{"id":"https://openalex.org/W1987990369","doi":"https://doi.org/10.1155/asp/2006/37349","title":"Towards Inferring Protein Interactions: Challenges and Solutions","display_name":"Towards Inferring Protein Interactions: Challenges and Solutions","publication_year":2006,"publication_date":"2006-04-05","ids":{"openalex":"https://openalex.org/W1987990369","doi":"https://doi.org/10.1155/asp/2006/37349","mag":"1987990369"},"language":"en","primary_location":{"id":"doi:10.1155/asp/2006/37349","is_oa":true,"landing_page_url":"https://doi.org/10.1155/asp/2006/37349","pdf_url":"https://asp-eurasipjournals.springeropen.com/counter/pdf/10.1155/ASP/2006/37349","source":{"id":"https://openalex.org/S35920007","display_name":"EURASIP Journal on Advances in Signal Processing","issn_l":"1687-6172","issn":["1687-6172","1687-6180"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"EURASIP Journal on Advances in Signal Processing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://asp-eurasipjournals.springeropen.com/counter/pdf/10.1155/ASP/2006/37349","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100342828","display_name":"Ya Zhang","orcid":"https://orcid.org/0000-0002-5390-9053"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ya Zhang","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, The University of Kansas, Lawrence, KS, 66045, USA","Information and Telecommunication Technology Center, The University of Kansas, Lawrence, KS, 66045, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, The University of Kansas, Lawrence, KS, 66045, USA","institution_ids":["https://openalex.org/I146416000"]},{"raw_affiliation_string":"Information and Telecommunication Technology Center, The University of Kansas, Lawrence, KS, 66045, USA","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046703129","display_name":"Hongyuan Zha","orcid":"https://orcid.org/0000-0001-7493-0911"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongyuan Zha","raw_affiliation_strings":["Department of Computer Science and Engineering, School of Engineering, Pennsylvania State University, University Park, PA, 16802, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, School of Engineering, Pennsylvania State University, University Park, PA, 16802, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091632693","display_name":"Chao\u2010Hsien Chu","orcid":"https://orcid.org/0000-0001-6274-5153"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chao-Hsien Chu","raw_affiliation_strings":["College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, 16802-6823, USA"],"affiliations":[{"raw_affiliation_string":"College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, 16802-6823, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101627715","display_name":"Xiang Ji","orcid":"https://orcid.org/0000-0002-0539-8244"},"institutions":[{"id":"https://openalex.org/I4210107353","display_name":"NEC (United States)","ror":"https://ror.org/01v791m31","country_code":"US","type":"company","lineage":["https://openalex.org/I118347220","https://openalex.org/I4210107353"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiang Ji","raw_affiliation_strings":["NEC Laboratories America, Inc., Cupertino, CA, 95014, USA"],"affiliations":[{"raw_affiliation_string":"NEC Laboratories America, Inc., Cupertino, CA, 95014, USA","institution_ids":["https://openalex.org/I4210107353"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100342828"],"corresponding_institution_ids":["https://openalex.org/I146416000"],"apc_list":{"value":1140,"currency":"GBP","value_usd":1398},"apc_paid":{"value":1140,"currency":"GBP","value_usd":1398},"fwci":0.681,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.66780133,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"2006","issue":"1","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":0.9990000128746033,"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":0.9990000128746033,"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":0.9948999881744385,"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":0.9915000200271606,"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/interactome","display_name":"Interactome","score":0.8735835552215576},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.732191801071167},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6217113733291626},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5873475670814514},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5754328370094299},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.49936962127685547},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4951113760471344},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.47634580731391907},{"id":"https://openalex.org/keywords/satisfiability","display_name":"Satisfiability","score":0.46791985630989075},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.452075719833374},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3571890592575073},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.26931434869766235},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1557619273662567},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10053858160972595}],"concepts":[{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.8735835552215576},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.732191801071167},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6217113733291626},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5873475670814514},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5754328370094299},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.49936962127685547},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4951113760471344},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.47634580731391907},{"id":"https://openalex.org/C168773769","wikidata":"https://www.wikidata.org/wiki/Q1350299","display_name":"Satisfiability","level":2,"score":0.46791985630989075},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.452075719833374},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3571890592575073},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26931434869766235},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1557619273662567},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10053858160972595},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1155/asp/2006/37349","is_oa":true,"landing_page_url":"https://doi.org/10.1155/asp/2006/37349","pdf_url":"https://asp-eurasipjournals.springeropen.com/counter/pdf/10.1155/ASP/2006/37349","source":{"id":"https://openalex.org/S35920007","display_name":"EURASIP