{"id":"https://openalex.org/W16133278","doi":null,"title":"Statistical calibration and differential gene expression analysis of RNA-Seq data","display_name":"Statistical calibration and differential gene expression analysis of RNA-Seq data","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W16133278","mag":"16133278"},"language":"en","primary_location":{"id":"pmh:oai:docs.lib.purdue.edu:dissertations-15351","doi":null,"is_oa":false,"landing_page_url":"https://docs.lib.purdue.edu/dissertations/AAI3669610","pdf_url":null,"source":{"id":"https://openalex.org/S4377196310","display_name":"Purdue e-Pubs (Purdue University System)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801333002","host_organization_name":"Purdue University System","host_organization_lineage":["https://openalex.org/I2801333002"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Theses and Dissertations Available from ProQuest","raw_type":"text"},"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/A5000182790","display_name":"Zhaonan Sun","orcid":"https://orcid.org/0000-0003-4471-3478","observed_orcids":["https://orcid.org/0000-0003-4471-3478"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Zhaonan Sun","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-4471-3478","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5000182790"],"corresponding_institution_ids":[],"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/T10885","display_name":"Gene expression and cancer classification","score":0.8755000233650208,"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/T10885","display_name":"Gene expression and cancer classification","score":0.8755000233650208,"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":0.11259999871253967,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.005499999970197678,"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/rna-seq","display_name":"RNA-seq","score":0.8939999938011169},{"id":"https://openalex.org/keywords/differential-gene-expression","display_name":"differential gene expression","score":0.8399999737739563},{"id":"https://openalex.org/keywords/gene-expression-quantification","display_name":"gene expression quantification","score":0.8830000162124634},{"id":"https://openalex.org/keywords/statistical-calibration","display_name":"statistical calibration","score":0.6980000138282776},{"id":"https://openalex.org/keywords/errors-in-variables-model","display_name":"measurement error models","score":0.9150000214576721},{"id":"https://openalex.org/keywords/qrt-pcr","display_name":"qRT-PCR","score":0.859000027179718},{"id":"https://openalex.org/keywords/microarray-normalization","display_name":"microarray normalization","score":0.7239999771118164},{"id":"https://openalex.org/keywords/rna-seq-normalization","display_name":"RNA-seq normalization","score":0.6909999847412109},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"alternative splicing","score":0.9660000205039978},{"id":"https://openalex.org/keywords/covariance-structure","display_name":"covariance structure","score":0.5529999732971191},{"id":"https://openalex.org/keywords/recurrence-relations","display_name":"recurrence relations","score":0.4959999918937683}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.7468551397323608},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5630630850791931},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5043586492538452},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46773844957351685},{"id":"https://openalex.org/C165838908","wikidata":"https://www.wikidata.org/wiki/Q736777","display_name":"Calibration","level":2,"score":0.4503272771835327},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43414241075515747},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39283692836761475},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3330245316028595},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3101576864719391},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2125658094882965},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.14977872371673584}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:docs.lib.purdue.edu:dissertations-15351","doi":null,"is_oa":false,"landing_page_url":"https://docs.lib.purdue.edu/dissertations/AAI3669610","pdf_url":null,"source":{"id":"https://openalex.org/S4377196310","display_name":"Purdue e-Pubs (Purdue University