{"id":"https://openalex.org/W2150902060","doi":"https://doi.org/10.1093/bioinformatics/btn036","title":"From pull-down data to protein interaction networks and complexes with biological relevance","display_name":"From pull-down data to protein interaction networks and complexes with biological relevance","publication_year":2008,"publication_date":"2008-02-26","ids":{"openalex":"https://openalex.org/W2150902060","doi":"https://doi.org/10.1093/bioinformatics/btn036","mag":"2150902060"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn036","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn036","pdf_url":null,"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"],"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/A5100389664","display_name":"Bing Zhang","orcid":"https://orcid.org/0000-0001-8676-2425"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bing Zhang","raw_affiliation_strings":["1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2Computer Science Department, North Carolina State University, Raleigh, NC 27695, USA"],"affiliations":[{"raw_affiliation_string":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2Computer Science Department, North Carolina State University, Raleigh, NC 27695, USA","institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075057162","display_name":"Byung Hoon Park","orcid":"https://orcid.org/0000-0002-0342-4656"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Byung-Hoon Park","raw_affiliation_strings":["1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2Computer Science Department, North Carolina State University, Raleigh, NC 27695, USA"],"affiliations":[{"raw_affiliation_string":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2Computer Science Department, North Carolina State University, Raleigh, NC 27695, USA","institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087636420","display_name":"Tatiana V. Karpinets","orcid":"https://orcid.org/0000-0002-3668-8148"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]},{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tatiana Karpinets","raw_affiliation_strings":["1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2Computer Science Department, North Carolina State University, Raleigh, NC 27695, USA"],"affiliations":[{"raw_affiliation_string":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2Computer Science Department, North Carolina State University, Raleigh, NC 27695, USA","institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I137902535"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040551107","display_name":"Nagiza F. Samatova","orcid":null},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]},{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nagiza F. Samatova","raw_affiliation_strings":["1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2Computer Science Department, North Carolina State University, Raleigh, NC 27695, USA"],"affiliations":[{"raw_affiliation_string":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2Computer Science Department, North Carolina State University, Raleigh, NC 27695, USA","institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I137902535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100389664"],"corresponding_institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I137902535"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":6.6387,"has_fulltext":false,"cited_by_count":152,"citation_normalized_percentile":{"value":0.97531255,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"24","issue":"7","first_page":"979","last_page":"986"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9976999759674072,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9976000189781189,"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/false-positive-paradox","display_name":"False positive paradox","score":0.7586085796356201},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6512433290481567},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.6502853035926819},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.5995182991027832},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5614806413650513},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5501238107681274},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.48967626690864563},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4595860540866852},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.28107982873916626},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2680026888847351},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2634879946708679},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19181343913078308},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1537914276123047}],"concepts":[{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.7586085796356201},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6512433290481567},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.6502853035926819},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.5995182991027832},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5614806413650513},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5501238107681274},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.48967626690864563},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4595860540866852},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.28107982873916626},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2680026888847351},