{"id":"https://openalex.org/W2131057697","doi":"https://doi.org/10.1093/bioinformatics/bti148","title":"Quantile smoothing of array CGH data","display_name":"Quantile smoothing of array CGH data","publication_year":2004,"publication_date":"2004-11-30","ids":{"openalex":"https://openalex.org/W2131057697","doi":"https://doi.org/10.1093/bioinformatics/bti148","mag":"2131057697","pmid":"https://pubmed.ncbi.nlm.nih.gov/15572474"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti148","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti148","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081914769","display_name":"Paul H.C. Eilers","orcid":"https://orcid.org/0000-0003-3480-5918"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Paul H. C. Eilers","raw_affiliation_strings":["Department of Medical Statistics, Leiden University Medical Centre PO Box 9604, 2300 RC, Leiden, The Netherlands","Department of Medical Statistics, Leiden University Medical Centre PO Box 9604, 2300 RC, Leiden, The Netherlands#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Statistics, Leiden University Medical Centre PO Box 9604, 2300 RC, Leiden, The Netherlands","institution_ids":["https://openalex.org/I2800006345"]},{"raw_affiliation_string":"Department of Medical Statistics, Leiden University Medical Centre PO Box 9604, 2300 RC, Leiden, The Netherlands#TAB#","institution_ids":["https://openalex.org/I121797337"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054621707","display_name":"Ren\u00e9e X. de Menezes","orcid":"https://orcid.org/0000-0002-1378-2721"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Ren\u00e9e X. de Menezes","raw_affiliation_strings":["Department of Medical Statistics, Leiden University Medical Centre PO Box 9604, 2300 RC, Leiden, The Netherlands","Department of Medical Statistics, Leiden University Medical Centre PO Box 9604, 2300 RC, Leiden, The Netherlands#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Statistics, Leiden University Medical Centre PO Box 9604, 2300 RC, Leiden, The Netherlands","institution_ids":["https://openalex.org/I2800006345"]},{"raw_affiliation_string":"Department of Medical Statistics, Leiden University Medical Centre PO Box 9604, 2300 RC, Leiden, The Netherlands#TAB#","institution_ids":["https://openalex.org/I121797337"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5081914769"],"corresponding_institution_ids":["https://openalex.org/I121797337","https://openalex.org/I2800006345"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":5.8765,"has_fulltext":false,"cited_by_count":149,"citation_normalized_percentile":{"value":0.96656803,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"21","issue":"7","first_page":"1146","last_page":"1153"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.7702999711036682,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.7702999711036682,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.05270000174641609,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11901","display_name":"Bayesian Methods and Mixture Models","score":0.026000000536441803,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/quantile","display_name":"Quantile","score":0.8093416094779968},{"id":"https://openalex.org/keywords/smoothing","display_name":"Smoothing","score":0.8057238459587097},{"id":"https://openalex.org/keywords/comparative-genomic-hybridization","display_name":"Comparative genomic hybridization","score":0.6679385900497437},{"id":"https://openalex.org/keywords/rounding","display_name":"Rounding","score":0.6465203762054443},{"id":"https://openalex.org/keywords/quartile","display_name":"Quartile","score":0.6213517785072327},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6130639314651489},{"id":"https://openalex.org/keywords/quantile-regression","display_name":"Quantile regression","score":0.5909398794174194},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.524397075176239},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.48405689001083374},{"id":"https://openalex.org/keywords/noisy-data","display_name":"Noisy data","score":0.4196145236492157},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3419397175312042},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2658218741416931},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11850625276565552},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.06375953555107117}],"concepts":[{"id":"https://openalex.org/C118671147","wikidata":"https://www.wikidata.org/wiki/Q578714","display_name":"Quantile","level":2,"score":0.8093416094779968},{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.8057238459587097},{"id":"https://openalex.org/C124942203","wikidata":"https://www.wikidata.org/wiki/Q656638","display_name":"Comparative genomic