{"id":"https://openalex.org/W3166475282","doi":"https://doi.org/10.1093/bioinformatics/btab440","title":"Detecting copy number alterations in RNA-Seq using SuperFreq","display_name":"Detecting copy number alterations in RNA-Seq using SuperFreq","publication_year":2021,"publication_date":"2021-06-15","ids":{"openalex":"https://openalex.org/W3166475282","doi":"https://doi.org/10.1093/bioinformatics/btab440","mag":"3166475282","pmid":"https://pubmed.ncbi.nlm.nih.gov/34132781"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab440","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab440","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/A5015244755","display_name":"Christoffer Flensburg","orcid":"https://orcid.org/0000-0002-3280-8966"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Christoffer Flensburg","raw_affiliation_strings":["Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia","Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville, VIC 3010, Australia"],"affiliations":[{"raw_affiliation_string":"Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville, VIC 3010, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066632434","display_name":"Alicia Oshlack","orcid":"https://orcid.org/0000-0001-9788-5690"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Alicia Oshlack","raw_affiliation_strings":["Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia","Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville, VIC 3010, Australia"],"affiliations":[{"raw_affiliation_string":"Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville, VIC 3010, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I2800555584"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002572034","display_name":"Ian J. Majewski","orcid":"https://orcid.org/0000-0002-6087-635X"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Ian J Majewski","raw_affiliation_strings":["Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia","Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville, VIC 3010, Australia"],"affiliations":[{"raw_affiliation_string":"Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville, VIC 3010, Australia","institution_ids":["https://openalex.org/I165779595"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5002572034","https://openalex.org/A5015244755"],"corresponding_institution_ids":["https://openalex.org/I165779595","https://openalex.org/I196021976"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8737,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.6796807,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"37","issue":"22","first_page":"4023","last_page":"4032"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9983000159263611,"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":0.9983000159263611,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9962999820709229,"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/rna-seq","display_name":"RNA-Seq","score":0.6612898111343384},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4970126450061798},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.4963296055793762},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46709105372428894},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40234166383743286},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3307744860649109},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.227321058511734},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.18170660734176636},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.15897488594055176},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11653012037277222}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6612898111343384},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4970126450061798},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.4963296055793762},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46709105372428894},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40234166383743286},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3307744860649109},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.227321058511734},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.18170660734176636},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.15897488594055176},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11653012037277222}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":"D015470","descriptor_name":"Leukemia, Myeloid, Acute","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015470","descriptor_name":"Leukemia, Myeloid, Acute","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015470","descriptor_name":"Leukemia, Myeloid, Acute","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab440","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab440","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:34132781","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34132781","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}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7200000286102295,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G8315856671","display_name":null,"funder_award_id":"1124178","funder_id":"https://openalex.org/F4320334707","funder_display_name":"Cancer Council Victoria"}],"funders":[{"id":"https://openalex.org/F4320334707","display_name":"Cancer Council Victoria","ror":"https://ror.org/023m51b03"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1255676896","https://openalex.org/W1973665555","https://openalex.org/W2016661249","https://openalex.org/W2112683411","https://openalex.org/W2116041602","https://openalex.org/W2137526110","https://openalex.org/W2146512944","https://openalex.org/W2153056550","https://openalex.org/W2155943701","https://openalex.org/W2158485828","https://openalex.org/W2170490448","https://openalex.org/W2211416430","https://openalex.org/W2262414037","https://openalex.org/W2298992290","https://openalex.org/W2332292689","https://openalex.org/W2802963454","https://openalex.org/W2807848287","https://openalex.org/W2891891425","https://openalex.org/W2909547032","https://openalex.org/W2978053672","https://openalex.org/W2997123690","https://openalex.org/W3005774532","https://openalex.org/W4253347679","https://openalex.org/W6643423274","https://openalex.org/W6755063849"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
