{"id":"https://openalex.org/W4391020796","doi":"https://doi.org/10.1109/lca.2024.3350701","title":"Efficient Memory Layout for Pre-Alignment Filtering of Long DNA Reads Using Racetrack Memory","display_name":"Efficient Memory Layout for Pre-Alignment Filtering of Long DNA Reads Using Racetrack Memory","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W4391020796","doi":"https://doi.org/10.1109/lca.2024.3350701"},"language":"en","primary_location":{"id":"doi:10.1109/lca.2024.3350701","is_oa":false,"landing_page_url":"https://doi.org/10.1109/lca.2024.3350701","pdf_url":null,"source":{"id":"https://openalex.org/S17643076","display_name":"IEEE Computer Architecture Letters","issn_l":"1556-6056","issn":["1556-6056","1556-6064","2473-2575"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Computer Architecture Letters","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090070224","display_name":"Asif Ali Khan","orcid":"https://orcid.org/0000-0002-5130-9855"},"institutions":[{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Asif Ali Khan","raw_affiliation_strings":["TU Dresden, Dresden, Germany"],"affiliations":[{"raw_affiliation_string":"TU Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070038996","display_name":"Fazal Hameed","orcid":"https://orcid.org/0000-0002-2763-8755"},"institutions":[{"id":"https://openalex.org/I199440890","display_name":"American University of Sharjah","ror":"https://ror.org/001g2fj96","country_code":"AE","type":"education","lineage":["https://openalex.org/I199440890"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Fazal Hameed","raw_affiliation_strings":["American University of Sharjah (AUS), Sharjah, UAE"],"affiliations":[{"raw_affiliation_string":"American University of Sharjah (AUS), Sharjah, UAE","institution_ids":["https://openalex.org/I199440890"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045031453","display_name":"Taha Shahroodi","orcid":"https://orcid.org/0000-0003-4576-0030"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Taha Shahroodi","raw_affiliation_strings":["TU Delft, Delft, The Netherlands"],"affiliations":[{"raw_affiliation_string":"TU Delft, Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030875484","display_name":"Alex K. Jones","orcid":"https://orcid.org/0000-0001-7498-0206"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alex K. Jones","raw_affiliation_strings":["University of Pittsburgh, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030115692","display_name":"Jer\u00f3nimo Castrill\u00f3n","orcid":"https://orcid.org/0000-0002-5007-445X"},"institutions":[{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jeronimo Castrillon","raw_affiliation_strings":["TU Dresden, Dresden, Germany"],"affiliations":[{"raw_affiliation_string":"TU Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5090070224"],"corresponding_institution_ids":["https://openalex.org/I78650965"],"apc_list":null,"apc_paid":null,"fwci":0.2339,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.52659656,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"23","issue":"1","first_page":"129","last_page":"132"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9977999925613403,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9977999925613403,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9944999814033508,"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/T12029","display_name":"DNA and Biological Computing","score":0.9922999739646912,"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/computer-science","display_name":"Computer science","score":0.7372729182243347},{"id":"https://openalex.org/keywords/overhead","display_name":"Overhead (engineering)","score":0.7052323818206787},{"id":"https://openalex.org/keywords/dram","display_name":"Dram","score":0.5945075750350952},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5515621900558472},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.48116549849510193},{"id":"https://openalex.org/keywords/von-neumann-architecture","display_name":"Von Neumann architecture","score":0.4360795319080353},{"id":"https://openalex.org/keywords/content-addressable-memory","display_name":"Content-addressable