{"id":"https://openalex.org/W4392518441","doi":"https://doi.org/10.1007/s11227-024-05956-7","title":"Accelerating the detection of DNA differentially methylated regions using multiple GPUs","display_name":"Accelerating the detection of DNA differentially methylated regions using multiple GPUs","publication_year":2024,"publication_date":"2024-03-06","ids":{"openalex":"https://openalex.org/W4392518441","doi":"https://doi.org/10.1007/s11227-024-05956-7"},"language":"en","primary_location":{"id":"doi:10.1007/s11227-024-05956-7","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1007/s11227-024-05956-7","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11227-024-05956-7.pdf","source":{"id":"https://openalex.org/S32326811","display_name":"The Journal of Supercomputing","issn_l":"0920-8542","issn":["0920-8542","1573-0484"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"The Journal of Supercomputing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s11227-024-05956-7.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054612127","display_name":"Carlos Rea\u00f1o","orcid":"https://orcid.org/0000-0001-7871-9152"},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Carlos Rea\u00f1o","raw_affiliation_strings":["Departament d\u2019Inform\u00e0tica, Escola T\u00e8cnica Superior d\u2019Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain","Departament d'Inform\u00e0tica, Escola T\u00e8cnica Superior d'Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain"],"affiliations":[{"raw_affiliation_string":"Departament d\u2019Inform\u00e0tica, Escola T\u00e8cnica Superior d\u2019Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain","institution_ids":["https://openalex.org/I16097986"]},{"raw_affiliation_string":"Departament d'Inform\u00e0tica, Escola T\u00e8cnica Superior d'Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain","institution_ids":["https://openalex.org/I16097986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074941315","display_name":"Ricardo Olanda","orcid":"https://orcid.org/0000-0002-1088-8109"},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Ricardo Olanda","raw_affiliation_strings":["Departament d\u2019Inform\u00e0tica, Escola T\u00e8cnica Superior d\u2019Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain","Departament d'Inform\u00e0tica, Escola T\u00e8cnica Superior d'Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain"],"affiliations":[{"raw_affiliation_string":"Departament d\u2019Inform\u00e0tica, Escola T\u00e8cnica Superior d\u2019Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain","institution_ids":["https://openalex.org/I16097986"]},{"raw_affiliation_string":"Departament d'Inform\u00e0tica, Escola T\u00e8cnica Superior d'Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain","institution_ids":["https://openalex.org/I16097986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085278703","display_name":"Elvira Baydal","orcid":"https://orcid.org/0000-0003-3261-7227"},"institutions":[{"id":"https://openalex.org/I60053951","display_name":"Universitat Polit\u00e8cnica de Val\u00e8ncia","ror":"https://ror.org/01460j859","country_code":"ES","type":"education","lineage":["https://openalex.org/I60053951"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Elvira Baydal","raw_affiliation_strings":["Departament d\u2019Inform\u00e0tica de Sistemes i Computadors (DISCA), Universitat Polit\u00e8cnica de Val\u00e8ncia, Cam\u00ed de Vera s/n, 46022, Val\u00e8ncia, Val\u00e8ncia, Spain","Departament d'Inform\u00e0tica de Sistemes i Computadors (DISCA), Universitat Polit\u00e8cnica de Val\u00e8ncia, Cam\u00ed de Vera s/n, 46022, Val\u00e8ncia, Val\u00e8ncia, Spain"],"affiliations":[{"raw_affiliation_string":"Departament d\u2019Inform\u00e0tica de Sistemes i Computadors (DISCA), Universitat Polit\u00e8cnica de Val\u00e8ncia, Cam\u00ed de Vera s/n, 46022, Val\u00e8ncia, Val\u00e8ncia, Spain","institution_ids":["https://openalex.org/I60053951"]},{"raw_affiliation_string":"Departament d'Inform\u00e0tica de Sistemes i Computadors (DISCA), Universitat Polit\u00e8cnica de Val\u00e8ncia, Cam\u00ed de Vera s/n, 46022, Val\u00e8ncia, Val\u00e8ncia, Spain","institution_ids":["https://openalex.org/I60053951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057445351","display_name":"Mariano P\u00e9rez","orcid":"https://orcid.org/0000-0002-0380-451X"},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Mariano P\u00e9rez","raw_affiliation_strings":["Departament d\u2019Inform\u00e0tica, Escola T\u00e8cnica Superior d\u2019Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain","Departament d'Inform\u00e0tica, Escola T\u00e8cnica Superior d'Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain"],"affiliations":[{"raw_affiliation_string":"Departament d\u2019Inform\u00e0tica, Escola