{"id":"https://openalex.org/W2968810249","doi":"https://doi.org/10.1186/s12859-019-3017-9","title":"Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods","display_name":"Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods","publication_year":2019,"publication_date":"2019-08-13","ids":{"openalex":"https://openalex.org/W2968810249","doi":"https://doi.org/10.1186/s12859-019-3017-9","mag":"2968810249","pmid":"https://pubmed.ncbi.nlm.nih.gov/31409293"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3017-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3017-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3017-9","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/track/pdf/10.1186/s12859-019-3017-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078316898","display_name":"Shintaro Katayama","orcid":"https://orcid.org/0000-0001-7581-5157"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Shintaro Katayama","raw_affiliation_strings":["Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden. shintaro.katayama@ki.se","Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden"],"raw_orcid":"https://orcid.org/0000-0001-7581-5157","affiliations":[{"raw_affiliation_string":"Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden. shintaro.katayama@ki.se","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034830859","display_name":"Tiina Skoog","orcid":"https://orcid.org/0000-0002-0148-0654"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Tiina Skoog","raw_affiliation_strings":["Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040807511","display_name":"Cilla S\u00f6derh\u00e4ll","orcid":"https://orcid.org/0000-0002-8397-3080"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Cilla S\u00f6derh\u00e4ll","raw_affiliation_strings":["Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden","Department of Women's and Children's Health, Karolinska Institutet, 17177, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Department of Women's and Children's Health, Karolinska Institutet, 17177, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017764037","display_name":"El\u00edsabet Einarsd\u00f3ttir","orcid":"https://orcid.org/0000-0003-3101-2285"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["FI","SE"],"is_corresponding":false,"raw_author_name":"Elisabet Einarsdottir","raw_affiliation_strings":["Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden","Folkh\u00e4lsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, 00014, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Folkh\u00e4lsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, 00014, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012737483","display_name":"Kaarel Krjut\u0161kov","orcid":"https://orcid.org/0000-0003-1297-1464"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I4210165715","display_name":"Competence Centre on Health Technologies (Estonia)","ror":"https://ror.org/05kagrs11","country_code":"EE","type":"company","lineage":["https://openalex.org/I4210165715"]}],"countries":["EE","FI","SE"],"is_corresponding":false,"raw_author_name":"Kaarel Krjut\u0161kov","raw_affiliation_strings":["Competence Centre on Health Technologies, 50410, Tartu, Estonia","Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden","Folkh\u00e4lsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, 00014, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Competence Centre on Health Technologies, 50410, Tartu, Estonia","institution_ids":["https://openalex.org/I4210165715"]},{"raw_affiliation_string":"Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Folkh\u00e4lsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, 00014, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100712980","display_name":"Juha Kere","orcid":"https://orcid.org/0000-0003-1974-0271"},"institutions":[{"id":"https://openalex.org/I1298207432","display_name":"Guy's Hospital","ror":"https://ror.org/04r33pf22","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I1298207432","https://openalex.org/I200166805","https://openalex.org/I4210111135"]},{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I4210153400","display_name":"King's College Hospital","ror":"https://ror.org/044nptt90","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I4210111135","https://openalex.org/I4210153400"]}],"countries":["FI","GB","SE"],"is_corresponding":false,"raw_author_name":"Juha Kere","raw_affiliation_strings":["Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden","Folkh\u00e4lsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, 00014, Helsinki, Finland","School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, SE1 9RT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Folkh\u00e4lsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, 00014, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, SE1 9RT, UK","institution_ids":["https://openalex.org/I1298207432","https://openalex.org/I4210153400"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5078316898"],"corresponding_institution_ids":["https://openalex.org/I28166907"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5983,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.67152788,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"20","issue":"1","first_page":"418","last_page":"418"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.7908999919891357,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.7908999919891357,"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":0.13109999895095825,"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":0.01899999938905239,"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/dna-microarray","display_name":"DNA microarray","score":0.6876408457756042},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.6688473224639893},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.626255214214325},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.499103307723999},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4907139539718628},{"id":"https://openalex.org/keywords/multiplexing","display_name":"Multiplexing","score":0.4352595806121826},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.379216730594635},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.379115492105484},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3559408187866211},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2585429549217224},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.20273590087890625},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.164081871509552},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.1029973030090332},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.1008433997631073},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.08246347308158875}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.6876408457756042},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6688473224639893},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.626255214214325},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.499103307723999},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4907139539718628},{"id":"https://openalex.org/C19275194","wikidata":"https://www.wikidata.org/wiki/Q222903","display_name":"Multiplexing","level":2,"score":0.4352595806121826},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.379216730594635},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.379115492105484},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3559408187866211},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2585429549217224},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.20273590087890625},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.164081871509552},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.1029973030090332},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.1008433997631073},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.08246347308158875}],"mesh":[{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1186/s12859-019-3017-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3017-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3017-9","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:31409293","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31409293","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:doaj.org/article:043e8dac8a1a436db127b1c2770db1c5","is_oa":true,"landing_page_url":"https://doaj.org/article/043e8dac8a1a436db127b1c2770db1c5","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 