Journal on Advances in Signal Processing","issn_l":"1687-6172","issn":["1687-6172","1687-6180"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"EURASIP Journal on Advances in Signal Processing","raw_type":"journal-article"},{"id":"pmh:oai:ink.library.smu.edu.sg:sis_research-2789","is_oa":true,"landing_page_url":"https://ink.library.smu.edu.sg/sis_research/1790","pdf_url":null,"source":{"id":"https://openalex.org/S4377196871","display_name":"Institutional Knowledge (InK) - Institutional Knowledge at Singapore Management University (Singapore Management University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79891267","host_organization_name":"Singapore Management University","host_organization_lineage":["https://openalex.org/I79891267"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://dx.doi.org/10.1155/ASP/2006/37349","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:7d8fa3a2635b40439edfcedd0ea87df4","is_oa":true,"landing_page_url":"https://doaj.org/article/7d8fa3a2635b40439edfcedd0ea87df4","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"EURASIP Journal on Advances in Signal Processing, Vol 2006, Iss 1, p 037349 (2006)","raw_type":"article"},{"id":"pmh:oai:kuscholarworks.ku.edu:1808/14064","is_oa":true,"landing_page_url":"http://hdl.handle.net/1808/14064","pdf_url":null,"source":{"id":"https://openalex.org/S4306400421","display_name":"KU ScholarWorks (The University of Kansas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I146416000","host_organization_name":"University of Kansas","host_organization_lineage":["https://openalex.org/I146416000"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1155/asp/2006/37349","is_oa":true,"landing_page_url":"https://doi.org/10.1155/asp/2006/37349","pdf_url":"https://asp-eurasipjournals.springeropen.com/counter/pdf/10.1155/ASP/2006/37349","source":{"id":"https://openalex.org/S35920007","display_name":"EURASIP Journal on Advances in Signal Processing","issn_l":"1687-6172","issn":["1687-6172","1687-6180"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"EURASIP Journal on Advances in Signal Processing","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1987990369.pdf","grobid_xml":"https://content.openalex.org/works/W1987990369.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W140201965","https://openalex.org/W156009831","https://openalex.org/W1559606743","https://openalex.org/W1966421023","https://openalex.org/W1980334039","https://openalex.org/W1993837454","https://openalex.org/W2015961921","https://openalex.org/W2036185701","https://openalex.org/W2037036397","https://openalex.org/W2048762035","https://openalex.org/W2055043387","https://openalex.org/W2057885377","https://openalex.org/W2065304353","https://openalex.org/W2080922074","https://openalex.org/W2107340752","https://openalex.org/W2107424557","https://openalex.org/W2107811186","https://openalex.org/W2109715166","https://openalex.org/W2111669058","https://openalex.org/W2123206403","https://openalex.org/W2133654213","https://openalex.org/W2137786672","https://openalex.org/W2141885858","https://openalex.org/W2144231753","https://openalex.org/W2145753039","https://openalex.org/W2146312020","https://openalex.org/W2150926065","https://openalex.org/W2154975737","https://openalex.org/W2155436344","https://openalex.org/W2166558964","https://openalex.org/W2167869241","https://openalex.org/W4210400672","https://openalex.org/W4237572013","https://openalex.org/W4250915400","https://openalex.org/W4252706339","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2152546257","https://openalex.org/W2018720220","https://openalex.org/W1500663296","https://openalex.org/W4252442860","https://openalex.org/W3159731292","https://openalex.org/W2178844921","https://openalex.org/W2162117109","https://openalex.org/W2392586760","https://openalex.org/W4319230148","https://openalex.org/W2157795344"],"abstract_inverted_index":{"Discovering":[0],"interacting":[1,181],"proteins":[2],"has":[3],"been":[4,62],"an":[5],"essential":[6],"part":[7],"of":[8,20,46,53,82,111,140,171,186,193],"functional":[9],"genomics.":[10],"However,":[11],"existing":[12],"experimental":[13],"techniques":[14],"only":[15],"uncover":[16],"a":[17,28,42,147,159],"small":[18],"portion":[19],"any":[21],"interactome.":[22],"Furthermore,":[23],"these":[24],"data":[25,162],"often":[26],"have":[27,61,164],"very":[29],"high":[30],"false":[31],"rate.":[32],"By":[33],"conceptualizing":[34],"the":[35,51,80,109,130,166,169,172,191],"interactions":[36,73,91,106,114,134],"at":[37],"domain":[38,72,103,113,136],"level,":[39],"we":[40,176],"provide":[41],"more":[43],"abstract":[44],"representation":[45,125],"interactome,":[47],"which":[48,115],"also":[49,177],"facilitates":[50],"discovery":[52],"unobserved":[54],"protein-protein":[55,66],"interactions.":[56,104,137],"Although":[57],"several":[58],"domain-based":[59],"approaches":[60],"proposed":[63,93,173],"to":[64,88,128,183,189],"predict":[65,89],"interactions,":[67],"they":[68],"usually":[69],"assume":[70],"that":[71],"are":[74,116],"independent":[75],"on":[76,118,158],"each":[77,119],"other":[78],"for":[79],"convenience":[81],"computational":[83],"modeling.":[84],"A":[85,121],"new":[86],"framework":[87],"protein":[90,133,187],"is":[92,100,126,143],"in":[94],"this":[95],"paper,":[96],"where":[97],"no":[98],"assumption":[99],"made":[101],"about":[102],"Protein":[105],"may":[107],"be":[108],"result":[110],"multiple":[112],"dependent":[117],"other.":[120],"conjunctive":[122],"norm":[123],"form":[124],"used":[127],"capture":[129],"relationships":[131],"between":[132],"and":[135,151,168],"The":[138],"problem":[139,150],"interaction":[141],"inference":[142],"then":[144],"modeled":[145],"as":[146],"constraint":[148],"satisfiability":[149],"solved":[152],"via":[153],"linear":[154],"programing.":[155],"Experimental":[156],"results":[157],"combined":[160],"yeast":[161],"set":[163],"demonstrated":[165],"robustness":[167],"accuracy":[170],"algorithm.":[174],"Moreover,":[175],"map":[178],"some":[179],"predicted":[180],"domains":[182],"three-dimensional":[184],"structures":[185],"complexes":[188],"show":[190],"validity":[192],"our":[194],"predictions.":[195]},"counts_by_year":[{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
