{"id":"https://openalex.org/W4414474889","doi":"https://doi.org/10.1093/bioinformatics/btag366","title":"LCR-modules: a collection of workflows for cancer genome analysis","display_name":"LCR-modules: a collection of workflows for cancer genome analysis","publication_year":2025,"publication_date":"2025-09-24","ids":{"openalex":"https://openalex.org/W4414474889","doi":"https://doi.org/10.1093/bioinformatics/btag366","pmid":"https://pubmed.ncbi.nlm.nih.gov/42271624"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag366","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag366","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"preprint","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag366","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091399178","display_name":"Kostiantyn Dreval","orcid":"https://orcid.org/0000-0002-6214-2843"},"institutions":[{"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/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":"Kostiantyn Dreval","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada;","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013858831","display_name":"Laura K. Hilton","orcid":"https://orcid.org/0000-0002-6413-6586"},"institutions":[{"id":"https://openalex.org/I2801953985","display_name":"Spinal Cord Injury BC","ror":"https://ror.org/0357ts970","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I2801953985"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Laura K. Hilton","raw_affiliation_strings":["Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada;","institution_ids":["https://openalex.org/I2801953985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075297650","display_name":"Bruno M. Grande","orcid":"https://orcid.org/0000-0002-4621-1589"},"institutions":[{"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"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Bruno M. Grande","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046392619","display_name":"Krysta M. Coyle","orcid":"https://orcid.org/0000-0002-1309-4873"},"institutions":[{"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"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Krysta M. Coyle","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010354858","display_name":"Manuela Cruz","orcid":null},"institutions":[{"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"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Manuela Cruz","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037847727","display_name":"Sierra Gillis","orcid":"https://orcid.org/0000-0002-3418-4958"},"institutions":[{"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":"Sierra Gillis","raw_affiliation_strings":["Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada; Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada; Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada;","institution_ids":["https://openalex.org/I4210133112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027874476","display_name":"Prasath Pararajalingam","orcid":"https://orcid.org/0000-0003-3945-3552"},"institutions":[{"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"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Prasath Pararajalingam","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002945228","display_name":"Christopher Rushton","orcid":"https://orcid.org/0000-0001-6306-9361"},"institutions":[{"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"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Christopher K. Rushton","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066408059","display_name":"Haya Shaalan","orcid":null},"institutions":[{"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"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Haya Shaalan","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113361465","display_name":"Nicole Thomas","orcid":"https://orcid.org/0009-0007-9026-2715"},"institutions":[{"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"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nicole Thomas","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024192852","display_name":"Helena Winata","orcid":"https://orcid.org/0000-0002-1001-5316"},"institutions":[{"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"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Helena Winata","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082331388","display_name":"Jasper Wong","orcid":"https://orcid.org/0000-0002-8140-6517"},"institutions":[{"id":"https://openalex.org/I2801953985","display_name":"Spinal Cord Injury BC","ror":"https://ror.org/0357ts970","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I2801953985"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jasper Wong","raw_affiliation_strings":["Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada;","institution_ids":["https://openalex.org/I2801953985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119718241","display_name":"Jacky Yiu","orcid":null},"institutions":[{"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"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jacky Yiu","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada;","institution_ids":["https://openalex.org/I18014758"]}]},{"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/I2801953985","display_name":"Spinal Cord Injury BC","ror":"https://ror.org/0357ts970","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I2801953985"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Christian Steidl","raw_affiliation_strings":["Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada;","institution_ids":["https://openalex.org/I2801953985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058249371","display_name":"David W. Scott","orcid":"https://orcid.org/0000-0003-4918-2610"},"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/I2801953985","display_name":"Spinal Cord Injury BC","ror":"https://ror.org/0357ts970","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I2801953985"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"David W. Scott","raw_affiliation_strings":["Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada; Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada; Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada;","institution_ids":["https://openalex.org/I1289530486","https://openalex.org/I2801953985"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081644676","display_name":"Ryan D. Morin","orcid":"https://orcid.org/0000-0003-2932-7800"},"institutions":[{"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/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":"Ryan D. Morin","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada; Centre for Lymphoid Cancer, BC Cancer Research Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada; Centre for Lymphoid Cancer, BC Cancer Research