{"id":"https://openalex.org/W782572168","doi":null,"title":"Innovative algorithms and evaluation methods for biological motif finding","display_name":"Innovative algorithms and evaluation methods for biological motif finding","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W782572168","mag":"782572168"},"language":"en","primary_location":{"id":"mag:782572168","doi":null,"is_oa":false,"landing_page_url":"https://scholarworks.gsu.edu/cgi/viewcontent.cgi?article=1066&context=cs_diss","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"volume":null,"type":"article","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/A5101465265","display_name":"Yi Feng Pan","orcid":"https://orcid.org/0000-0002-2766-3096","observed_orcids":["https://orcid.org/0000-0002-2766-3096"]},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi Pan","raw_affiliation_strings":["Georgia State University,"],"raw_orcid":"https://orcid.org/0000-0002-2766-3096","affiliations":[{"raw_affiliation_string":"Georgia State University,","institution_ids":["https://openalex.org/I181565077"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5118844306","display_name":"Wooyoung Kim","orcid":"https://orcid.org/0000-0002-9993-8431","observed_orcids":["https://orcid.org/0000-0002-9993-8431","https://orcid.org/0000-0002-6015-7064"]},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wooyoung Kim","raw_affiliation_strings":["Georgia State University,"],"raw_orcid":"https://orcid.org/0000-0002-9993-8431","affiliations":[{"raw_affiliation_string":"Georgia State University,","institution_ids":["https://openalex.org/I181565077"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I181565077"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"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":0.9740999937057495,"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":0.9740999937057495,"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/T10064","display_name":"Complex Network Analysis Techniques","score":0.0038999998942017555,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.003000000026077032,"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/network-motifs","display_name":"network motifs","score":0.8650000095367432},{"id":"https://openalex.org/keywords/sequence-motifs","display_name":"sequence motifs","score":0.7269999980926514},{"id":"https://openalex.org/keywords/structural-motifs","display_name":"structural motifs","score":0.7799999713897705},{"id":"https://openalex.org/keywords/sparse-non-negative-matrix-factorization","display_name":"sparse non-negative matrix factorization","score":0.9150000214576721},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene Ontology","score":0.8460000157356262},{"id":"https://openalex.org/keywords/protein-protein-interaction-network","display_name":"protein-protein interaction network","score":0.718999981880188},{"id":"https://openalex.org/keywords/essential-protein-prediction","display_name":"essential protein prediction","score":0.972000002861023},{"id":"https://openalex.org/keywords/clustering-algorithms","display_name":"clustering algorithms","score":0.46399998664855957}],"concepts":[{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.788905143737793},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.7141820788383484},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.6585806608200073},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.614599347114563},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.6061950325965881},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.5896856784820557},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5766223073005676},{"id":"https://openalex.org/C60723933","wikidata":"https://www.wikidata.org/wiki/Q7001080","display_name":"Network motif","level":3,"score":0.44385087490081787},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.42902517318725586},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.40059730410575867},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38351547718048096},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3543030619621277},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3249226212501526},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21128395199775696},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16812387108802795},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.116854727268219},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","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}],"mesh":[],"locations_count":1,"locations":[{"id":"mag:782572168","doi":null,"is_oa":false,"landing_page_url":"https://scholarworks.gsu.edu/cgi/viewcontent.cgi?article=1066&context=cs_diss","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"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":187,"referenced_works":["https://openalex.org/W87092222","https://openalex.org/W135311109","https://openalex.org/W158805393","https://openalex.org/W249159571","https://openalex.org/W339865234","https://openalex.org/W598987462","https://openalex.org/W1207633162","https://openalex.org/W1490239928","https://openalex.org/W1497256448","https://openalex.org/W1499476884","https://