{"id":"https://openalex.org/W2165909549","doi":"https://doi.org/10.1093/bib/bbs046","title":"A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis","display_name":"A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis","publication_year":2012,"publication_date":"2012-09-17","ids":{"openalex":"https://openalex.org/W2165909549","doi":"https://doi.org/10.1093/bib/bbs046","mag":"2165909549"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbs046","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbs046","pdf_url":"https://academic.oup.com/bib/article-pdf/14/6/671/467651/bbs046.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/14/6/671/467651/bbs046.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078354187","display_name":"Marie\u2010Agn\u00e8s Dillies","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"M.-A. Dillies","raw_affiliation_strings":["PF2 - Puces \u00e0 ADN (Plate-Forme 2) (25-28 rue du Docteur Roux 75724 Paris Cedex 15 - France)"],"affiliations":[{"raw_affiliation_string":"PF2 - Puces \u00e0 ADN (Plate-Forme 2) (25-28 rue du Docteur Roux 75724 Paris Cedex 15 - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014679436","display_name":"Andr\u00e9a Rau","orcid":"https://orcid.org/0000-0001-6469-488X"},"institutions":[{"id":"https://openalex.org/I22248866","display_name":"AgroParisTech","ror":"https://ror.org/02kbmgc12","country_code":"FR","type":"education","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210129272","display_name":"G\u00e9n\u00e9tique Animale et Biologie Int\u00e9grative","ror":"https://ror.org/03rkgeb39","country_code":"FR","type":"facility","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4210129272"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"A. Rau","raw_affiliation_strings":["GABI - G\u00e9n\u00e9tique Animale et Biologie Int\u00e9grative (Domaine de Vilvert F-78252 Jouy-en-Josas - France)"],"affiliations":[{"raw_affiliation_string":"GABI - G\u00e9n\u00e9tique Animale et Biologie Int\u00e9grative (Domaine de Vilvert F-78252 Jouy-en-Josas - France)","institution_ids":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I4210129272","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048149985","display_name":"Julie Aubert","orcid":"https://orcid.org/0000-0001-5203-5748"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I4210102957","display_name":"D\u00e9partement Math\u00e9matiques et Informatique Appliqu\u00e9es","ror":"https://ror.org/011emb038","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210102957"]},{"id":"https://openalex.org/I4387153087","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es","ror":"https://ror.org/00780az30","country_code":null,"type":"facility","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4387153087"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"J. Aubert","raw_affiliation_strings":["MIA-Paris - Math\u00e9matiques et Informatique Appliqu\u00e9es (16 rue Claude Bernard 75231 PARIS CEDEX 05 - France)"],"affiliations":[{"raw_affiliation_string":"MIA-Paris - Math\u00e9matiques et Informatique Appliqu\u00e9es (16 rue Claude Bernard 75231 PARIS CEDEX 05 - France)","institution_ids":["https://openalex.org/I4210102957","https://openalex.org/I100532134","https://openalex.org/I4387153087"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090278719","display_name":"Christelle Hennequet\u2010Antier","orcid":"https://orcid.org/0000-0001-5836-2803"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"C. Hennequet-Antier","raw_affiliation_strings":["CMIP - Centre M\u00e9dical de l'Institut Pasteur (209-211 rue de Vaugirard F-75015 Paris - France)"],"affiliations":[{"raw_affiliation_string":"CMIP - Centre M\u00e9dical de l'Institut Pasteur (209-211 rue de Vaugirard F-75015 Paris - France)","institution_ids":["https://openalex.org/I157536573"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004315548","display_name":"Marine Jeanmougin","orcid":"https://orcid.org/0000-0001-6239-4357"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Jeanmougin","raw_affiliation_strings":["LSG - Laboratoire Statistique et G\u00e9nome (23 boulevard de France 91 037 \u00c9vry, France - France)"],"affiliations":[{"raw_affiliation_string":"LSG - Laboratoire Statistique et G\u00e9nome (23 boulevard de France 91 037 \u00c9vry, France - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047327833","display_name":"Nicolas Servant","orcid":"https://orcid.org/0000-0003-1678-7410"},"institutions":[{"id":"https://openalex.org/I4210113863","display_name":"G\u00e9nomique Bioinformatique et Applications","ror":"https://ror.org/0264vhs54","country_code":"FR","type":"facility","lineage":["https://openalex.org/I124158823","https://openalex.org/I4210113863","https://openalex.org/I4210134562"]},{"id":"https://openalex.org/I4387153074","display_name":"Cancer et g\u00e9nome: Bioinformatique, biostatistiques et \u00e9pid\u00e9miologie des syst\u00e8mes