{"id":"https://openalex.org/W2102778186","doi":"https://doi.org/10.1186/1471-2105-14-258","title":"Differential expression analysis with global network adjustment","display_name":"Differential expression analysis with global network adjustment","publication_year":2013,"publication_date":"2013-08-23","ids":{"openalex":"https://openalex.org/W2102778186","doi":"https://doi.org/10.1186/1471-2105-14-258","mag":"2102778186","pmid":"https://pubmed.ncbi.nlm.nih.gov/23968143"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-258","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-258","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-258","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":null,"license_id":null,"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/10.1186/1471-2105-14-258","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024582072","display_name":"Jonathan Gelfond","orcid":"https://orcid.org/0000-0002-0773-3683"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan A Gelfond","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA. gelfondjal@uthscsa.edu","Department of Epidemiology and Biostatistics, University of Texas Health Science Center San Antonio, San Antonio, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA. gelfondjal@uthscsa.edu","institution_ids":["https://openalex.org/I165951966"]},{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, University of Texas Health Science Center San Antonio, San Antonio, USA","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078399867","display_name":"Joseph G. Ibrahim","orcid":"https://orcid.org/0000-0003-2428-6552"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph G Ibrahim","raw_affiliation_strings":["Department of Biostatistics, University of North Carolina School of Public Health, Chapel Hill, North Carolina, USA","Department of Biostatistics, University of North Carolina School of Public Health, Chapel Hill, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of North Carolina School of Public Health, Chapel Hill, North Carolina, USA","institution_ids":[]},{"raw_affiliation_string":"Department of Biostatistics, University of North Carolina School of Public Health, Chapel Hill, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003955241","display_name":"Mayetri Gupta","orcid":"https://orcid.org/0000-0003-1052-6738"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mayetri Gupta","raw_affiliation_strings":["School of Mathematics and Statistics, University of Glasgow, Glasgow, Scotland, UK","University of Glasgow"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Glasgow, Glasgow, Scotland, UK","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"University of Glasgow","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100678189","display_name":"Ming\u2010Hui Chen","orcid":"https://orcid.org/0000-0003-1935-2447"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ming-Hui Chen","raw_affiliation_strings":["Department of Statistics, University of Connecticut, Storrs, Connecticut, USA","University of Connecticut"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Connecticut, Storrs, Connecticut, USA","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"University of Connecticut","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083485626","display_name":"Jannine D. Cody","orcid":"https://orcid.org/0000-0002-3034-8687"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jannine D Cody","raw_affiliation_strings":["Department of Pediatrics, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA","Department of Pediatrics, University of Texas Health Science Center San Antonio, San Antonio, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA","institution_ids":["https://openalex.org/I165951966"]},{"raw_affiliation_string":"Department of Pediatrics, University of Texas Health Science Center San Antonio, San Antonio, USA","institution_ids":["https://openalex.org/I165951966"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2790},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2790},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08922318,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"14","issue":"1","first_page":"258","last_page":"258"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.7843000292778015,"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":0.7843000292778015,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.10350000113248825,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.03319999948143959,"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/lasso","display_name":"Lasso (programming language)","score":0.6723203659057617},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6425540447235107},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.558716893196106},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5577239394187927},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5061821341514587},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5050867199897766},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4938371777534485},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.45798978209495544},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4425663948059082},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43496212363243103},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.423685759305954},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.4200282096862793},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.41320565342903137},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.41147270798683167},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3880082368850708},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3099743127822876},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2829778790473938},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.26680201292037964},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1796925961971283}],"concepts":[{"id":"https://openalex.org/C37616216","wikidata":"https://www.wikidata.org/wiki/Q3218363","display_name":"Lasso (programming language)","level":2,"score":0.6723203659057617},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6425540447235107},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.558716893196106},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5577239394187927},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5061821341514587},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5050867199897766},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4938371777534485},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.45798978209495544},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4425663948059082},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43496212363243103},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.423685759305954},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.4200282096862793},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.41320565342903137},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.41147270798683167},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3880082368850708},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3099743127822876},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2829778790473938},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26680201292037964},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1796925961971283},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059629","descriptor_name":"Signal-To-Noise