System)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801333002","host_organization_name":"Purdue University System","host_organization_lineage":["https://openalex.org/I2801333002"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Theses and Dissertations Available from ProQuest","raw_type":"text"},{"id":"mag:16133278","doi":null,"is_oa":false,"landing_page_url":"https://docs.lib.purdue.edu/cgi/viewcontent.cgi?article=15351&context=dissertations","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":0,"referenced_works":[],"related_works":["https://openalex.org/W3102372221","https://openalex.org/W1980482597","https://openalex.org/W2129271620","https://openalex.org/W2276921915","https://openalex.org/W2081600396","https://openalex.org/W7099970607","https://openalex.org/W2106171838","https://openalex.org/W56029280","https://openalex.org/W4415926293","https://openalex.org/W3107199668"],"abstract_inverted_index":{"The":[0,282],"rapid":[1],"development":[2],"of":[3,20,36,123,200,232,239,289,316],"the":[4,21,29,33,79,135,173,187,198,230,237,246,271,276,287,295,304,310,317],"next":[5],"generation":[6],"sequencing":[7],"(NGS)":[8],"technologies":[9],"has":[10,67,111],"revolutionized":[11],"how":[12],"genomic":[13],"research":[14],"is":[15,26,149,176,190,224,294,322],"conducted.":[16],"An":[17,314],"important":[18,150],"application":[19,315],"NGS":[22],"technologies,":[23],"named":[24],"RNA-Seq,":[25,37],"to":[27,90,100,128,146,151,180,193,213,229,244,255,269,309],"study":[28],"RNA":[30],"transcripts.":[31],"Despite":[32],"increasing":[34],"popularity":[35],"statistical":[38],"challenges":[39],"still":[40],"exist":[41],"for":[42,74,78],"analyzing":[43],"RNA-Seq":[44,63,84,138,142,209,217,258],"data.":[45,64],"This":[46],"thesis":[47],"focuses":[48],"on":[49,205],"three":[50],"specific":[51,266],"problems":[52],"in":[53,226,303],"gene":[54,59,75,130,210,221],"expression":[55,60,76,131,211,222,263],"quantification":[56,77],"and":[57,83,95,133,137,162,178,208,215,236,260,275,324],"differential":[58,262],"analysis":[61,223],"using":[62],"Microarray":[65,207],"technology":[66],"been":[68],"used":[69],"as":[70,86,270],"a":[71,87,105,121,168,300],"main":[72],"platform":[73],"last":[80],"few":[81],"decades,":[82],"emerged":[85],"promising":[88],"alternative":[89,233],"microarrays.":[91],"Unfortunately,":[92],"both":[93],"microarray":[94,136],"RNA-seq":[96],"data":[97,212,259],"are":[98,160,280],"subject":[99,192],"various":[101],"measurement":[102,117,125,194,201],"errors.":[103],"Using":[104],"third":[106],"platform,":[107],"called":[108],"qRT-PCR,":[109,206],"which":[110],"low":[112],"throughput":[113],"capacity":[114],"but":[115],"high":[116],"accuracy,":[118],"we":[119],"propose":[120,243],"system":[122,199],"functional":[124],"error":[126,202],"models":[127,203],"model":[129,256,274,321],"measurements":[132],"calibrate":[134],"platforms.":[139],"As":[140],"new":[141],"normalization":[143,158,218],"methods":[144,159],"continue":[145],"appear,":[147],"it":[148,182],"systematically":[152],"compare":[153,214],"different":[154,157],"methods.":[155,219],"Currently,":[156],"compared":[161],"validated":[163],"by":[164],"their":[165],"correlations":[166],"with":[167,251],"certain":[169,252],"gold":[170,188],"standard.":[171],"Although":[172],"current":[174],"approach":[175],"intuitive":[177],"easy":[179],"implement,":[181],"becomes":[183],"statistically":[184],"inadequate":[185],"when":[186],"standard":[189],"also":[191],"error.":[195],"We":[196,242,298],"utilize":[197],"based":[204],"validate":[216],"Differential":[220],"complicated":[225],"eukaryotes":[227],"due":[228],"prevalence":[231],"splicing":[234],"events":[235],"incompleteness":[238],"transcript":[240],"annotations.":[241],"use":[245,288],"multivariate":[247,290],"negative":[248,291,306],"binomial":[249,292,307],"distributions":[250],"covariance":[253,278],"structures":[254],"exon-level":[257],"perform":[261],"analysis.":[264],"Two":[265],"models,":[267],"referred":[268],"first-order":[272],"adjacent":[273,320],"common":[277],"model,":[279],"discussed.":[281,325],"major":[283],"barrier":[284],"that":[285],"hurdles":[286],"distribution":[293,308],"computational":[296],"burden.":[297],"generalized":[299],"recursive":[301],"relation":[302],"bivariate":[305],"two":[311],"proposed":[312],"models.":[313],"first":[318],"order":[319],"presented":[323]},"counts_by_year":[],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2016-06-24T00:00:00"}