memory","score":0.42559242248535156},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3940490782260895},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.30936288833618164},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2705681324005127},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2634243369102478}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7372729182243347},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.7052323818206787},{"id":"https://openalex.org/C7366592","wikidata":"https://www.wikidata.org/wiki/Q1255620","display_name":"Dram","level":2,"score":0.5945075750350952},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5515621900558472},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.48116549849510193},{"id":"https://openalex.org/C80469333","wikidata":"https://www.wikidata.org/wiki/Q189088","display_name":"Von Neumann architecture","level":2,"score":0.4360795319080353},{"id":"https://openalex.org/C53442348","wikidata":"https://www.wikidata.org/wiki/Q745101","display_name":"Content-addressable memory","level":3,"score":0.42559242248535156},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3940490782260895},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.30936288833618164},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2705681324005127},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2634243369102478},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/lca.2024.3350701","is_oa":false,"landing_page_url":"https://doi.org/10.1109/lca.2024.3350701","pdf_url":null,"source":{"id":"https://openalex.org/S17643076","display_name":"IEEE Computer Architecture Letters","issn_l":"1556-6056","issn":["1556-6056","1556-6064","2473-2575"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Computer Architecture Letters","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4591874914","display_name":null,"funder_award_id":"1822085","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5527412688","display_name":null,"funder_award_id":"2133267","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W2087064593","https://openalex.org/W2216509856","https://openalex.org/W2753463544","https://openalex.org/W2766890412","https://openalex.org/W2789843538","https://openalex.org/W2913174568","https://openalex.org/W2971559821","https://openalex.org/W3013588319","https://openalex.org/W3033870872","https://openalex.org/W3103269557","https://openalex.org/W3111187134","https://openalex.org/W4221049439","https://openalex.org/W4247044463","https://openalex.org/W4288064720"],"related_works":["https://openalex.org/W3120961607","https://openalex.org/W2098207691","https://openalex.org/W3148568549","https://openalex.org/W1648516568","https://openalex.org/W361036515","https://openalex.org/W2269474412","https://openalex.org/W4386903460","https://openalex.org/W4211178602","https://openalex.org/W2433923775","https://openalex.org/W2537599394"],"abstract_inverted_index":{"DNA":[0,86],"sequence":[1],"alignment":[2,29],"is":[3,45],"a":[4,37,103,115],"fundamental":[5],"and":[6,68,110,123,135],"computationally":[7],"expensive":[8],"operation":[9,43],"in":[10,36,131],"bioinformatics.":[11],"Researchers":[12],"have":[13],"developed":[14],"<italic":[15,75,95],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[16,76,96],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">pre-alignment</i>":[17],"filters":[18],"that":[19,34,119],"effectively":[20],"reduce":[21],"the":[22,28,41,49,141],"amount":[23],"of":[24,88],"data":[25],"consumed":[26],"by":[27,31],"process":[30],"discarding":[32],"locations":[33],"result":[35],"poor":[38],"match.":[39],"However,":[40,80],"filtering":[42],"itself":[44],"memory-intensive":[46],"for":[47,106],"which":[48],"conventional":[50],"Von-Neumann":[51],"architectures":[52],"perform":[53],"poorly.":[54],"Therefore,":[55],"recent":[56],"designs":[57,82],"advocate":[58],"compute":[59],"near":[60],"memory":[61,71],"(CNM)":[62],"accelerators":[63],"based":[64],"on":[65],"stacked":[66],"DRAM":[67],"more":[69],"exotic":[70],"technologies":[72],"such":[73],"as":[74,94],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">racetrack":[77],"memories</i>":[78],"(RTM).":[79],"these":[81],"only":[83],"support":[84],"small":[85],"reads":[87],"circa":[89],"100":[90],"nucleotides,":[91],"referred":[92],"to":[93,140],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">short":[97],"reads</i>":[98],".":[99],"This":[100],"paper":[101],"proposes":[102],"CNM":[104],"system":[105],"handling":[107],"both":[108],"long":[109],"short":[111],"reads.":[112],"It":[113],"introduces":[114],"novel":[116],"data-placement":[117],"solution":[118],"significantly":[120],"increases":[121],"parallelism":[122],"reduces":[124],"overhead.":[125],"Evaluation":[126],"results":[127],"show":[128],"substantial":[129],"reductions":[130],"execution":[132],"time":[133],"(1.32\u00d7)":[134],"energy":[136],"consumption":[137],"(50%),":[138],"compared":[139],"state-of-the-art.":[142]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}