{"id":"https://openalex.org/W4391822770","doi":"https://doi.org/10.1186/s12859-024-05670-4","title":"Torch-eCpG: a fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units","display_name":"Torch-eCpG: a fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units","publication_year":2024,"publication_date":"2024-02-14","ids":{"openalex":"https://openalex.org/W4391822770","doi":"https://doi.org/10.1186/s12859-024-05670-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/38355413"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05670-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05670-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05670-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05670-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039761997","display_name":"Kord M. Kober","orcid":"https://orcid.org/0000-0001-9732-3321"},"institutions":[{"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/I4210167126","display_name":"UCSF Helen Diller Family Comprehensive Cancer Center","ror":"https://ror.org/05yndxy10","country_code":"US","type":"facility","lineage":["https://openalex.org/I180670191","https://openalex.org/I4210110664","https://openalex.org/I4210167126"]},{"id":"https://openalex.org/I76766440","display_name":"University of San Francisco","ror":"https://ror.org/029m7xn54","country_code":"US","type":"education","lineage":["https://openalex.org/I76766440"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kord M. Kober","raw_affiliation_strings":["Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA. kord.kober@ucsf.edu","Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. kord.kober@ucsf.edu","School of Nursing, University of California San Francisco, San Francisco, CA, USA. kord.kober@ucsf.edu","School of Nursing, University of California San Francisco, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA. kord.kober@ucsf.edu","institution_ids":[]},{"raw_affiliation_string":"Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. kord.kober@ucsf.edu","institution_ids":["https://openalex.org/I4210167126"]},{"raw_affiliation_string":"School of Nursing, University of California San Francisco, San Francisco, CA, USA. kord.kober@ucsf.edu","institution_ids":["https://openalex.org/I180670191","https://openalex.org/I76766440"]},{"raw_affiliation_string":"School of Nursing, University of California San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031681478","display_name":"Liam Berger","orcid":null},"institutions":[{"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liam Berger","raw_affiliation_strings":["School of Nursing, University of California San Francisco, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Nursing, University of California San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077152188","display_name":"Ritu Roy","orcid":"https://orcid.org/0000-0003-2065-7846"},"institutions":[{"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/I4210167126","display_name":"UCSF Helen Diller Family Comprehensive Cancer Center","ror":"https://ror.org/05yndxy10","country_code":"US","type":"facility","lineage":["https://openalex.org/I180670191","https://openalex.org/I4210110664","https://openalex.org/I4210167126"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ritu Roy","raw_affiliation_strings":["Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I4210167126","https://openalex.org/I180670191"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016883047","display_name":"Adam B. Olshen","orcid":"https://orcid.org/0000-0002-8998-4514"},"institutions":[{"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/I4210167126","display_name":"UCSF Helen Diller Family Comprehensive Cancer Center","ror":"https://ror.org/05yndxy10","country_code":"US","type":"facility","lineage":["https://openalex.org/I180670191","https://openalex.org/I4210110664","https://openalex.org/I4210167126"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam Olshen","raw_affiliation_strings":["Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA","Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I4210167126","https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5039761997"],"corresponding_institution_ids":["https://openalex.org/I180670191","https://openalex.org/I4210167126","https://openalex.org/I76766440"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.9331,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.72097438,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"25","issue":"1","first_page":"71","last_page":"71"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.6948000192642212,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.6948000192642212,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.13860000669956207,"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":0.03909999877214432,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/torch","display_name":"Torch","score":0.6989753842353821},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.6930896639823914},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6269767880439758},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5744702816009521},{"id":"https://openalex.org/keywords/cpg-site","display_name":"CpG site","score":0.5490255951881409},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5465320348739624},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5382594466209412},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.534910261631012},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.4931187331676483},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4924215078353882},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.452648401260376},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3377259373664856},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3370756506919861},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3351062536239624},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.2186695635318756},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2088325321674347},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20628580451011658},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1564123034477234}],"concepts":[{"id":"https://openalex.org/C946207","wikidata":"https://www.wikidata.org/wiki/Q327954","display_name":"Torch","level":3,"score":0.6989753842353821},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.6930896639823914},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6269767880439758},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5744702816009521},{"id":"https://openalex.org/C140173407","wikidata":"https://www.wikidata.org/wiki/Q1138358","display_name":"CpG