{"id":"https://openalex.org/W2059738726","doi":"https://doi.org/10.1109/bibmw.2011.6112354","title":"Evaluation of normalization methods for RNA-Seq gene expression estimation","display_name":"Evaluation of normalization methods for RNA-Seq gene expression estimation","publication_year":2011,"publication_date":"2011-11-01","ids":{"openalex":"https://openalex.org/W2059738726","doi":"https://doi.org/10.1109/bibmw.2011.6112354","mag":"2059738726","pmid":"https://pubmed.ncbi.nlm.nih.gov/27532058"},"language":"en","primary_location":{"id":"doi:10.1109/bibmw.2011.6112354","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2011.6112354","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5050846682","display_name":"Po-Yen Wu","orcid":"https://orcid.org/0000-0002-3552-5152"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Po-Yen Wu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Georgia Institute of Technology","Department of Electrical and Computer Engineering, Georgia Institute of Technology, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Georgia Institute of Technology","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Georgia Institute of Technology, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074230084","display_name":"John H. Phan","orcid":"https://orcid.org/0000-0002-4670-2660"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]},{"id":"https://openalex.org/I2802612298","display_name":"The Wallace H. Coulter Department of Biomedical Engineering","ror":"https://ror.org/02j15s898","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444","https://openalex.org/I150468666","https://openalex.org/I2802612298"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. H. Phan","raw_affiliation_strings":["The Wallace H. Coulter Biomedical Engineering Department, Georgia Institute of Technology and Emory University","The Wallace H. Coulter Biomedical Engineering Department, Georgia Institute of Technology and Emory University, USA"],"affiliations":[{"raw_affiliation_string":"The Wallace H. Coulter Biomedical Engineering Department, Georgia Institute of Technology and Emory University","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"The Wallace H. Coulter Biomedical Engineering Department, Georgia Institute of Technology and Emory University, USA","institution_ids":["https://openalex.org/I2802612298","https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058786170","display_name":"Fengfeng Zhou","orcid":"https://orcid.org/0000-0002-8108-6007"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]},{"id":"https://openalex.org/I2802612298","display_name":"The Wallace H. Coulter Department of Biomedical Engineering","ror":"https://ror.org/02j15s898","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444","https://openalex.org/I150468666","https://openalex.org/I2802612298"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fengfeng Zhou","raw_affiliation_strings":["Research Center for Biomedical Information Technology, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences","The Wallace H. Coulter Biomedical Engineering Department, Georgia Institute of Technology and Emory University, USA"],"affiliations":[{"raw_affiliation_string":"Research Center for Biomedical Information Technology, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences","institution_ids":[]},{"raw_affiliation_string":"The Wallace H. Coulter Biomedical Engineering Department, Georgia Institute of Technology and Emory University, USA","institution_ids":["https://openalex.org/I2802612298","https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030096887","display_name":"May D. Wang","orcid":"https://orcid.org/0000-0003-3961-3608"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]},{"id":"https://openalex.org/I2802612298","display_name":"The Wallace H. Coulter Department of Biomedical Engineering","ror":"https://ror.org/02j15s898","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444","https://openalex.org/I150468666","https://openalex.org/I2802612298"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. D. Wang","raw_affiliation_strings":["The Wallace H. Coulter Biomedical Engineering Department, Georgia Institute of Technology and Emory University","The Wallace H. Coulter Biomedical Engineering Department, Georgia Institute of Technology and Emory University, USA"],"affiliations":[{"raw_affiliation_string":"The Wallace H. Coulter Biomedical Engineering Department, Georgia Institute of Technology and Emory University","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"The Wallace H. Coulter Biomedical Engineering Department, Georgia Institute of Technology and Emory University, USA","institution_ids":["https://openalex.org/I2802612298","https://openalex.org/I130701444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5050846682"],"corresponding_institution_ids":["https://openalex.org/I130701444"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.10562562,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"36","issue":null,"first_page":"50","last_page":"57"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9997000098228455,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9997000098228455,"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":0.9979000091552734,"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":0.9921000003814697,"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/normalization","display_name":"Normalization (sociology)","score":0.905074954032898},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.7209261655807495},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5343023538589478},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.526803731918335},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5159288644790649},{"id":"https://openalex.org/keywords/database-normalization","display_name":"Database normalization","score":0.4824957847595215},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.48162025213241577},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.46949127316474915},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4374249577522278},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40506649017333984},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38376715779304504},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33845606446266174},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.26212072372436523},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20567595958709717},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.195491760969162},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.1329669952392578}],"concepts":[{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.905074954032898},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.7209261655807495},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5343023538589478},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.526803731918335},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5159288644790649},{"id":"https://openalex.org/C162984825","wikidata":"https://www.wikidata.org/wiki/Q339072","display_name":"Database normalization","level":3,"score":0.4824957847595215},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.48162025213241577},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.46949127316474915},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4374249577522278},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40506649017333984},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38376715779304504},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33845606446266174},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.26212072372436523},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20567595958709717},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.195491760969162},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.1329669952392578},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bibmw.2011.6112354","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2011.6112354","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","raw_type":"proceedings-article"},{"id":"pmid:27532058","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27532058","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":"IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine","raw_type":null},{"id":"pmh:oai:europepmc.org:3945100","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4983420","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1118098720","https://openalex.org/W1981509058","https://openalex.org/W1996021314","https://openalex.org/W2010262162","https://openalex.org/W2044010294","https://openalex.org/W2048368626","https://openalex.org/W2057614798","https://openalex.org/W2060842569","https://openalex.org/W2065255559","https://openalex.org/W2094678200","https://openalex.org/W2096525273","https://openalex.org/W2103441770","https://openalex.org/W2107018762","https://openalex.org/W2109972881","https://openalex.org/W2118473681","https://openalex.org/W2118526609","https://openalex.org/W2121211805","https://openalex.org/W2126385616","https://openalex.org/W2136145671","https://openalex.org/W2138773756","https://openalex.org/W2146898272","https://openalex.org/W2154431984","https://openalex.org/W2156631105","https://openalex.org/W4239678514","https://openalex.org/W6813364610"],"related_works":["https://openalex.org/W4241705247","https://openalex.org/W2107018762","https://openalex.org/W2145362441","https://openalex.org/W2101622345","https://openalex.org/W2069695727","https://openalex.org/W1996185163","https://openalex.org/W3134304369","https://openalex.org/W2582603276","https://openalex.org/W2084813257","https://openalex.org/W2096302356"],"abstract_inverted_index":{"Statistical":[0],"inferences":[1],"on":[2,80],"RNA-Seq":[3,35,42,69,74,128],"data,":[4],"e.g.,":[5],"detecting":[6],"differential":[7,56],"gene":[8,57,83],"expression,":[9],"are":[10,110],"meaningful":[11],"only":[12],"after":[13],"proper":[14],"normalization.":[15],"However,":[16,99],"there":[17],"is":[18],"no":[19],"consensus":[20],"for":[21,126],"choosing":[22],"a":[23],"normalization":[24,36,75,108,129],"procedure":[25],"from":[26],"among":[27],"the":[28,51,60,65,100],"many":[29],"existing":[30],"procedures.":[31,130],"We":[32],"evaluated":[33],"several":[34],"procedures":[37,66,76,109],"by":[38],"(1)":[39],"correlating":[40],"estimated":[41],"expression":[43,84],"values":[44],"to":[45,67,113],"those":[46],"of":[47,53,91,102,117],"microarrays,":[48],"(2)":[49],"examining":[50],"concordance":[52,90],"stable":[54],"and":[55,62],"detection":[58],"between":[59],"platforms,":[61],"(3)":[63],"applying":[64],"simulated":[68,103],"data.":[70],"Results":[71],"suggested":[72,105],"that":[73,106],"have":[77],"little":[78],"effect":[79],"both":[81],"inter-platform":[82,89],"correlation":[85],"as":[86,88,94],"well":[87],"genes":[92],"detected":[93],"stably":[95],"or":[96],"differentially":[97,118],"expressed.":[98],"results":[101,122],"analysis":[104],"some":[107],"more":[111],"robust":[112],"changes":[114],"in":[115],"distribution":[116],"expressed":[119],"genes.":[120],"These":[121],"may":[123],"provide":[124],"guidance":[125],"selecting":[127]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