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2634879946708679},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19181343913078308},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1537914276123047},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btn036","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn036","pdf_url":null,"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"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.44999998807907104,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W119257584","https://openalex.org/W1530803355","https://openalex.org/W1644749979","https://openalex.org/W1975304761","https://openalex.org/W1980548655","https://openalex.org/W1987604884","https://openalex.org/W1997504014","https://openalex.org/W2010577059","https://openalex.org/W2018642282","https://openalex.org/W2040411864","https://openalex.org/W2050721857","https://openalex.org/W2053906518","https://openalex.org/W2063543381","https://openalex.org/W2076710572","https://openalex.org/W2083872341","https://openalex.org/W2084619201","https://openalex.org/W2091181826","https://openalex.org/W2101833102","https://openalex.org/W2103017472","https://openalex.org/W2106119591","https://openalex.org/W2110587743","https://openalex.org/W2116117181","https://openalex.org/W2116447934","https://openalex.org/W2122536523","https://openalex.org/W2123898323","https://openalex.org/W2124166542","https://openalex.org/W2127563440","https://openalex.org/W2133894503","https://openalex.org/W2136850043","https://openalex.org/W2138247507","https://openalex.org/W2142084170","https://openalex.org/W2145144660","https://openalex.org/W2152495216","https://openalex.org/W2155335955","https://openalex.org/W2163480486","https://openalex.org/W2164928285","https://openalex.org/W2914844703","https://openalex.org/W6632011196","https://openalex.org/W6671541239"],"related_works":["https://openalex.org/W2800059693","https://openalex.org/W37860747","https://openalex.org/W2066232588","https://openalex.org/W4377086792","https://openalex.org/W2099913238","https://openalex.org/W2767490506","https://openalex.org/W1987705964","https://openalex.org/W4226462951","https://openalex.org/W2069244164","https://openalex.org/W2106286319"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Recent":[2],"improvements":[3],"in":[4,25,46,169,183,228,238],"high-throughput":[5],"Mass":[6],"Spectrometry":[7],"(MS)":[8],"technology":[9],"have":[10],"expedited":[11],"genome-wide":[12],"discovery":[13,65],"of":[14,21,31,55,61,66,71,101,149,190,199,204,222],"protein\u2013protein":[15,56],"interactions":[16],"by":[17,115,165,210],"providing":[18],"a":[19,26,111,117,136,141,211,220],"capability":[20],"detecting":[22],"protein":[23,32,36,62,67,83,112,128,174,206],"complexes":[24,37,68,84,129,175,192,207],"physiological":[27],"setting.":[28],"Computational":[29],"inference":[30],"interaction":[33,57,63,93,113],"networks":[34],"and":[35,49,69,130,171],"from":[38,85,106],"MS":[39,86,107],"data":[40,88,246],"are":[41,44,247],"challenging.":[42],"Advances":[43],"required":[45],"developing":[47],"robust":[48],"seamlessly":[50],"integrated":[51],"procedures":[52],"for":[53,81],"assessment":[54],"affinities,":[58],"mathematical":[59],"representation":[60],"networks,":[64],"evaluation":[70,143],"their":[72,102,132],"biological":[73,147],"relevance.":[74],"Results:":[75],"A":[76],"multi-step":[77],"but":[78],"easy-to-follow":[79],"framework":[80,159],"identifying":[82],"pull-down":[87,156,229],"is":[89],"introduced.":[90],"It":[91,109,139],"assesses":[92],"affinity":[94],"between":[95],"two":[96],"proteins":[97],"based":[98,179],"on":[99,123,180,197],"similarity":[100],"co-purification":[103,203],"patterns":[104],"derived":[105],"data.":[108],"constructs":[110],"network":[114],"adopting":[116],"knowledge-guided":[118],"threshold":[119],"selection":[120],"method.":[121],"Based":[122],"the":[124,158,181,191,195,233],"network,":[125],"it":[126],"identifies":[127],"infers":[131],"core":[133],"components":[134],"using":[135],"graph-theoretical":[137],"approach.":[138],"deploys":[140],"statistical":[142],"procedure":[144],"to":[145],"assess":[146],"relevance":[148],"each":[150],"found":[151],"complex.":[152],"On":[153],"Saccharomyces":[154],"cerevisiae":[155],"data,":[157],"outperformed":[160],"other":[161],"more":[162],"complicated":[163],"schemes":[164],"at":[166,249],"least":[167],"10%":[168],"F1-measure":[170],"identified":[172],"610":[173],"with":[176],"high-functional":[177],"homogeneity":[178],"enrichment":[182],"Gene":[184],"Ontology":[185],"(GO)":[186],"annotation.":[187],"Manual":[188],"examination":[189],"brought":[193],"forward":[194],"hypotheses":[196],"cause":[198],"false":[200,223,239],"identifications.":[201],"Namely,":[202],"different":[205],"as":[208,216,232],"mediated":[209],"common":[212],"non-protein":[213],"molecule,":[214],"such":[215,231],"DNA,":[217],"might":[218],"be":[219],"source":[221],"positives.":[224],"Protein":[225],"identification":[226],"bias":[227,235],"technology,":[230],"hydrophilic":[234],"could":[236],"result":[237],"negatives.":[240],"Contact:":[241],"samatovan@ornl.gov":[242],"Supplementary":[243,245],"information:":[244],"available":[248],"Bioinformatics":[250],"online.":[251]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":23},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":14},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":10}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}