complexes","ror":"https://ror.org/0095dt357","country_code":null,"type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I2746051580","https://openalex.org/I4387153074","https://openalex.org/I70768539","https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"N. Servant","raw_affiliation_strings":["Cancer et g\u00e9nome: Bioinformatique, biostatistiques et \u00e9pid\u00e9miologie d'un syst\u00e8me complexe (26 rue d'Ulm - 75248 Paris cedex 05 - France)"],"affiliations":[{"raw_affiliation_string":"Cancer et g\u00e9nome: Bioinformatique, biostatistiques et \u00e9pid\u00e9miologie d'un syst\u00e8me complexe (26 rue d'Ulm - 75248 Paris cedex 05 - France)","institution_ids":["https://openalex.org/I4210113863","https://openalex.org/I4387153074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056295276","display_name":"C\u00e9line Keime","orcid":"https://orcid.org/0000-0001-7604-3814"},"institutions":[{"id":"https://openalex.org/I4210086872","display_name":"Institut de g\u00e9n\u00e9tique et de biologie mol\u00e9culaire et cellulaire","ror":"https://ror.org/0015ws592","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I4210086872","https://openalex.org/I4210096427","https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"C. Keime","raw_affiliation_strings":["Institute of Genetics [Illkirch] (1, rue Laurent Fries, 67404 Illkirch - France)"],"affiliations":[{"raw_affiliation_string":"Institute of Genetics [Illkirch] (1, rue Laurent Fries, 67404 Illkirch - France)","institution_ids":["https://openalex.org/I4210086872"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044537062","display_name":"Guillemette Marot","orcid":"https://orcid.org/0000-0002-7437-8239"},"institutions":[{"id":"https://openalex.org/I4387155751","display_name":"Evaluation des technologies de sant\u00e9 et des pratiques m\u00e9dicales","ror":"https://ror.org/01qygwc68","country_code":null,"type":"facility","lineage":["https://openalex.org/I2279609970","https://openalex.org/I3018718406","https://openalex.org/I4387155751"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"G. Marot","raw_affiliation_strings":["METRICS - Evaluation des technologies de sant\u00e9 et des pratiques m\u00e9dicales - ULR 2694 (1, place de Verdun 59045 - Lille cedex - France)","MODAL - MOdel for Data Analysis and Learning (France)"],"affiliations":[{"raw_affiliation_string":"METRICS - Evaluation des technologies de sant\u00e9 et des pratiques m\u00e9dicales - ULR 2694 (1, place de Verdun 59045 - Lille cedex - France)","institution_ids":["https://openalex.org/I4387155751"]},{"raw_affiliation_string":"MODAL - MOdel for Data Analysis and Learning (France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073066369","display_name":"David Castel","orcid":"https://orcid.org/0000-0003-0247-080X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"D. Castel","raw_affiliation_strings":["LEFG - Laboratoire d'Exploration Fonctionnelle des G\u00e9nomes (2, rue Gaston Cr\u00e9mieux 91000 EVRY - France)"],"affiliations":[{"raw_affiliation_string":"LEFG - Laboratoire d'Exploration Fonctionnelle des G\u00e9nomes (2, rue Gaston Cr\u00e9mieux 91000 EVRY - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018660599","display_name":"Jordi Estell\u00e9","orcid":"https://orcid.org/0000-0002-6241-1732"},"institutions":[{"id":"https://openalex.org/I157913058","display_name":"Generalitat de Catalunya","ror":"https://ror.org/01bg62x04","country_code":"ES","type":"government","lineage":["https://openalex.org/I157913058"]},{"id":"https://openalex.org/I4210095713","display_name":"Departament de Salut","ror":"https://ror.org/00nyrjc53","country_code":"ES","type":"government","lineage":["https://openalex.org/I157913058","https://openalex.org/I4210095713"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"J. Estelle","raw_affiliation_strings":["CNAG - Centro Nacional de An\u00e1lisi Gen\u00f3mico (Generalitat de Catalunya - Departament de SalutGeneralitat de Catalunya - Departament d'Innovaci\u00f3Ministerio de Ciendia e Innovaci\u00f3nParc Cient\u00edfic de Barcelona baldiri reixac, 4 pcb - tower i 08028 Barcelona - Spain)"],"affiliations":[{"raw_affiliation_string":"CNAG - Centro Nacional de An\u00e1lisi Gen\u00f3mico (Generalitat de Catalunya - Departament de SalutGeneralitat de Catalunya - Departament d'Innovaci\u00f3Ministerio de Ciendia e Innovaci\u00f3nParc Cient\u00edfic de Barcelona baldiri reixac, 4 pcb - tower i 08028 Barcelona - Spain)","institution_ids":["https://openalex.org/I157913058","https://openalex.org/I4210095713"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059218890","display_name":"Gr\u00e9gory Guernec","orcid":null},"institutions":[{"id":"https://openalex.org/I4210128915","display_name":"Centre d'Immunologie et des Maladies Infectieuses","ror":"https://ror.org/0375b8f90","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210128915"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"G. Guernec","raw_affiliation_strings":["ESIM - Epid\u00e9miologie