{"id":"https://openalex.org/W6887971855","doi":"https://doi.org/10.17877/de290r-19925","title":"Bioinformatics from genetic variants to methylation","display_name":"Bioinformatics from genetic variants to methylation","publication_year":2018,"publication_date":"2018-01-01","ids":{"openalex":"https://openalex.org/W6887971855","doi":"https://doi.org/10.17877/de290r-19925"},"language":"en","primary_location":{"id":"pmh:oai:eldorado.tu-dortmund.de:2003/37940","is_oa":true,"landing_page_url":"http://hdl.handle.net/2003/37940","pdf_url":"http://hdl.handle.net/2003/37940","source":{"id":"https://openalex.org/S4306400811","display_name":"Technische Universit\u00e4t Dortmund Eldorado (Technische Universit\u00e4t Dortmund)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210148506","host_organization_name":"Erich-Brost-Institut","host_organization_lineage":["https://openalex.org/I4210148506"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doc-type:doctoralThesis"},"type":"dissertation","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2003/37940","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Schr\u00f6der, Christopher","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Schr\u00f6der, Christopher","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"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":true,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.295199990272522,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.295199990272522,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.11180000007152557,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.03680000081658363,"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/dna-methylation","display_name":"DNA methylation","score":0.7583000063896179},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.5674999952316284},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5641000270843506},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"Bisulfite sequencing","score":0.5595999956130981},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5383999943733215},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.41780000925064087},{"id":"https://openalex.org/keywords/illumina-methylation-assay","display_name":"Illumina Methylation Assay","score":0.4124999940395355},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.37459999322891235},{"id":"https://openalex.org/keywords/5-methylcytosine","display_name":"5-Methylcytosine","score":0.3319999873638153}],"concepts":[{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.7583000063896179},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5837000012397766},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.5674999952316284},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5641000270843506},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.5595999956130981},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5587000250816345},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5383999943733215},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4636000096797943},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41780000925064087},{"id":"https://openalex.org/C136953436","wikidata":"https://www.wikidata.org/wiki/Q6000286","display_name":"Illumina Methylation Assay","level":5,"score":0.4124999940395355},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.37459999322891235},{"id":"https://openalex.org/C2775926025","wikidata":"https://www.wikidata.org/wiki/Q238563","display_name":"5-Methylcytosine","level":5,"score":0.3319999873638153},{"id":"https://openalex.org/C116114238","wikidata":"https://www.wikidata.org/wiki/Q6823960","display_name":"Methylated DNA immunoprecipitation","level":5,"score":0.33079999685287476},{"id":"https://openalex.org/C51064596","wikidata":"https://www.wikidata.org/wiki/Q7452482","display_name":"Sequencing by hybridization","level":5,"score":0.3303999900817871},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.3260999917984009},{"id":"https://openalex.org/C163002167","wikidata":"https://www.wikidata.org/wiki/Q7277124","display_name":"RNA-Directed DNA Methylation","level":5,"score":0.3208000063896179},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.3156999945640564},{"id":"https://openalex.org/C2775959680","wikidata":"https://www.wikidata.org/wiki/Q2718222","display_name":"Bisulfite","level":5,"score":0.3012000024318695},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.3003999888896942},{"id":"https://openalex.org/C54887055","wikidata":"https://www.wikidata.org/wiki/Q5205758","display_name":"DNA nanoball sequencing","level":5,"score":0.289900004863739},{"id":"https://openalex.org/C52182516","wikidata":"https://www.wikidata.org/wiki/Q17144128","display_name":"Sequencing by