{"id":"https://openalex.org/W2240572358","doi":null,"title":"Protein functionality analysis through protein-protein interaction networks","display_name":"Protein functionality analysis through protein-protein interaction networks","publication_year":2011,"publication_date":"2011-01-01","ids":{"openalex":"https://openalex.org/W2240572358","mag":"2240572358"},"language":"en","primary_location":{"id":"mag:2240572358","doi":null,"is_oa":false,"landing_page_url":"https://dl.acm.org/citation.cfm?id=2231461","pdf_url":null,"source":{"id":"https://openalex.org/S4306508160","display_name":"Dissertations & Theses @ SUNY Buffalo,ProQuest Dissertations & Theses Global","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":"Dissertations & Theses @ SUNY Buffalo,ProQuest Dissertations & Theses Global","raw_type":null},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"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/A5013588572","display_name":"Aidong Zhang","orcid":"https://orcid.org/0000-0001-9723-3246","observed_orcids":["https://orcid.org/0000-0001-9723-3246"]},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aidong Zhang","raw_affiliation_strings":["State University of New York at Buffalo"],"raw_orcid":"https://orcid.org/0000-0001-9723-3246","affiliations":[{"raw_affiliation_string":"State University of New York at Buffalo","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100658547","display_name":"Lei Shi","orcid":"https://orcid.org/0000-0002-1965-2602","observed_orcids":["https://orcid.org/0000-0002-1965-2602"]},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lei Shi","raw_affiliation_strings":["State University of New York at Buffalo"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State University of New York at Buffalo","institution_ids":["https://openalex.org/I63190737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I63190737"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":9.999999747378752e-05,"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":9.999999747378752e-05,"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/protein-function-prediction","display_name":"protein function prediction","score":0.8999999761581421},{"id":"https://openalex.org/keywords/protein-protein-interaction-network","display_name":"protein-protein interaction network","score":0.9890000224113464},{"id":"https://openalex.org/keywords/protein-complexes","display_name":"protein complexes","score":0.5070000290870667},{"id":"https://openalex.org/keywords/protein-localization","display_name":"protein localization","score":0.48100000619888306},{"id":"https://openalex.org/keywords/yeast-two-hybrid","display_name":"yeast two-hybrid","score":0.6150000095367432},{"id":"https://openalex.org/keywords/synthetic-lethality-screen","display_name":"synthetic lethality screen","score":0.7009999752044678},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"mass spectrometry","score":0.6890000104904175},{"id":"https://openalex.org/keywords/domain-fusion","display_name":"domain fusion","score":0.4090000092983246},{"id":"https://openalex.org/keywords/gene-coevolution","display_name":"gene coevolution","score":0.4959999918937683}],"concepts":[{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.7575234770774841},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6324752569198608},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.6257190704345703},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5607877969741821},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5273094177246094},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5049534440040588},{"id":"https://openalex.org/C2994604686","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell function","level":3,"score":0.4378674030303955},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.35665827989578247},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2740349769592285},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.18289127945899963}],"mesh":[],"locations_count":1,"locations":[{"id":"mag:2240572358","doi":null,"is_oa":false,"landing_page_url":"https://dl.acm.org/citation.cfm?id=2231461","pdf_url":null,"source":{"id":"https://openalex.org/S4306508160","display_name":"Dissertations & Theses @ SUNY Buffalo,ProQuest Dissertations & Theses Global","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":"Dissertations & Theses @ SUNY Buffalo,ProQuest Dissertations & Theses Global","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W295615070","https://openalex.org/W2172453422","https://openalex.org/W1999888532","https://openalex.org/W2110115297","https://openalex.org/W2130179418","https://openalex.org/W7100256444","https://openalex.org/W2427798428","https://openalex.org/W2022693294","https://openalex.org/W2754307534","https://openalex.org/W3001481682"],"abstract_inverted_index":{"Since":[0],"the":[1,4,13,20,38,44,54,57,98,109,133,138,149,160,164,174,177,185,194,204,213,278,287,309,331,366,387,396,406,417,462,481,494,498,507,531,547,561,579,587,591,598,603,606,617,665],"sequencing":[2],"of":[3,15,22,37,43,56,59,66,100,108,127,137,148,159,166,176,191,196,206,215,229,238,277,305,317,340,369,389,408,419,426,450,456,483,497,536,552,565,576,581,590,610,657,668],"human":[5],"genome":[6],"was":[7],"brought":[8],"to":[9,29,71,249,254,286,490,596,619,627],"fruition":[10],"[142,":[11],"66],":[12],"field":[14],"genetics":[16],"now":[17],"stands":[18],"on":[19,301,546,560,638],"threshold":[21],"significant":[23,434],"theoretical":[24,548],"and":[25,41,68,89,105,124,130,173,188,193,211,261,272,323,359,466,476,492,516,533,549,631,643,659,675],"practical":[26],"advances.":[27],"Crucial":[28],"furthering":[30],"these":[31],"investigations":[32],"is":[33,53,199,253,544,600],"a":[34,63,79,128,200,226,315,427,447,501,573,623,662],"comprehensive":[35],"understanding":[36,52],"expression,":[39],"function,":[40],"regulation":[42],"proteins":[45,183,263,289,318,379,393,410,451,658],"encoded":[46],"by":[47,348,453,615],"an":[48,154,258],"organism":[49],"[155].":[50],"This":[51,648],"subject":[55],"discipline":[58],"proteomics.":[60],"Proteomics":[61],"encompasses":[62],"wide":[64],"range":[65],"approaches":[67,297],"applications":[69],"intended":[70],"explicate":[72],"how":[73,82,90],"complex":[74,448,457,484,524],"biological":[75,467,669],"processes":[76,399],"occur":[77],"at":[78,235],"molecular":[80],"level,":[81],"they":[83,91],"differ":[84],"in":[85,94,113,153,203,386,395,500,523,541],"various":[86],"cell":[87],"types,":[88],"are":[92,117,144,184,298,584,613,625,646],"altered":[93],"disease":[95],"states.\r\nIn":[96],"particular,":[97,557],"elucidation":[99],"protein":[101,251,260,280,341,438,440,477,537,553,566,569,633],"function":[102,276],"has":[103,234,375],"been,":[104],"remains,":[106],"one":[107],"most":[110,150,186],"central":[111],"problems":[112],"computational":[114,296],"biology.":[115],"Proteins":[116,143],"macromolecules":[118,190],"that":[119,225,314,378],"serve":[120],"as":[121,157,219,269,382,446,470,622,672],"building":[122],"blocks":[123],"functional":[125,370,629,655],"components":[126],"cell,":[129],"account":[131],"for":[132,146,170,338,654,664],"second":[134],"largest":[135],"fraction":[136,228],"cellular":[139,178,398],"weight":[140],"after":[141],"water.":[142],"responsible":[145],"some":[147],"important":[151,367],"functions":[152,198,252,327,407],"organism,":[155],"such":[156,218,268,469,671],"constitution":[158],"organs":[161],"(structural":[162],"proteins),":[163],"catalysis":[165],"biochemical":[167],"reactions":[168],"necessary":[169],"metabolism":[171],"(enzymes),":[172],"maintenance":[175],"environment":[179],"(transmembrane":[180],"proteins).":[181],"Thus,":[182],"essential":[187],"versatile":[189],"life,":[192],"knowledge":[195],"their":[197,239,390],"crucial":[201],"link":[202],"development":[205,214],"new":[207,435],"drugs,":[208],"better":[209],"crops,":[210],"even":[212],"synthetic":[216,360],"biochemicals":[217],"biofuels":[220],"[49].