{"id":"https://openalex.org/W2045916345","doi":"https://doi.org/10.1186/1752-0509-5-121","title":"Inferring causal genomic alterations in breast cancer using gene expression data","display_name":"Inferring causal genomic alterations in breast cancer using gene expression data","publication_year":2011,"publication_date":"2011-08-01","ids":{"openalex":"https://openalex.org/W2045916345","doi":"https://doi.org/10.1186/1752-0509-5-121","mag":"2045916345","pmid":"https://pubmed.ncbi.nlm.nih.gov/21806811"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-5-121","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-121","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-121","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-121","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053537520","display_name":"Linh M. Tran","orcid":"https://orcid.org/0000-0001-8597-643X"},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]},{"id":"https://openalex.org/I1323236076","display_name":"Sage Bionetworks","ror":"https://ror.org/049ncjx51","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1323236076"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Linh M Tran","raw_affiliation_strings":["Sage Bionetworks, Seattle, WA 98109, USA","Sage Bionetworks, Seattle, USA","Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sage Bionetworks, Seattle, WA 98109, USA","institution_ids":["https://openalex.org/I1323236076"]},{"raw_affiliation_string":"Sage Bionetworks, Seattle, USA","institution_ids":["https://openalex.org/I1323236076"]},{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100392792","display_name":"Bin Zhang","orcid":"https://orcid.org/0000-0001-8835-8370"},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]},{"id":"https://openalex.org/I1323236076","display_name":"Sage Bionetworks","ror":"https://ror.org/049ncjx51","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1323236076"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bin Zhang","raw_affiliation_strings":["Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","Sage Bionetworks, Seattle, WA, 98109, USA","Sage Bionetworks, Seattle, USA","Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I1285764155"]},{"raw_affiliation_string":"Sage Bionetworks, Seattle, WA, 98109, USA","institution_ids":["https://openalex.org/I1323236076"]},{"raw_affiliation_string":"Sage Bionetworks, Seattle, USA","institution_ids":["https://openalex.org/I1323236076"]},{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100393427","display_name":"Zhan Zhang","orcid":"https://orcid.org/0000-0002-9685-5753"},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhan Zhang","raw_affiliation_strings":["Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I1285764155"]},{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101796817","display_name":"Chunsheng Zhang","orcid":"https://orcid.org/0000-0001-7782-0355"},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chunsheng Zhang","raw_affiliation_strings":["Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I1285764155"]},{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063855097","display_name":"Tao Xie","orcid":"https://orcid.org/0000-0001-7658-6587"},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tao Xie","raw_affiliation_strings":["Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I1285764155"]},{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103204753","display_name":"John R. Lamb","orcid":"https://orcid.org/0000-0002-6584-7697"},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John R Lamb","raw_affiliation_strings":["Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I1285764155"]},{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101790056","display_name":"Hongyue Dai","orcid":"https://orcid.org/0000-0002-6609-9141"},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongyue Dai","raw_affiliation_strings":["Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I1285764155"]},{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071946434","display_name":"Eric E. Schadt","orcid":"https://orcid.org/0000-0002-7892-8808"},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]},{"id":"https://openalex.org/I1323236076","display_name":"Sage Bionetworks","ror":"https://ror.org/049ncjx51","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1323236076"]},{"id":"https://openalex.org/I68554272","display_name":"Pacific Biosciences (United States)","ror":"https://ror.org/00fcszb13","country_code":"US","type":"company","lineage":["https://openalex.org/I68554272"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric E Schadt","raw_affiliation_strings":["Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","Pacific Biosciences, 1505 Adams Drive, Menlo Park, California, 94025, USA","Sage Bionetworks, Seattle, WA, 98109, USA","Pacific Biosciences, Menlo Park, USA","Merck Research Laboratories, Merck & Co., Inc., Boston, USA","Sage Bionetworks, Seattle, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I1285764155"]},{"raw_affiliation_string":"Pacific Biosciences, 1505 Adams Drive, Menlo Park, California, 94025, USA","institution_ids":["https://openalex.org/I68554272"]},{"raw_affiliation_string":"Sage Bionetworks, Seattle, WA, 98109, USA","institution_ids":["https://openalex.org/I1323236076"]},{"raw_affiliation_string":"Pacific