{"id":"https://openalex.org/W81776794","doi":null,"title":"Machine Learning Approaches to Transcription Factor Binding Site Search and Visualization","display_name":"Machine Learning Approaches to Transcription Factor Binding Site Search and Visualization","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W81776794","mag":"81776794"},"language":"en","primary_location":{"id":"pmh:oai:opencommons.uconn.edu:dissertations-6505","doi":null,"is_oa":true,"landing_page_url":"https://opencommons.uconn.edu/dissertations/304","pdf_url":"https://opencommons.uconn.edu/cgi/viewcontent.cgi?article=6505&context=dissertations","source":{"id":"https://openalex.org/S4377196438","display_name":"OpenCommons - UConn (University of Connecticut)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I140172145","host_organization_name":"University of Connecticut","host_organization_lineage":["https://openalex.org/I140172145"],"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":"Doctoral Dissertations","raw_type":"text"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://opencommons.uconn.edu/cgi/viewcontent.cgi?article=6505&context=dissertations","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081092601","display_name":"Chih Lee","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chih Lee","raw_affiliation_strings":["University of Connecticut"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5081092601"],"corresponding_institution_ids":["https://openalex.org/I140172145"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.961899995803833,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.961899995803833,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.01080000028014183,"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":0.010599999688565731,"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/lasagna","display_name":"lasagna","score":0.8080000281333923},{"id":"https://openalex.org/keywords/web-based-tool","display_name":"web-based tool","score":0.5350000262260437},{"id":"https://openalex.org/keywords/one-class-classification","display_name":"one-class classification","score":0.8539999723434448},{"id":"https://openalex.org/keywords/binary-classification","display_name":"binary classification","score":0.8889999985694885},{"id":"https://openalex.org/keywords/dna-sequence-analysis","display_name":"DNA sequence analysis","score":0.45899999141693115}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.554077684879303},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5482497811317444},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4367883801460266},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.41259095072746277},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40272262692451477},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17955949902534485},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14811021089553833},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.11634781956672668},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10874900221824646},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10200545191764832}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:opencommons.uconn.edu:dissertations-6505","doi":null,"is_oa":true,"landing_page_url":"https://opencommons.uconn.edu/dissertations/304","pdf_url":"https://opencommons.uconn.edu/cgi/viewcontent.cgi?article=6505&context=dissertations","source":{"id":"https://openalex.org/S4377196438","display_name":"OpenCommons - UConn (University of Connecticut)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I140172145","host_organization_name":"University of Connecticut","host_organization_lineage":["https://openalex.org/I140172145"],"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":"Doctoral Dissertations","raw_type":"text"},{"id":"pmh:oai:digitalcommons.lib.uconn.edu:dissertations-6505","doi":null,"is_oa":false,"landing_page_url":"https://digitalcommons.lib.uconn.edu/dissertations/304","pdf_url":null,"source":{"id":"https://openalex.org/S4306401180","display_name":"OpenCommons at University of Connecticut (University of Connecticut)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I140172145","host_organization_name":"University of Connecticut","host_organization_lineage":["https://openalex.org/I140172145"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Doctoral Dissertations","raw_type":"text"},{"id":"mag:81776794","doi":null,"is_oa":false,"landing_page_url":"http://digitalcommons.uconn.edu/dissertations/304/","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":{"id":"pmh:oai:opencommons.uconn.edu:dissertations-6505","doi":null,"is_oa":true,"landing_page_url":"https://opencommons.uconn.edu/dissertations/304","pdf_url":"https://opencommons.uconn.edu/cgi/viewcontent.cgi?article=6505&context=dissertations","source":{"id":"https://openalex.org/S4377196438","display_name":"OpenCommons - UConn (University of Connecticut)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I140172145","host_organization_name":"University of Connecticut","host_organization_lineage":["https://openalex.org/I140172145"],"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":"Doctoral Dissertations","raw_type":"text"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W81776794.pdf","grobid_xml":"https://content.openalex.org/works/W81776794.grobid-xml"},"referenced_works_count":91,"referenced_works":["https://openalex.org/W1510549104","https://openalex.org/W1549994062","https://openalex.org/W1586476557","https://openalex.org/W1592870802","https://openalex.org/W1660390307","https://openalex.org/W1815199292","https://openalex.org/W1857789879","https://openalex.org/W1932107019","https://openalex.org/W1963553964","https://openalex.org/W1966448776","https://openalex.org/W1967512542","https://openalex.org/W1971216836","https://openalex.org/W1973247666","https://openalex.org/W1975612392","https://openalex.org/W1980425490","https://openalex.org/W1996112765","https://openalex.org/W2003967338","https://openalex.org/W2011430131","https://openalex.org/W2013739996","https://openalex.org/W2017200304","https://openalex.org/W2017309141","https://openalex.org/W2026731344","https://openalex.org/W2028904582","https://openalex.org/W2032695847","https://openalex.org/W2035564383","https://openalex.org/W2038473742","https://openalex.org/W2055632024","https://openalex.org/W2058912719","https://openalex.org/W2061834804","https://openalex.org/W2062340962","https://openalex.org/W2063447456","https://openalex.org/W2073850887","https://openalex.org/W2074703985","https://openalex.org/W2076439598","https://openalex.org/W2078381702","https://openalex.org/W2079659879","https://openalex.org/W2081277704","https://openalex.org/W2088990426","https://openalex.org/W2089026820","https://openalex.org/W2094036688","https://openalex.org/W2095718954","https://openalex.org/W2100628300","https://openalex.org/W2102000247","https://openalex.org/W2102137830","https://openalex.org/W2103777723","https://openalex.org/W2106882534","https://openalex.org/W2107249189","https://openalex.org/W2108187446","https://openalex.org/W2108407754","https://openalex.org/W2111164126","https://openalex.org/W2113071089","https://openalex.org/W2115577355","https://openalex.org/W2119572012","https://openalex.org/W2127057035","https://openalex.org/W2127640118","https://openalex.org/W2129795133","https://openalex.org/W2131741851","https://openalex.org/W2135030836","https://openalex.org/W2137015675","https://openalex.org/W2140885056","https://openalex.org/W2141179681","https://openalex.org/W2142067151","https://openalex.org/W2142570576","https://openalex.org/W2143885206","https://openalex.org/W2152210981","https://openalex.org/W2153550523","https://openalex.org/W2153562609","https://openalex.org/W2157009395","https://openalex.org/W2158221945","https://openalex.org/W2158356009","https://openalex.org/W2158698691","https://openalex.org/W2159934528","https://openalex.org/W2160379721","https://openalex.org/W2161849959","https://openalex.org/W2161893150","https://openalex.org/W2162836426","https://openalex.org/W2165612380","https://openalex.org/W2166937350","https://openalex.org/W2167827709","https://openalex