{"id":"https://openalex.org/W3203675953","doi":"https://doi.org/10.1109/tcbb.2021.3118018","title":"GeNVoM: Read Mapping Near Non-Volatile Memory","display_name":"GeNVoM: Read Mapping Near Non-Volatile Memory","publication_year":2021,"publication_date":"2021-10-06","ids":{"openalex":"https://openalex.org/W3203675953","doi":"https://doi.org/10.1109/tcbb.2021.3118018","mag":"3203675953","pmid":"https://pubmed.ncbi.nlm.nih.gov/34613917"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3118018","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3118018","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/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":true,"raw_author_name":"S. Karen Khatamifard","raw_affiliation_strings":["Department of Electrical Engineering, University of Minnesota, Minneapolis, MN, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","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 Chowdhury","raw_affiliation_strings":["Department of Electrical Engineering, University of Minnesota, Minneapolis, MN, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057468474","display_name":"Nakul Pande","orcid":"https://orcid.org/0000-0002-1753-0812"},"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":"Nakul Pande","raw_affiliation_strings":["Department of Electrical Engineering, University of Minnesota, Minneapolis, MN, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical 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":["Department of Industrial & Systems Engineering, University of Southern California, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Industrial & Systems Engineering, University of Southern California, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043025421","display_name":"Chris H. Kim","orcid":"https://orcid.org/0000-0002-4194-1347"},"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":"Chris Kim","raw_affiliation_strings":["Department of Electrical Engineering, University of Minnesota, Minneapolis, MN, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical 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 Engineering, University of Minnesota, Minneapolis, MN, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5069877491"],"corresponding_institution_ids":["https://openalex.org/I130238516"],"apc_list":null,"apc_paid":null,"fwci":1.0534,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.76362777,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"19","issue":"6","first_page":"3482","last_page":"3496"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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":0.9986000061035156,"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":0.9948999881744385,"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/T12326","display_name":"Network Packet Processing and Optimization","score":0.9930999875068665,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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":0.7307049632072449},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.4599560499191284},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4478333294391632},{"id":"https://openalex.org/keywords/energy-consumption","display_name":"Energy consumption","score":0.41387060284614563},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3341687321662903},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3309793174266815},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.266989141702652},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16452458500862122},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1255837082862854}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7307049632072449},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4599560499191284},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4478333294391632},{"id":"https://openalex.org/C2780165032","wikidata":"https://www.wikidata.org/wiki/Q16869822","display_name":"Energy consumption","level":2,"score":0.41387060284614563},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3341687321662903},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3309793174266815},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.266989141702652},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16452458500862122},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1255837082862854},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2021.3118018","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3118018","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34613917","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34613917","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.9100000262260437,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W148021875","https://openalex.org/W594283781","https://openalex.org/W1966711026","https://openalex.org/W1969349120","https://openalex.org/W1971584645","https://openalex.org/W2001725958","https://openalex.org/W2015831381","https://openalex.org/W2020704360","https://openalex.org/W2024975965","https://openalex.org/W2025583382","https://openalex.org/W2029195137","https://openalex.org/W2034798008","https://openalex.org/W2034861439","https://openalex.org/W2037748100","https