{"id":"https://openalex.org/W2099921417","doi":"https://doi.org/10.1093/bioinformatics/btr488","title":"Finding recurrent copy number alterations preserving within-sample homogeneity","display_name":"Finding recurrent copy number alterations preserving within-sample homogeneity","publication_year":2011,"publication_date":"2011-08-25","ids":{"openalex":"https://openalex.org/W2099921417","doi":"https://doi.org/10.1093/bioinformatics/btr488","mag":"2099921417","pmid":"https://pubmed.ncbi.nlm.nih.gov/21873327"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr488","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/21/2949/48864795/bioinformatics_27_21_2949.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/27/21/2949/48864795/bioinformatics_27_21_2949.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087559200","display_name":"Sandro Morganella","orcid":"https://orcid.org/0000-0003-4050-0985"},"institutions":[{"id":"https://openalex.org/I16337185","display_name":"University of Sannio","ror":"https://ror.org/04vc81p87","country_code":"IT","type":"education","lineage":["https://openalex.org/I16337185"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Sandro Morganella","raw_affiliation_strings":["1 Department of Science, University of Sannio, 82100, Benevento and 2Bioinformatics CORE, BIOGEM s.c.a.r.l., Contrada Camporeale, Ariano Irpino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Science, University of Sannio, 82100, Benevento and 2Bioinformatics CORE, BIOGEM s.c.a.r.l., Contrada Camporeale, Ariano Irpino, Italy","institution_ids":["https://openalex.org/I16337185"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082618284","display_name":"Stefano Maria Pagnotta","orcid":"https://orcid.org/0000-0002-8298-9777"},"institutions":[{"id":"https://openalex.org/I16337185","display_name":"University of Sannio","ror":"https://ror.org/04vc81p87","country_code":"IT","type":"education","lineage":["https://openalex.org/I16337185"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Stefano Maria Pagnotta","raw_affiliation_strings":["1 Department of Science, University of Sannio, 82100, Benevento and 2Bioinformatics CORE, BIOGEM s.c.a.r.l., Contrada Camporeale, Ariano Irpino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Science, University of Sannio, 82100, Benevento and 2Bioinformatics CORE, BIOGEM s.c.a.r.l., Contrada Camporeale, Ariano Irpino, Italy","institution_ids":["https://openalex.org/I16337185"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085527072","display_name":"Michele Ceccarelli","orcid":"https://orcid.org/0000-0002-4702-6617"},"institutions":[{"id":"https://openalex.org/I16337185","display_name":"University of Sannio","ror":"https://ror.org/04vc81p87","country_code":"IT","type":"education","lineage":["https://openalex.org/I16337185"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Michele Ceccarelli","raw_affiliation_strings":["1 Department of Science, University of Sannio, 82100, Benevento and 2Bioinformatics CORE, BIOGEM s.c.a.r.l., Contrada Camporeale, Ariano Irpino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Science, University of Sannio, 82100, Benevento and 2Bioinformatics CORE, BIOGEM s.c.a.r.l., Contrada Camporeale, Ariano Irpino, Italy","institution_ids":["https://openalex.org/I16337185"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5085527072","https://openalex.org/A5087559200"],"corresponding_institution_ids":["https://openalex.org/I16337185"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5535,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.83918124,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"27","issue":"21","first_page":"2949","last_page":"2956"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9872999787330627,"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":0.9872999787330627,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.004699999932199717,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.00139999995008111,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.623892605304718},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5824984312057495},{"id":"https://openalex.org/keywords/homogeneity","display_name":"Homogeneity (statistics)","score":0.5410363674163818},{"id":"https://openalex.org/keywords/comparative-genomic-hybridization","display_name":"Comparative genomic hybridization","score":0.48190194368362427},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47901052236557007},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.415793240070343},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3024083971977234},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.243784099817276},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19645482301712036},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.1915532350540161},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10411021113395691}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.623892605304718},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5824984312057495},{"id":"https://openalex.org/C142259097","wikidata":"https://www.wikidata.org/wiki/Q5891314","display_name":"Homogeneity (statistics)","level":2,"score":0.5410363674163818},{"id":"https://openalex.org/C124942203","wikidata":"https://www.wikidata.org/wiki/Q656638","display_name":"Comparative genomic hybridization","level":4,"score":0.48190194368362427},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47901052236557007},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.415793240070343},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3024083971977234},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.243784099817276},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19645482301712036},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.1915532350540161},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10411021113395691},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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":"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055028","descriptor_name":"Comparative Genomic Hybridization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055028","descriptor_name":"Comparative Genomic Hybridization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055028","descriptor_name":"Comparative Genomic Hybridization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btr488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr488","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/21/2949/48864795/bioinformatics_27_21_2949.