{"id":"https://openalex.org/W2132213882","doi":"https://doi.org/10.1093/bioinformatics/btt575","title":"Robust adjustment of sequence tag abundance","display_name":"Robust adjustment of sequence tag abundance","publication_year":2013,"publication_date":"2013-10-09","ids":{"openalex":"https://openalex.org/W2132213882","doi":"https://doi.org/10.1093/bioinformatics/btt575","mag":"2132213882","pmid":"https://pubmed.ncbi.nlm.nih.gov/24108185"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt575","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt575","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/5/601/48919142/bioinformatics_30_5_601.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/5/601/48919142/bioinformatics_30_5_601.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111742159","display_name":"Douglas D. Baumann","orcid":null},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Douglas D. Baumann","raw_affiliation_strings":["Department of Statistics, Purdue University, West Lafayette, IN 47907, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Purdue University, West Lafayette, IN 47907, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109392450","display_name":"R. W. Doerge","orcid":null},"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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rebecca W. Doerge","raw_affiliation_strings":["Department of Statistics, Purdue University, West Lafayette, IN 47907, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Purdue University, West Lafayette, IN 47907, USA","institution_ids":["https://openalex.org/I219193219"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5109392450"],"corresponding_institution_ids":["https://openalex.org/I219193219"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.4168,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.64200608,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"30","issue":"5","first_page":"601","last_page":"605"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9361000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9361000061035156,"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":0.018200000748038292,"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":0.007000000216066837,"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/computational-biology","display_name":"Computational biology","score":0.510384738445282},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.508941650390625},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5074726939201355},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5012316703796387},{"id":"https://openalex.org/keywords/censoring","display_name":"Censoring (clinical trials)","score":0.48562923073768616},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.43957749009132385},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34676074981689453},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.1924126148223877},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14114946126937866}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.510384738445282},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.508941650390625},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5074726939201355},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5012316703796387},{"id":"https://openalex.org/C137668524","wikidata":"https://www.wikidata.org/wiki/Q189813","display_name":"Censoring (clinical trials)","level":2,"score":0.48562923073768616},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.43957749009132385},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34676074981689453},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.1924126148223877},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14114946126937866},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt575","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt575","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/5/601/48919142/bioinformatics_30_5_601.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24108185","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24108185","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":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1034.3828","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1034.3828","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2013/10/09/bioinformatics.btt575.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt575","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt575","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/5/601/48919142/bioinformatics_30_5_601.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7599999904632568,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309036","display_name":"Purdue University","ror":"https://ror.org/02dqehb95"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2132213882.pdf"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W53657057","https://openalex.org/W1537947034","https://openalex.org/W1596515083","https://openalex.org/W1933293707","https://openalex.org/W1975922601","https://openalex.org/W1992512552","https://openalex.org/W2004078197","https://openalex.org/W2024081693","https://openalex.org/W2032118018","https://openalex.org/W2037780745","https://openalex.org/W2051406511","https://openalex.org/W2067151470","https://openalex.org/W2098758691","https://openalex.org/W2102813686","https://openalex.org/W2103903744","https://openalex.org/W2110065044","https://openalex.org/W2114104545","https://openalex.org/W2121211805","https://openalex.org/W2127081952","https://openalex.org/W2128114769","https://openalex.org/W2141425631","https://openalex.org/W2145416275","https://openalex.org/W2167865654","https://openalex.org/W2312890204","https://openalex.org/W2582743722","https://openalex.org/W2611775752","https://openalex.org/W4243977291"],"related_works":["https://openalex.org/W2363656491","https://openalex.org/W4376988598","https://openalex.org/W4388007941","https://openalex.org/W2884149040","https://openalex.org/W2159198570","https://openalex.org/W1581143638","https://openalex.org/W4231764023","https://openalex.org/W4386150570","https://openalex.org/W2039944302","https://openalex.org/W2034625591"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,22],"majority":[2],"of":[3,11],"next-generation":[4],"sequencing":[5],"technologies":[6],"effectively":[7,81],"sample":[8],"small":[9],"amounts":[10],"DNA":[12],"or":[13],"RNA":[14],"that":[15,73],"are":[16],"amplified":[17],"(i.e.":[18],"copied)":[19],"before":[20],"sequencing.":[21],"amplification":[23,44],"process":[24],"is":[25,134],"not":[26],"perfect,":[27],"leading":[28],"to":[29,41,88,107,129],"extreme":[30],"bias":[31,45],"in":[32,50,91,114],"sequenced":[33],"read":[34],"counts.":[35],"We":[36,61,103],"present":[37],"a":[38],"novel":[39],"procedure":[40],"account":[42],"for":[43,96],"and":[46,68,86],"demonstrate":[47],"its":[48],"effectiveness":[49],"mitigating":[51],"gene":[52,58,78,116,120],"length":[53],"dependence":[54],"when":[55],"estimating":[56],"true":[57,77],"expression.":[59],"RESULTS:":[60],"tested":[62],"the":[63,131,138],"proposed":[64],"method":[65,75,106],"on":[66,137],"simulated":[67],"real":[69],"data.":[70],"Simulations":[71],"indicated":[72],"our":[74,105],"captures":[76],"expression":[79,93],"more":[80],"than":[82],"classic":[83],"censoring-based":[84],"approaches":[85],"leads":[87],"power":[89],"gains":[90],"differential":[92],"testing,":[94],"particularly":[95],"shorter":[97],"genes":[98],"with":[99],"high":[100],"transcription":[101],"rates.":[102],"applied":[104],"an":[108],"unreplicated":[109],"Arabidopsis":[110],"RNA-seq":[111],"dataset":[112],"resulting":[113],"disparate":[115],"ontologies":[117],"arising":[118],"from":[119],"set":[121],"enrichment":[122],"analyses.":[123],"AVAILABILITY":[124],"AND":[125],"IMPLEMENTATION:":[126],"R":[127],"code":[128],"perform":[130],"RASTA":[132],"procedures":[133],"freely":[135],"available":[136],"web":[139],"at":[140],"www.stat.purdue.edu/\u223cdoerge/.":[141]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}