{"id":"https://openalex.org/W2343452498","doi":"https://doi.org/10.1109/tpds.2015.2513053","title":"RAMPS: A Reconfigurable Architecture for Minimal Perfect Sequencing","display_name":"RAMPS: A Reconfigurable Architecture for Minimal Perfect Sequencing","publication_year":2015,"publication_date":"2015-12-29","ids":{"openalex":"https://openalex.org/W2343452498","doi":"https://doi.org/10.1109/tpds.2015.2513053","mag":"2343452498"},"language":"en","primary_location":{"id":"doi:10.1109/tpds.2015.2513053","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tpds.2015.2513053","pdf_url":null,"source":{"id":"https://openalex.org/S97130795","display_name":"IEEE Transactions on Parallel and Distributed Systems","issn_l":"1045-9219","issn":["1045-9219","1558-2183","2161-9883"],"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 Transactions on Parallel and Distributed Systems","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/A5000347228","display_name":"C NELSON","orcid":null},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chad Nelson","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Iowa State University, Ames, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032062942","display_name":"Kevin R. Townsend","orcid":null},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin R. Townsend","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Iowa State University, Ames, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078669544","display_name":"Osama G. Attia","orcid":"https://orcid.org/0000-0002-7663-5534"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Osama G. Attia","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Iowa State University, Ames, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026774201","display_name":"Phillip H. Jones","orcid":"https://orcid.org/0000-0002-8220-7552"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Phillip H. Jones","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Iowa State University, Ames, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081541206","display_name":"Joseph Zambreno","orcid":"https://orcid.org/0000-0002-0566-5744"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph Zambreno","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Iowa State University, Ames, IA"],"raw_orcid":"https://orcid.org/0000-0002-0566-5744","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1506,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.58668152,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"27","issue":"10","first_page":"3029","last_page":"3043"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9994000196456909,"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":0.9937999844551086,"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":0.8321726322174072},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.7667334675788879},{"id":"https://openalex.org/keywords/memory-footprint","display_name":"Memory footprint","score":0.6314975619316101},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5962556600570679},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.5771849155426025},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5226597189903259},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.49907898902893066},{"id":"https://openalex.org/keywords/footprint","display_name":"Footprint","score":0.4933537542819977},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.45039480924606323},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.44240593910217285},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4208543300628662},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.16702553629875183},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1419047713279724},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.13562077283859253},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1173868179321289},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08155113458633423},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07759198546409607}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8321726322174072},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.7667334675788879},{"id":"https://openalex.org/C74912251","wikidata":"https://www.wikidata.org/wiki/Q6815727","display_name":"Memory footprint","level":2,"score":0.6314975619316101},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5962556600570679},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.5771849155426025},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5226597189903259},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49907898902893066},{"id":"https://openalex.org/C132943942","wikidata":"https://www.wikidata.org/wiki/Q2562511","display_name":"Footprint","level":2,"score":0.4933537542819977},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.45039480924606323},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.44240593910217285},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4208543300628662},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.16702553629875183},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1419047713279724},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13562077283859253},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1173868179321289},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08155113458633423},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07759198546409607},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tpds.2015.2513053","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tpds.2015.2513053","pdf_url":null,"source":{"id":"https://openalex.org/S97130795","display_name":"IEEE Transactions on Parallel and Distributed Systems","issn_l":"1045-9219","issn":["1045-9219","1558-2183","2161-9883"],"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 Transactions on Parallel and Distributed Systems","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4300000071525574,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G6473885579","display_name":null,"funder_award_id":"CNS-1116810","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6973344255","display_name":null,"funder_award_id":"CCF-1149539","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":37,"referenced_works":["https://openalex.org/W62638829","https://openalex.org/W1535755777","https://openalex.org/W1979726029","https://openalex.org/W2011175593","https://openalex.org/W2025516544","https://openalex.org/W2031445984","https://openalex.org/W2034798008","https://openalex.org/W2037113830","https://openalex.org/W2044899448","https://openalex.org/W2054882590","https://openalex.org/W2055043387","https://openalex.org/W2060790568","https://openalex.org/W2074282129","https://openalex.org/W2087064593","https://openalex.org/W2097341408","https://openalex.org/W2103441770","https://openalex.org/W2107745473","https://openalex.org/W2112113834","https://openalex.org/W2117683095","https://openalex.org/W2121853166","https://openalex.org/W2124985265","https://openalex.org/W2148294372","https://openalex.org/W2156976066","https://openalex.org/W2158322625","https://openalex.org/W2161488606","https://openalex.org/W2171977947","https://openalex.org/W2318397367","https://openalex.org/W2319458729","https://openalex.org/W2554162996","https://openalex.org/W3151256199","https://openalex.org/W3203992401","https://openalex.org/W4236236547","https://openalex.org/W6656594533","https://openalex.org/W6683504902","https://openalex.org/W6700229322","https://openalex.org/W6700321065","https://openalex.org/W6730253985"],"related_works":["https://openalex.org/W2120447654","https://openalex.org/W2977179488","https://openalex.org/W2144453115","https://openalex.org/W2128223750","https://openalex.org/W4238532390","https://openalex.org/W2188872161","https://openalex.org/W3137434606","https://openalex.org/W4372263373","https://openalex.org/W2105035271","https://openalex.org/W2107233609"],"abstract_inverted_index":{"The":[0],"alignment":[1],"of":[2,6,31,33,62,89,91,138],"many":[3],"short":[4,86],"sequences":[5],"DNA,":[7],"called":[8],"reads,":[9,34],"to":[10,27,57,120,148],"a":[11,16,44,59,66,82,105,132],"long":[12],"reference":[13,122,128,141],"genome":[14,80,130],"is":[15,25],"common":[17],"task":[18],"in":[19,131],"molecular":[20],"biology.":[21],"When":[22],"the":[23,63,78,127,136,149],"problem":[24],"expanded":[26],"handle":[28],"typical":[29],"workloads":[30],"billions":[32],"execution":[35],"time":[36],"becomes":[37],"critical.":[38],"In":[39],"this":[40],"paper":[41],"we":[42],"present":[43],"novel":[45],"reconfigurable":[46],"architecture":[47],"for":[48],"minimal":[49],"perfect":[50],"sequencing":[51],"(RAMPS).":[52],"While":[53],"existing":[54],"solutions":[55],"attempt":[56],"align":[58],"high":[60],"percentage":[61],"reads":[64,87],"using":[65,139],"small":[67],"memory":[68],"footprint,":[69],"RAMPS":[70,84,124],"focuses":[71],"on":[72],"performing":[73],"fast":[74],"exact":[75],"matching.":[76],"Using":[77],"human":[79,129],"as":[81,99,113],"reference,":[83],"aligns":[85],"hundreds":[88],"thousands":[90],"times":[92,107],"faster":[93,108],"than":[94,109],"current":[95],"software":[96],"implementations":[97,111],"such":[98,112],"SOAP2":[100],"or":[101],"Bowtie,":[102],"and":[103],"about":[104],"thousand":[106],"GPU":[110],"SOAP3.":[114],"Whereas":[115],"other":[116],"aligners":[117],"require":[118],"hours":[119],"preprocess":[121,126],"genomes,":[123],"can":[125],"few":[133],"minutes,":[134],"opening":[135],"possibility":[137],"new":[140],"sources":[142],"that":[143],"are":[144],"more":[145],"genetically":[146],"similar":[147],"newly":[150],"sequenced":[151],"data.":[152]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
