{"id":"https://openalex.org/W4309322228","doi":"https://doi.org/10.1186/s12859-022-05023-z","title":"Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes","display_name":"Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes","publication_year":2022,"publication_date":"2022-11-16","ids":{"openalex":"https://openalex.org/W4309322228","doi":"https://doi.org/10.1186/s12859-022-05023-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/36384457"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-05023-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-05023-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-05023-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-05023-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044381779","display_name":"Igor V. Deyneko","orcid":"https://orcid.org/0000-0002-3173-9604"},"institutions":[{"id":"https://openalex.org/I4210133056","display_name":"Timiryazev Institute of Plant Physiology","ror":"https://ror.org/03hg8g849","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210133056"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Igor V. Deyneko","raw_affiliation_strings":["Laboratory of Functional Genomics, \u041a.\u0410. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276. igor.deyneko@inbox.ru","Laboratory of Functional Genomics, \u041a.\u0410. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276"],"raw_orcid":"https://orcid.org/0000-0002-3173-9604","affiliations":[{"raw_affiliation_string":"Laboratory of Functional Genomics, \u041a.\u0410. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276. igor.deyneko@inbox.ru","institution_ids":["https://openalex.org/I4210133056"]},{"raw_affiliation_string":"Laboratory of Functional Genomics, \u041a.\u0410. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276","institution_ids":["https://openalex.org/I4210133056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025021312","display_name":"\u041e. \u041d. \u041c\u0443\u0441\u0442\u0430\u0444\u0430\u0435\u0432","orcid":null},"institutions":[{"id":"https://openalex.org/I126595936","display_name":"Azerbaijan National Academy of Sciences","ror":"https://ror.org/006m4q736","country_code":"AZ","type":"government","lineage":["https://openalex.org/I126595936"]}],"countries":["AZ"],"is_corresponding":false,"raw_author_name":"Orkhan N. Mustafaev","raw_affiliation_strings":["Genetic Resources Institute, Azerbaijan National Academy of Sciences, AZ1106, Baku, Azerbaijan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genetic Resources Institute, Azerbaijan National Academy of Sciences, AZ1106, Baku, Azerbaijan","institution_ids":["https://openalex.org/I126595936"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026593115","display_name":"A. A. Tyurin","orcid":"https://orcid.org/0000-0001-5206-0775"},"institutions":[{"id":"https://openalex.org/I4210133056","display_name":"Timiryazev Institute of Plant Physiology","ror":"https://ror.org/03hg8g849","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210133056"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Alexander \u0410. Tyurin","raw_affiliation_strings":["Laboratory of Functional Genomics, \u041a.\u0410. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Functional Genomics, \u041a.\u0410. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276","institution_ids":["https://openalex.org/I4210133056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087030175","display_name":"Ksenya V. Zhukova","orcid":null},"institutions":[{"id":"https://openalex.org/I4210133056","display_name":"Timiryazev Institute of Plant Physiology","ror":"https://ror.org/03hg8g849","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210133056"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ksenya V. Zhukova","raw_affiliation_strings":["Laboratory of Functional Genomics, \u041a.\u0410. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Functional Genomics, \u041a.\u0410. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276","institution_ids":["https://openalex.org/I4210133056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063837188","display_name":"Alexander Varzari","orcid":"https://orcid.org/0000-0003-1855-3095"},"institutions":[{"id":"https://openalex.org/I4210114834","display_name":"Phthisiopneumology Institute \"Chiril Draganiuc\"","ror":"https://ror.org/02j0at714","country_code":"MD","type":"healthcare","lineage":["https://openalex.org/I4210114834"]}],"countries":["MD"],"is_corresponding":false,"raw_author_name":"Alexander Varzari","raw_affiliation_strings":["Laboratory of Human Genetics, Chiril Draganiuc Institute of Phthisiopneumology, MD2025, Kishinev, Republic of Moldova"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Human Genetics, Chiril Draganiuc Institute of Phthisiopneumology, MD2025, Kishinev, Republic of Moldova","institution_ids":["https://openalex.org/I4210114834"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075181672","display_name":"\u0418. \u0412. \u0413\u043e\u043b\u0434\u0435\u043d\u043a\u043e\u0432\u0430-\u041f\u0430\u0432\u043b\u043e\u0432\u0430","orcid":"https://orcid.org/0000-0003-2270-065X"},"institutions":[{"id":"https://openalex.org/I4210133056","display_name":"Timiryazev Institute of Plant Physiology","ror":"https://ror.org/03hg8g849","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210133056"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Irina V. Goldenkova-Pavlova","raw_affiliation_strings":["Laboratory of Functional Genomics, \u041a.\u0410. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276. irengold58@gmail.com","Laboratory of Functional Genomics, \u041a.\u0410. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Functional Genomics, \u041a.\u0410. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276. irengold58@gmail.com","institution_ids":["https://openalex.org/I4210133056"]},{"raw_affiliation_string":"Laboratory of Functional Genomics, \u041a.\u0410. