{"id":"https://openalex.org/W2112683411","doi":"https://doi.org/10.1093/bioinformatics/btt521","title":"Precise inference of copy number alterations in tumor samples from SNP arrays","display_name":"Precise inference of copy number alterations in tumor samples from SNP arrays","publication_year":2013,"publication_date":"2013-09-09","ids":{"openalex":"https://openalex.org/W2112683411","doi":"https://doi.org/10.1093/bioinformatics/btt521","mag":"2112683411","pmid":"https://pubmed.ncbi.nlm.nih.gov/24021380"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt521","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt521","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/23/2964/17123169/btt521.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/29/23/2964/17123169/btt521.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089243860","display_name":"Gary K. Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gary K. Chen","raw_affiliation_strings":["1 Department of Preventive Medicine, 2Zilkha Neurogenetic Institute and 3Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Preventive Medicine, 2Zilkha Neurogenetic Institute and 3Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032354393","display_name":"Xiao Chang","orcid":"https://orcid.org/0000-0002-0230-0416"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiao Chang","raw_affiliation_strings":["1 Department of Preventive Medicine, 2Zilkha Neurogenetic Institute and 3Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Preventive Medicine, 2Zilkha Neurogenetic Institute and 3Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036849769","display_name":"Christina Curtis","orcid":"https://orcid.org/0000-0003-0166-3802"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christina Curtis","raw_affiliation_strings":["1 Department of Preventive Medicine, 2Zilkha Neurogenetic Institute and 3Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Preventive Medicine, 2Zilkha Neurogenetic Institute and 3Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100437036","display_name":"Kai Wang","orcid":"https://orcid.org/0000-0002-6170-4744"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kai Wang","raw_affiliation_strings":["1 Department of Preventive Medicine, 2Zilkha Neurogenetic Institute and 3Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Preventive Medicine, 2Zilkha Neurogenetic Institute and 3Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA","institution_ids":["https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5089243860","https://openalex.org/A5100437036"],"corresponding_institution_ids":["https://openalex.org/I1174212"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6928,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.73050606,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"29","issue":"23","first_page":"2964","last_page":"2970"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9997000098228455,"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"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9997000098228455,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9995999932289124,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.998199999332428,"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/inference","display_name":"Inference","score":0.7486653327941895},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.6444941163063049},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46943238377571106},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4518170654773712},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.4216388165950775},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40997424721717834},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3565020263195038},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3302555978298187},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32419446110725403},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.31143444776535034},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2555326819419861},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.24941083788871765},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.12928563356399536},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09034290909767151},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.0677100121974945}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7486653327941895},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.6444941163063049},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46943238377571106},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4518170654773712},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.4216388165950775},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40997424721717834},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3565020263195038},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3302555978298187},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32419446110725403},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.31143444776535034},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2555326819419861},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.24941083788871765},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.12928563356399536},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09034290909767151},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0677100121974945}],"mesh":[{"descriptor_ui":"D000782","descriptor_name":"Aneuploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000782","descriptor_name":"Aneuploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000782","descriptor_name":"Aneuploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D002869","descriptor_name":"Chromosome Aberrations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002869","descriptor_name":"Chromosome Aberrations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002869","descriptor_name":"Chromosome Aberrations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017154","descriptor_name":"Stromal Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017154","descriptor_name":"Stromal Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017154","descriptor_name":"Stromal Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017154","descriptor_name":"Stromal Cells","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D017154","descriptor_name":"Stromal Cells","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D017154","descriptor_name":"Stromal Cells","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt521","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt521","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/23/2964/17123169/btt521.