Institute","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5081644676"],"corresponding_institution_ids":["https://openalex.org/I18014758","https://openalex.org/I4210133112"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5022,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.67597322,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":97},"biblio":{"volume":"42","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.8442999720573425,"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"}},"topics":[{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.8442999720573425,"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/T10885","display_name":"Gene expression and cancer classification","score":0.7350999712944031,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.7031999826431274,"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/workflow","display_name":"Workflow","score":0.7890999913215637},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.6118000149726868},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.5695000290870667},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.5558000206947327},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5325999855995178},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5034000277519226},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.47589999437332153},{"id":"https://openalex.org/keywords/exome","display_name":"Exome","score":0.4546000063419342},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4219000041484833}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7890999913215637},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6187999844551086},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6118000149726868},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.5695000290870667},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.5558000206947327},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5325999855995178},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5286999940872192},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5034000277519226},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.47589999437332153},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.4546000063419342},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4219000041484833},{"id":"https://openalex.org/C205270622","wikidata":"https://www.wikidata.org/wiki/Q17082639","display_name":"Cancer genome sequencing","level":5,"score":0.3756999969482422},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3427000045776367},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.34209999442100525},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.34060001373291016},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3330000042915344},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3167000114917755},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.2992999851703644},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.2840999960899353},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2806999981403351},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.2782000005245209},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.26980000734329224},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.262800008058548},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2563999891281128},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.2533999979496002},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.2515000104904175},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.25029999017715454}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag366","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag366","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.1101/2025.09.19.676923","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.09.19.676923","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/09/24/2025.09.19.676923.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:42271624","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42271624","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":{"id":"doi:10.1093/bioinformatics/btag366","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag366","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320319965","display_name":"Michael Smith Health Research BC","ror":"https://ror.org/020x39229"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1596936080","https://openalex.org/W1964807436","https://openalex.org/W2158485828","https://openalex.org/W2169456326","https://openalex.org/W2235737683","https://openalex.org/W2573966335","https://openalex.org/W2592811885","https://openalex.org/W2867868648","https://openalex.org/W2951635356","https://openalex.org/W2980774213","https://openalex.org/W2990871782","https://openalex.org/W3157952000","https://openalex.org/W3200776886","https://openalex.org/W4210644165","https://openalex.org/W4214621353","https://openalex.org/W4284878948","https://openalex.org/W4285742812","https://openalex.org/W4302742543","https://openalex.org/W4366609228","https://openalex.org/W4380740721","https://openalex.org/W4384341779","https://openalex.org/W4385741590","https://openalex.org/W4386416915","https://openalex.org/W4390878940","https://openalex.org/W4392122317","https://openalex.org/W4406539224","https://openalex.org/W4410192422"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,44,128],"surge":[2],"of":[3,21,37,108,125],"genomic":[4,91],"data":[5,31,41,92,120],"from":[6,56,112],"advanced":[7],"sequencing":[8,67],"technologies":[9],"is":[10,134],"outpacing":[11],"current":[12],"analytical":[13],"pipelines.":[14],"We":[15],"introduce":[16],"LCR-modules,":[17],"an":[18],"open-source":[19],"suite":[20,45],"bioinformatics":[22],"tools":[23],"designed":[24],"for":[25,131],"flexible":[26],"and":[27,69,78,83,98,100,110],"automated":[28],"cancer":[29,39],"genome":[30],"analysis.":[32],"LCR-modules":[33,64,85,133],"enables":[34],"reproducible":[35],"analysis":[36],"diverse":[38],"genomics":[40],"at":[42,137],"scale.":[43],"comprises":[46],"49":[47],"Snakemake-based":[48],"workflows":[49],"organized":[50],"into":[51],"three":[52],"levels,":[53],"facilitating":[54],"tasks":[55],"low-level":[57],"quality":[58],"control":[59],"to":[60,105],"complex":[61],"cohort-level":[62,79],"analyses.":[63],"supports":[65],"various":[66],"types":[68],"integrates":[70],"pipelines":[71],"such":[72],"as":[73],"mutation":[74],"calling,":[75],"expression":[76],"quantification,":[77],"aggregation,":[80],"ensuring":[81],"flexibility":[82],"reproducibility.":[84],"represents":[86],"a":[87,106],"significant":[88],"advancement":[89],"in":[90,96,123],"analysis,":[93],"reducing":[94],"barriers":[95],"reproducibility":[97],"scalability":[99],"has":[101],"already":[102],"been":[103],"applied":[104],"combination":[107],"exomes":[109],"genomes":[111],"over":[113],"10":[114],"800":[115],"samples.":[116],"AVAILABILITY:":[117],"No":[118],"new":[119],"were":[121],"generated":[122],"support":[124],"this":[126],"research.":[127],"source":[129],"code":[130],"the":[132],"openly":[135],"available":[136],"https://github.com/LCR-BCCRC/lcr-modules.":[138]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-06T08:01:05.025921","created_date":"2025-10-10T00:00:00"}
