{"id":"https://openalex.org/W4214923637","doi":"https://doi.org/10.1109/tetc.2022.3153613","title":"CRAM-Seq: Accelerating RNA-Seq Abundance Quantification Using Computational RAM","display_name":"CRAM-Seq: Accelerating RNA-Seq Abundance Quantification Using Computational RAM","publication_year":2022,"publication_date":"2022-03-01","ids":{"openalex":"https://openalex.org/W4214923637","doi":"https://doi.org/10.1109/tetc.2022.3153613"},"language":"en","primary_location":{"id":"doi:10.1109/tetc.2022.3153613","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tetc.2022.3153613","pdf_url":null,"source":{"id":"https://openalex.org/S2496326734","display_name":"IEEE Transactions on Emerging Topics in Computing","issn_l":"2168-6750","issn":["2168-6750","2376-4562"],"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 Emerging Topics in Computing","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/A5080806544","display_name":"Zamshed I. Chowdhury","orcid":"https://orcid.org/0000-0002-4096-7000"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zamshed I. Chowdhury","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA"],"raw_orcid":"https://orcid.org/0000-0002-4096-7000","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069877491","display_name":"S. Karen Khatamifard","orcid":"https://orcid.org/0000-0002-7574-8975"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Karen Khatamifard","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA"],"raw_orcid":"https://orcid.org/0000-0002-7574-8975","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089021376","display_name":"Salonik Resch","orcid":"https://orcid.org/0000-0002-9050-3685"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Salonik Resch","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA"],"raw_orcid":"https://orcid.org/0000-0002-9050-3685","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071436787","display_name":"H\u00fcsrev C\u0131lasun","orcid":"https://orcid.org/0000-0002-5421-1159"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Husrev Cilasun","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA"],"raw_orcid":"https://orcid.org/0000-0002-5421-1159","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081856566","display_name":"Zhengyang Zhao","orcid":"https://orcid.org/0000-0002-8017-3635"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhengyang Zhao","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA"],"raw_orcid":"https://orcid.org/0000-0002-8017-3635","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013347279","display_name":"Masoud Zabihi","orcid":"https://orcid.org/0000-0003-1916-901X"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Masoud Zabihi","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA"],"raw_orcid":"https://orcid.org/0000-0003-1916-901X","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041237539","display_name":"Meisam Razaviyayn","orcid":"https://orcid.org/0000-0003-4342-6661"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Meisam Razaviyayn","raw_affiliation_strings":["University of Southern California, Los Angeles, CA, USA"],"raw_orcid":"https://orcid.org/0000-0003-4342-6661","affiliations":[{"raw_affiliation_string":"University of Southern California, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062474441","display_name":"Jian\u2010Ping Wang","orcid":"https://orcid.org/0000-0003-2815-6624"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jian-Ping Wang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA"],"raw_orcid":"https://orcid.org/0000-0003-2815-6624","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068714995","display_name":"Sachin S. Sapatnekar","orcid":"https://orcid.org/0000-0002-5353-2364"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sachin S. Sapatnekar","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA"],"raw_orcid":"https://orcid.org/0000-0002-5353-2364","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018104631","display_name":"Ulya R. Karpuzcu","orcid":"https://orcid.org/0000-0001-9238-4256"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ulya