{"id":"https://openalex.org/W2562042122","doi":"https://doi.org/10.1093/bioinformatics/btw810","title":"Defining the clonality of peripheral T cell lymphomas using RNA-seq","display_name":"Defining the clonality of peripheral T cell lymphomas using RNA-seq","publication_year":2016,"publication_date":"2016-12-15","ids":{"openalex":"https://openalex.org/W2562042122","doi":"https://doi.org/10.1093/bioinformatics/btw810","mag":"2562042122","pmid":"https://pubmed.ncbi.nlm.nih.gov/28003262"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw810","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw810","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/8/1111/25150317/btw810.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/8/1111/25150317/btw810.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032706379","display_name":"Scott D. Brown","orcid":"https://orcid.org/0000-0003-4000-4148"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]},{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210132220","display_name":"Genome British Columbia","ror":"https://ror.org/03gne5057","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210132220"]},{"id":"https://openalex.org/I4210133112","display_name":"Canada's Michael Smith Genome Sciences Centre","ror":"https://ror.org/0333j0897","country_code":"CA","type":"other","lineage":["https://openalex.org/I4210133112"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Scott D Brown","raw_affiliation_strings":["Canada\u2019s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada","Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada","Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Canada\u2019s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I4210132220","https://openalex.org/I141945490"]},{"raw_affiliation_string":"Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082085036","display_name":"Greg Hapgood","orcid":"https://orcid.org/0000-0002-7980-8496"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Greg Hapgood","raw_affiliation_strings":["Centre for Lymphoid Cancer, Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Lymphoid Cancer, Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048030695","display_name":"Christian Steidl","orcid":"https://orcid.org/0000-0001-9842-9750"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Christian Steidl","raw_affiliation_strings":["Centre for Lymphoid Cancer, Department of Lymphoid Cancer Research, British Columbia Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Lymphoid Cancer, Department of Lymphoid Cancer Research, British Columbia Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069512440","display_name":"Andrew P. Weng","orcid":"https://orcid.org/0000-0001-7394-5425"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Andrew P Weng","raw_affiliation_strings":["Terry Fox Laboratory and Department of Pathology, British Columbia Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Terry Fox Laboratory and Department of Pathology, British Columbia Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017873196","display_name":"Kerry J. Savage","orcid":"https://orcid.org/0000-0002-5835-9863"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Kerry J Savage","raw_affiliation_strings":["Centre for Lymphoid Cancer, Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Lymphoid Cancer, Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065733774","display_name":"Robert A. Holt","orcid":"https://orcid.org/0000-0002-7259-1247"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]},{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I4210132220","display_name":"Genome British Columbia","ror":"https://ror.org/03gne5057","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210132220"]},{"id":"https://openalex.org/I4210133112","display_name":"Canada's Michael Smith Genome Sciences Centre","ror":"https://ror.org/0333j0897","country_code":"CA","type":"other","lineage":["https://openalex.org/I4210133112"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Robert A Holt","raw_affiliation_strings":["Canada\u2019s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada","Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada","Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada","Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada","Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Canada\u2019s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I4210132220","https://openalex.org/I141945490"]},{"raw_affiliation_string":"Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I1289530486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5017873196","https://openalex.org/A5065733774"],"corresponding_institution_ids":["https://openalex.org/I1289530486","https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I4210132220","https://openalex.org/I4210133112"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.7044,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.84136745,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"33","issue":"8","first_page":"1111","last_page":"1115"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10185","display_name":"Lymphoma Diagnosis and Treatment","score":0.8991000056266785,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10185","display_name":"Lymphoma Diagnosis and Treatment","score":0.8991000056266785,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11811","display_name":"Cutaneous lymphoproliferative disorders research","score":0.03500000014901161,"subfield":{"id":"https://openalex.org/subfields/2708","display_name":"Dermatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12159","display_name":"T-cell and Retrovirus Studies","score":0.019099999219179153,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.6262491941452026},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5438821911811829},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5265001654624939},{"id":"https://openalex.org/keywords/peripheral-t-cell-lymphoma","display_name":"Peripheral T-cell lymphoma","score":0.4957805573940277},{"id":"https://openalex.org/keywords/peripheral","display_name":"Peripheral","score":0.4897487163543701},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46244579553604126},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.4044435918331146},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39195334911346436},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.3288404643535614},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.28958866000175476},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24793320894241333},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1872197389602661},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1782325804233551},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.07517853379249573}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6262491941452026},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5438821911811829},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5265001654624939},{"id":"https://openalex.org/C2777891184","wikidata":"https://www.wikidata.org/wiki/Q7168693","display_name":"Peripheral T-cell