{"id":"https://openalex.org/W2120778579","doi":"https://doi.org/10.1093/bioinformatics/btt143","title":"Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size","display_name":"Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size","publication_year":2013,"publication_date":"2013-04-14","ids":{"openalex":"https://openalex.org/W2120778579","doi":"https://doi.org/10.1093/bioinformatics/btt143","mag":"2120778579"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt143","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt143","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/10/1275/48886853/bioinformatics_29_10_1275.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/10/1275/48886853/bioinformatics_29_10_1275.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077738572","display_name":"Danni Yu","orcid":"https://orcid.org/0000-0002-4550-6510"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]},{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Danni Yu","raw_affiliation_strings":["1 Genome Biology Unit, European Molecular Biology Laboratory, Mayerhofstra\u00dfe 1, Heidelberg 69117, Germany 2Department of Statistics and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"],"affiliations":[{"raw_affiliation_string":"1 Genome Biology Unit, European Molecular Biology Laboratory, Mayerhofstra\u00dfe 1, Heidelberg 69117, Germany 2Department of Statistics and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA","institution_ids":["https://openalex.org/I219193219","https://openalex.org/I4210138560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029601108","display_name":"Wolfgang Huber","orcid":"https://orcid.org/0000-0002-0474-2218"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]},{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Wolfgang Huber","raw_affiliation_strings":["1 Genome Biology Unit, European Molecular Biology Laboratory, Mayerhofstra\u00dfe 1, Heidelberg 69117, Germany 2Department of Statistics and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"],"affiliations":[{"raw_affiliation_string":"1 Genome Biology Unit, European Molecular Biology Laboratory, Mayerhofstra\u00dfe 1, Heidelberg 69117, Germany 2Department of Statistics and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA","institution_ids":["https://openalex.org/I219193219","https://openalex.org/I4210138560"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088073215","display_name":"Olga Vitek","orcid":"https://orcid.org/0000-0003-1728-1104"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]},{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Olga Vitek","raw_affiliation_strings":["1 Genome Biology Unit, European Molecular Biology Laboratory, Mayerhofstra\u00dfe 1, Heidelberg 69117, Germany 2Department of Statistics and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"],"affiliations":[{"raw_affiliation_string":"1 Genome Biology Unit, European Molecular Biology Laboratory, Mayerhofstra\u00dfe 1, Heidelberg 69117, Germany 2Department of Statistics and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA","institution_ids":["https://openalex.org/I219193219","https://openalex.org/I4210138560"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5077738572"],"corresponding_institution_ids":["https://openalex.org/I219193219","https://openalex.org/I4210138560"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.7913,"has_fulltext":true,"cited_by_count":150,"citation_normalized_percentile":{"value":0.95869546,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"29","issue":"10","first_page":"1275","last_page":"1282"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9980000257492065,"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"}},"topics":[{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9940000176429749,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9879000186920166,"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/negative-binomial-distribution","display_name":"Negative binomial distribution","score":0.7220937609672546},{"id":"https://openalex.org/keywords/sample-size-determination","display_name":"Sample size determination","score":0.719007670879364},{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.7189509868621826},{"id":"https://openalex.org/keywords/count-data","display_name":"Count data","score":0.5444775819778442},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.5284851789474487},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4672154486179352},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4612608551979065},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4302806258201599},{"id":"https://openalex.org/keywords/binomial-distribution","display_name":"Binomial distribution","score":0.42681336402893066},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3856961727142334},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14244717359542847},{"id":"https://openalex.org/keywords/poisson-distribution","display_name":"Poisson distribution","score":0.09814015030860901}],"concepts":[{"id":"https://openalex.org/C199335787","wikidata":"https://www.wikidata.org/wiki/Q743364","display_name":"Negative binomial distribution","level":3,"score":0.7220937609672546},{"id":"https://openalex.org/C129848803","wikidata":"https://www.wikidata.org/wiki/Q2564360","display_name":"Sample size determination","level":2,"score":0.719007670879364},{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.7189509868621826},{"id":"https://openalex.org/C33643355","wikidata":"https://www.wikidata.org/wiki/Q5176731","display_name":"Count data","level":3,"score":0.5444775819778442},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.5284851789474487},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4672154486179352},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4612608551979065},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4302806258201599},{"id":"https://openalex.org/C41054675","wikidata":"https://www.wikidata.org/wiki/Q185547","display_name":"Binomial distribution","level":2,"score":0.42681336402893066},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3856961727142334},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14244717359542847},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.09814015030860901},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btt143","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt143","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/10/1275/48886853/bioinformatics_29_10_1275.