{"id":"https://openalex.org/W4211191452","doi":"https://doi.org/10.1145/3490422.3502366","title":"Co-Design for Energy Efficient and Fast Genomic Search","display_name":"Co-Design for Energy Efficient and Fast Genomic Search","publication_year":2022,"publication_date":"2022-02-11","ids":{"openalex":"https://openalex.org/W4211191452","doi":"https://doi.org/10.1145/3490422.3502366"},"language":"en","primary_location":{"id":"doi:10.1145/3490422.3502366","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3490422.3502366","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3490422.3502366","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2022 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3490422.3502366","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073868028","display_name":"Marius Knaust","orcid":null},"institutions":[{"id":"https://openalex.org/I195893171","display_name":"Zuse Institute Berlin","ror":"https://ror.org/02eva5865","country_code":"DE","type":"facility","lineage":["https://openalex.org/I195893171"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Marius Knaust","raw_affiliation_strings":["Zuse Institute Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Zuse Institute Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I195893171"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047231982","display_name":"Enrico Seiler","orcid":"https://orcid.org/0000-0003-4270-1086"},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Enrico Seiler","raw_affiliation_strings":["Freie Universit\u00e4t Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Freie Universit\u00e4t Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078948324","display_name":"Knut Reinert","orcid":"https://orcid.org/0000-0003-3078-8129"},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Knut Reinert","raw_affiliation_strings":["Freie Universit\u00e4t Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Freie Universit\u00e4t Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090438638","display_name":"Thomas Steinke","orcid":"https://orcid.org/0000-0002-0338-8042"},"institutions":[{"id":"https://openalex.org/I195893171","display_name":"Zuse Institute Berlin","ror":"https://ror.org/02eva5865","country_code":"DE","type":"facility","lineage":["https://openalex.org/I195893171"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas Steinke","raw_affiliation_strings":["Zuse Institute Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Zuse Institute Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I195893171"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5073868028"],"corresponding_institution_ids":["https://openalex.org/I195893171"],"apc_list":null,"apc_paid":null,"fwci":0.2763,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.53353545,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"180","last_page":"189"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11478","display_name":"Caching and Content Delivery","score":0.9972000122070312,"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"}},"topics":[{"id":"https://openalex.org/T11478","display_name":"Caching and Content Delivery","score":0.9972000122070312,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9876000285148621,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9829000234603882,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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":0.8456828594207764},{"id":"https://openalex.org/keywords/bloom-filter","display_name":"Bloom filter","score":0.5956703424453735},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.575195848941803},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.544165849685669},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.5134733319282532},{"id":"https://openalex.org/keywords/efficient-energy-use","display_name":"Efficient energy use","score":0.49501413106918335},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.45207950472831726},{"id":"https://openalex.org/keywords/partition","display_name":"Partition (number theory)","score":0.43035072088241577},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.36746490001678467},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.26688724756240845},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.22309574484825134},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19366022944450378},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.11420595645904541}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8456828594207764},{"id":"https://openalex.org/C147224247","wikidata":"https://www.wikidata.org/wiki/Q885373","display_name":"Bloom filter","level":2,"score":0.5956703424453735},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.575195848941803},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.544165849685669},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.5134733319282532},{"id":"https://openalex.org/C2742236","wikidata":"https://www.wikidata.org/wiki/Q924713","display_name":"Efficient energy use","level":2,"score":0.49501413106918335},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.45207950472831726},{"id":"https://openalex.org/C42812","wikidata":"https://www.wikidata.org/wiki/Q1082910","display_name":"Partition (number theory)","level":2,"score":0.43035072088241577},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.36746490001678467},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.26688724756240845},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.22309574484825134},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19366022944450378},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.11420595645904541},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3490422.3502366","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3490422.3502366","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3490422.3502366","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2022 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3490422.3502366","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3490422.3502366","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3490422.3502366","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2022 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays","raw_type":"proceedings-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8899999856948853,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4211191452.pdf","grobid_xml":"https://content.openalex.org/works/W4211191452.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1985681048","https://openalex.org/W1997446138","https://openalex.org/W2123845384","https://openalex.org/W2159954944","https://openalex.org/W2266239166","https://openalex.org/W2560269863","https://openalex.org/W2731118616","https://openalex.org/W2753396470","https://openalex.org/W2761496944","https://openalex.org/W3043424179","https://openalex.org/W3160765884","https://openalex.org/W3176125632"],"related_works":["https://openalex.org/W2081869611","https://openalex.org/W2150999591","https://openalex.org/W2011343125","https://openalex.org/W1564712904","https://openalex.org/W2113436622","https://openalex.org/W2623698249","https://openalex.org/W2099972273","https://openalex.org/W2156338408","https://openalex.org/W2086458297","https://openalex.org/W2069074882"],"abstract_inverted_index":{"Next-Generation":[0],"Sequencing":[1],"technologies":[2],"generate":[3],"a":[4,19,38,72,89,127,172],"vast":[5],"and":[6,67,106,117,161],"exponentially":[7],"increasing":[8],"amount":[9],"of":[10,41,75,111,121,156,164],"sequence":[11,42,56,101],"data.":[12],"The":[13],"Interleaved":[14],"Bloom":[15],"Filter":[16],"(IBF)":[17],"is":[18,25],"novel":[20],"indexing":[21],"data":[22,34,49,78,132],"structure":[23,79],"which":[24],"state-of-the-art":[26],"for":[27,51,99],"distributing":[28],"approximate":[29],"queries":[30],"with":[31],"an":[32],"in-memory":[33],"structure.":[35],"With":[36],"it,":[37],"main":[39],"task":[40],"analysis":[43],"pipelines,":[44],"(approximately)":[45],"searching":[46],"large":[47],"reference":[48],"sets":[50],"sequencing":[52],"reads":[53],"or":[54],"short":[55],"patterns":[57],"like":[58,114],"genes,":[59],"can":[60,149],"be":[61],"significantly":[62],"accelerated.":[63],"To":[64],"meet":[65],"performance":[66,163],"energy-efficiency":[68],"requirements,":[69],"we":[70],"chose":[71],"co-design":[73],"approach":[74],"the":[76,81,93,118,134,139,143],"IBF":[77],"on":[80,138],"FPGA":[82,140],"platform.":[83],"Further,":[84],"our":[85],"OpenCL-based":[86],"implementation":[87],"allows":[88],"seamless":[90],"integration":[91],"into":[92],"widely":[94],"used":[95],"SeqAn":[96],"C++":[97],"library":[98],"biological":[100],"analysis.":[102],"Our":[103],"algorithmic":[104],"design":[105],"optimization":[107],"strategy":[108],"takes":[109],"advantage":[110],"FPGA-specific":[112],"features":[113],"shift":[115],"register":[116],"parallelization":[119],"potential":[120],"many":[122],"bitwise":[123],"operations.":[124],"We":[125,148],"designed":[126],"well-chosen":[128],"schema":[129],"to":[130,158,166,171],"partition":[131],"across":[133],"different":[135],"memory":[136],"domains":[137],"platform":[141],"using":[142],"Shared":[144],"Virtual":[145],"Memory":[146],"concept.":[147],"demonstrate":[150],"significant":[151],"improvements":[152],"in":[153,162],"energy":[154],"efficiency":[155],"up":[157,165],"19":[159],"times":[160],"5.6":[167],"times,":[168],"respectively,":[169],"compared":[170],"well-tuned,":[173],"multithreaded":[174],"CPU":[175],"reference.":[176]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}