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276","institution_ids":["https://openalex.org/I4210133056"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5044381779"],"corresponding_institution_ids":["https://openalex.org/I4210133056"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.5601,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.83198053,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"23","issue":"1","first_page":"488","last_page":"488"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.33180001378059387,"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":0.33180001378059387,"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":0.12630000710487366,"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":0.11869999766349792,"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/rna-seq","display_name":"RNA-Seq","score":0.8158438205718994},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6848912835121155},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6130883693695068},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5997838973999023},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5818533301353455},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.44588813185691833},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.42306971549987793},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.41122496128082275},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3995402753353119},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3623386025428772}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.8158438205718994},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6848912835121155},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6130883693695068},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5997838973999023},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5818533301353455},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.44588813185691833},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.42306971549987793},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.41122496128082275},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3995402753353119},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3623386025428772}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-022-05023-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-05023-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-05023-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36384457","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36384457","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9670425","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9670425","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:f176899df60449148035161160517f88","is_oa":true,"landing_page_url":"https://doaj.org/article/f176899df60449148035161160517f88","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 23, Iss 1, Pp 1-14 (2022)","raw_type":"article"},{"id":"pmh:oai:ibn.idsi.md:168432","is_oa":true,"landing_page_url":"https://ibn.idsi.md/vizualizare_articol/168432","pdf_url":null,"source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics  1-14","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-05023-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-05023-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-05023-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4399999976158142}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4309322228.pdf","grobid_xml":"https://content.openalex.org/works/W4309322228.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1993684198","https://openalex.org/W2027099754","https://openalex.org/W2046065484","https://openalex.org/W2053427298","https://openalex.org/W2058358568","https://openalex.org/W2072602203","https://openalex.org/W2079166554","https://openalex.org/W2097117811","https://openalex.org/W2114104545","https://openalex.org/W2119034410","https://openalex.org/W2121211805","https://openalex.org/W2130116522","https://openalex.org/W2143689381","https://openalex.org/W2146516445","https://openalex.org/W2150782426","https://openalex.org/W2152239989","https://openalex.org/W2163871842","https://openalex.org/W2164883482","https://openalex.org/W2179438025","https://openalex.org/W2323326409","https://openalex.org/W2906053276","https://openalex.org/W2917207851","https://openalex.org/W2932166412","https://openalex.org/W2950101275","https://openalex.org/W3080195127","https://openalex.org/W3092050064","https://openalex.org/W3098132351","https://openalex.org/W3112995414","https://openalex.org/W3154460765","https://openalex.org/W3173362574"],"related_works":["https://openalex.org/W4362511917","https://openalex.org/W3018634223","https://openalex.org/W2904597490","https://openalex.org/W4362530199","https://openalex.org/W4362511560","https://openalex.org/W4377231761","https://openalex.org/W4285162488","https://openalex.org/W4362512073","https://openalex.org/W4362485908","https://openalex.org/W2268123450"],"abstract_inverted_index":{"BACKGROUND:":[0],"RNA-seq":[1,60,138,146,182],"has":[2],"become":[3],"a":[4,56,79],"standard":[5],"technology":[6],"to":[7,75,111,136],"quantify":[8],"mRNA.":[9],"The":[10,180],"measured":[11],"values":[12,28],"usually":[13],"vary":[14],"by":[15,44],"several":[16,144],"orders":[17],"of":[18,24,35,47,66,84,106,118,134,165,174,189],"magnitude,":[19],"and":[20,49,70,91,126,143,154,160,169,187,196],"while":[21],"the":[22,33,36,45,64,104,112,116,171,193],"detection":[23,65,164],"differences":[25,37],"at":[26,197],"high":[27],"is":[29],"statistically":[30],"well":[31],"grounded,":[32],"significance":[34],"for":[38,58,151,176],"rare":[39],"mRNAs":[40],"can":[41],"be":[42],"weakened":[43],"presence":[46],"biological":[48],"technical":[50,97],"noise.":[51],"RESULTS:":[52],"We":[53,101],"have":[54],"developed":[55],"method":[57],"cleaning":[59],"data,":[61,183],"which":[62],"improves":[63],"differentially":[67,120,166],"expressed":[68,121,167],"genes":[69,72],"specifically":[71],"with":[73],"low":[74],"moderate":[76],"transcription.":[77],"Using":[78],"data":[80,139,195],"modeling":[81],"approach,":[82],"parameters":[83],"randomly":[85],"distributed":[86],"mRNA":[87],"counts":[88],"are":[89,99,191],"identified":[90],"reads,":[92],"most":[93],"probably":[94],"originating":[95],"from":[96],"noise,":[98],"removed.":[100],"demonstrate":[102],"that":[103],"removal":[105],"this":[107],"random":[108],"component":[109],"leads":[110],"significant":[113,124],"increase":[114],"in":[115,192],"number":[117],"detected":[119],"genes,":[122,168],"more":[123],"pvalues":[125],"no":[127],"bias":[128],"towards":[129],"low-count":[130],"genes.":[131],"CONCLUSION:":[132],"Application":[133],"RNAdeNoise":[135],"our":[137],"on":[140],"polysome":[141],"profiling":[142],"published":[145],"datasets":[147],"reveals":[148],"its":[149],"suitability":[150],"different":[152],"organisms":[153],"sequencing":[155],"technologies":[156],"such":[157],"as":[158],"Illumina":[159],"BGI,":[161],"shows":[162],"improved":[163],"excludes":[170],"subjective":[172],"setting":[173],"thresholds":[175],"minimal":[177],"RNA":[178],"counts.":[179],"program,":[181],"resulted":[184],"gene":[185],"lists":[186],"examples":[188],"use":[190],"supplementary":[194],"https://github.com/Deyneko/RNAdeNoise":[198],".":[199]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}