des maladies infectieuses et mod\u00e9lisation (Faculte de M\u00e9decine Saint-Antoine 27, Rue Chaligny 75571 Paris Cedex 12 - France)"],"affiliations":[{"raw_affiliation_string":"ESIM - Epid\u00e9miologie des maladies infectieuses et mod\u00e9lisation (Faculte de M\u00e9decine Saint-Antoine 27, Rue Chaligny 75571 Paris Cedex 12 - France)","institution_ids":["https://openalex.org/I4210128915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001676921","display_name":"Bernd Jagla","orcid":null},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"B. Jagla","raw_affiliation_strings":["CMIP - Centre M\u00e9dical de l'Institut Pasteur (209-211 rue de Vaugirard F-75015 Paris - France)"],"affiliations":[{"raw_affiliation_string":"CMIP - Centre M\u00e9dical de l'Institut Pasteur (209-211 rue de Vaugirard F-75015 Paris - France)","institution_ids":["https://openalex.org/I157536573"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006948865","display_name":"Luc Jouneau","orcid":"https://orcid.org/0000-0002-5094-7302"},"institutions":[{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210099460","https://openalex.org/I4210159481"]},{"id":"https://openalex.org/I4387153087","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es","ror":"https://ror.org/00780az30","country_code":null,"type":"facility","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4387153087"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"L. Jouneau","raw_affiliation_strings":["Unit\u00e9 MIAJ - INRA - Math\u00e9matiques et Informatique Appliqu\u00e9es (Centre de Jouy-en-Josas Domaine de Vilvert F78352 JOUY-EN-JOSAS Cedex - France)"],"affiliations":[{"raw_affiliation_string":"Unit\u00e9 MIAJ - INRA - Math\u00e9matiques et Informatique Appliqu\u00e9es (Centre de Jouy-en-Josas Domaine de Vilvert F78352 JOUY-EN-JOSAS Cedex - France)","institution_ids":["https://openalex.org/I4210159481","https://openalex.org/I4387153087"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016868874","display_name":"D\u00e9nis Lalo\u00eb","orcid":"https://orcid.org/0000-0001-8359-0760"},"institutions":[{"id":"https://openalex.org/I22248866","display_name":"AgroParisTech","ror":"https://ror.org/02kbmgc12","country_code":"FR","type":"education","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210129272","display_name":"G\u00e9n\u00e9tique Animale et Biologie Int\u00e9grative","ror":"https://ror.org/03rkgeb39","country_code":"FR","type":"facility","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4210129272"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"D. Laloe","raw_affiliation_strings":["GABI - G\u00e9n\u00e9tique Animale et Biologie Int\u00e9grative (Domaine de Vilvert F-78252 Jouy-en-Josas - France)"],"affiliations":[{"raw_affiliation_string":"GABI - G\u00e9n\u00e9tique Animale et Biologie Int\u00e9grative (Domaine de Vilvert F-78252 Jouy-en-Josas - France)","institution_ids":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I4210129272","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010350182","display_name":"Caroline Le Gall","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"C. Le Gall","raw_affiliation_strings":["Methodomics (Toulouse - France)"],"affiliations":[{"raw_affiliation_string":"Methodomics (Toulouse - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105842320","display_name":"Brigitte Schaeffer","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210099460","https://openalex.org/I4210159481"]},{"id":"https://openalex.org/I4387153087","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es","ror":"https://ror.org/00780az30","country_code":null,"type":"facility","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4387153087"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"B. Schaeffer","raw_affiliation_strings":["INRA (INRA, UR 0341 Math\u00e9matiques et Informatique Appliqu\u00e9es, F-78352, Jouy-en-Josas, France - France)"],"affiliations":[{"raw_affiliation_string":"INRA (INRA, UR 0341 Math\u00e9matiques et Informatique Appliqu\u00e9es, F-78352, Jouy-en-Josas, France - France)","institution_ids":["https://openalex.org/I4210159481","https://openalex.org/I4387153087"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052835091","display_name":"St\u00e9phane Le Crom","orcid":"https://orcid.org/0000-0002-0534-7797"},"institutions":[{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"S. Le Crom","raw_affiliation_strings":["Genomique ENS - GenomiqueENS (GenomiqueENS\r\nInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS\r\n46, rue d'Ulm\r\n75230 Paris Cedex 05\r\nFrance - France)"],"affiliations":[{"raw_affiliation_string":"Genomique ENS - GenomiqueENS (GenomiqueENS\r\nInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS\r\n46, rue d'Ulm\r\n75230 Paris Cedex 05\r\nFrance - France)","institution_ids":["https://openalex.org/I4210129409"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075313108","display_name":"Micka\u00ebl