Biosciences, Menlo Park, USA","institution_ids":["https://openalex.org/I68554272"]},{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc., Boston, USA","institution_ids":["https://openalex.org/I1285764155"]},{"raw_affiliation_string":"Sage Bionetworks, Seattle, USA","institution_ids":["https://openalex.org/I1323236076"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058745924","display_name":"Jun Zhu","orcid":"https://orcid.org/0000-0003-0834-8178"},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]},{"id":"https://openalex.org/I1323236076","display_name":"Sage Bionetworks","ror":"https://ror.org/049ncjx51","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1323236076"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jun Zhu","raw_affiliation_strings":["Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","Sage Bionetworks, Seattle, WA, 98109, USA","Sage Bionetworks, Seattle, USA","Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I1285764155"]},{"raw_affiliation_string":"Sage Bionetworks, Seattle, WA, 98109, USA","institution_ids":["https://openalex.org/I1323236076"]},{"raw_affiliation_string":"Sage Bionetworks, Seattle, USA","institution_ids":["https://openalex.org/I1323236076"]},{"raw_affiliation_string":"Merck Research Laboratories, Merck & Co., Inc.,, Boston, USA","institution_ids":["https://openalex.org/I1285764155"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5053537520"],"corresponding_institution_ids":["https://openalex.org/I1285764155","https://openalex.org/I1323236076"],"apc_list":null,"apc_paid":null,"fwci":4.9518,"has_fulltext":true,"cited_by_count":69,"citation_normalized_percentile":{"value":0.95448465,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"5","issue":"1","first_page":"121","last_page":"121"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.8654000163078308,"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":0.8654000163078308,"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/T10492","display_name":"Microtubule and mitosis dynamics","score":0.022199999541044235,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.021400000900030136,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.8110004663467407},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6594088077545166},{"id":"https://openalex.org/keywords/carcinogenesis","display_name":"Carcinogenesis","score":0.5891040563583374},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5811475515365601},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5301495790481567},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5296960473060608},{"id":"https://openalex.org/keywords/breast-cancer","display_name":"Breast cancer","score":0.5254993438720703},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.501596212387085},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4875313937664032},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.48337334394454956},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.44088014960289},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3524263799190521},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2503548264503479}],"concepts":[{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.8110004663467407},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6594088077545166},{"id":"https://openalex.org/C555283112","wikidata":"https://www.wikidata.org/wiki/Q1637543","display_name":"Carcinogenesis","level":3,"score":0.5891040563583374},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5811475515365601},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5301495790481567},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5296960473060608},{"id":"https://openalex.org/C530470458","wikidata":"https://www.wikidata.org/wiki/Q128581","display_name":"Breast cancer","level":3,"score":0.5254993438720703},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.501596212387085},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4875313937664032},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.48337334394454956},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.44088014960289},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3524263799190521},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2503548264503479},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":"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":"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":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D052138","descriptor_name":"Genes, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D052138","descriptor_name":"Genes, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D052138","descriptor_name":"Genes, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","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},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1752-0509-5-121","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-121","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-121","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:21806811","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21806811","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:55bf0f1d3563487d88550e2042b0e44f","is_oa":false,"landing_page_url":"https://doaj.org/article/55bf0f1d3563487d88550e2042b0e44f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"BMC Systems Biology, Vol 5, Iss 1, p 121 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2166181","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3162519","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-5-121","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-121","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-121","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.47999998927116394,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2045916345.pdf","grobid_xml":"https://content.openalex.org/works/W2045916345.