T\u00e8cnica Superior d\u2019Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain","institution_ids":["https://openalex.org/I16097986"]},{"raw_affiliation_string":"Departament d'Inform\u00e0tica, Escola T\u00e8cnica Superior d'Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain","institution_ids":["https://openalex.org/I16097986"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032238726","display_name":"Juan M. Ordu\u00f1a","orcid":"https://orcid.org/0000-0002-2932-0214"},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Juan M. Ordu\u00f1a","raw_affiliation_strings":["Departament d\u2019Inform\u00e0tica, Escola T\u00e8cnica Superior d\u2019Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain","Departament d'Inform\u00e0tica, Escola T\u00e8cnica Superior d'Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain"],"affiliations":[{"raw_affiliation_string":"Departament d\u2019Inform\u00e0tica, Escola T\u00e8cnica Superior d\u2019Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain","institution_ids":["https://openalex.org/I16097986"]},{"raw_affiliation_string":"Departament d'Inform\u00e0tica, Escola T\u00e8cnica Superior d'Enginyeria (ETSE), Universitat de Val\u00e8ncia, Avinguda de la Universitat s/n, 46100, Burjassot, Val\u00e8ncia, Spain","institution_ids":["https://openalex.org/I16097986"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5032238726","https://openalex.org/A5054612127","https://openalex.org/A5057445351","https://openalex.org/A5074941315","https://openalex.org/A5085278703"],"corresponding_institution_ids":["https://openalex.org/I16097986","https://openalex.org/I60053951"],"apc_list":{"value":2390,"currency":"EUR","value_usd":2990},"apc_paid":{"value":2390,"currency":"EUR","value_usd":2990},"fwci":0.2313,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.53407946,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"80","issue":"9","first_page":"13386","last_page":"13410"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9983999729156494,"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":0.9983999729156494,"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/T11478","display_name":"Caching and Content Delivery","score":0.9714999794960022,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11896","display_name":"Opportunistic and Delay-Tolerant Networks","score":0.9577999711036682,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7577872276306152},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6918262243270874},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.6203950047492981},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6129680275917053},{"id":"https://openalex.org/keywords/differentially-methylated-regions","display_name":"Differentially methylated regions","score":0.49274304509162903},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.48558539152145386},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.41404667496681213},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13174745440483093},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07531687617301941},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06988874077796936}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7577872276306152},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6918262243270874},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.6203950047492981},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6129680275917053},{"id":"https://openalex.org/C154253233","wikidata":"https://www.wikidata.org/wiki/Q14862240","display_name":"Differentially methylated regions","level":5,"score":0.49274304509162903},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.48558539152145386},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.41404667496681213},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13174745440483093},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07531687617301941},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06988874077796936},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1007/s11227-024-05956-7","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1007/s11227-024-05956-7","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11227-024-05956-7.pdf","source":{"id":"https://openalex.org/S32326811","display_name":"The Journal of Supercomputing","issn_l":"0920-8542","issn":["0920-8542","1573-0484"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"The Journal of Supercomputing","raw_type":"journal-article"},{"id":"pmh:oai:riunet.upv.es:10251/209237","is_oa":true,"landing_page_url":"http://hdl.handle.net/10251/209237","pdf_url":"https://riunet.upv.es/bitstream/10251/209237/1/ReanoOlandaBaydal%20-%20Accelerating%20the%20detection%20of%20DNA%20differentially%20methylated%20regions%20using%20mul....pdf","source":{"id":"https://openalex.org/S4306400639","display_name":"RiuNet (Universitat Polit\u00e8cnica de Val\u00e8ncia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I60053951","host_organization_name":"Universitat Polit\u00e8cnica de Val\u00e8ncia","host_organization_lineage":["https://openalex.org/I60053951"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:roderic.uv.es:10550/96449","is_oa":true,"landing_page_url":"https://hdl.handle.net/10550/96449","pdf_url":null,"source":{"id":"https://openalex.org/S4306400245","display_name":"Repository of Digital Objects for Teaching Research and Culture (University of Valencia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I16097986","host_organization_name":"Universitat de Val\u00e8ncia","host_organization_lineage":["https://openalex.org/I16097986"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Rea\u00f1o, Carlos Olanda Rodr\u00edguez, Ricardo Baydal Cardona, Elvira P\u00e9rez Mart\u00ednez, Mariano Ordu\u00f1a Huertas, Juan Manuel 2024 Accelerating the detection of DNA differentially methylated regions using multiple GPUs Journal of Supercomputing","raw_type":"journal article"}],"best_oa_location":{"id":"doi:10.1007/s11227-024-05956-7","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1007/s11227-024-05956-7","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11227-024-05956-7.pdf","source":{"id":"https://openalex.org/S32326811","display_name":"The Journal of Supercomputing","issn_l":"0920-8542","issn":["0920-8542","1573-0484"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"The Journal of Supercomputing","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4868821653","display_name":null,"funder_award_id":"CIGE/2021/132","funder_id":"https://openalex.org/F4320321864","funder_display_name":"Generalitat Valenciana"}],"funders":[{"id":"https://openalex.org/F4320321864","display_name":"Generalitat Valenciana","ror":"https://ror.org/0097mvx21"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4392518441.pdf"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W59652542","https://openalex.org/W1596936080","https://openalex.org/W1993419284","https://openalex.org/W1997866877","https://openalex.org/W2004078197","https://openalex.org/W2067897366","https://openalex.org/W2200334237","https://openalex.org/W2591635079","https://openalex.org/W2897136628","https://openalex.org/W2913397029","https://openalex.org/W2937563420","https://openalex.org/W2947341884","https://openalex.org/W3011491274","https://openalex.org/W3038141998","https://openalex.org/W3158911208"],"related_works":["https://openalex.org/W2317245370","https://openalex.org/W4249323025","https://openalex.org/W198851386","https://openalex.org/W2030310580","https://openalex.org/W947442053","https://openalex.org/W1980160788","https://openalex.org/W2148915962","https://openalex.org/W2283866686","https://openalex.org/W4287182096","https://openalex.org/W27867058"],"abstract_inverted_index":{"Abstract":[0],"DNA":[1],"methylation":[2],"analysis":[3],"has":[4],"become":[5],"an":[6,51],"important":[7],"topic":[8],"in":[9,145],"the":[10,90,113,116,122,128,132,137],"study":[11],"of":[12,22,37,47,54,105,139],"human":[13],"health.":[14],"In":[15],"previous":[16],"work,":[17],"we":[18],"developed":[19],"a":[20,31,72,77],"suite":[21],"tools":[23],"to":[24,57,101,115,136,143],"perform":[25],"this":[26],"analysis.":[27],"It":[28],"includes":[29],"HPG-Dhunter,":[30],"web-based":[32],"tool":[33,49],"for":[34],"automatic":[35],"detection":[36],"differentially":[38],"methylated":[39],"regions":[40],"(DMRs)":[41],"between":[42],"different":[43,61],"samples.":[44],"The":[45,103],"back-end":[46],"that":[48,121],"receives":[50],"undefined":[52],"number":[53,104,138],"simultaneous":[55,64],"requests":[56,65,84,97],"detect":[58],"DMRs":[59],"on":[60],"datasets.":[62],"Currently,":[63],"are":[66],"queued":[67],"and":[68,98],"processed":[69],"one":[70],"at":[71],"time.":[73,130],"This":[74],"paper":[75],"proposes":[76],"parallel":[78,124],"architecture":[79,114,125],"where":[80],"multiple":[81],"daemons":[82,106],"serve":[83],"simultaneously.":[85],"Daemons":[86],"can":[87],"also":[88],"share":[89],"same":[91],"physical":[92],"GPUs.":[93],"A":[94],"scheduler":[95],"manages":[96],"forwards":[99],"them":[100],"daemons.":[102],"per":[107],"GPU":[108],"is":[109],"configurable,":[110],"thus":[111],"adapting":[112],"available":[117,140],"hardware.":[118],"Results":[119],"show":[120],"proposed":[123],"hugely":[126],"reduces":[127],"execution":[129],"Furthermore,":[131],"speedup":[133],"increases":[134],"proportionally":[135],"GPUs":[141],"(up":[142],"7.47x":[144],"our":[146],"experimental":[147],"setup).":[148]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-04T08:04:53.788161","created_date":"2025-10-10T00:00:00"}