{"id":"https://openalex.org/W4385898657","doi":"https://doi.org/10.1093/bioinformatics/btad498","title":"Adjusting for gene-specific covariates to improve RNA-seq analysis","display_name":"Adjusting for gene-specific covariates to improve RNA-seq analysis","publication_year":2023,"publication_date":"2023-08-01","ids":{"openalex":"https://openalex.org/W4385898657","doi":"https://doi.org/10.1093/bioinformatics/btad498","pmid":"https://pubmed.ncbi.nlm.nih.gov/37589589"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad498","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad498","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad498/51135264/btad498.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad498/51135264/btad498.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041958648","display_name":"Hyeongseon Jeon","orcid":"https://orcid.org/0000-0002-3539-4332"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]},{"id":"https://openalex.org/I2799885155","display_name":"The Ohio State University Comprehensive Cancer Center \u2013 Arthur G. James Cancer Hospital and Richard J. Solove Research Institute","ror":"https://ror.org/028t46f04","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799885155"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hyeongseon Jeon","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University , Columbus, OH, United States","Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University , Columbus, OH 43210, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University , Columbus, OH, United States","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University , Columbus, OH 43210, United States","institution_ids":["https://openalex.org/I2799885155","https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043896734","display_name":"Kyu\u2010Sang Lim","orcid":"https://orcid.org/0000-0001-5406-266X"},"institutions":[{"id":"https://openalex.org/I206597221","display_name":"Kongju National University","ror":"https://ror.org/0373nm262","country_code":"KR","type":"education","lineage":["https://openalex.org/I206597221"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kyu-Sang Lim","raw_affiliation_strings":["Department of Animal Resources Science, Kongju National University , Yesan-gun, Chungnam 32439, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Department of Animal Resources Science, Kongju National University , Yesan-gun, Chungnam 32439, Republic of Korea","institution_ids":["https://openalex.org/I206597221"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070374369","display_name":"Yet Nguyen","orcid":null},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yet Nguyen","raw_affiliation_strings":["Department of Mathematics and Statistics, Old Dominion University , Norfolk, VA 23529, United States"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, Old Dominion University , Norfolk, VA 23529, United States","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047522477","display_name":"Dan Nettleton","orcid":"https://orcid.org/0000-0002-6045-1036"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dan Nettleton","raw_affiliation_strings":["Department of Statistics, Iowa State University , Ames, IA 50011, Unites States"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, Iowa State University , Ames, IA 50011, Unites States","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5041958648"],"corresponding_institution_ids":["https://openalex.org/I2799885155","https://openalex.org/I52357470"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.27668295,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"39","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.998199999332428,"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/T10885","display_name":"Gene expression and cancer classification","score":0.998199999332428,"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":0.9980000257492065,"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/T11235","display_name":"Statistical Methods in Clinical Trials","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/covariate","display_name":"Covariate","score":0.920091986656189},{"id":"https://openalex.org/keywords/estimator","display_name":"Estimator","score":0.6542236804962158},{"id":"https://openalex.org/keywords/null","display_name":"Null (SQL)","score":0.57066410779953},{"id":"https://openalex.org/keywords/type-i-and-type-ii-errors","display_name":"Type I and type II errors","score":0.5457146167755127},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5404513478279114},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5205919742584229},{"id":"https://openalex.org/keywords/null-hypothesis","display_name":"Null hypothesis","score":0.5054452419281006},{"id":"https://openalex.org/keywords/variable","display_name":"Variable (mathematics)","score":0.505403995513916},{"id":"https://openalex.org/keywords/null-model","display_name":"Null model","score":0.4959588944911957},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.4766705334186554},{"id":"https://openalex.org/keywords/multiple-comparisons-problem","display_name":"Multiple comparisons problem","score":0.41651177406311035},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3756541311740875},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3467087149620056},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1186985969543457}],"concepts":[{"id":"https://openalex.org/C119043178","wikidata":"https://www.wikidata.org/wiki/Q320723","display_name":"Covariate","level":2,"score":0.920091986656189},{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.6542236804962158},{"id":"https://openalex.org/C203763787","wikidata":"https://www.wikidata.org/wiki/Q371029","display_name":"Null (SQL)","level":2,"score":0.57066410779953},{"id":"https://openalex.org/C40696583","wikidata":"https://www.wikidata.org/wiki/Q989120","display_name":"Type I and type II errors","level":2,"score":0.5457146167755127},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5404513478279114},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5205919742584229},{"id":"https://openalex.org/C191988596","wikidata":"https://www.wikidata.org/wiki/Q628374","display_name":"Null hypothesis","level":2,"score":0.5054452419281006},{"id":"https://openalex.org/C182365436","wikidata":"https://www.wikidata.org/wiki/Q50701","display_name":"Variable (mathematics)","level":2,"score":0.505403995513916},{"id":"https://openalex.org/C36382193","wikidata":"https://www.wikidata.org/wiki/Q7068966","display_name":"Null model","level":2,"score":0.4959588944911957},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.4766705334186554},{"id":"https://openalex.org/C183905921","wikidata":"https://www.wikidata.org/wiki/Q1038757","display_name":"Multiple comparisons problem","level":2,"score":0.41651177406311035},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3756541311740875},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3467087149620056},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1186985969543457},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad498","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad498","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad498/51135264/btad498.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37589589","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37589589","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10460482","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10460482","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10460482/pdf/btad498.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:digitalcommons.odu.edu:mathstat_fac_pubs-1236","is_oa":true,"landing_page_url":"https://digitalcommons.odu.edu/mathstat_fac_pubs/234","pdf_url":null,"source":{"id":"https://openalex.org/S4377196314","display_name":"ODU Digital Commons (Old Dominion University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I81365321","host_organization_name":"Old Dominion University","host_organization_lineage":["https://openalex.org/I81365321"],"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":"Mathematics & Statistics Faculty Publications","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad498","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad498","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad498/51135264/btad498.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1912461434","display_name":null,"funder_award_id":"IOW03717","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G3890658974","display_name":null,"funder_award_id":"Hatch","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G4366873263","display_name":null,"funder_award_id":"2017-67007-26144","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G4534757481","display_name":null,"funder_award_id":"IOW05658","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G4846987069","display_name":null,"funder_award_id":"IOW03717","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"}],"funders":[{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320326646","display_name":"Genome Alberta","ror":null},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4385898657.pdf"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1978103519","https://openalex.org/W2049113394","https://openalex.org/W2073622765","https://openalex.org/W2105381419","https://openalex.org/W2110065044","https://openalex.org/W2418024629","https://openalex.org/W2829554817","https://openalex.org/W2904560543","https://openalex.org/W2951144892","https://openalex.org/W2962981429","https://openalex.org/W2963642566","https://openalex.org/W3127140457","https://openalex.org/W3193233062"],"related_works":["https://openalex.org/W3003558595","https://openalex.org/W4361270669","https://openalex.org/W154531455","https://openalex.org/W2915316750","https://openalex.org/W3069995450","https://openalex.org/W4249473446","https://openalex.org/W2153630450","https://openalex.org/W2113330311","https://openalex.org/W1995992573","https://openalex.org/W4200219293"],"abstract_inverted_index":{"The":[0],"source":[1],"code":[2],"repository":[3],"is":[4],"publicly":[5],"available":[6],"at":[7],"https://github.com/hsjeon1217/conditional_method.":[8]},"counts_by_year":[],"updated_date":"2026-03-25T14:56:36.534964","created_date":"2025-10-10T00:00:00"}