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1607267312","https://openalex.org/W1658679052","https://openalex.org/W1853389192","https://openalex.org/W1968667083","https://openalex.org/W1971422405","https://openalex.org/W1981076054","https://openalex.org/W1999951331","https://openalex.org/W2000420450","https://openalex.org/W2007978156","https://openalex.org/W2008395997","https://openalex.org/W2014606320","https://openalex.org/W2016440433","https://openalex.org/W2017642141","https://openalex.org/W2034032177","https://openalex.org/W2034979835","https://openalex.org/W2036760996","https://openalex.org/W2037416530","https://openalex.org/W2042921949","https://openalex.org/W2044499590","https://openalex.org/W2054035764","https://openalex.org/W2059300459","https://openalex.org/W2060705109","https://openalex.org/W2060749612","https://openalex.org/W2065485562","https://openalex.org/W2073968654","https://openalex.org/W2074465378","https://openalex.org/W2076876150","https://openalex.org/W2078637334","https://openalex.org/W2080460005","https://openalex.org/W2090808827","https://openalex.org/W2096606586","https://openalex.org/W2100665415","https://openalex.org/W2110359348","https://openalex.org/W2117007075","https://openalex.org/W2118303980","https://openalex.org/W2118413367","https://openalex.org/W2123621576","https://openalex.org/W2128985829","https://openalex.org/W2136940727","https://openalex.org/W2138180163","https://openalex.org/W2141452279","https://openalex.org/W2144654038","https://openalex.org/W2150599921","https://openalex.org/W2152227081","https://openalex.org/W2154361640","https://openalex.org/W2155399095","https://openalex.org/W2158631553","https://openalex.org/W2159796173","https://openalex.org/W2161959295","https://openalex.org/W2162765154","https://openalex.org/W2163563958","https://openalex.org/W2166468869","https://openalex.org/W2169404013","https://openalex.org/W2171927996","https://openalex.org/W4245024447"],"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/W2106650442"],"abstract_inverted_index":{"BACKGROUND:":[0],"One":[1],"of":[2,54,66,99,129,156,194,240],"the":[3,52,70,75,79,127,145,171,191,203],"primary":[4],"objectives":[5],"in":[6,78,107,118,126,185],"cancer":[7,71,115,136,140,158,241],"research":[8],"is":[9,170],"to":[10,34,42,91,133,174,215,229],"identify":[11,92,176,216],"causal":[12],"genomic":[13,32,213],"alterations,":[14],"such":[15,243],"as":[16,244,250,252],"somatic":[17,23],"copy":[18,195],"number":[19,155,196],"variation":[20],"(CNV)":[21],"and":[22,68,114,177,220,236],"mutations,":[24],"during":[25],"tumor":[26],"development.":[27],"Many":[28,98],"valuable":[29],"studies":[30,235],"lack":[31],"data":[33,48,214,242],"detect":[35],"CNV;":[36],"therefore,":[37],"methods":[38],"that":[39],"are":[40,102],"able":[41,90],"infer":[43],"CNVs":[44],"from":[45,74],"gene":[46,130,204,221,233],"expression":[47,181,200,234,248],"would":[49],"help":[50],"maximize":[51],"value":[53],"these":[55,100,119],"studies.":[56],"RESULTS:":[57],"We":[58],"developed":[59],"a":[60,154,209],"framework":[61,146,189],"for":[62,104,180,211],"identifying":[63],"recurrent":[64,94,120],"regions":[65,84,101,122,184],"CNV":[67,83,96,121,183,253],"distinguishing":[69],"driver":[72,137,141],"genes":[73,77,105,142,160],"passenger":[76],"regions.":[80,97],"By":[81],"inferring":[82],"across":[85],"many":[86,108,230],"datasets":[87],"we":[88],"were":[89,123],"109":[93],"amplified/deleted":[95],"enriched":[103],"involved":[106],"important":[109],"processes":[110],"associated":[111],"with":[112,202],"tumorigenesis":[113],"progression.":[116],"Genes":[117],"then":[124],"examined":[125],"context":[128],"regulatory":[131,205,218],"networks":[132],"prioritize":[134],"putative":[135],"genes.":[138],"The":[139,188],"uncovered":[143],"by":[144],"include":[147],"not":[148],"only":[149],"well-known":[150],"oncogenes":[151],"but":[152],"also":[153],"novel":[157,238],"susceptibility":[159],"validated":[161],"via":[162],"siRNA":[163],"experiments.":[164],"CONCLUSIONS:":[165],"To":[166],"our":[167],"knowledge,":[168],"this":[169],"first":[172],"effort":[173],"systematically":[175],"validate":[178],"drivers":[179],"based":[182,198,247],"breast":[186],"cancer.":[187],"where":[190],"wavelet":[192],"analysis":[193],"alteration":[197],"on":[199],"coupled":[201],"network":[206],"analysis,":[207],"provides":[208],"blueprint":[210],"leveraging":[212],"key":[217],"components":[219],"targets.":[222],"This":[223],"integrative":[224],"approach":[225],"can":[226],"be":[227],"applied":[228],"other":[231,237],"large-scale":[232],"types":[239],"next-generation":[245],"sequencing":[246],"(RNA-Seq)":[249],"well":[251],"data.":[254]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":11}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}