Ratio","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059629","descriptor_name":"Signal-To-Noise Ratio","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059629","descriptor_name":"Signal-To-Noise Ratio","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-14-258","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-258","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-258","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23968143","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23968143","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:eprints.gla.ac.uk:85826","is_oa":false,"landing_page_url":"https://eprints.gla.ac.uk/view/author/29274.html>","pdf_url":null,"source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":false,"is_in_doaj":true,"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Articles"},{"id":"pmh:oai:cdr.lib.unc.edu:uuid:4f9913bd-c487-4973-9d8d-ceac53cae1fb","is_oa":true,"landing_page_url":"https://cdr.lib.unc.edu/record/uuid:4f9913bd-c487-4973-9d8d-ceac53cae1fb","pdf_url":null,"source":{"id":"https://openalex.org/S4306401075","display_name":"Carolina Digital Repository (University of North Carolina at Chapel Hill)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I114027177","host_organization_name":"University of North Carolina at Chapel Hill","host_organization_lineage":["https://openalex.org/I114027177"],"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":"","raw_type":"Text"},{"id":"pmh:oai:europepmc.org:2762406","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3766173","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3766173","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3766173","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-14-258","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-258","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-258","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4515346447","display_name":null,"funder_award_id":"AI087520","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2102778186.pdf","grobid_xml":"https://content.openalex.org/works/W2102778186.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1998544165","https://openalex.org/W2011117766","https://openalex.org/W2014725748","https://openalex.org/W2024103316","https://openalex.org/W2040724884","https://openalex.org/W2047028564","https://openalex.org/W2088645589","https://openalex.org/W2088961728","https://openalex.org/W2094678200","https://openalex.org/W2101163066","https://openalex.org/W2102054988","https://openalex.org/W2122825543","https://openalex.org/W2132555912","https://openalex.org/W2135046866","https://openalex.org/W2136979045","https://openalex.org/W2139602588","https://openalex.org/W2140954822","https://openalex.org/W2143076232","https://openalex.org/W2148070020","https://openalex.org/W2154362705","https://openalex.org/W2164201990","https://openalex.org/W2164683872","https://openalex.org/W2167167845","https://openalex.org/W2170264612","https://openalex.org/W2582743722","https://openalex.org/W4229762230","https://openalex.org/W4234698323"],"related_works":["https://openalex.org/W2069695727","https://openalex.org/W1996185163","https://openalex.org/W1515021623","https://openalex.org/W2084813257","https://openalex.org/W3155171010","https://openalex.org/W2045929470","https://openalex.org/W2081127504","https://openalex.org/W2119862467","https://openalex.org/W2122223946","https://openalex.org/W4233500668"],"abstract_inverted_index":{"BACKGROUND:":[0],"Large-scale":[1],"chromosomal":[2],"deletions":[3],"or":[4,17],"other":[5,48],"non-specific":[6],"perturbations":[7],"of":[8,15,19,24,47,55,62,81,93,98,106,138,167,188,202,226,265,289,301],"the":[9,13,53,60,79,91,96,104,164,168,171,178,192,205,223,242,271,287,290,297],"transcriptome":[10],"can":[11,116,143],"alter":[12],"expression":[14,43,113,149,230,252,281,303],"hundreds":[16],"thousands":[18],"genes,":[20,295],"and":[21,95,151,181,234,299],"it":[22],"is":[23,77,89,101,160,196,231],"biological":[25,99,272],"interest":[26],"to":[27,67,119,154,176,183,254],"understand":[28],"which":[29,274],"genes":[30,49,63],"are":[31,110,268,305],"most":[32],"profoundly":[33],"affected.":[34],"We":[35,134,258],"present":[36],"a":[37,41,45,68,86,136,184,199,238,262],"method":[38,210],"for":[39,52,286],"predicting":[40],"gene's":[42],"as":[44],"function":[46],"thereby":[50],"accounting":[51],"effect":[54],"transcriptional":[56,128],"regulation":[57,129],"that":[58,78,115,122,142,222,261],"confounds":[59],"identification":[61],"differentially":[64],"expressed":[65],"relative":[66],"regulatory":[69],"network.":[70],"The":[71,157],"challenge":[72],"in":[73,126,130,170,229,237,241],"constructing":[74],"such":[75],"models":[76],"number":[80,97],"possible":[82],"regulator":[83],"transcripts":[84],"within":[85],"global":[87,291],"network":[88,292],"on":[90,103,249,270,293],"order":[92,105],"thousands,":[94],"samples":[100],"typically":[102],"10.":[107],"Nevertheless,":[108,204],"there":[109],"large":[111,147,263],"gene":[112,148,251,266],"databases":[114],"be":[117,124,144,276],"used":[118,213],"construct":[120],"networks":[121],"could":[123],"helpful":[125],"modeling":[127],"smaller":[131,155],"experiments.":[132,156],"RESULTS:":[133],"demonstrate":[135],"type":[137],"penalized":[139],"regression":[140],"model":[141,179],"estimated":[145],"from":[146],"databases,":[150],"then":[152],"applied":[153],"ridge":[158],"parameter":[159,189],"selected":[161],"by":[162,198],"minimizing":[163],"cross-validation":[165],"error":[166],"predictions":[169],"independent":[172,218],"out-sample.":[173],"This":[174],"tends":[175],"increase":[177,240],"stability":[180],"leads":[182],"much":[185],"greater":[186],"degree":[187],"shrinkage,":[190],"but":[191],"resulting":[193],"biased":[194],"estimation":[195],"mitigated":[197],"second":[200],"round":[201],"regression.":[203],"proposed":[206],"computationally":[207],"efficient":[208],"\"over-shrinkage\"":[209],"outperforms":[211],"previously":[212],"LASSO-based":[214],"techniques.":[215],"In":[216],"two":[217],"datasets,":[219],"we":[220],"find":[221],"median":[224],"proportion":[225,264],"explained":[227],"variability":[228],"approximately":[232],"25%,":[233],"this":[235],"results":[236],"substantial":[239],"signal-to-noise":[243],"ratio":[244],"allowing":[245],"more":[246],"powerful":[247],"inferences":[248],"differential":[250,280,302],"leading":[253],"biologically":[255],"intuitive":[256],"findings.":[257],"also":[259],"show":[260],"dependencies":[267],"conditional":[269],"state,":[273],"would":[275],"impossible":[277],"with":[278],"standard":[279],"methods.":[282],"CONCLUSIONS:":[283],"By":[284],"adjusting":[285],"effects":[288],"individual":[294],"both":[296],"sensitivity":[298],"reliability":[300],"measures":[304],"greatly":[306],"improved.":[307]},"counts_by_year":[],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
