{"id":"https://openalex.org/W3096046178","doi":"https://doi.org/10.1093/bioinformatics/btaa930","title":"Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach","display_name":"Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach","publication_year":2020,"publication_date":"2020-10-21","ids":{"openalex":"https://openalex.org/W3096046178","doi":"https://doi.org/10.1093/bioinformatics/btaa930","mag":"3096046178","pmid":"https://pubmed.ncbi.nlm.nih.gov/33135072"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa930","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa930","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/8/1052/38157307/btaa930.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/8/1052/38157307/btaa930.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100446728","display_name":"Weiwei Zhang","orcid":"https://orcid.org/0000-0001-7836-8874"},"institutions":[{"id":"https://openalex.org/I4210119674","display_name":"East China University of Technology","ror":"https://ror.org/027385r44","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210119674"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiwei Zhang","raw_affiliation_strings":["School of Science , East China University of Technology, Nanchang, Jiangxi 330013, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science , East China University of Technology, Nanchang, Jiangxi 330013, China","institution_ids":["https://openalex.org/I4210119674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083170497","display_name":"Hao Wu","orcid":"https://orcid.org/0000-0003-1269-7354"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hao Wu","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics , Emory University, Atlanta, GA 30322, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics , Emory University, Atlanta, GA 30322, USA","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100389131","display_name":"Ziyi Li","orcid":"https://orcid.org/0000-0001-8359-0533"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ziyi Li","raw_affiliation_strings":["Department of Biostatistics , The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics , The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I1343551460"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5083170497","https://openalex.org/A5100389131"],"corresponding_institution_ids":["https://openalex.org/I1343551460","https://openalex.org/I150468666"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1668,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.51147665,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"37","issue":"8","first_page":"1052","last_page":"1059"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.7982000112533569,"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":0.7982000112533569,"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":0.07150000333786011,"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/T10885","display_name":"Gene expression and cancer classification","score":0.02199999988079071,"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/deconvolution","display_name":"Deconvolution","score":0.7022220492362976},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.7008944153785706},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5524284243583679},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5423132181167603},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5240240693092346},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.4789755344390869},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3913132846355438},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34669917821884155},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33718395233154297},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32898926734924316},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.32034292817115784},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12212827801704407}],"concepts":[{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.7022220492362976},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.7008944153785706},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5524284243583679},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5423132181167603},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5240240693092346},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.4789755344390869},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3913132846355438},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34669917821884155},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33718395233154297},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32898926734924316},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32034292817115784},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12212827801704407},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa930","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa930","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/8/1052/38157307/btaa930.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33135072","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33135072","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8150138","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8150138","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa930","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa930","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/8/1052/38157307/btaa930.