ligation","level":5,"score":0.27000001072883606},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.2694999873638153},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2648000121116638},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.2599000036716461}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:eldorado.tu-dortmund.de:2003/37940","is_oa":true,"landing_page_url":"http://hdl.handle.net/2003/37940","pdf_url":"http://hdl.handle.net/2003/37940","source":{"id":"https://openalex.org/S4306400811","display_name":"Technische Universit\u00e4t Dortmund Eldorado (Technische Universit\u00e4t Dortmund)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210148506","host_organization_name":"Erich-Brost-Institut","host_organization_lineage":["https://openalex.org/I4210148506"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doc-type:doctoralThesis"},{"id":"doi:10.17877/de290r-19925","is_oa":true,"landing_page_url":"https://doi.org/10.17877/de290r-19925","pdf_url":null,"source":{"id":"https://openalex.org/S4306400811","display_name":"Technische Universit\u00e4t Dortmund Eldorado (Technische Universit\u00e4t Dortmund)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210148506","host_organization_name":"Erich-Brost-Institut","host_organization_lineage":["https://openalex.org/I4210148506"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:eldorado.tu-dortmund.de:2003/37940","is_oa":true,"landing_page_url":"http://hdl.handle.net/2003/37940","pdf_url":"http://hdl.handle.net/2003/37940","source":{"id":"https://openalex.org/S4306400811","display_name":"Technische Universit\u00e4t Dortmund Eldorado (Technische Universit\u00e4t Dortmund)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210148506","host_organization_name":"Erich-Brost-Institut","host_organization_lineage":["https://openalex.org/I4210148506"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doc-type:doctoralThesis"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1640141467","display_name":null,"funder_award_id":"01KU1216","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W6887971855.pdf","grobid_xml":"https://content.openalex.org/works/W6887971855.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"An":[0,76],"important":[1,77],"research":[2],"topic":[3],"in":[4,29,45,51,58,88,126,230,288,482],"bioinformatics":[5,382],"is":[6,25,36,83,153,209,250,462,559,570,634],"the":[7,11,15,31,41,46,67,98,109,168,210,225,247,272,282,320,328,334,355,360,364,378,384,395,421,427,468,546,552,557,593,603,606,614,655],"analysis":[8,68,207,553],"of":[9,18,33,43,65,69,79,112,116,138,191,212,224,275,284,337,344,366,377,381,394,401,435,551,556,582,605,619,657,673,685],"DNA,":[10],"molecule":[12],"that":[13,160,269,287,458,679],"encodes":[14],"genetic":[16,497,543,690],"information":[17,111],"all":[19,369,610],"organisms.":[20],"The":[21,142,392,416,520,549,580],"basis":[22],"for":[23,135,146,188,217,312,323,419,423,432,464,508,514,527,534,599,613],"this":[24,175,447,460,583],"sequencing,":[26,512],"a":[27,55,81,86,158,222,261,265,405,413,425,504,532,562,683],"procedure":[28],"which":[30,89,218,439],"sequence":[32,48,99],"DNA":[34,84,95,114,139,148,162,177,192],"bases":[35],"determined.":[37],"In":[38],"addition":[39,483],"to":[40,94,173,232,255,292,306,318,363,478,484,539,596,627,689],"identification":[42],"variations":[44],"base":[47],"itself,":[49],"advances":[50],"sequencing":[52,59,244,329],"methods":[53,187,611],"and":[54,108,124,133,178,195,241,252,309,317,390,473,537,554,591,617,647,654,675],"steady":[56],"reduction":[57],"costs":[60],"open":[61],"up":[62,240],"new":[63,243],"fields":[64],"research:":[66],"functionally":[70],"relevant":[71],"non-base-related":[72],"changes,":[73],"so-called":[74],"epigenetics.":[75],"example":[78,515],"such":[80,347,424,651],"mechanism":[82],"methylation,":[85,367],"process":[87,174],"methyl":[90],"groups":[91],"are":[92,375,440,518,687],"added":[93],"without":[96],"altering":[97],"itself.":[100],"Methylation":[101],"takes":[102],"place":[103],"only":[104,316,491,516],"at":[105,163,404],"specific":[106,406],"sites,":[107],"methylation":[110,120,140,149,193,335,397,444,485,674],"human":[113],"consists":[115],"approximately":[117],"30":[118],"million":[119],"levels":[121,194],"between":[122,622],"0":[123,436],"1":[125],"total.":[127],"This":[128,277,352,487,625],"thesis":[129],"deals":[130,489],"with":[131,199,234,492,496],"problems":[132,431],"solutions":[134],"each":[136],"phase":[137],"analysis.":[141,298],"most":[143,289],"advanced":[144],"method":[145,228,262],"detecting":[147],"based":[150,263,455,572],"on":[151,264,456,573,576,637,666],"resolution":[152],"Whole-Genome":[154],"Bisulfite":[155],"Sequencing":[156],"(WGBS),":[157],"technique":[159],"modifies":[161],"unmethylated":[164],