R. Karpuzcu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA"],"raw_orcid":"https://orcid.org/0000-0001-9238-4256","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6929,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.65793008,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"10","issue":"4","first_page":"2055","last_page":"2071"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9890999794006348,"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":0.9868000149726868,"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":0.7575434446334839},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7331276535987854},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5358549356460571},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4781675934791565},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3250964879989624},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1067863404750824}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7575434446334839},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7331276535987854},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5358549356460571},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4781675934791565},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3250964879989624},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1067863404750824},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","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/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tetc.2022.3153613","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tetc.2022.3153613","pdf_url":null,"source":{"id":"https://openalex.org/S2496326734","display_name":"IEEE Transactions on Emerging Topics in Computing","issn_l":"2168-6750","issn":["2168-6750","2376-4562"],"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 Emerging Topics in Computing","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.9100000262260437}],"awards":[{"id":"https://openalex.org/G1193618548","display_name":null,"funder_award_id":"SPX-1725420","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"}],"funders":[{"id":"https://openalex.org/F4320335353","display_name":"National Science Foundation of Sri Lanka","ror":"https://ror.org/010xaa060"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1574447377","https://openalex.org/W2008792512","https://openalex.org/W2010202670","https://openalex.org/W2024122052","https://openalex.org/W2049633694","https://openalex.org/W2065128082","https://openalex.org/W2096465161","https://openalex.org/W2104846587","https://openalex.org/W2117683095","https://openalex.org/W2121873871","https://openalex.org/W2140729960","https://openalex.org/W2141458291","https://openalex.org/W2151671981","https://openalex.org/W2323326409","https://openalex.org/W2330100020","https://openalex.org/W2606268188","https://openalex.org/W2756167909","https://openalex.org/W2870561134","https://openalex.org/W2883676000","https://openalex.org/W2884190866","https://openalex.org/W2886462352","https://openalex.org/W2900776157","https://openalex.org/W2942415134","https://openalex.org/W2944735424","https://openalex.org/W2946017187","https://openalex.org/W2980249334","https://openalex.org/W3009680524","https://openalex.org/W3016287095","https://openalex.org/W3105003914","https://openalex.org/W4233376872","https://openalex.org/W4242222372","https://openalex.org/W6753687140"],"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/W2389214306"],"abstract_inverted_index":{"RNA":[0],"Sequence":[1],"(RNA-Seq)":[2],"abundance":[3,39,104,141],"quantification":[4,57,105,142],"is":[5,42],"an":[6,100,112],"important":[7],"application":[8,25,58],"in":[9,20,146],"different":[10],"fields":[11],"of":[12,30,33,55,90,117,120,148],"genomic":[13,92],"studies,":[14],"e.g.,":[15],"analysis":[16],"offunctionally":[17],"similar":[18],"genes":[19],"a":[21,79,136],"biological":[22],"sample.":[23],"This":[24],"depends":[26],"on":[27,107],"the":[28,91],"availability":[29],"high":[31,37,118],"volume":[32],"sequence":[34],"data":[35,52,69],"for":[36,102],"accuracy":[38],"estimation,":[40],"which":[41],"made":[43],"possible":[44],"by":[45],"next":[46],"generation":[47],"sequencing":[48],"platforms.":[49],"Large":[50],"scale":[51],"processing":[53,73,89,114,122],"requirements":[54],"this":[56,83,95],"push":[59],"conventional":[60],"computing":[61],"systems":[62],"to":[63,67,82],"their":[64],"limits":[65],"due":[66],"excessive":[68],"movement":[70],"required":[71],"between":[72],"and":[74,150],"memory":[75],"elements.":[76],"Processing-In-memory":[77],"presents":[78],"viable":[80],"solution":[81],"drawback,":[84],"through":[85],"<italic":[86],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[87],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">in-situ</i>":[88],"data.":[93],"In":[94],"paper,":[96],"we":[97,131],"present":[98],"CRAM-Seq,":[99],"accelerator":[101],"RNA-Seq":[103],"based":[106],"Computational":[108],"RAM":[109],"(CRAM)":[110],"\u2013":[111,145],"in-memory":[113],"substrate":[115],"capable":[116],"degree":[119],"parallel":[121],"with":[123],"very":[124],"low":[125],"energy":[126,151],"consumption.":[127],"Through":[128],"hardware/software":[129],"co-design,":[130],"demonstrate":[132],"that":[133],"CRAM-Seq":[134],"outperforms":[135],"commonly":[137],"used":[138],"state-of-the-art":[139],"software":[140],"algorithm,":[143],"Kallisto":[144],"terms":[147],"throughput":[149],"efficiency,":[152],"while":[153],"being":[154],"highly":[155],"scalable.":[156]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}