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:24021380","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24021380","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:pubmedcentral.nih.gov:3834792","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3834792","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt521","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt521","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/23/2964/17123169/btt521.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":[{"id":"https://openalex.org/G3182266129","display_name":null,"funder_award_id":"R01HG006465","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G3931858097","display_name":null,"funder_award_id":"R01 HG006465","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1967621681","https://openalex.org/W1979617384","https://openalex.org/W1986522151","https://openalex.org/W2005405893","https://openalex.org/W2005895632","https://openalex.org/W2006288875","https://openalex.org/W2023369015","https://openalex.org/W2049942970","https://openalex.org/W2060084956","https://openalex.org/W2063281610","https://openalex.org/W2065141457","https://openalex.org/W2071734901","https://openalex.org/W2076918641","https://openalex.org/W2081093887","https://openalex.org/W2083870688","https://openalex.org/W2098469535","https://openalex.org/W2104224322","https://openalex.org/W2105061544","https://openalex.org/W2115919763","https://openalex.org/W2122769974","https://openalex.org/W2141393790","https://openalex.org/W2142769937","https://openalex.org/W2143671737","https://openalex.org/W2149127222","https://openalex.org/W2149681218","https://openalex.org/W2150575159","https://openalex.org/W2153056550","https://openalex.org/W2154361640","https://openalex.org/W2159595235","https://openalex.org/W2163022769","https://openalex.org/W2167064353","https://openalex.org/W2262414037","https://openalex.org/W2262954332","https://openalex.org/W2567002812","https://openalex.org/W4232497309","https://openalex.org/W6692729735"],"related_works":["https://openalex.org/W2513883126","https://openalex.org/W3118014344","https://openalex.org/W2160911017","https://openalex.org/W2763474833","https://openalex.org/W2387464095","https://openalex.org/W2507940864","https://openalex.org/W1526237818","https://openalex.org/W4281746656","https://openalex.org/W2005336569","https://openalex.org/W2996064479"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"The":[2],"accurate":[3,72],"detection":[4,26,74],"of":[5,22,127,147],"copy":[6],"number":[7],"alterations":[8],"(CNAs)":[9],"in":[10,27,162],"human":[11],"genomes":[12],"is":[13,36],"important":[14],"for":[15,69,109],"understanding":[16],"susceptibility":[17],"to":[18,41,123,143],"cancer":[19,153],"and":[20,50,66,71,112,131,155,164,175],"mechanisms":[21],"tumor":[23],"progression.":[24],"CNA":[25,73],"tumors":[28],"from":[29,79,152],"single":[30],"nucleotide":[31],"polymorphism":[32],"(SNP)":[33],"genotyping":[34,81],"arrays":[35],"a":[37,89,119],"challenging":[38],"problem":[39],"due":[40],"phenomena":[42],"such":[43],"as":[44,138,140],"aneuploidy,":[45],"stromal":[46,85],"contamination,":[47],"genomic":[48,96,113],"waves":[49],"intra-tumor":[51],"heterogeneity,":[52],"issues":[53],"that":[54],"leading":[55],"methods":[56,65],"do":[57],"not":[58],"optimally":[59],"address.":[60],"Results:":[61],"Here":[62],"we":[63,158],"introduce":[64],"software":[67],"(PennCNV-tumor)":[68],"fast":[70],"using":[75],"signal":[76,101,133],"intensity":[77,102,134],"data":[78,151,190],"SNP":[80],"arrays.":[82],"We":[83],"estimate":[84],"contamination":[86],"by":[87],"applying":[88],"maximum":[90],"likelihood":[91],"approach":[92],"over":[93],"multiple":[94,125],"discrete":[95],"intervals.":[97],"By":[98],"conditioning":[99],"on":[100],"across":[103],"the":[104],"genome,":[105],"our":[106,116],"method":[107,117],"accounts":[108],"both":[110],"aneuploidy":[111],"waves.":[114],"Finally,":[115],"uses":[118],"hidden":[120],"Markov":[121],"model":[122],"integrate":[124],"sources":[126],"information,":[128],"including":[129],"total":[130],"allele-specific":[132],"at":[135,181,193],"each":[136],"SNP,":[137],"well":[139],"physical":[141],"maps":[142],"make":[144],"posterior":[145],"inferences":[146],"CNAs.":[148],"Using":[149],"real":[150],"cell-lines":[154],"patient":[156],"tumors,":[157],"demonstrate":[159],"substantial":[160],"improvements":[161],"accuracy":[163],"computational":[165],"efficiency":[166],"compared":[167],"with":[168],"existing":[169],"methods.":[170],"Availability:":[171],"Source":[172],"code,":[173],"documentation":[174],"example":[176],"datasets":[177],"are":[178,191],"freely":[179],"available":[180,192],"http://sourceforge.net/projects/penncnv-2.":[182],"Contact:":[183],"gary.k.chen@usc.edu":[184],"or":[185],"kaichop@gmail.com":[186],"Supplementary":[187,189],"information:":[188],"Bioinformatics":[194],"online.":[195]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}