openalex.org/W1503938960","https://openalex.org/W1516536009","https://openalex.org/W1527854642","https://openalex.org/W1531182450","https://openalex.org/W1548843388","https://openalex.org/W1558136956","https://openalex.org/W1560541823","https://openalex.org/W1573579329","https://openalex.org/W1575476631","https://openalex.org/W1592870802","https://openalex.org/W1602731994","https://openalex.org/W1673310716","https://openalex.org/W1766157213","https://openalex.org/W1808967201","https://openalex.org/W1965687403","https://openalex.org/W1965893904","https://openalex.org/W1966638085","https://openalex.org/W1970737407","https://openalex.org/W1971421925","https://openalex.org/W1971912858","https://openalex.org/W1974436271","https://openalex.org/W1975586684","https://openalex.org/W1975948225","https://openalex.org/W1976672440","https://openalex.org/W1977186059","https://openalex.org/W1977496278","https://openalex.org/W1978486653","https://openalex.org/W1980317569","https://openalex.org/W1980800453","https://openalex.org/W1981722151","https://openalex.org/W1982428412","https://openalex.org/W1984220047","https://openalex.org/W1985416968","https://openalex.org/W1987815409","https://openalex.org/W1989011685","https://openalex.org/W1990368529","https://openalex.org/W1990600049","https://openalex.org/W1991645955","https://openalex.org/W1992419399","https://openalex.org/W1992543421","https://openalex.org/W1992595091","https://openalex.org/W1998300401","https://openalex.org/W2000503761","https://openalex.org/W2005443451","https://openalex.org/W2005740247","https://openalex.org/W2006038621","https://openalex.org/W2006683252","https://openalex.org/W2008708467","https://openalex.org/W2008808389","https://openalex.org/W2009566340","https://openalex.org/W2009570821","https://openalex.org/W2011186028","https://openalex.org/W2012139697","https://openalex.org/W2012852001","https://openalex.org/W2015705446","https://openalex.org/W2018642282","https://openalex.org/W2025971310","https://openalex.org/W2030404924","https://openalex.org/W2031869443","https://openalex.org/W2036131961","https://openalex.org/W2038518475","https://openalex.org/W2041877620","https://openalex.org/W2049695588","https://openalex.org/W2051224630","https://openalex.org/W2052464097","https://openalex.org/W2053096433","https://openalex.org/W2055043387","https://openalex.org/W2056002855","https://openalex.org/W2057680921","https://openalex.org/W2057712948","https://openalex.org/W2059044327","https://openalex.org/W2059505358","https://openalex.org/W2062402656","https://openalex.org/W2066235893","https://openalex.org/W2069611131","https://openalex.org/W2073583237","https://openalex.org/W2073661767","https://openalex.org/W2073693914","https://openalex.org/W2074182576","https://openalex.org/W2074443723","https://openalex.org/W2076566842","https://openalex.org/W2081709066","https://openalex.org/W2081927170","https://openalex.org/W2083391480","https://openalex.org/W2084908610","https://openalex.org/W2089783852","https://openalex.org/W2090305799","https://openalex.org/W2090754786","https://openalex.org/W2095617232","https://openalex.org/W2098567615","https://openalex.org/W2099651125","https://openalex.org/W2102122585","https://openalex.org/W2104080300","https://openalex.org/W2106202847","https://openalex.org/W2107412629","https://openalex.org/W2108078368","https://openalex.org/W2109110326","https://openalex.org/W2109745408","https://openalex.org/W2110017370","https://openalex.org/W2110699703","https://openalex.org/W2112204996","https://openalex.org/W2112262143","https://openalex.org/W2113076747","https://openalex.org/W2113654464","https://openalex.org/W2115761267","https://openalex.org/W2117022273","https://openalex.org/W2118587067","https://openalex.org/W2119843070","https://openalex.org/W2123280311","https://openalex.org/W2123854512","https://openalex.org/W2124073224","https://openalex.org/W2124145810","https://openalex.org/W2124533460","https://openalex.org/W2124866671","https://openalex.org/W2126602684","https://openalex.org/W2126975650","https://openalex.org/W2127218421","https://openalex.org/W2127464112","https://openalex.org/W2127971792","https://openalex.org/W2128601422","https://openalex.org/W2130790725","https://openalex.org/W2130832525","https://openalex.org/W2131035027","https://openalex.org/W2131984349","https://openalex.org/W2132692097","https://openalex.org/W2134873429","https://openalex.org/W2134923619","https://openalex.org/W2135030836","https://openalex.org/W2137786672","https://openalex.org/W2138270253","https://openalex.org/W2140462113","https://openalex.org/W2140948740","https://openalex.org/W2141012957","https://openalex.org/W2141224484","https://openalex.org/W2142437744","https://openalex.org/W2142465702","https://openalex.org/W2144885342","https://openalex.org/W2145100112","https://openalex.org/W2147623464","https://openalex.org/W2148762636","https://openalex.org/W2149769193","https://openalex.org/W2150744251","https://openalex.org/W2153020710","https://openalex.org/W2153153865","https://openalex.org/W2155320925","https://openalex.org/W2155331065","https://openalex.org/W2156345326","https://openalex.org/W2157556292","https://openalex.org/W2157735020","https://openalex.org/W2160319713","https://openalex.org/W2161708849","https://openalex.org/W2161917555","https://openalex.org/W2161965550","https://openalex.org/W2162891889","https://openalex.org/W2162979438","https://openalex.org/W2163480486","https://openalex.org/W2164393635","https://openalex.org/W2164928285","https://openalex.org/W2164958334","https://openalex.org/W2164997719","https://openalex.org/W2165533101","https://openalex.org/W2165685007","https://openalex.org/W2166344835","https://openalex.org/W2166898290","https://openalex.org/W2167164103","https://openalex.org/W2168157678","https://openalex.org/W2168157737","https://openalex.org/W2168164063","https://openalex.org/W2171081680","https://openalex.org/W2481427704","https://openalex.org/W2482276862","https://openalex.org/W2548060058","https://openalex.org/W2612166593","https://openalex.org/W2765633603","https://openalex.org/W2999729612","https://openalex.org/W3128894147","https://openalex.org/W3216731846"],"related_works":["https://openalex.org/W2008014943","https://openalex.org/W1976722121","https://openalex.org/W2004865576","https://openalex.org/W3021093342","https://openalex.org/W2394144662","https://openalex.org/W2104703309","https://openalex.org/W2955615924","https://openalex.org/W2215639193","https://openalex.org/W2177477930","https://openalex.org/W4246614746"],"abstract_inverted_index":{"Biological":[0,158,332,348],"motifs":[1,15,18,75,102,160,209,285,316,334],"are":[2,19,63,76,161,210,335],"defined":[3],"as":[4,185,263],"overly":[5],"recurring":[6],"short-sized":[7],"patterns":[8],"in":[9,86,94,216,232,274,295,321],"biological":[10,23,32,56,98,117,129,148,205,207,284,299,313,319],"systems.":[11],"Sequence":[12],"motifs,":[13],"structural":[14,70,80],"and":[16,92,106,181,224,298,324],"network":[17,101,159,208,333,349],"the":[20,40,45,55,59,87,97,116,120,154,174,191,281,305,312,322],"examples":[21],"of":[22,58,73,100,150,202,204,245,283,315,342,344],"motifs.":[24,46,121],"Due":[25],"to":[26,43,53,127,212,229,260,270,280,338],"its":[27],"expensive":[28],"searching":[29],"process,":[30],"many":[31],"motif":[33,156],"finding":[34],"algorithms":[35,166,175,180,184,192,197,259,323],"have":[36,277],"been":[37],"focusing":[38],"on":[39,115,311],"computational":[41],"efficiency":[42],"discover":[44],"However,":[47,96],"there":[48],"is":[49,103,144,253,292,301],"no":[50,107],"comprehensive":[51],"benchmark":[52],"validate":[54],"significance":[57],"\u201ccandidate":[60],"motifs,\u201d":[61],"which":[62],"discovered":[64],"computationally":[65],"with":[66,131,146,167,248,256,304],"their":[67,79,83],"sequential":[68],"or":[69,82,89],"similarities.":[71],"Some":[72],"sequence":[74],"verified":[77],"by":[78,163,198,317,325],"similarities":[81],"functional":[84],"roles":[85],"DNA":[88],"protein":[90,155],"sequences,":[91],"stored":[93],"databases.":[95],"role":[99],"still":[104],"invalidated":[105],"databases":[108],"exist.\r\nIn":[109],"this":[110,287,296],"dissertation,":[111],"we":[112],"emphasize":[113],"more":[114,200,222,310],"meanings":[118,314],"for":[119,153,265],"We":[122,219,308],"provide":[123],"an":[124],"efficient":[125],"way":[126],"incorporate":[128],"information":[130,149,300],"clustering":[132,165],"analysis":[133,291],"methods:":[134],"For":[135],"example,":[136],"a":[137,147,221,233,266,275,339],"sparse":[138],"nonnegative":[139],"matrix":[140],"factorization":[141],"(SNMF)":[142],"method":[143],"used":[145,294],"Chou-Fasman":[151],"parameters":[152],"finding.":[157],"searched":[162],"various":[164],"Gene":[168,353],"ontology":[169],"(GO)":[170],"information.":[171],"In":[172],"addition,":[173],"can":[176],"replace":[177],"existing":[178,196,249],"approximation":[179],"parallel":[182],"search":[183],"well.":[186],"Experimental":[187],"results":[188],"show":[189,240],"that":[190,241],"perform":[193],"better":[194],"than":[195],"producing":[199],"number":[201],"high-quality":[203],"motifs.\r\nAdditionally,":[206],"applied":[211,337],"predict":[213,271],"essential":[214,272,345],"proteins":[215,231,273],"two":[217],"ways.":[218],"design":[220],"robust":[223],"biologically":[225,327],"meaningful":[226],"centrality":[227,250,258],"algorithm":[228,269],"rank":[230],"PPI":[234],"network,":[235],"name":[236],"it":[237],"MCGO,":[238],"then":[239,254],"highest":[242],"detection":[243],"rate":[244],"MCGO":[246,252],"compared":[247],"algorithms.":[251],"combined":[255],"other":[257],"be":[261],"plugged":[262],"features":[264],"machine":[267],"learning":[268],"network.\r\nWe":[276],"three":[278],"contributions":[279],"study":[282],"through":[286],"thesis;":[288],"1)":[289],"Clustering":[290,351],"efficiently":[293],"work":[297],"easily":[302],"integrated":[303],"analysis;":[306],"2)":[307],"focus":[309],"adding":[318],"knowledge":[320],"suggesting":[326],"related":[328],"evaluation":[329],"methods.":[330],"3)":[331],"successfully":[336],"practical":[340],"application":[341],"prediction":[343],"proteins.\r\nINDEX":[346],"WORDS:":[347],"motif,":[350],"analysis,":[352],"ontology,":[354],"Essential":[355],"protein,":[356],"Machine":[357],"learning.":[358]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