"sites.":[165],"We":[166,258],"describe":[167],"special":[169],"in-silico":[170],"treatment":[171],"required":[172],"altered":[176],"existing":[179],"concepts":[180],"as":[181,183,342,348,412,443,525,652,682],"well":[182],"newly":[184],"developed":[185,201,260,451,642],"bioinformatic":[186],"efficient":[189],"determination":[190],"their":[196],"further":[197,297],"processing":[198],"our":[200,301,349,528],"tool":[202,533],"camel.":[203],"A":[204],"common":[205,236,442],"downstream":[206],"step":[208],"detection":[211,633],"differentially":[213],"methylated":[214],"regions":[215],"(DMRs),":[216],"we":[219,449,502,608,677],"have":[220,259,450],"implemented":[221],"modification":[223],"widely":[226],"used":[227,341],"BSmooth":[229],"order":[231],"deal":[233],"today\u2019s":[235],"data":[237,286,362,433,465,480,509,586,671],"sizes.":[238],"Setting":[239],"creating":[242],"protocols,":[245],"e.g.,":[246,399],"mentioned":[248],"WGBS,":[249],"complicated":[251],"requires":[253],"adjustments":[254],"several":[256,402,623],"parameters.":[257],"linear":[266],"program":[267],"(LP)":[268],"can":[270,339,408,474],"predict":[271],"duplicate":[273],"rate":[274,322],"supersamples.":[276],"critical":[278],"quality":[279],"measure":[280],"represents":[281],"proportion":[283],"redundant":[285],"cases":[290],"needs":[291],"be":[293,340,387,410,476],"removed":[294],"from":[295,359,510],"any":[296],"By":[299],"using":[300],"method,":[302],"it":[303],"becomes":[304],"possible":[305,541],"test,":[307],"adjust":[308],"improve":[310],"parameters":[311,422],"small":[313],"test":[314],"libraries":[315],"estimate":[319],"duplication":[321],"potential":[324],"full-size":[325],"samples.":[326],"Once":[327],"protocol":[330],"has":[331,430],"been":[332],"established,":[333],"recognition":[336],"camel":[338],"part":[343],"automated":[345],"workflows,":[346],"mosquito":[350],"workflow.":[351],"pipeline":[353,506],"processes":[354,644],"generated":[356],"WGBS":[357],"samples":[358,403,646],"raw":[361],"degree":[365],"including":[368],"essential":[370],"intermediate":[371],"steps.":[372],"Such":[373],"workflows":[374],"one":[376],"central":[379],"components":[380],"since":[383],"calculation":[385],"must":[386],"parallel,":[388],"reproducible":[389],"scalable.":[391],"distribution":[393],"detected":[396],"levels,":[398],"values":[400],"location,":[407],"often":[409],"described":[411],"beta-mixture":[414],"model.":[415],"standard":[417],"approach":[418,643],"estimating":[420],"model,":[426],"EM":[428],"algorithm,":[429],"points":[434,466],"or":[437],"1,":[438],"very":[441],"levels.":[445,486],"For":[446],"reason,":[448],"an":[452],"alternative":[453],"algorithm":[454],"moments":[457],"overcome":[459],"disadvantage.It":[461],"robust":[463],"within":[467],"closed":[469],"interval":[470],"[0;":[471],"1]":[472],"also":[475,495],"applied":[477],"similar":[479],"sets":[481,672],"work":[488],"not":[490,571],"epigenetic":[493],"but":[494,575],"variants.":[498,544],"To":[499],"analyze":[500],"these,":[501],"present":[503],"second":[505],"(ape)":[507],"targeted":[511],"where":[513],"genes":[517],"sequenced.":[519],"recognized":[521],"variants":[522],"then":[523],"serve":[524],"input":[526],"graphical":[529,563],"environment":[530],"eagle,":[531],"computer":[535],"scientists":[536],"geneticists":[538],"recognize":[540],"causal":[542],"As":[545],"name":[547],"implies:":[548],"configuration":[550],"presentation":[555],"results":[558],"done":[560],"via":[561],"user":[564],"interface.":[565],"Unlike":[566],"other":[567],"tools,":[568],"eagle":[569],"databases,":[574],"encapsulated":[577],"hdf5":[578],"files.":[579],"use":[581,597,609],"universal":[584],"file-system-like":[585],"structure":[587],"offers":[588],"some":[589,628],"advantages":[590],"makes":[592],"system":[594],"easy":[595],"especially":[598],"non-computer":[600],"scientists.":[601],"At":[602],"end":[604],"thesis,":[607],"presented":[612],"detection,":[615],"analysis,":[616],"characterization":[618],"interindividual":[620],"DMRs":[621,681],"donors.":[624],"leads":[626],"computational":[629],"challenges":[630],"because":[631],"DMR":[632],"usually":[635],"performed":[636],"two":[638],"different":[639],"groups.":[640],"Our":[641],"independent":[645],"calculates":[648],"key":[649],"metrics":[650],"p-values":[653],"number":[656],"undetectable":[658],"DMRs.":[659],"Through":[660],"whole":[661],"genome":[662],"association":[663],"studies":[664],"(GWAS)":[665],"more":[667],"than":[668],"1000":[669],"array":[670],"variants,":[676],"show":[678],"(interindividual)":[680],"subtype":[684],"epigenetics":[686],"related":[688],"variation.":[691]},"counts_by_year":[{"year":2020,"cited_by_count":1}],"updated_date":"2026-08-04T08:18:43.703281","created_date":"2025-10-10T00:00:00"}