Guedj","orcid":"https://orcid.org/0000-0002-9742-957X"},"institutions":[{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210099460","https://openalex.org/I4210159481"]},{"id":"https://openalex.org/I4387153087","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es","ror":"https://ror.org/00780az30","country_code":null,"type":"facility","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4387153087"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"M. Guedj","raw_affiliation_strings":["INRA (INRA, UR 0341 Math\u00e9matiques et Informatique Appliqu\u00e9es, F-78352, Jouy-en-Josas, France - France)"],"affiliations":[{"raw_affiliation_string":"INRA (INRA, UR 0341 Math\u00e9matiques et Informatique Appliqu\u00e9es, F-78352, Jouy-en-Josas, France - France)","institution_ids":["https://openalex.org/I4210159481","https://openalex.org/I4387153087"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061290573","display_name":"Florence Jaffr\u00e9zic","orcid":"https://orcid.org/0000-0001-7579-6419"},"institutions":[{"id":"https://openalex.org/I22248866","display_name":"AgroParisTech","ror":"https://ror.org/02kbmgc12","country_code":"FR","type":"education","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210129272","display_name":"G\u00e9n\u00e9tique Animale et Biologie Int\u00e9grative","ror":"https://ror.org/03rkgeb39","country_code":"FR","type":"facility","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4210129272"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"F. Jaffrezic","raw_affiliation_strings":["GABI - G\u00e9n\u00e9tique Animale et Biologie Int\u00e9grative (Domaine de Vilvert F-78252 Jouy-en-Josas - France)"],"affiliations":[{"raw_affiliation_string":"GABI - G\u00e9n\u00e9tique Animale et Biologie Int\u00e9grative (Domaine de Vilvert F-78252 Jouy-en-Josas - France)","institution_ids":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I4210129272","https://openalex.org/I4210088668"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":19,"corresponding_author_ids":["https://openalex.org/A5078354187"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":36.0363,"has_fulltext":true,"cited_by_count":1372,"citation_normalized_percentile":{"value":0.99896489,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"14","issue":"6","first_page":"671","last_page":"683"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983000159263611,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983000159263611,"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":0.9961000084877014,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9922000169754028,"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":0.9183228015899658},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6070961952209473},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5525736808776855},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.480047345161438},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4484977424144745},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36064034700393677},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20071765780448914},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11918801069259644},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.10253360867500305},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08554226160049438},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.06731489300727844}],"concepts":[{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.9183228015899658},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6070961952209473},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5525736808776855},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.480047345161438},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4484977424144745},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36064034700393677},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20071765780448914},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11918801069259644},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.10253360867500305},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08554226160049438},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.06731489300727844},{"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":4,"locations":[{"id":"doi:10.1093/bib/bbs046","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbs046","pdf_url":"https://academic.oup.com/bib/article-pdf/14/6/671/467651/bbs046.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:HAL:hal-00782486v1","is_oa":false,"landing_page_url":"https://inria.hal.science/hal-00782486","pdf_url":null,"source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bib.oxfordjournals.org/","raw_type":"Journal articles"},{"id":"pmh:oai:HAL:hal-01521274v1","is_oa":false,"landing_page_url":"https://hal.archives-ouvertes.fr/hal-01521274","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1467-5463","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:HAL:hal-01661260v1","is_oa":false,"landing_page_url":"https://hal.science/hal-01661260","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"4 Workshop of StatSeq COST Action TD0801, Apr 2012, V\u00e9rone, Italy. &#x27E8;10.1093/bib/bbs046&#x27E9;","raw_type":"Conference papers"}],"best_oa_location":{"id":"doi:10.1093/bib/bbs046","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbs046","pdf_url":"https://academic.oup.com/bib/article-pdf/14/6/671/467651/bbs046.