{"id":"https://openalex.org/W4413158608","doi":"https://doi.org/10.1109/ipdpsw66978.2025.00146","title":"Protein database search using Processing-in-Memory architecture","display_name":"Protein database search using Processing-in-Memory architecture","publication_year":2025,"publication_date":"2025-06-03","ids":{"openalex":"https://openalex.org/W4413158608","doi":"https://doi.org/10.1109/ipdpsw66978.2025.00146"},"language":"en","primary_location":{"id":"doi:10.1109/ipdpsw66978.2025.00146","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdpsw66978.2025.00146","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hal.science/hal-05375748","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5119285287","display_name":"Charly Airault","orcid":null},"institutions":[{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Charly Airault","raw_affiliation_strings":["IRISA / CNRS,Rennes,France"],"affiliations":[{"raw_affiliation_string":"IRISA / CNRS,Rennes,France","institution_ids":["https://openalex.org/I2802519937","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015132134","display_name":"Charles Deltel","orcid":null},"institutions":[{"id":"https://openalex.org/I4210133778","display_name":"Centre Inria de l'Universit\u00e9 de Rennes","ror":"https://ror.org/04040yw90","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210133778"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Charles Deltel","raw_affiliation_strings":["Inria,Rennes,France"],"affiliations":[{"raw_affiliation_string":"Inria,Rennes,France","institution_ids":["https://openalex.org/I4210133778"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115046995","display_name":"Florestan De Moor","orcid":null},"institutions":[{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Florestan De Moor","raw_affiliation_strings":["IRISA / CNRS,Rennes,France"],"affiliations":[{"raw_affiliation_string":"IRISA / CNRS,Rennes,France","institution_ids":["https://openalex.org/I2802519937","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083018584","display_name":"Erwan Drezen","orcid":null},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Erwan Drezen","raw_affiliation_strings":["Pasteur Institute,Paris,France"],"affiliations":[{"raw_affiliation_string":"Pasteur Institute,Paris,France","institution_ids":["https://openalex.org/I157536573"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106355539","display_name":"Meven Mognol","orcid":null},"institutions":[{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Meven Mognol","raw_affiliation_strings":["IRISA / UPMEM,Rennes,France"],"affiliations":[{"raw_affiliation_string":"IRISA / UPMEM,Rennes,France","institution_ids":["https://openalex.org/I2802519937"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008215565","display_name":"Dominique Lavenier","orcid":"https://orcid.org/0000-0003-2557-680X"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Dominique Lavenier","raw_affiliation_strings":["IRISA / CNRS,Rennes,France"],"affiliations":[{"raw_affiliation_string":"IRISA / CNRS,Rennes,France","institution_ids":["https://openalex.org/I2802519937","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5119285287"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.22400409,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"939","last_page":"948"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9679999947547913,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9679999947547913,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.967199981212616,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9182999730110168,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.791080117225647},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.5833941102027893},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.4898771643638611},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.42195791006088257},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.37966203689575195}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.791080117225647},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.5833941102027893},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.4898771643638611},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.42195791006088257},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.37966203689575195},{"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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/ipdpsw66978.2025.00146","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdpsw66978.2025.00146","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)","raw_type":"proceedings-article"},{"id":"pmh:oai:HAL:hal-05375748v1","is_oa":true,"landing_page_url":"https://hal.science/hal-05375748","pdf_url":null,"source":{"id":"https://openalex.org/S4406922461","display_name":"SPIRE - Sciences Po Institutional REpository","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://www.ipdps.org/ipdps2025/index.html","raw_type":"Conference papers"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-05375748v1","is_oa":true,"landing_page_url":"https://hal.science/hal-05375748","pdf_url":null,"source":{"id":"https://openalex.org/S4406922461","display_name":"SPIRE - Sciences Po Institutional REpository","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://www.ipdps.org/ipdps2025/index.html","raw_type":"Conference papers"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1981409766","https://openalex.org/W2045204781","https://openalex.org/W2068448872","https://openalex.org/W2074231493","https://openalex.org/W2092608522","https://openalex.org/W2095439426","https://openalex.org/W2125369168","https://openalex.org/W2158714788","https://openalex.org/W2163680465","https://openalex.org/W2466826145","https://openalex.org/W2471092755","https://openalex.org/W2769613207","https://openalex.org/W2981619930","https://openalex.org/W2982008795","https://openalex.org/W3105003914","https://openalex.org/W3130152469","https://openalex.org/W4236236547","https://openalex.org/W4285548014","https://openalex.org/W4313289674","https://openalex.org/W4319334382","https://openalex.org/W4327615886","https://openalex.org/W4361017256","https://openalex.org/W4386710083","https://openalex.org/W4394788044","https://openalex.org/W4401408782","https://openalex.org/W4403597825","https://openalex.org/W4403998417","https://openalex.org/W4404404667","https://openalex.org/W4404458588"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2038503502"],"abstract_inverted_index":{"This":[0],"paper":[1],"describes":[2],"the":[3,14,35,45,55,62],"implementation":[4],"of":[5,57,66],"alignment":[6],"search":[7],"within":[8],"a":[9,23,40],"protein":[10],"sequence":[11],"database":[12],"using":[13],"Processing-in-Memory":[15],"concept.":[16],"The":[17,29],"PiM":[18,58],"memory":[19],"component":[20],"used":[21],"is":[22],"specialized":[24],"DRAM":[25],"developed":[26],"by":[27,49],"UPMEM.":[28],"study":[30],"examines":[31],"two":[32],"main":[33],"aspects:":[34],"acceleration":[36],"achieved":[37],"compared":[38],"to":[39],"traditional":[41],"multi-core":[42],"server":[43],"and":[44,64],"energy":[46],"savings":[47],"enabled":[48],"this":[50],"architecture.":[51],"These":[52],"evaluations":[53],"highlight":[54],"potential":[56],"technology":[59],"for":[60],"enhancing":[61],"performance":[63],"efficiency":[65],"computationally":[67],"intensive":[68],"bioinformatics":[69],"applications.":[70]},"counts_by_year":[],"updated_date":"2025-12-28T23:10:05.387466","created_date":"2025-10-10T00:00:00"}