\r\nA":[221],"recent":[222,329],"review":[223],"noted":[224],"large":[227],"currently":[230],"sequenced":[231],"complete":[232],"genomes":[233],"least":[236],"half":[237],"gene":[240,473],"entries":[241],"having":[242],"ambiguous":[243],"annotations":[244],"[59].":[245],"The":[246,275],"classical":[247],"way":[248],"predict":[250,632],"find":[255],"homologies":[256],"between":[257,372],"unannotated":[259,279],"other":[262,322],"using":[264,586],"sequence":[265],"similarity":[266],"algorithms,":[267,636],"FASTA":[270],"[106]":[271],"PSI-BLAST":[273],"[85].":[274],"can":[281,411,431,443,529,650],"then":[282],"be":[283,412,444,651],"assigned":[284],"according":[285],"annotated":[288],"with":[290,320,402,416],"similar":[291,420],"sequences.":[292],"In":[293,556,602],"addition,":[294],"several":[295],"proposed":[299],"based":[300,545,637],"correlated":[302],"evolution":[303],"mechanisms":[304],"genes.":[306],"For":[307],"example,":[308],"domain":[310],"fusion":[311],"analysis":[312,354,535,564,667],"infers":[313],"pair":[316],"interacts":[319],"each":[321,403,620],"thus":[324,432],"performs":[325],"related":[326],"[88].\r\nIn":[328],"years,":[330],"high-throughput":[332,349],"bio-techniques":[333],"have":[334,364,488,520],"provided":[335,365],"additional":[336],"opportunities":[337],"inference":[339,674],"functions.":[342,634],"Protein-protein":[343],"interaction":[344,429,441,478,538,554,570,599,608],"(PPI)":[345],"data,":[346],"enriched":[347],"experiments":[350],"including":[351],"yeast":[352],"two-hybrid":[353],"[67][139],":[355],"mass":[356],"spectrometry":[357],"[50][62]":[358],"lethality":[361],"screen":[362],"[3],":[363],"clues":[368],"associations":[371],"proteins.":[373,422],"It":[374],"been":[376,521],"observed":[377,522],"seldom":[380],"act":[381],"single":[383],"isolated":[384],"species":[385],"performance":[388],"functions;":[391],"rather,":[392],"involved":[394],"same":[397],"often":[400],"interact":[401],"other.":[404],"Therefore,":[405],"uncharacterized":[409],"predicted":[413],"through":[414,568],"comparison":[415],"interactions":[418,583],"known":[421],"A":[423,593],"detailed":[424],"examination":[425],"protein-protein":[428,582],"network":[430,442,673,676],"yield":[433],"insights":[436],"into":[437],"functions.\r\nThe":[439],"described":[445],"system":[449],"linked":[452],"interactions.":[454],"Examples":[455],"systems":[458,468,485,499],"include":[459],"social":[460],"networks,":[461,472],"World":[463],"Wide":[464],"Web":[465],"metabolic":[471],"regulatory":[474],"networks":[475,609,645,670],"networks.":[479,555,571],"Recently,":[480],"studies":[482],"[4,":[486],"96]":[487],"attempted":[489],"understand":[491],"characterize":[493],"structural":[495],"behaviors":[496],"topological":[502,588],"perspective.":[503],"As":[504,572],"interesting":[505],"features,":[506],"small-world":[508],"properties":[509],"[147],":[510],"scale-free":[511],"degree":[512],"distributions":[513],"[14,":[514],"15]":[515],"hierarchical":[517],"modularity":[518],"[115]":[519],"systems.":[525],"These":[526],"unique":[527],"characteristics":[528],"facilitate":[530],"efficient":[532],"accurate":[534,563],"networks.\r\nThe":[539],"study":[540,649],"this":[542,577],"dissertation":[543],"quantitative":[550],"characterization":[551,656],"it":[558],"focuses":[559],"efficientand":[562],"functionality":[567],"preliminary":[574],"work":[575],"dissertation,":[578],"reliabilities":[580],"assessed":[585],"features":[589],"network.":[592],"novel":[594],"measurement":[595],"quantify":[597],"proposed.":[601,647],"next":[604],"step,":[605],"weighted":[607],"proteins,":[611],"which":[612],"created":[614],"assigning":[616],"reliability":[618],"edge":[621],"weight,":[624],"used":[626],"detect":[628],"modules":[630],"Novel":[635],"information":[639],"flow,":[640],"spanning":[641],"tree,":[642],"neural":[644],"underlying":[652],"bases":[653],"also":[660],"provides":[661],"guideline":[663],"deeper":[666],"dynamics.":[677]},"counts_by_year":[],"updated_date":"2025-10-10T17:16:08.811792","created_date":"2016-06-24T00:00:00"}