site","level":5,"score":0.5490255951881409},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5465320348739624},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5382594466209412},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.534910261631012},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.4931187331676483},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4924215078353882},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.452648401260376},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3377259373664856},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3370756506919861},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3351062536239624},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2186695635318756},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2088325321674347},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20628580451011658},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1564123034477234},{"id":"https://openalex.org/C191897082","wikidata":"https://www.wikidata.org/wiki/Q11467","display_name":"Metallurgy","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C19474535","wikidata":"https://www.wikidata.org/wiki/Q131172","display_name":"Welding","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-024-05670-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05670-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05670-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38355413","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38355413","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt9m35k5sz","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/9m35k5sz","pdf_url":"https://escholarship.org/content/qt9m35k5sz/qt9m35k5sz.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, vol 25, iss 1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10867984","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10867984","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10867984/pdf/12859_2024_Article_5670.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:fb93a795857a423f8913c63189944807","is_oa":true,"landing_page_url":"https://doaj.org/article/fb93a795857a423f8913c63189944807","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-9 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05670-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05670-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05670-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4000000059604645,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1601389486","display_name":null,"funder_award_id":"P30 CA082103","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3295524100","display_name":null,"funder_award_id":"CA082103","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5513746999","display_name":null,"funder_award_id":"CA233774","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6258283449","display_name":null,"funder_award_id":"CA233774","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7178345801","display_name":null,"funder_award_id":"CA082103","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G8011927044","display_name":null,"funder_award_id":"R37 CA233774","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391822770.pdf"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W2128016314","https://openalex.org/W2466930524","https://openalex.org/W2618311580","https://openalex.org/W2794542396","https://openalex.org/W2796298565","https://openalex.org/W2808448636","https://openalex.org/W2944117578","https://openalex.org/W2950903530","https://openalex.org/W2983859156","https://openalex.org/W3036029599","https://openalex.org/W3184642093","https://openalex.org/W4212796217","https://openalex.org/W4220782328","https://openalex.org/W4220813379","https://openalex.org/W4225414542","https://openalex.org/W4226336441","https://openalex.org/W4229059471","https://openalex.org/W4229336814","https://openalex.org/W4229453107"],"related_works":["https://openalex.org/W4319736389","https://openalex.org/W1963684754","https://openalex.org/W2379527315","https://openalex.org/W2388213899","https://openalex.org/W2113128227","https://openalex.org/W632256878","https://openalex.org/W2491403535","https://openalex.org/W2479811461","https://openalex.org/W2104915799","https://openalex.org/W4311938462"],"abstract_inverted_index":{"BACKGROUND:":[0],"Gene":[1],"expression":[2,30,35,43],"may":[3,70],"be":[4],"regulated":[5],"by":[6],"the":[7,23,32,72,99,110,113,123],"DNA":[8,26],"methylation":[9,27,38,130],"of":[10,34,67,77],"regulatory":[11],"elements":[12],"in":[13],"cis,":[14],"distal,":[15],"and":[16,28,125,138],"trans":[17],"regions.":[18],"One":[19],"method":[20],"to":[21,54,75,87,104,118,141],"evaluate":[22],"relationship":[24],"between":[25],"gene":[29],"is":[31,134,149],"mapping":[33,61,90],"quantitative":[36],"trait":[37],"(eQTM)":[39],"loci":[40],"(also":[41],"called":[42],"associated":[44],"CpG":[45],"loci,":[46],"eCpG).":[47],"However,":[48],"no":[49],"open-source":[50,85],"tools":[51],"are":[52,115],"available":[53,150],"provide":[55],"eQTM":[56,60,89,143],"mapping.":[57,144],"In":[58],"addition,":[59],"can":[62,97],"involve":[63],"a":[64,135],"large":[65],"number":[66],"comparisons":[68],"which":[69],"prevent":[71],"analyses":[73,111],"due":[74],"limitations":[76],"computational":[78],"resources.":[79],"Here,":[80],"we":[81],"describe":[82],"Torch-eCpG,":[83],"an":[84,93],"tool":[86,114,140],"perform":[88,142],"that":[91,96],"includes":[92],"optimized":[94],"implementation":[95],"use":[98],"graphical":[100],"processing":[101],"unit":[102],"(GPU)":[103],"reduce":[105],"runtime.":[106],"RESULTS:":[107],"We":[108],"demonstrate":[109],"using":[112,122],"reproducible,":[116],"up":[117],"18":[119],"\u00d7":[120],"faster":[121],"GPU,":[124],"scale":[126],"linearly":[127],"with":[128],"increasing":[129],"loci.":[131],"CONCLUSIONS:":[132],"Torch-eCpG":[133,148],"fast,":[136],"reliable,":[137],"scalable":[139],"Source":[145],"code":[146],"for":[147],"at":[151],"https://github.com/kordk/torch-ecpg":[152],".":[153]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3}],"updated_date":"2026-06-17T06:14:20.161405","created_date":"2025-10-10T00:00:00"}