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7240651115","display_name":null,"funder_award_id":"ANR-10","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2165909549.pdf","grobid_xml":"https://content.openalex.org/works/W2165909549.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W641275596","https://openalex.org/W1533335653","https://openalex.org/W1537947034","https://openalex.org/W1546952499","https://openalex.org/W1593470657","https://openalex.org/W1608062813","https://openalex.org/W1840387029","https://openalex.org/W1945743004","https://openalex.org/W1981509058","https://openalex.org/W1984375010","https://openalex.org/W1996064069","https://openalex.org/W1999574084","https://openalex.org/W2000875411","https://openalex.org/W2004419591","https://openalex.org/W2008083733","https://openalex.org/W2011920499","https://openalex.org/W2027455260","https://openalex.org/W2042954443","https://openalex.org/W2061537056","https://openalex.org/W2064469303","https://openalex.org/W2067931814","https://openalex.org/W2072532688","https://openalex.org/W2081304299","https://openalex.org/W2104503053","https://openalex.org/W2107018762","https://openalex.org/W2107060225","https://openalex.org/W2107598685","https://openalex.org/W2110065044","https://openalex.org/W2112888168","https://openalex.org/W2114504176","https://openalex.org/W2119204091","https://openalex.org/W2120865735","https://openalex.org/W2126419817","https://openalex.org/W2128985829","https://openalex.org/W2133111499","https://openalex.org/W2141458291","https://openalex.org/W2149517369","https://openalex.org/W2152045787","https://openalex.org/W2152239989","https://openalex.org/W2154431984","https://openalex.org/W2155804510","https://openalex.org/W2156631105","https://openalex.org/W2156841387","https://openalex.org/W2157840751","https://openalex.org/W2164683872","https://openalex.org/W2168342464","https://openalex.org/W2170152604","https://openalex.org/W2170219300","https://openalex.org/W2417670899","https://openalex.org/W3191599952"],"related_works":["https://openalex.org/W2591697403","https://openalex.org/W2944728705","https://openalex.org/W2904022177","https://openalex.org/W2359348847","https://openalex.org/W3011538607","https://openalex.org/W4294432981","https://openalex.org/W4321441197","https://openalex.org/W2953716828","https://openalex.org/W2469820710","https://openalex.org/W3185081511"],"abstract_inverted_index":{"During":[0],"the":[1,10,19,24,31,48,56,63,82,92,124,135],"last":[2],"3":[3],"years,":[4],"a":[5,59,72],"number":[6],"of":[7,12,26,58,75,85,94,138],"approaches":[8],"for":[9,81],"normalization":[11,50,79,126],"RNA":[13],"sequencing":[14],"data":[15,37,108],"have":[16],"emerged":[17],"in":[18,23,30,112],"literature,":[20],"differing":[21],"both":[22],"type":[25],"bias":[27],"adjustment":[28],"and":[29,97,103,131],"statistical":[32],"strategy":[33],"adopted.":[34],"However,":[35],"as":[36],"continue":[38],"to":[39,52,106,128],"accumulate,":[40],"there":[41],"has":[42],"been":[43],"no":[44],"clear":[45],"consensus":[46],"on":[47,62,71,91,115,123,134],"appropriate":[49,125],"method":[51,61,127],"be":[53,129],"used":[54,130],"or":[55],"impact":[57,133],"chosen":[60],"downstream":[64],"analysis.":[65],"In":[66],"this":[67,116],"work,":[68],"we":[69,119],"focus":[70],"comprehensive":[73],"comparison":[74,117],"seven":[76],"recently":[77],"proposed":[78],"methods":[80],"differential":[83,136],"analysis":[84,137],"RNA-seq":[86,139],"data,":[87],"with":[88],"an":[89],"emphasis":[90],"use":[93],"varied":[95],"real":[96],"simulated":[98],"datasets":[99],"involving":[100],"different":[101],"species":[102],"experimental":[104],"designs":[105],"represent":[107],"characteristics":[109],"commonly":[110],"observed":[111],"practice.":[113],"Based":[114],"study,":[118],"propose":[120],"practical":[121],"recommendations":[122],"its":[132],"data.":[140]},"counts_by_year":[{"year":2026,"cited_by_count":16},{"year":2025,"cited_by_count":67},{"year":2024,"cited_by_count":113},{"year":2023,"cited_by_count":75},{"year":2022,"cited_by_count":112},{"year":2021,"cited_by_count":127},{"year":2020,"cited_by_count":117},{"year":2019,"cited_by_count":105},{"year":2018,"cited_by_count":129},{"year":2017,"cited_by_count":114},{"year":2016,"cited_by_count":127},{"year":2015,"cited_by_count":115},{"year":2014,"cited_by_count":113},{"year":2013,"cited_by_count":36},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-23T09:07:50.710637","created_date":"2016-06-24T00:00:00"}