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:21873327","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21873327","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:open-archive.highwire.org:bioinfo:27/21/2949","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/21/2949","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:zenodo.org:100735","is_oa":true,"landing_page_url":"https://www.openaccessrepository.it/record/100735","pdf_url":null,"source":{"id":"https://openalex.org/S4306402478","display_name":"INFM-OAR (INFN Catania)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210116497","host_organization_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Catania","host_organization_lineage":["https://openalex.org/I4210116497"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr488","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/21/2949/48864795/bioinformatics_27_21_2949.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":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2099921417.pdf"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1967073729","https://openalex.org/W1978645448","https://openalex.org/W2033990985","https://openalex.org/W2056937433","https://openalex.org/W2060084956","https://openalex.org/W2071551825","https://openalex.org/W2085755265","https://openalex.org/W2087841183","https://openalex.org/W2088608458","https://openalex.org/W2089473025","https://openalex.org/W2091066174","https://openalex.org/W2091220038","https://openalex.org/W2092343534","https://openalex.org/W2099512426","https://openalex.org/W2100083515","https://openalex.org/W2100725331","https://openalex.org/W2103987317","https://openalex.org/W2106983577","https://openalex.org/W2107751484","https://openalex.org/W2108081301","https://openalex.org/W2110065044","https://openalex.org/W2116530373","https://openalex.org/W2118184985","https://openalex.org/W2122769974","https://openalex.org/W2124277850","https://openalex.org/W2126043934","https://openalex.org/W2133174470","https://openalex.org/W2134034024","https://openalex.org/W2136109165","https://openalex.org/W2136119414","https://openalex.org/W2138978405","https://openalex.org/W2139478442","https://openalex.org/W2145629225","https://openalex.org/W2146273335","https://openalex.org/W2149681218","https://openalex.org/W2153056550","https://openalex.org/W2153825609","https://openalex.org/W2155319189","https://openalex.org/W2160697532","https://openalex.org/W2167001416","https://openalex.org/W2167544405","https://openalex.org/W2187886502","https://openalex.org/W2796349379","https://openalex.org/W2796856748","https://openalex.org/W4248673725","https://openalex.org/W6686980263"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W4223449272","https://openalex.org/W2978247079","https://openalex.org/W2166887457","https://openalex.org/W2148708580","https://openalex.org/W3037604406","https://openalex.org/W2140163842","https://openalex.org/W2036870935"],"abstract_inverted_index":{"MOTIVATION:":[0],"Copy":[1],"number":[2,91],"alterations":[3],"(CNAs)":[4],"represent":[5],"an":[6,176,206],"important":[7],"component":[8],"of":[9,22,37,49,89,103,109,119,127,131,147],"genetic":[10],"variation":[11],"and":[12,77,170,215],"play":[13],"a":[14,47,86,128,141,156,195,216],"significant":[15],"role":[16],"in":[17,63,93,187],"many":[18],"human":[19],"diseases.":[20],"Development":[21],"array":[23],"comparative":[24],"genomic":[25,50],"hybridization":[26],"(aCGH)":[27],"technology":[28],"has":[29,134,223],"made":[30],"it":[31,96],"possible":[32],"to":[33,45,69,72,105,151,162,179,198],"identify":[34],"CNAs.":[35],"Identification":[36],"recurrent":[38,64,120,153],"CNAs":[39,65,121,154],"represents":[40,85,194],"the":[41,54,70,107,110,117,181,234],"first":[42],"fundamental":[43],"step":[44],"provide":[46],"list":[48],"regions":[51,182],"which":[52],"form":[53],"basis":[55],"for":[56],"further":[57],"biological":[58],"investigations.":[59],"The":[60],"main":[61],"problem":[62],"discovery":[66],"is":[67,160],"related":[68],"need":[71],"distinguish":[73],"between":[74],"functional":[75,188],"changes":[76],"random":[78],"events":[79],"without":[80],"pathological":[81],"relevance.":[82],"Within-sample":[83],"homogeneity":[84,172],"common":[87],"feature":[88],"copy":[90],"profile":[92],"cancer,":[94],"so":[95],"can":[97,230],"be":[98,231],"used":[99],"as":[100,226],"additional":[101],"source":[102],"information":[104],"increase":[106],"accuracy":[108],"results.":[111],"Although":[112],"several":[113],"algorithms":[114],"aimed":[115],"at":[116,247],"identification":[118],"have":[122],"been":[123,136,224],"proposed,":[124],"no":[125],"attempt":[126],"comprehensive":[129],"comparison":[130,208],"different":[132],"approaches":[133],"yet":[135],"published.":[137],"RESULTS:":[138],"We":[139],"propose":[140],"new":[142],"approach,":[143],"called":[144],"Genomic":[145],"Analysis":[146],"Important":[148],"Alterations":[149],"(GAIA),":[150],"find":[152],"where":[155],"statistical":[157],"hypothesis":[158],"framework":[159],"extended":[161],"take":[163],"into":[164,175],"account":[165],"within-sample":[166,171],"homogeneity.":[167],"Statistical":[168],"significance":[169],"are":[173,185,245],"combined":[174],"iterative":[177],"procedure":[178],"extract":[180],"that":[183,192],"likely":[184],"involved":[186],"changes.":[189],"Results":[190],"show":[191],"GAIA":[193,222],"valid":[196],"alternative":[197],"other":[199],"proposed":[200],"approaches.":[201],"In":[202],"addition,":[203],"we":[204],"perform":[205],"accurate":[207],"by":[209],"using":[210],"two":[211],"real":[212],"aCGH":[213],"datasets":[214],"carefully":[217],"planned":[218],"simulation":[219],"study.":[220],"AVAILABILITY:":[221],"implemented":[225],"R/Bioconductor":[227],"package.":[228],"It":[229],"downloaded":[232],"from":[233],"following":[235],"page":[236],"http://bioinformatics.biogem.it/download/gaia.":[237],"CONTACT:":[238],"ceccarelli@unisannio.it;":[239],"morganella@unisannio.it.":[240],"SUPPLEMENTARY":[241],"INFORMATION:":[242],"Supplementary":[243],"data":[244],"available":[246],"Bioinformatics":[248],"online.":[249]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}