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2653729","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3654711","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt143","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt143","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/10/1275/48886853/bioinformatics_29_10_1275.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1171700966","display_name":null,"funder_award_id":"NSF CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3482151097","display_name":null,"funder_award_id":"DBI-1054826","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7618292881","display_name":"CAREER: Sparse-sampling inference for functional proteomics, metabolomics and ionomics","funder_award_id":"1054826","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2120778579.pdf","grobid_xml":"https://content.openalex.org/works/W2120778579.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W9032326","https://openalex.org/W1528905581","https://openalex.org/W1537947034","https://openalex.org/W1546952499","https://openalex.org/W1584444527","https://openalex.org/W1598266570","https://openalex.org/W1968475238","https://openalex.org/W1973628995","https://openalex.org/W1981509058","https://openalex.org/W1989367702","https://openalex.org/W1990643384","https://openalex.org/W1996984681","https://openalex.org/W2006138378","https://openalex.org/W2010637767","https://openalex.org/W2026112119","https://openalex.org/W2027874981","https://openalex.org/W2031205682","https://openalex.org/W2035653829","https://openalex.org/W2055770801","https://openalex.org/W2061537056","https://openalex.org/W2072602203","https://openalex.org/W2074414424","https://openalex.org/W2081098333","https://openalex.org/W2087107100","https://openalex.org/W2097117811","https://openalex.org/W2097449851","https://openalex.org/W2098734857","https://openalex.org/W2103903744","https://openalex.org/W2107018762","https://openalex.org/W2110065044","https://openalex.org/W2114104545","https://openalex.org/W2118526609","https://openalex.org/W2119034410","https://openalex.org/W2121211805","https://openalex.org/W2122759946","https://openalex.org/W2129172482","https://openalex.org/W2130116522","https://openalex.org/W2140116490","https://openalex.org/W2142165994","https://openalex.org/W2145416275","https://openalex.org/W2148167644","https://openalex.org/W2152239989","https://openalex.org/W2155115337","https://openalex.org/W2156631105","https://openalex.org/W2160164696","https://openalex.org/W2161790708","https://openalex.org/W2313427692","https://openalex.org/W2320103898","https://openalex.org/W2326040775","https://openalex.org/W2332156311","https://openalex.org/W4301861531","https://openalex.org/W4302853952","https://openalex.org/W6634927326","https://openalex.org/W6635777585","https://openalex.org/W6674864170"],"related_works":["https://openalex.org/W2599805416","https://openalex.org/W3210390693","https://openalex.org/W4214644238","https://openalex.org/W2556931687","https://openalex.org/W3135460725","https://openalex.org/W2152239989","https://openalex.org/W2138071539","https://openalex.org/W2485412231","https://openalex.org/W2586858414","https://openalex.org/W2605857286"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"RNA-seq":[2],"experiments":[3,41,163],"produce":[4],"digital":[5],"counts":[6,30],"of":[7,49,79,125,146],"reads":[8],"that":[9,92,145],"are":[10,31,53,84,184],"affected":[11],"by":[12,34],"both":[13],"biological":[14],"and":[15,60,102,118,137,140,154,171,176],"technical":[16],"variation.":[17],"To":[18],"distinguish":[19],"the":[20,29,35,46,50,65,70,77,82,94,99,103,122,131],"systematic":[21],"changes":[22],"in":[23,40,168],"expression":[24],"between":[25,98],"conditions":[26],"from":[27],"noise,":[28],"frequently":[32],"modeled":[33],"Negative":[36],"Binomial":[37],"distribution.":[38],"However,":[39],"with":[42,121,144,164],"small":[43,165],"sample":[44,166],"size,":[45],"per-gene":[47],"estimates":[48,72,83,101],"dispersion":[51],"parameter":[52],"unreliable.":[54],"Method:":[55],"We":[56,129],"propose":[57],"a":[58,89],"simple":[59],"effective":[61],"approach":[62,107,133],"for":[63,73,162],"estimating":[64],"dispersions.":[66],"First,":[67],"we":[68],"obtain":[69],"initial":[71,100],"each":[74],"gene":[75],"using":[76,134],"method":[78],"moments.":[80],"Second,":[81],"regularized,":[85],"i.e.":[86],"shrunk":[87],"towards":[88],"common":[90],"value":[91],"minimizes":[93],"average":[95],"squared":[96],"difference":[97],"shrinkage":[104],"estimates.":[105],"The":[106],"does":[108],"not":[109],"require":[110],"extra":[111],"modeling":[112],"assumptions,":[113],"is":[114,119],"easy":[115],"to":[116],"compute":[117],"compatible":[120],"exact":[123],"test":[124],"differential":[126],"expression.":[127],"Results:":[128],"evaluated":[130],"proposed":[132],"10":[135],"simulated":[136],"experimental":[138],"datasets":[139],"compared":[141],"its":[142],"performance":[143],"currently":[147],"popular":[148],"packages":[149],"edgeR,":[150],"DESeq,":[151],"baySeq,":[152],"BBSeq":[153],"SAMseq.":[155],"For":[156],"these":[157],"datasets,":[158],"sSeq":[159],"performed":[160],"favorably":[161],"size":[167],"sensitivity,":[169],"specificity":[170],"computational":[172],"time.":[173],"Availability:":[174],"http://www.stat.purdue.edu/\u223covitek/Software.html":[175],"Bioconductor.":[177],"Contact:":[178],"ovitek@purdue.edu":[179],"Supplementary":[180,182],"information:":[181],"data":[183],"available":[185],"at":[186],"Bioinformatics":[187],"online.":[188]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":17},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":20},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":18},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}