lymphoma","level":4,"score":0.4957805573940277},{"id":"https://openalex.org/C46762472","wikidata":"https://www.wikidata.org/wiki/Q178648","display_name":"Peripheral","level":2,"score":0.4897487163543701},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46244579553604126},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.4044435918331146},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39195334911346436},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.3288404643535614},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.28958866000175476},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24793320894241333},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1872197389602661},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1782325804233551},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.07517853379249573},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002999","descriptor_name":"Clone Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002999","descriptor_name":"Clone Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002999","descriptor_name":"Clone Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005434","descriptor_name":"Flow Cytometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005434","descriptor_name":"Flow Cytometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005434","descriptor_name":"Flow Cytometry","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":"D013601","descriptor_name":"T-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D013601","descriptor_name":"T-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D013601","descriptor_name":"T-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D016130","descriptor_name":"Immunophenotyping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016130","descriptor_name":"Immunophenotyping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016130","descriptor_name":"Immunophenotyping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016411","descriptor_name":"Lymphoma, T-Cell, Peripheral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016411","descriptor_name":"Lymphoma, T-Cell, Peripheral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016411","descriptor_name":"Lymphoma, T-Cell, Peripheral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016411","descriptor_name":"Lymphoma, T-Cell, Peripheral","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D016411","descriptor_name":"Lymphoma, T-Cell, Peripheral","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D016411","descriptor_name":"Lymphoma, T-Cell, Peripheral","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw810","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw810","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/8/1111/25150317/btw810.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28003262","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28003262","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:5408843","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5408843","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/btw810","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw810","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/8/1111/25150317/btw810.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G134014912","display_name":null,"funder_award_id":"MOP-102679","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G2368354742","display_name":null,"funder_award_id":"CIHR; MOP-102679","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"}],"funders":[{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1605230984","https://openalex.org/W1964372737","https://openalex.org/W1978391087","https://openalex.org/W1995875735","https://openalex.org/W1999574084","https://openalex.org/W2020094108","https://openalex.org/W2020206419","https://openalex.org/W2041617648","https://openalex.org/W2043071551","https://openalex.org/W2072624318","https://openalex.org/W2084781910","https://openalex.org/W2094883326","https://openalex.org/W2104108814","https://openalex.org/W2138968719","https://openalex.org/W2163510906","https://openalex.org/W2170551349","https://openalex.org/W2188890094","https://openalex.org/W2250255440","https://openalex.org/W2276803021","https://openalex.org/W2416844197","https://openalex.org/W2993383518","https://openalex.org/W4313146863","https://openalex.org/W6648982606"],"related_works":["https://openalex.org/W4200033037","https://openalex.org/W3213655218","https://openalex.org/W2907260191","https://openalex.org/W2147993839","https://openalex.org/W1840103016","https://openalex.org/W3147425560","https://openalex.org/W2233436997","https://openalex.org/W2319221584","https://openalex.org/W54859794","https://openalex.org/W3018517591"],"abstract_inverted_index":{"Motivation:":[0],"In":[1],"T-cell":[2],"lymphoma,":[3],"malignant":[4],"T":[5,15,38,58,83,101,104,109,117,128,156],"cells":[6],"arising":[7],"from":[8,32,47,86,143],"a":[9,52,154,177,201],"founding":[10],"clone":[11,158,179],"share":[12],"an":[13],"identical":[14],"cell":[16,59,84,90,102,129,157],"receptor":[17],"(TCR)":[18],"and":[19,80,115,131,134,140,187,195,209],"can":[20,50],"be":[21],"identified":[22],"by":[23,65,161,172,180],"the":[24,33,144,149,164,184,198,215,218],"over-representation":[25],"of":[26,36,56,148,190,200,217],"this":[27],"TCR":[28,44,132],"relative":[29],"to":[30,78,98],"TCRs":[31],"patient's":[34],"repertoire":[35],"normal":[37,202],"cells.":[39],"Here,":[40],"we":[41],"demonstrate":[42],"that":[43,63,94,197],"information":[45],"extracted":[46,139],"RNA-seq":[48,123,145,191],"data":[49,219,232],"provide":[51],"higher":[53],"resolution":[54],"view":[55],"peripheral":[57],"lymphomas":[60],"(PTCLs)":[61],"than":[62],"provided":[64],"conventional":[66],"methods.":[67],"Results:":[68],"For":[69,92],"60":[70],"subjects":[71],"with":[72],"PTCL,":[73],"flow":[74,173,193],"cytometry/FACS":[75],"was":[76,124,170],"used":[77,213],"identify":[79],"sort":[81],"aberrant":[82,100,151,168],"populations":[85],"diagnostic":[87,188],"lymph":[88],"node":[89],"suspensions.":[91],"samples":[93,152,165],"did":[95],"not":[96,205],"appear":[97],"contain":[99],"populations,":[103,130],"helper":[105,111],"(T":[106,112],"H":[107],"),":[108],"follicular":[110],"FH":[113],")":[114],"cytotoxic":[116],"lymphocyte":[118],"(CTL)":[119],"subsets":[120],"were":[121,138],"sorted.":[122],"performed":[125],"on":[126],"sorted":[127],"alpha":[133],"beta":[135],"chain":[136],"sequences":[137],"quantified":[141],"directly":[142],"data.":[146],"96%":[147],"immunophenotypically":[150],"had":[153,176],"dominant":[155,178],"readily":[159],"identifiable":[160],"RNA-seq.":[162,181],"Of":[163],"where":[166],"no":[167],"population":[169],"found":[171],"cytometry,":[174],"80%":[175],"This":[182],"demonstrates":[183],"increased":[185],"sensitivity":[186],"ability":[189],"over":[192],"cytometry":[194],"shows":[196],"presence":[199],"immunophenotype":[203],"does":[204],"exclude":[206],"clonality.":[207],"Availability":[208],"Implementation:":[210],"R":[211],"scripts":[212],"in":[214],"processing":[216],"are":[220,233],"available":[221,234],"online":[222],"at":[223,235],"https://www.github.com/scottdbrown/RNAseq-TcellClonality.":[224],"Contacts:":[225],"rholt@bcgsc.ca":[226],"or":[227],"ksavage@bccancer.bc.ca.":[228],"Supplementary":[229,231],"information:":[230],"Bioinformatics":[236],"online.":[237]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}