.org/W2168249156","https://openalex.org/W2168817939","https://openalex.org/W2169783907","https://openalex.org/W2170942986","https://openalex.org/W2259938310","https://openalex.org/W2293652778","https://openalex.org/W2414421951","https://openalex.org/W2765633603","https://openalex.org/W2798766386","https://openalex.org/W2916083703","https://openalex.org/W3099514962","https://openalex.org/W7095841607"],"related_works":["https://openalex.org/W1971216836","https://openalex.org/W1967512542","https://openalex.org/W2102137830","https://openalex.org/W1989988018","https://openalex.org/W2097464046","https://openalex.org/W7100673715","https://openalex.org/W2162836426","https://openalex.org/W4313527127","https://openalex.org/W7097972088","https://openalex.org/W6908495310"],"abstract_inverted_index":{"A":[0],"transcription":[1,69],"factor":[2,70,113],"(TF)":[3],"is":[4,65,117,132,156],"a":[5,32,36,49,51,68,95,107,150,177,180,215,249,263,291],"protein":[6,8],"or":[7,39],"complex.":[9],"It":[10],"regulates":[11],"the":[12,22,81,90,128,140,173,228,232,253,278,301,305],"expression":[13],"of":[14,25,31,48,94,98,142,146,176,248,252,262],"its":[15],"target":[16],"genes":[17],"by":[18,163,187],"physically":[19],"binding":[20,29,46,62,71,92,114,130,151,174,184,246,260,312],"to":[21,57,103,171,207,226],"regulatory":[23],"regions":[24],"these":[26],"genes.":[27],"The":[28,153,192],"sites":[30,47,93,131,175,185,247,261,274,284,313],"TF":[33,52,96,178,196,264,279],"naturally":[34],"share":[35],"common":[37],"pattern":[38],"motif":[40],"with":[41,268],"one":[42],"another.":[43],"Given":[44],"known":[45,66,91,259],"TF,":[50],"model":[53,108,197],"can":[54,109],"be":[55,104,110],"built":[56],"scan":[58],"sequences":[59],"for":[60,288],"putative":[61],"sites.":[63,316],"This":[64,221],"as":[67,280],"site":[72,115],"(TFBS)":[73],"search":[74,83,169,234,255],"problem.":[75,294],"In":[76],"this":[77],"dissertation,":[78],"we":[79,213],"investigate":[80],"TFBS":[82,168,211,254],"problem":[84,122],"using":[85],"machine":[86],"learning":[87,121,239],"approaches.\\nIn":[88],"general,":[89],"are":[97,189,236,285],"variable":[99],"lengths":[100,141],"and":[101,144,202,265,304,314],"have":[102],"aligned":[105],"before":[106],"built.":[111],"Transcription":[112],"alignment":[116],"considered":[118,237],"an":[119,136],"unsupervised":[120],"since":[123,241],"no":[124],"other":[125],"information":[126,276],"about":[127,277],"unaligned":[129],"given.":[133],"We":[134,295],"propose":[135,296],"algorithm":[137],"that":[138],"considers":[139],"TFBSs":[143,289],"dependencies":[145],"nucleotide":[147],"positions":[148],"in":[149,179],"site.":[152],"novel":[154,216,298],"method":[155],"named":[157,219,300],"LASAGNA":[158],"(Length-Aware":[159],"Site":[160],"Alignment":[161],"Guided":[162],"Nucleotide":[164],"Association).\\nStudies":[165],"often":[166,194],"utilize":[167],"tools":[170,206],"predict":[172],"DNA":[181],"sequence":[182,200],"when":[183],"found":[186],"assays":[188],"not":[190],"available.":[191],"analysis":[193,229],"involves":[195],"collection,":[198],"promoter":[199],"retrieval":[201],"visualization,":[203],"requiring":[204],"several":[205],"accomplish.":[208],"To":[209],"accelerate":[210],"analyses,":[212],"developed":[214],"integrated":[217],"webtool":[218],"LASAGNA-Search.":[220],"user-friendly":[222],"tool":[223],"allows":[224],"users":[225],"perform":[227],"without":[230],"leaving":[231],"site.\\nTFBS":[233],"methods":[235,256,299],"supervised":[238],"algorithms":[240],"they":[242],"learn":[243],"from":[244],"example":[245],"TF.":[250],"Most":[251],"consider":[257],"only":[258],"hence":[266],"deal":[267],"one-class":[269],"classification":[270,293],"problems.":[271],"However,":[272],"non-binding":[273,283,315],"contain":[275],"well.":[281],"When":[282],"available,":[286],"searching":[287],"becomes":[290],"two-class":[292],"two":[297],"negative-to-positive":[302],"vector":[303,308],"optimal":[306],"discriminating":[307],"methods,":[309],"utilizing":[310],"both":[311]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2016-06-24T00:00:00"}