"matrix\"":[152],"representation":[153],"within":[156],"co-purified":[157],"groups":[158],"proteins":[160],"achieve":[162],"rate.":[168]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
