{"id":"https://openalex.org/W2789784730","doi":"https://doi.org/10.1145/3173162.3173193","title":"Darwin","display_name":"Darwin","publication_year":2018,"publication_date":"2018-03-19","ids":{"openalex":"https://openalex.org/W2789784730","doi":"https://doi.org/10.1145/3173162.3173193","mag":"2789784730"},"language":"en","primary_location":{"id":"doi:10.1145/3173162.3173193","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3173162.3173193","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Twenty-Third International Conference on Architectural Support for Programming Languages and Operating Systems","raw_type":"proceedings-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/A5080797757","display_name":"Yatish Turakhia","orcid":"https://orcid.org/0000-0001-5600-2900"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yatish Turakhia","raw_affiliation_strings":["Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085525898","display_name":"Gill Bejerano","orcid":"https://orcid.org/0000-0001-5179-3635"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gill Bejerano","raw_affiliation_strings":["Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084342236","display_name":"William J. Dally","orcid":"https://orcid.org/0000-0003-4632-2876"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]},{"id":"https://openalex.org/I4210127875","display_name":"Nvidia (United States)","ror":"https://ror.org/03jdj4y14","country_code":"US","type":"company","lineage":["https://openalex.org/I4210127875"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William J. Dally","raw_affiliation_strings":["Stanford University, NVIDIA Research, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University, NVIDIA Research, Stanford, CA, USA","institution_ids":["https://openalex.org/I4210127875","https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5080797757"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":null,"apc_paid":null,"fwci":6.3095,"has_fulltext":false,"cited_by_count":111,"citation_normalized_percentile":{"value":0.97457198,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":null,"issue":null,"first_page":"199","last_page":"213"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9750000238418579,"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"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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"}}],"keywords":[{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.852057933807373},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.781990110874176},{"id":"https://openalex.org/keywords/darwin","display_name":"Darwin (ADL)","score":0.6492587327957153},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5341593027114868},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4807145893573761},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.45408254861831665},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.33419930934906006},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.1927606463432312},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09887111186981201},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08992224931716919}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.852057933807373},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.781990110874176},{"id":"https://openalex.org/C206118921","wikidata":"https://www.wikidata.org/wiki/Q5225921","display_name":"Darwin (ADL)","level":2,"score":0.6492587327957153},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5341593027114868},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4807145893573761},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.45408254861831665},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.33419930934906006},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.1927606463432312},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09887111186981201},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08992224931716919},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3173162.3173193","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3173162.3173193","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Twenty-Third International Conference on Architectural Support for Programming Languages and Operating Systems","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions","score":0.6200000047683716}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":84,"referenced_works":["https://openalex.org/W35674199","https://openalex.org/W344138311","https://openalex.org/W938539187","https://openalex.org/W1487227630","https://openalex.org/W1501077214","https://openalex.org/W1546528060","https://openalex.org/W1566539040","https://openalex.org/W1573552135","https://openalex.org/W1579534339","https://openalex.org/W1599106035","https://openalex.org/W1634605944","https://openalex.org/W1689369637","https://openalex.org/W1786896381","https://openalex.org/W1976878754","https://openalex.org/W1982579644","https://openalex.org/W1990061958","https://openalex.org/W1992440403","https://openalex.org/W1997246534