://openalex.org/W2047822307","https://openalex.org/W2096143664","https://openalex.org/W2097341408","https://openalex.org/W2103441770","https://openalex.org/W2104846587","https://openalex.org/W2112113834","https://openalex.org/W2114094169","https://openalex.org/W2121716038","https://openalex.org/W2124985265","https://openalex.org/W2129504003","https://openalex.org/W2131417499","https://openalex.org/W2139760555","https://openalex.org/W2160515792","https://openalex.org/W2170551349","https://openalex.org/W2290939274","https://openalex.org/W2295828257","https://openalex.org/W2536491920","https://openalex.org/W2560228154","https://openalex.org/W2561721141","https://openalex.org/W2577617591","https://openalex.org/W2613567208","https://openalex.org/W2759742634","https://openalex.org/W2762749859","https://openalex.org/W2766890412","https://openalex.org/W2771835478","https://openalex.org/W2789784730","https://openalex.org/W2794757234","https://openalex.org/W2870561134","https://openalex.org/W2883847355","https://openalex.org/W2896262061","https://openalex.org/W2907390641","https://openalex.org/W2907707247","https://openalex.org/W2913747979","https://openalex.org/W2920013165","https://openalex.org/W2928905502","https://openalex.org/W2932607048","https://openalex.org/W2952956051","https://openalex.org/W3005304875","https://openalex.org/W3015825547","https://openalex.org/W3019010333","https://openalex.org/W3103269557","https://openalex.org/W4232675554","https://openalex.org/W4236302577","https://openalex.org/W4247053599","https://openalex.org/W4300601563","https://openalex.org/W6605926476","https://openalex.org/W6757249731"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2389214306","https://openalex.org/W2965083567","https://openalex.org/W4235240664","https://openalex.org/W1838576100","https://openalex.org/W2095886385","https://openalex.org/W2889616422","https://openalex.org/W2089704382","https://openalex.org/W1983399550","https://openalex.org/W4401278057"],"abstract_inverted_index":{"DNA":[0,20,28,52,58],"sequencing":[1,29],"is":[2,97],"the":[3,8,11,61,91,142,175,206,215,222,228,245],"physical/biochemical":[4],"process":[5],"of":[6,10,48,50,63,90,107,148,163,167,194,244],"identifying":[7],"location":[9],"four":[12],"bases":[13],"(Adenine,":[14],"Guanine,":[15],"Cytosine,":[16],"Thymine)":[17],"in":[18,54,76,103,179],"a":[19,40,87,98,104,113,187],"strand.":[21],"As":[22,39],"semiconductor":[23],"technology":[24,30],"revolutionized":[25,36],"computing,":[26],"modern":[27,42],"(termed":[31],"Next":[32],"Generation":[33],"Sequencing,":[34],"NGS)":[35],"genomic":[37,70,156],"research.":[38],"result,":[41],"NGS":[43,64,72,154],"platforms":[44],"can":[45,120,173,220],"sequence":[46],"hundreds":[47],"millions":[49],"short":[51],"fragments":[53],"parallel.":[55],"The":[56],"sequenced":[57],"fragments,":[59],"representing":[60],"output":[62],"platforms,":[65],"are":[66],"termed":[67],"reads.":[68,77],"Besides":[69],"variations,":[71],"imperfections":[73],"induce":[74],"noise":[75],"Mapping":[78,111],"each":[79],"read":[80,95],"to":[81,226,233,237],"(the":[82],"most":[83],"similar":[84],"portion":[85],"of)":[86],"reference":[88],"genome":[89],"same":[92],"species,":[93],"i.e.,":[94],"mapping,":[96],"common":[99],"critical":[100],"first":[101],"step":[102],"diverse":[105],"set":[106],"emerging":[108],"bioinformatics":[109],"applications.":[110],"represents":[112,242],"search-heavy":[114],"memory-intensive":[115],"similarity":[116,151],"matching":[117,152],"problem,":[118],"therefore,":[119],"greatly":[121],"benefit":[122],"from":[123,214],"near-memory":[124],"processing.":[125],"Intuition":[126],"suggests":[127],"using":[128],"fast":[129],"associative":[130],"search":[131],"enabled":[132],"by":[133,139,224,231],"Ternary":[134],"Content":[135],"Addressable":[136],"Memory":[137],"(TCAM)":[138],"construction.":[140],"However,":[141],"excessive":[143],"energy":[144,229],"consumption":[145],"and":[146,155,190,208],"lack":[147],"support":[149],"for":[150,199],"(under":[153],"variation":[157],"induced":[158],"noise)":[159],"renders":[160],"direct":[161],"application":[162],"TCAM":[164,172],"infeasible,":[165],"irrespective":[166],"volatility,":[168],"where":[169],"only":[170],"non-volatile":[171,209],"accommodate":[174],"large":[176],"memory":[177],"footprint":[178],"an":[180,196,238],"area-efficient":[181],"way.":[182],"This":[183],"paper":[184],"introduces":[185],"GeNVoM,":[186],"scalable,":[188],"energy-efficient":[189],"high-throughput":[191],"solution.":[192],"Instead":[193],"optimizing":[195],"algorithm":[197,207],"developed":[198],"general-purpose":[200],"computers":[201],"or":[202],"GPUs,":[203],"GeNVoM":[204,219],"rethinks":[205],"TCAM-based":[210],"accelerator":[211],"design":[212],"together":[213],"ground":[216],"up.":[217],"Thereby":[218],"improve":[221],"throughput":[223],"up":[225,232],"3.67\u00d7;":[227],"consumption,":[230],"1.36\u00d7,":[234],"when":[235],"compared":[236],"ASIC":[239],"baseline,":[240],"which":[241],"one":[243],"highest-throughput":[246],"implementations":[247],"known.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4}],"updated_date":"2026-03-06T13:50:29.536080","created_date":"2025-10-10T00:00:00"}