{"id":"https://openalex.org/W2112861424","doi":"https://doi.org/10.1093/bioinformatics/btt744","title":"ALEA: a toolbox for allele-specific epigenomics analysis","display_name":"ALEA: a toolbox for allele-specific epigenomics analysis","publication_year":2013,"publication_date":"2013-12-26","ids":{"openalex":"https://openalex.org/W2112861424","doi":"https://doi.org/10.1093/bioinformatics/btt744","mag":"2112861424","pmid":"https://pubmed.ncbi.nlm.nih.gov/24371156"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt744","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt744","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/8/1172/48922698/bioinformatics_30_8_1172.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/8/1172/48922698/bioinformatics_30_8_1172.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037328673","display_name":"Hamid Younesy","orcid":null},"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/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"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/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"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":["AT","CA","US"],"is_corresponding":false,"raw_author_name":"Hamid Younesy","raw_affiliation_strings":["1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I129774422","https://openalex.org/I180670191","https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060664606","display_name":"Torsten M\u00f6ller","orcid":"https://orcid.org/0000-0003-1192-0710"},"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/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"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/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"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":["AT","CA","US"],"is_corresponding":false,"raw_author_name":"Torsten M\u00f6ller","raw_affiliation_strings":["1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I129774422","https://openalex.org/I180670191","https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042682747","display_name":"Alireza Heravi\u2010Moussavi","orcid":null},"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/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"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/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"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":["AT","CA","US"],"is_corresponding":false,"raw_author_name":"Alireza Heravi-Moussavi","raw_affiliation_strings":["1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I129774422","https://openalex.org/I180670191","https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043939880","display_name":"Jeffrey B. Cheng","orcid":"https://orcid.org/0000-0001-9821-4549"},"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/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"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/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"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":["AT","CA","US"],"is_corresponding":false,"raw_author_name":"Jeffrey B. Cheng","raw_affiliation_strings":["1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I129774422","https://openalex.org/I180670191","https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088197113","display_name":"J Costello","orcid":"https://orcid.org/0000-0003-3189-584X"},"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/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"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/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"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":["AT","CA","US"],"is_corresponding":false,"raw_author_name":"Joseph F. Costello","raw_affiliation_strings":["1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I129774422","https://openalex.org/I180670191","https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024279129","display_name":"Matthew C. Lorincz","orcid":"https://orcid.org/0000-0003-0885-0467"},"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/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"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/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"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":["AT","CA","US"],"is_corresponding":false,"raw_author_name":"Matthew C. Lorincz","raw_affiliation_strings":["1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I129774422","https://openalex.org/I180670191","https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076209108","display_name":"Mohammad M. Karimi","orcid":"https://orcid.org/0000-0001-5017-1252"},"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/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"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/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"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":["AT","CA","US"],"is_corresponding":true,"raw_author_name":"Mohammad M. Karimi","raw_affiliation_strings":["1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I129774422","https://openalex.org/I180670191","https://openalex.org/I1289530486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100728059","display_name":"Steven J.M. Jones","orcid":"https://orcid.org/0000-0003-3394-2208"},"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/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"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/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"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":["AT","CA","US"],"is_corresponding":true,"raw_author_name":"Steven J. M. Jones","raw_affiliation_strings":["1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, 2Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, 3Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, 4Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, 5Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and 6Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I129774422","https://openalex.org/I180670191","https://openalex.org/I1289530486"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5076209108","https://openalex.org/A5100728059"],"corresponding_institution_ids":["https://openalex.org/I1289530486","https://openalex.org/I129774422","https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I180670191","https://openalex.org/I4210133112"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.3466,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.8067687,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"30","issue":"8","first_page":"1172","last_page":"1174"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.5910999774932861,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.5910999774932861,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.15279999375343323,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.10589999705553055,"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/epigenomics","display_name":"Epigenomics","score":0.8251273036003113},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.573968768119812},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.5734551548957825},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.5406894087791443},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5277515053749084},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.47209662199020386},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4602760970592499},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4509262442588806},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4328252673149109},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4097920060157776},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2980837821960449},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22401002049446106},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.19895699620246887},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.10509791970252991},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07243236899375916}],"concepts":[{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.8251273036003113},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.573968768119812},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.5734551548957825},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.5406894087791443},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5277515053749084},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.47209662199020386},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4602760970592499},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4509262442588806},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4328252673149109},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4097920060157776},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2980837821960449},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22401002049446106},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.19895699620246887},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10509791970252991},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07243236899375916},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt744","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt744","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/8/1172/48922698/bioinformatics_30_8_1172.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24371156","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24371156","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:kclpure.kcl.ac.uk:publications/e11bc370-b4cb-4963-866c-679ca299c565","is_oa":true,"landing_page_url":"https://kclpure.kcl.ac.uk/portal/en/publications/e11bc370-b4cb-4963-866c-679ca299c565","pdf_url":"https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btt744","source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Younesy , H , M\u00f6ller , T , Heravi-moussavi , A , Cheng , J B , Costello , J F , Lorincz , M C , Karimi , M M &amp; Jones , S J M 2014 , ' ALEA: a toolbox for allele-specific epigenomics analysis ' , BIOINFORMATICS , vol. 30 , no. 8 , pp. 1172-1174 . https://doi.org/10.1093/bioinformatics/btt744","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt744","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt744","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/8/1172/48922698/bioinformatics_30_8_1172.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6550747558","display_name":null,"funder_award_id":"120591","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"}],"funders":[{"id":"https://openalex.org/F4320306673","display_name":"Dermatology Foundation","ror":"https://ror.org/04xy3z086"},{"id":"https://openalex.org/F4320319973","display_name":"Genome British Columbia","ror":"https://ror.org/03gne5057"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2112861424.pdf","grobid_xml":"https://content.openalex.org/works/W2112861424.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1978116054","https://openalex.org/W2005501593","https://openalex.org/W2035997482","https://openalex.org/W2083736279","https://openalex.org/W2096791516","https://openalex.org/W2108666233","https://openalex.org/W2134199796"],"related_works":["https://openalex.org/W2057739827","https://openalex.org/W2520779216","https://openalex.org/W3035076328","https://openalex.org/W2795212387","https://openalex.org/W3153821214","https://openalex.org/W1996341957","https://openalex.org/W2107680358","https://openalex.org/W3198770482","https://openalex.org/W2563699781","https://openalex.org/W2967439527"],"abstract_inverted_index":{"The":[0,98,113],"assessment":[1],"of":[2,46,66,73],"expression":[3],"and":[4,17,52,58,86,105,109,117],"epigenomic":[5,22],"status":[6],"using":[7,103],"sequencing":[8,75,84],"based":[9],"methods":[10],"provides":[11,62],"an":[12],"unprecedented":[13],"opportunity":[14],"to":[15,92],"identify":[16],"correlate":[18],"allelic":[19,36,54,89],"differences":[20],"with":[21],"status.":[23],"We":[24],"present":[25],"ALEA,":[26],"a":[27,63],"computational":[28],"toolbox":[29],"for":[30,43,70],"allele-specific":[31,71],"epigenomics":[32],"analysis,":[33],"which":[34],"incorporates":[35],"variation":[37],"data":[38,76,85,116,133],"within":[39],"existing":[40],"resources,":[41],"allowing":[42],"the":[44,82],"identification":[45],"significant":[47],"associations":[48],"between":[49],"epigenetic":[50],"modifications":[51],"specific":[53],"variants":[55],"in":[56],"human":[57,104],"mouse":[59,107],"cells.":[60],"ALEA":[61],"customizable":[64],"pipeline":[65,99],"command":[67],"line":[68],"tools":[69],"analysis":[72],"next-generation":[74],"(ChIP-seq,":[77],"RNA-seq,":[78],"etc.)":[79],"that":[80],"takes":[81],"raw":[83],"produces":[87],"separate":[88],"tracks":[90],"ready":[91],"be":[93],"viewed":[94],"on":[95],"genome":[96],"browsers.":[97],"has":[100],"been":[101],"validated":[102],"hybrid":[106],"ChIP-seq":[108],"RNA-seq":[110],"data.":[111],"AVAILABILITY:":[112],"package,":[114],"test":[115],"usage":[118],"instructions":[119],"are":[120,134],"available":[121,135],"online":[122],"at":[123,136],"http://www.bcgsc.ca/platform/bioinfo/software/alea":[124],"CONTACT:":[125],":":[126],"mkarimi1@interchange.ubc.ca":[127],"or":[128],"sjones@bcgsc.ca":[129],"Supplementary":[130,132],"information:":[131],"Bioinformatics":[137],"online.":[138]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}