","https://openalex.org/W2001496424","https://openalex.org/W2034861439","https://openalex.org/W2039693716","https://openalex.org/W2054399325","https://openalex.org/W2055043387","https://openalex.org/W2055666215","https://openalex.org/W2068448872","https://openalex.org/W2069458148","https://openalex.org/W2072763119","https://openalex.org/W2075996757","https://openalex.org/W2076189890","https://openalex.org/W2081763928","https://openalex.org/W2082346787","https://openalex.org/W2087064593","https://openalex.org/W2089610326","https://openalex.org/W2093065590","https://openalex.org/W2095680943","https://openalex.org/W2095824228","https://openalex.org/W2100751585","https://openalex.org/W2100990361","https://openalex.org/W2102714321","https://openalex.org/W2103914320","https://openalex.org/W2104846587","https://openalex.org/W2106811687","https://openalex.org/W2106882534","https://openalex.org/W2109034006","https://openalex.org/W2109692166","https://openalex.org/W2116495135","https://openalex.org/W2126525177","https://openalex.org/W2127230663","https://openalex.org/W2129497695","https://openalex.org/W2129713651","https://openalex.org/W2132341951","https://openalex.org/W2134800079","https://openalex.org/W2136102082","https://openalex.org/W2136145671","https://openalex.org/W2137759177","https://openalex.org/W2141978199","https://openalex.org/W2144560237","https://openalex.org/W2146496959","https://openalex.org/W2147783737","https://openalex.org/W2150677022","https://openalex.org/W2152882637","https://openalex.org/W2154826966","https://openalex.org/W2158714788","https://openalex.org/W2165654401","https://openalex.org/W2168909179","https://openalex.org/W2189047836","https://openalex.org/W2323608404","https://openalex.org/W2337261418","https://openalex.org/W2516234899","https://openalex.org/W2682773473","https://openalex.org/W2741321474","https://openalex.org/W2784619191","https://openalex.org/W2937032166","https://openalex.org/W2950354111","https://openalex.org/W2953174564","https://openalex.org/W4247053599","https://openalex.org/W4285719527","https://openalex.org/W6634012511","https://openalex.org/W6638274289","https://openalex.org/W6664263360","https://openalex.org/W6664387049","https://openalex.org/W6672364634","https://openalex.org/W6680235326","https://openalex.org/W6842402754"],"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/W2148915962","https://openalex.org/W2283866686","https://openalex.org/W4287182096","https://openalex.org/W27867058","https://openalex.org/W1980160788"],"abstract_inverted_index":{"Genomics":[0,12],"is":[1,15,171],"transforming":[2],"medicine":[3],"and":[4,31,40,63,120,143,176,183],"our":[5],"understanding":[6],"of":[7,38,59,101,133,148,158,188],"life":[8],"in":[9],"fundamental":[10],"ways.":[11],"data,":[13],"however,":[14],"far":[16],"outpacing":[17],"Moore\u00bbs":[18],"Law.":[19],"Third-generation":[20],"sequencing":[21,181],"technologies":[22,30,44,182],"produce":[23],"100X":[24],"longer":[25],"reads":[26],"than":[27],"second":[28],"generation":[29],"reveal":[32],"a":[33,79,130,135,145,150],"much":[34],"broader":[35],"mutation":[36],"spectrum":[37],"disease":[39],"evolution.":[41],"However,":[42],"these":[43],"incur":[45],"prohibitively":[46],"high":[47,141],"computational":[48],"costs.":[49],"Over":[50],"1,300":[51],"CPU":[52,66],"hours":[53,67],"are":[54,68],"required":[55,69],"for":[56,70,81,98,116,126,166],"reference-guided":[57,99],"assembly":[58,100],"the":[60,95,123,167,186],"human":[61],"genome,":[62],"over":[64,94],"15,600":[65],"de":[71],"novo":[72],"assembly.":[73,193],"This":[74],"paper":[75],"describes":[76],"\"Darwin\"":[77],"---":[78],"co-processor":[80],"genomic":[82,161,189],"sequence":[83],"alignment":[84,115,139,152],"that,":[85],"without":[86],"sacrificing":[87],"sensitivity,":[88],"provides":[89],"up":[90],"to":[91,178,184],"$15,000X":[92],"speedup":[93,107],"state-of-the-art":[96],"software":[97],"third-generation":[102],"reads.":[103],"Darwin":[104,128,170],"achieves":[105],"this":[106],"through":[108],"hardware/algorithm":[109],"co-design,":[110],"trading":[111],"more":[112],"easily":[113],"accelerated":[114],"less":[117],"memory-intensive":[118],"filtering,":[119],"by":[121],"optimizing":[122],"memory":[124,165],"system":[125],"filtering.":[127],"combines":[129],"hardware-accelerated":[131,146],"version":[132,147],"D-SOFT,":[134],"novel":[136,151],"filtering":[137],"algorithm,":[138],"at":[140],"speed,":[142],"with":[144,173],"GACT,":[149],"algorithm.":[153],"GACT":[154],"generates":[155],"near-optimal":[156],"alignments":[157],"arbitrarily":[159],"long":[160],"sequences":[162],"using":[163],"constant":[164],"compute-intensive":[168],"step.":[169],"adaptable,":[172],"tunable":[174],"speed":[175],"sensitivity":[177],"match":[179],"emerging":[180],"meet":[185],"requirements":[187],"applications":[190],"beyond":[191],"read":[192]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":19},{"year":2020,"cited_by_count":29},{"year":2019,"cited_by_count":14},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2018-03-29T00:00:00"}