hybridization","level":4,"score":0.6679385900497437},{"id":"https://openalex.org/C136625980","wikidata":"https://www.wikidata.org/wiki/Q663208","display_name":"Rounding","level":2,"score":0.6465203762054443},{"id":"https://openalex.org/C68443243","wikidata":"https://www.wikidata.org/wiki/Q2786686","display_name":"Quartile","level":3,"score":0.6213517785072327},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6130639314651489},{"id":"https://openalex.org/C63817138","wikidata":"https://www.wikidata.org/wiki/Q3455889","display_name":"Quantile regression","level":2,"score":0.5909398794174194},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.524397075176239},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.48405689001083374},{"id":"https://openalex.org/C2781170535","wikidata":"https://www.wikidata.org/wiki/Q30587856","display_name":"Noisy data","level":2,"score":0.4196145236492157},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3419397175312042},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2658218741416931},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11850625276565552},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.06375953555107117},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C44249647","wikidata":"https://www.wikidata.org/wiki/Q208498","display_name":"Confidence interval","level":2,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017403","descriptor_name":"In Situ Hybridization","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017403","descriptor_name":"In Situ Hybridization","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017403","descriptor_name":"In Situ Hybridization","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/bti148","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti148","pdf_url":null,"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:15572474","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15572474","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":"Comparative Study"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.103.3447","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.103.3447","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/cgi/reprint/bti148v1.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions","score":0.6299999952316284}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332622","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1488591768","https://openalex.org/W1691300750","https://openalex.org/W1836952553","https://openalex.org/W1909097318","https://openalex.org/W1967542684","https://openalex.org/W2043517539","https://openalex.org/W2047992909","https://openalex.org/W2066721762","https://openalex.org/W2072011344","https://openalex.org/W2100725331","https://openalex.org/W2118711140","https://openalex.org/W2124277850","https://openalex.org/W2133174470","https://openalex.org/W2136119414","https://openalex.org/W2151820600","https://openalex.org/W2162894628","https://openalex.org/W2911329779"],"related_works":["https://openalex.org/W4206511378","https://openalex.org/W4206618949","https://openalex.org/W2526321210","https://openalex.org/W3205863630","https://openalex.org/W3014605311","https://openalex.org/W2364275385","https://openalex.org/W4318833145","https://openalex.org/W2007977664","https://openalex.org/W4252013513","https://openalex.org/W4376874882"],"abstract_inverted_index":{"MOTIVATION:":[0],"Plots":[1],"of":[2,14,85,96,112,119],"array":[3,124],"Comparative":[4],"Genomic":[5],"Hybridization":[6],"(CGH)":[7],"data":[8,101],"often":[9],"show":[10,72,109],"special":[11],"patterns:":[12],"stretches":[13],"constant":[15],"level":[16],"(copy":[17],"number)":[18],"with":[19],"sharp":[20],"jumps":[21],"between":[22],"them.":[23],"There":[24],"can":[25,60],"also":[26],"be":[27],"much":[28,41],"noise.":[29],"Classic":[30],"smoothing":[31,52],"algorithms":[32],"do":[33],"not":[34],"work":[35],"well,":[36],"because":[37],"they":[38],"introduce":[39,47],"too":[40],"rounding.":[42],"To":[43],"remedy":[44],"this,":[45],"we":[46,66],"a":[48,103],"fast":[49],"and":[50,75,78,102],"effective":[51],"algorithm":[53],"based":[54],"on":[55,68],"penalized":[56],"quantile":[57,63],"regression.":[58],"It":[59],"compute":[61],"arbitrary":[62],"curves,":[64],"but":[65],"concentrate":[67],"the":[69,73,76,83,86,94,97,110,113,117],"median":[70],"to":[71,108,115],"trend":[74],"lower":[77],"upper":[79],"quartile":[80],"curves":[81],"showing":[82],"spread":[84],"data.":[87,126],"Two-fold":[88],"cross-validation":[89],"is":[90],"used":[91,107],"for":[92],"optimizing":[93],"weight":[95],"penalties.":[98],"RESULTS:":[99],"Simulated":[100],"published":[104],"dataset":[105],"are":[106],"capabilities":[111],"method":[114],"detect":[116],"segments":[118],"changed":[120],"copy":[121],"numbers":[122],"in":[123],"CGH":[125]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":11}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