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1389117987","display_name":null,"funder_award_id":"U01 MH116441","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G1928029749","display_name":null,"funder_award_id":"P01NS097206","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2748096557","display_name":null,"funder_award_id":"R01GM122083","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4978443175","display_name":null,"funder_award_id":"R01 GM122083","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6761798547","display_name":null,"funder_award_id":"P01 NS097206","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G7184533123","display_name":null,"funder_award_id":"61902061","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7211878532","display_name":null,"funder_award_id":"R01 GM124061","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7417640436","display_name":null,"funder_award_id":"U01MH116441","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1555549210","https://openalex.org/W1765766961","https://openalex.org/W1771887010","https://openalex.org/W1963970354","https://openalex.org/W1966453802","https://openalex.org/W1976615758","https://openalex.org/W1987557775","https://openalex.org/W1997719110","https://openalex.org/W2000217106","https://openalex.org/W2004078197","https://openalex.org/W2011988545","https://openalex.org/W2022142157","https://openalex.org/W2028934624","https://openalex.org/W2066792703","https://openalex.org/W2067606868","https://openalex.org/W2069169522","https://openalex.org/W2090384073","https://openalex.org/W2107665951","https://openalex.org/W2112500414","https://openalex.org/W2121091193","https://openalex.org/W2121417064","https://openalex.org/W2126453701","https://openalex.org/W2126882378","https://openalex.org/W2130002311","https://openalex.org/W2130523009","https://openalex.org/W2140360759","https://openalex.org/W2140501674","https://openalex.org/W2149312162","https://openalex.org/W2157043395","https://openalex.org/W2163886442","https://openalex.org/W2165414304","https://openalex.org/W2169556367","https://openalex.org/W2170324063","https://openalex.org/W2170490448","https://openalex.org/W2185207072","https://openalex.org/W2309685155","https://openalex.org/W2329659234","https://openalex.org/W2510420694","https://openalex.org/W2553677484","https://openalex.org/W2580601263","https://openalex.org/W2610326370","https://openalex.org/W2890558526","https://openalex.org/W2920020242","https://openalex.org/W2921126124","https://openalex.org/W2945415170","https://openalex.org/W2950086703","https://openalex.org/W2950687473","https://openalex.org/W2952240309","https://openalex.org/W2972265392","https://openalex.org/W3012143942","https://openalex.org/W4283726509","https://openalex.org/W6633261909","https://openalex.org/W6644515432","https://openalex.org/W6701881206"],"related_works":["https://openalex.org/W4251527294","https://openalex.org/W2902329290","https://openalex.org/W2052355316","https://openalex.org/W2046964473","https://openalex.org/W2107880877","https://openalex.org/W2151182744","https://openalex.org/W2024490794","https://openalex.org/W2221018455","https://openalex.org/W2054863651","https://openalex.org/W1998349112"],"abstract_inverted_index":{"MOTIVATION:":[0],"It":[1,114],"is":[2,17,97,128,162],"a":[3,19,72,98],"common":[4],"practice":[5],"in":[6],"epigenetics":[7],"research":[8],"to":[9,61,101],"profile":[10],"DNA":[11,51,83],"methylation":[12,52,84],"on":[13],"tissue":[14],"samples,":[15],"which":[16,77],"usually":[18],"mixture":[20],"of":[21,63,90,104,135,143,166],"different":[22],"cell":[23,32,48,80,91,105,107,118],"types.":[24],"To":[25],"properly":[26],"account":[27],"for":[28,46],"the":[29,140,167],"mixture,":[30],"estimating":[31],"compositions":[33,49,81,108],"has":[34],"been":[35],"recognized":[36],"as":[37,164],"an":[38],"important":[39],"first":[40],"step.":[41],"Many":[42],"methods":[43,151],"were":[44],"developed":[45],"quantifying":[47],"from":[50,82],"data,":[53],"but":[54],"they":[55],"mostly":[56],"have":[57],"limited":[58],"applications":[59],"due":[60],"lack":[62],"reference":[64,126],"or":[65,93,123],"prior":[66,88],"information.":[67],"RESULTS:":[68],"We":[69],"develop":[70],"Tsisal,":[71],"novel":[73],"complete":[74],"deconvolution":[75,150],"method":[76,146,160],"accurately":[78],"estimate":[79,102],"data":[85,176],"without":[86],"any":[87],"knowledge":[89],"types":[92],"their":[94],"proportions.":[95],"Tsisal":[96,161],"full":[99],"pipeline":[100],"number":[103],"types,":[106],"and":[109,133],"identify":[110],"cell-type-specific":[111],"CpG":[112],"sites.":[113],"can":[115],"also":[116],"assign":[117],"type":[119],"labels":[120],"when":[121],"(full":[122],"part":[124,165],"of)":[125],"panel":[127],"available.":[129],"Extensive":[130],"simulation":[131],"studies":[132],"analyses":[134],"seven":[136],"real":[137],"datasets":[138],"demonstrate":[139],"favorable":[141],"performance":[142],"our":[144],"proposed":[145,159],"compared":[147],"with":[148],"existing":[149],"serving":[152],"similar":[153],"purpose.":[154],"AVAILABILITY":[155],"AND":[156],"IMPLEMENTATION:":[157],"The":[158],"implemented":[163],"R/Bioconductor":[168],"package":[169],"TOAST":[170],"at":[171,179],"https://bioconductor.org/packages/TOAST.":[172],"SUPPLEMENTARY":[173],"INFORMATION:":[174],"Supplementary":[175],"are":[177],"available":[178],"Bioinformatics":[180],"online.":[181]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":2}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
