{"id":"https://openalex.org/W2156840892","doi":"https://doi.org/10.1093/bioinformatics/btp471","title":"Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication","display_name":"Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication","publication_year":2009,"publication_date":"2009-08-10","ids":{"openalex":"https://openalex.org/W2156840892","doi":"https://doi.org/10.1093/bioinformatics/btp471","mag":"2156840892","pmid":"https://pubmed.ncbi.nlm.nih.gov/19667080"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp471","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp471","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/19/2486/48995599/bioinformatics_25_19_2486.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/25/19/2486/48995599/bioinformatics_25_19_2486.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101832672","display_name":"Youngchul Kim","orcid":"https://orcid.org/0000-0002-2307-0330"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]},{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR","US"],"is_corresponding":false,"raw_author_name":"Youngchul Kim","raw_affiliation_strings":["1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I51556381","https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048872833","display_name":"Stefan Bekiranov","orcid":"https://orcid.org/0000-0002-3177-4346"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]},{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["KR","US"],"is_corresponding":false,"raw_author_name":"Stefan Bekiranov","raw_affiliation_strings":["1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I51556381","https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066164452","display_name":"Jae K. Lee","orcid":null},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]},{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR","US"],"is_corresponding":true,"raw_author_name":"Jae K. Lee","raw_affiliation_strings":["1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I51556381","https://openalex.org/I139264467"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100643662","display_name":"Taesung Park","orcid":"https://orcid.org/0000-0002-8294-590X"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]},{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR","US"],"is_corresponding":true,"raw_author_name":"Taesung Park","raw_affiliation_strings":["1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I51556381","https://openalex.org/I139264467"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5066164452","https://openalex.org/A5100643662"],"corresponding_institution_ids":["https://openalex.org/I139264467","https://openalex.org/I51556381"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2688,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.60802462,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"25","issue":"19","first_page":"2486","last_page":"2491"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9993000030517578,"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":0.9993000030517578,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9987000226974487,"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":0.987500011920929,"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/replication","display_name":"Replication (statistics)","score":0.6641577482223511},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.590714156627655},{"id":"https://openalex.org/keywords/variance","display_name":"Variance (accounting)","score":0.5252040028572083},{"id":"https://openalex.org/keywords/chip","display_name":"Chip","score":0.5216962695121765},{"id":"https://openalex.org/keywords/tiling-array","display_name":"Tiling array","score":0.5200176239013672},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.46700724959373474},{"id":"https://openalex.org/keywords/error-detection-and-correction","display_name":"Error detection and correction","score":0.4310833811759949},{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.42793524265289307},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.407469242811203},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35432857275009155},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.33069342374801636},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3212270736694336},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.26568323373794556},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2259797751903534},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.16744175553321838},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09387964010238647}],"concepts":[{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.6641577482223511},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.590714156627655},{"id":"https://openalex.org/C196083921","wikidata":"https://www.wikidata.org/wiki/Q7915758","display_name":"Variance (accounting)","level":2,"score":0.5252040028572083},{"id":"https://openalex.org/C165005293","wikidata":"https://www.wikidata.org/wiki/Q1074500","display_name":"Chip","level":2,"score":0.5216962695121765},{"id":"https://openalex.org/C119401833","wikidata":"https://www.wikidata.org/wiki/Q7802158","display_name":"Tiling array","level":5,"score":0.5200176239013672},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.46700724959373474},{"id":"https://openalex.org/C103088060","wikidata":"https://www.wikidata.org/wiki/Q1062839","display_name":"Error detection and correction","level":2,"score":0.4310833811759949},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.42793524265289307},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.407469242811203},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35432857275009155},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.33069342374801636},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3212270736694336},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26568323373794556},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2259797751903534},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.16744175553321838},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09387964010238647},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C121955636","wikidata":"https://www.wikidata.org/wiki/Q4116214","display_name":"Accounting","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004261","descriptor_name":"DNA Replication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004261","descriptor_name":"DNA Replication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004261","descriptor_name":"DNA Replication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","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":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","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":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp471","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp471","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/19/2486/48995599/bioinformatics_25_19_2486.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:19667080","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19667080","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:europepmc.org:1899741","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2800349","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/btp471","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp471","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/19/2486/48995599/bioinformatics_25_19_2486.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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2156840892.pdf","grobid_xml":"https://content.openalex.org/works/W2156840892.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1488427658","https://openalex.org/W1964895626","https://openalex.org/W1983468797","https://openalex.org/W1989880978","https://openalex.org/W2052301225","https://openalex.org/W2053833990","https://openalex.org/W2077132193","https://openalex.org/W2080498142","https://openalex.org/W2083479872","https://openalex.org/W2096286842","https://openalex.org/W2097705100","https://openalex.org/W2100668965","https://openalex.org/W2107875796","https://openalex.org/W2116305918","https://openalex.org/W2118628540","https://openalex.org/W2123564569","https://openalex.org/W2132508108","https://openalex.org/W2139290043","https://openalex.org/W2141222206","https://openalex.org/W2163417603","https://openalex.org/W2167755634","https://openalex.org/W2168801969","https://openalex.org/W4213167074","https://openalex.org/W4248318091","https://openalex.org/W6647581434"],"related_works":["https://openalex.org/W2898002554","https://openalex.org/W2080053800","https://openalex.org/W2377727084","https://openalex.org/W2078156175","https://openalex.org/W2306587515","https://openalex.org/W2046627901","https://openalex.org/W4298218313","https://openalex.org/W2057460369","https://openalex.org/W1589515948","https://openalex.org/W2106848411"],"abstract_inverted_index":{"Applying":[0],"DES":[1,72],"to":[2,51],"ChIP-chip":[3],"tiling":[4],"array":[5],"study":[6],"for":[7,79],"discovering":[8],"genome-wide":[9],"protein-binding":[10],"sites,":[11],"we":[12],"identified":[13,45],"8400":[14],"target":[15],"regions":[16],"that":[17],"include":[18],"highly":[19],"likely":[20],"TFIID":[21],"binding":[22,54,83],"sites.":[23,84],"About":[24],"33%":[25],"of":[26,63,71],"these":[27],"were":[28],"well":[29],"matched":[30],"with":[31,74],"the":[32,38,68],"known":[33],"transcription":[34],"starting":[35],"sites":[36,46,55],"on":[37,57],"DBTSS":[39],"library,":[40],"while":[41],"many":[42],"other":[43,75],"newly":[44],"have":[47],"a":[48,58],"high":[49,59],"chance":[50],"be":[52],"real":[53],"based":[56],"positive":[60],"predictive":[61],"value":[62],"DES.":[64],"We":[65],"also":[66],"showed":[67],"superior":[69],"performance":[70],"compared":[73],"commonly":[76],"used":[77],"methods":[78],"detecting":[80],"actual":[81],"protein":[82]},"counts_by_year":[{"year":2012,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}