{"id":"https://openalex.org/W2051464515","doi":"https://doi.org/10.1109/globalsip.2014.7032349","title":"Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test","display_name":"Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test","publication_year":2014,"publication_date":"2014-12-01","ids":{"openalex":"https://openalex.org/W2051464515","doi":"https://doi.org/10.1109/globalsip.2014.7032349","mag":"2051464515"},"language":"en","primary_location":{"id":"doi:10.1109/globalsip.2014.7032349","is_oa":false,"landing_page_url":"https://doi.org/10.1109/globalsip.2014.7032349","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5100351875","display_name":"Lin Zhang","orcid":"https://orcid.org/0000-0002-7404-5231"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Zhang","raw_affiliation_strings":["Siee, China University of Mining and Technology, Xuzhou, China","Siee, China University of Mining and Technology, Xuzhou, 221116, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Siee, China University of Mining and Technology, Xuzhou, China","institution_ids":["https://openalex.org/I25757504"]},{"raw_affiliation_string":"Siee, China University of Mining and Technology, Xuzhou, 221116, China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062986831","display_name":"Jia Meng","orcid":"https://orcid.org/0000-0003-3455-205X"},"institutions":[{"id":"https://openalex.org/I69356397","display_name":"Xi\u2019an Jiaotong-Liverpool University","ror":"https://ror.org/03zmrmn05","country_code":"CN","type":"education","lineage":["https://openalex.org/I69356397"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jia Meng","raw_affiliation_strings":["Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China","Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China","institution_ids":["https://openalex.org/I69356397"]},{"raw_affiliation_string":"Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China","institution_ids":["https://openalex.org/I69356397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113566766","display_name":"Hui Liu","orcid":"https://orcid.org/0000-0001-8845-4813"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Liu","raw_affiliation_strings":["Siee, China University of Mining and Technology, Xuzhou, China","Siee, China University of Mining and Technology, Xuzhou, 221116, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Siee, China University of Mining and Technology, Xuzhou, China","institution_ids":["https://openalex.org/I25757504"]},{"raw_affiliation_string":"Siee, China University of Mining and Technology, Xuzhou, 221116, China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089852582","display_name":"Xiaodong Cui","orcid":"https://orcid.org/0000-0002-2280-4160"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Xiaodong Cui","raw_affiliation_strings":["Key Laboratory of Information Fusion Technology of Ministry of Education, Northwestern Poly technical University, Xian, China","Department of ECE, The University of Texas at San Antonio, San Antonio, TX 78249, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Information Fusion Technology of Ministry of Education, Northwestern Poly technical University, Xian, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Department of ECE, The University of Texas at San Antonio, San Antonio, TX 78249, USA","institution_ids":["https://openalex.org/I45438204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061712236","display_name":"Shao\u2010Wu Zhang","orcid":"https://orcid.org/0000-0003-1305-7447"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]},{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Shao-Wu Zhang","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, TX, USA","Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xian 710072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, TX, USA","institution_ids":["https://openalex.org/I165951966"]},{"raw_affiliation_string":"Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xian 710072, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100689057","display_name":"Yidong Chen","orcid":"https://orcid.org/0000-0001-6806-2185"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yidong Chen","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX, US","Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio TX, 78229, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX, US","institution_ids":["https://openalex.org/I165951966"]},{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio TX, 78229, USA","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103214311","display_name":"Yufei Huang","orcid":"https://orcid.org/0000-0002-1903-0838"},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yufei Huang","raw_affiliation_strings":["Dept. of ECE, University of Texas at San Antonio, San Antonio, TX, US","Department of ECE, The University of Texas at San Antonio, San Antonio, TX 78249, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of ECE, University of Texas at San Antonio, San Antonio, TX, US","institution_ids":["https://openalex.org/I45438204"]},{"raw_affiliation_string":"Department of ECE, The University of Texas at San Antonio, San Antonio, TX 78249, USA","institution_ids":["https://openalex.org/I45438204"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1368","last_page":"1371"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9970999956130981,"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/T11482","display_name":"RNA modifications and cancer","score":0.9970999956130981,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.987500011920929,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9800000190734863,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/negative-binomial-distribution","display_name":"Negative binomial distribution","score":0.723476231098175},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.5689622163772583},{"id":"https://openalex.org/keywords/likelihood-ratio-test","display_name":"Likelihood-ratio test","score":0.5217231512069702},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5036143660545349},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4914199113845825},{"id":"https://openalex.org/keywords/binomial","display_name":"Binomial (polynomial)","score":0.44815078377723694},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.44277462363243103},{"id":"https://openalex.org/keywords/rna-methylation","display_name":"RNA methylation","score":0.440601110458374},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41700413823127747},{"id":"https://openalex.org/keywords/exact-test","display_name":"Exact test","score":0.41581013798713684},{"id":"https://openalex.org/keywords/multinomial-distribution","display_name":"Multinomial distribution","score":0.4153374135494232},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2992911636829376},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2819634675979614},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2807929515838623},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25172245502471924},{"id":"https://openalex.org/keywords/poisson-distribution","display_name":"Poisson distribution","score":0.1072990894317627}],"concepts":[{"id":"https://openalex.org/C199335787","wikidata":"https://www.wikidata.org/wiki/Q743364","display_name":"Negative binomial distribution","level":3,"score":0.723476231098175},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.5689622163772583},{"id":"https://openalex.org/C9483764","wikidata":"https://www.wikidata.org/wiki/Q585740","display_name":"Likelihood-ratio test","level":2,"score":0.5217231512069702},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5036143660545349},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4914199113845825},{"id":"https://openalex.org/C2781315470","wikidata":"https://www.wikidata.org/wiki/Q193623","display_name":"Binomial (polynomial)","level":2,"score":0.44815078377723694},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.44277462363243103},{"id":"https://openalex.org/C2909856833","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"RNA methylation","level":5,"score":0.440601110458374},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41700413823127747},{"id":"https://openalex.org/C191093355","wikidata":"https://www.wikidata.org/wiki/Q9250577","display_name":"Exact test","level":2,"score":0.41581013798713684},{"id":"https://openalex.org/C192065140","wikidata":"https://www.wikidata.org/wiki/Q1147928","display_name":"Multinomial distribution","level":2,"score":0.4153374135494232},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2992911636829376},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2819634675979614},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2807929515838623},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25172245502471924},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.1072990894317627},{"id":"https://openalex.org/C91965660","wikidata":"https://www.wikidata.org/wiki/Q415875","display_name":"Methyltransferase","level":4,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/globalsip.2014.7032349","is_oa":false,"landing_page_url":"https://doi.org/10.1109/globalsip.2014.7032349","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.4000000059604645,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320310677","display_name":"University of Texas at San Antonio","ror":"https://ror.org/01kd65564"},{"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/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null},{"id":"https://openalex.org/F4320337534","display_name":"National Institute on Minority Health and Health Disparities","ror":"https://ror.org/0493hgw16"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1967656072","https://openalex.org/W1974225991","https://openalex.org/W2005100829","https://openalex.org/W2015696149","https://openalex.org/W2044676948","https://openalex.org/W2078964320","https://openalex.org/W2102904139","https://openalex.org/W2104162210","https://openalex.org/W2116709453","https://openalex.org/W2149118757","https://openalex.org/W2166153887","https://openalex.org/W2166843037","https://openalex.org/W2171808845","https://openalex.org/W4237941089","https://openalex.org/W4251448448"],"related_works":["https://openalex.org/W2279693271","https://openalex.org/W2955220190","https://openalex.org/W2355806151","https://openalex.org/W4320152868","https://openalex.org/W2805744880","https://openalex.org/W4400112320","https://openalex.org/W4395064841","https://openalex.org/W2021262032","https://openalex.org/W4238009488","https://openalex.org/W2122478484"],"abstract_inverted_index":{"The":[0,80,121],"study":[1],"of":[2,43,61,94],"mRNA":[3,34],"methylation":[4,46],"is":[5,74],"an":[6,86],"emerging":[7],"research":[8],"field":[9],"greatly":[10],"fueled":[11],"by":[12],"recent":[13],"advancement":[14],"in":[15,48],"high":[16],"throughput":[17],"sequencing":[18],"technology.":[19],"We":[20],"propose":[21],"here":[22],"a":[23,54],"binomial":[24,55,62],"likelihood":[25],"ratio":[26],"test":[27],"(\"bltest\")":[28],"aiming":[29],"at":[30,118],"detecting":[31],"differentially":[32,78],"methylated":[33],"with":[35,53,136],"MeRIP-Seq":[36,96],"data,":[37,130],"\"bltest\"":[38,82,111],"models":[39],"the":[40,58,71,95,103,128,132],"read":[41],"counts":[42],"each":[44],"RNA":[45,73],"site":[47],"IP":[49],"and":[50,131],"input":[51],"samples":[52],"distribution.":[56],"If":[57],"successful":[59],"rates":[60],"distributions":[63],"under":[64],"two":[65],"experimental":[66],"conditions":[67],"are":[68,134],"significantly":[69],"different,":[70],"corresponding":[72],"identified":[75],"to":[76,89,127],"be":[77],"methylated.":[79],"proposed":[81,122],"does":[83],"not":[84],"require":[85],"independent":[87],"procedure":[88],"unify":[90],"different":[91],"library":[92],"sizes":[93],"samples,":[97],"thus":[98],"retaining":[99],"maximal":[100],"information":[101],"from":[102],"data.":[104],"Our":[105],"simulation":[106],"results":[107],"clearly":[108],"showed":[109],"that":[110],"consistently":[112],"outperforms":[113],"classic":[114],"\"Fisher's":[115],"exact":[116],"test\"":[117],"all":[119],"settings.":[120],"method":[123],"was":[124],"also":[125],"applied":[126],"real":[129],"findings":[133],"consistent":[135],"previous":[137],"studies.":[138]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