20, Iss 1, Pp 1-9 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5645470","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6693229","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:helda.helsinki.fi:10138/304733","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/304733","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"http://purl.org/eprint/entityType/ScholarlyWork"},{"id":"pmh:oai:helda.helsinki.fi:10138/306360","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/306360","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:zenodo.org:3372402","is_oa":true,"landing_page_url":"https://zenodo.org/record/3372402","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics 20(1) 418","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-3017-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3017-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3017-9","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":[{"score":0.6700000166893005,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G1328989013","display_name":null,"funder_award_id":"2014fobi41753","funder_id":"https://openalex.org/F4320322315","funder_display_name":"Karolinska Institutet"},{"id":"https://openalex.org/G2423991038","display_name":null,"funder_award_id":"2016fobi50455","funder_id":"https://openalex.org/F4320322315","funder_display_name":"Karolinska Institutet"},{"id":"https://openalex.org/G7587496563","display_name":null,"funder_award_id":"KAW2015.0096","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G988683975","display_name":null,"funder_award_id":"2013fobi38282","funder_id":"https://openalex.org/F4320322315","funder_display_name":"Karolinska Institutet"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322169","display_name":"Hj\u00e4rt-Lungfonden","ror":"https://ror.org/052261q33"},{"id":"https://openalex.org/F4320322315","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691"},{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320324368","display_name":"Stiftelsen Sven Jerrings Fond","ror":"https://ror.org/055y0va06"},{"id":"https://openalex.org/F4320336376","display_name":"Uppsala Multidisciplinary Center for Advanced Computational Science","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2968810249.pdf","grobid_xml":"https://content.openalex.org/works/W2968810249.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W987420839","https://openalex.org/W1966327575","https://openalex.org/W2025828346","https://openalex.org/W2041677964","https://openalex.org/W2109389325","https://openalex.org/W2120865735","https://openalex.org/W2124985265","https://openalex.org/W2140729960","https://openalex.org/W2149031002","https://openalex.org/W2152239989","https://openalex.org/W2155536866","https://openalex.org/W2157795344","https://openalex.org/W2169575896","https://openalex.org/W2173732482","https://openalex.org/W2301339423","https://openalex.org/W2493948093","https://openalex.org/W2517071462","https://openalex.org/W2794891507","https://openalex.org/W2907783748","https://openalex.org/W2949275240","https://openalex.org/W2951638683","https://openalex.org/W3102458540","https://openalex.org/W4294107304"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W2982720988","https://openalex.org/W3150324899","https://openalex.org/W4388725868","https://openalex.org/W2104762330","https://openalex.org/W4379374180","https://openalex.org/W2523545060","https://openalex.org/W4229998356"],"abstract_inverted_index":{"BACKGROUND:":[0],"Standard":[1],"RNAseq":[2,10,40,98],"methods":[3,11,236],"using":[4,101,128,167],"bulk":[5],"RNA":[6],"and":[7,18,20,38,78,114,193,215,249],"recent":[8],"single-cell":[9,37],"use":[12,231],"DNA":[13],"barcodes":[14],"to":[15,180,222,244],"identify":[16],"samples":[17,57,243],"cells,":[19],"the":[21,42,50,74,102,108,129,136,163,194,205,224],"barcoded":[22],"cDNAs":[23],"are":[24],"pooled":[25],"into":[26],"a":[27,59,170,185,238],"library":[28,43,65,87,109,116,121,164,195,206,225],"pool":[29],"before":[30],"high":[31],"throughput":[32],"sequencing.":[33],"In":[34],"cases":[35],"of":[36,53,84,107,188],"low-input":[39],"methods,":[41],"is":[44,76,211,220],"further":[45],"amplified":[46],"by":[47,112,151],"PCR":[48],"after":[49],"pooling.":[51],"Preparation":[52],"hundreds":[54],"or":[55],"more":[56],"for":[58,184,204],"large":[60],"study":[61,187],"often":[62],"requires":[63,169],"multiple":[64],"pools.":[66],"However,":[67],"sometimes":[68],"correlation":[69],"between":[70,86],"expression":[71,182],"profiles":[72],"among":[73],"libraries":[75,99,153],"low":[77,156],"batch":[79],"effect":[80],"biases":[81,110,196,226],"make":[82],"integration":[83],"data":[85],"pools":[88],"difficult.":[89],"RESULTS:":[90],"We":[91],"investigated":[92],"166":[93],"technical":[94],"replicates":[95],"in":[96,135,227,253],"14":[97],"made":[100],"STRT":[103],"method.":[104],"The":[105,123,139,174,200],"patterns":[106],"differed":[111],"genes,":[113],"uneven":[115],"yields":[117],"were":[118,197],"associated":[119],"with":[120,154,237,242],"biases.":[122],"former":[124],"bias":[125,141,165,207],"was":[126,178],"corrected":[127,145],"NBGLM-LBC":[130,168,175,210],"algorithm,":[131],"which":[132],"we":[133],"present":[134],"current":[137],"study.":[138],"latter":[140],"could":[142,148],"not":[143],"be":[144,149,245],"directly,":[146],"but":[147],"solved":[150],"omitting":[152],"particularly":[155],"yields.":[157],"A":[158],"simulation":[159],"experiment":[160],"suggested":[161],"that":[162,230],"correction":[166,176,208],"consistent":[171,239],"sample":[172,240],"layout.":[173],"method":[177,219],"applied":[179],"an":[181],"profile":[183],"cohort":[186],"childhood":[189],"acute":[190],"respiratory":[191],"illness,":[192],"resolved.":[198],"CONCLUSIONS:":[199],"R":[201],"source":[202],"code":[203],"named":[209],"available":[212],"at":[213],"https://shka.github.io/NBGLM-LBC":[214],"https://shka.bitbucket.io/NBGLM-LBC":[216],".":[217],"This":[218],"applicable":[221],"correct":[223],"various":[228],"studies":[229],"highly":[232],"multiplexed":[233],"sequencing-based":[234],"profiling":[235],"layout":[241],"compared":[246],"(e.g.,":[247],"\"cases\"":[248],"\"controls\")":[250],"equally":[251],"distributed":[252],"each":[254],"library.":[255]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}