{"id":"https://openalex.org/W2981088532","doi":"https://doi.org/10.1109/tcbb.2019.2947059","title":"GenSeq+: A Scalable High-Performance Accelerator for Genome Sequencing","display_name":"GenSeq+: A Scalable High-Performance Accelerator for Genome Sequencing","publication_year":2019,"publication_date":"2019-10-14","ids":{"openalex":"https://openalex.org/W2981088532","doi":"https://doi.org/10.1109/tcbb.2019.2947059","mag":"2981088532","pmid":"https://pubmed.ncbi.nlm.nih.gov/31613776"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2947059","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2947059","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/A5011884768","display_name":"Chao Wang","orcid":"https://orcid.org/0000-0002-9403-5575"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chao Wang","raw_affiliation_strings":["University of Science and Technology of China, Hefei, Anhui, China"],"affiliations":[{"raw_affiliation_string":"University of Science and Technology of China, Hefei, Anhui, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072915437","display_name":"Lei Gong","orcid":"https://orcid.org/0000-0002-8391-5526"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lei Gong","raw_affiliation_strings":["Suzhou Institute for Advanced Study, University of Science and Technology of China, Suzhou, Jiangsu, China"],"affiliations":[{"raw_affiliation_string":"Suzhou Institute for Advanced Study, University of Science and Technology of China, Suzhou, Jiangsu, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110472160","display_name":"Shiming Lei","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shiming Lei","raw_affiliation_strings":["Suzhou Institute for Advanced Study, University of Science and Technology of China, Suzhou, Jiangsu, China"],"affiliations":[{"raw_affiliation_string":"Suzhou Institute for Advanced Study, University of Science and Technology of China, Suzhou, Jiangsu, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052893195","display_name":"Haijie Fang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Haijie Fang","raw_affiliation_strings":["Suzhou Institute for Advanced Study, University of Science and Technology of China, Suzhou, Jiangsu, China"],"affiliations":[{"raw_affiliation_string":"Suzhou Institute for Advanced Study, University of Science and Technology of China, Suzhou, Jiangsu, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100407758","display_name":"Xi Li","orcid":"https://orcid.org/0000-0003-3023-1662"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xi Li","raw_affiliation_strings":["University of Science and Technology of China, Hefei, Anhui, China"],"affiliations":[{"raw_affiliation_string":"University of Science and Technology of China, Hefei, Anhui, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100693070","display_name":"Aili Wang","orcid":"https://orcid.org/0000-0002-9118-230X"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Aili Wang","raw_affiliation_strings":["University of Science and Technology of China, Hefei, Anhui, China"],"affiliations":[{"raw_affiliation_string":"University of Science and Technology of China, Hefei, Anhui, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077322091","display_name":"Xuehai Zhou","orcid":"https://orcid.org/0000-0002-8360-3143"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuehai Zhou","raw_affiliation_strings":["University of Science and Technology of China, Hefei, Anhui, China"],"affiliations":[{"raw_affiliation_string":"University of Science and Technology of China, Hefei, Anhui, China","institution_ids":["https://openalex.org/I126520041"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5011884768"],"corresponding_institution_ids":["https://openalex.org/I126520041"],"apc_list":null,"apc_paid":null,"fwci":0.28,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.66342006,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"18","issue":"4","first_page":"1512","last_page":"1523"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9994999766349792,"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":0.9980999827384949,"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"}},{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9922999739646912,"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/scalability","display_name":"Scalability","score":0.8092772960662842},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8018335103988647},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.6763232946395874},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.663256049156189},{"id":"https://openalex.org/keywords/hardware-acceleration","display_name":"Hardware acceleration","score":0.59012770652771},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5284214615821838},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.524814248085022},{"id":"https://openalex.org/keywords/string-searching-algorithm","display_name":"String searching algorithm","score":0.49127286672592163},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4856323301792145},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.42682409286499023},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3546906113624573},{"id":"https://openalex.org/keywords/computer-engineering","display_name":"Computer engineering","score":0.32487910985946655},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.27302247285842896},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.23734867572784424},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1396302580833435},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11496198177337646}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.8092772960662842},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8018335103988647},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.6763232946395874},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.663256049156189},{"id":"https://openalex.org/C13164978","wikidata":"https://www.wikidata.org/wiki/Q600158","display_name":"Hardware acceleration","level":3,"score":0.59012770652771},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5284214615821838},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.524814248085022},{"id":"https://openalex.org/C7757238","wikidata":"https://www.wikidata.org/wiki/Q374040","display_name":"String searching algorithm","level":3,"score":0.49127286672592163},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4856323301792145},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.42682409286499023},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3546906113624573},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.32487910985946655},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.27302247285842896},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.23734867572784424},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1396302580833435},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11496198177337646},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2019.2947059","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2947059","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:31613776","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31613776","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":[{"id":"https://metadata.un.org/sdg/7","score":0.6700000166893005,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G354725111","display_name":null,"funder_award_id":"2017YFA0700900","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G4451411784","display_name":null,"funder_award_id":"2017497","funder_id":"https://openalex.org/F4320322847","funder_display_name":"Youth Innovation Promotion Association of the Chinese Academy of Sciences"},{"id":"https://openalex.org/G6823762549","display_name":null,"funder_award_id":"WK2150110003","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G7639841928","display_name":null,"funder_award_id":"BK20181193","funder_id":"https://openalex.org/F4320322769","funder_display_name":"Natural Science Foundation of Jiangsu Province"}],"funders":[{"id":"https://openalex.org/F4320322769","display_name":"Natural Science Foundation of Jiangsu Province","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322847","display_name":"Youth Innovation Promotion Association of the Chinese Academy of Sciences","ror":"https://ror.org/031141b54"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1503562643","https://openalex.org/W1543636183","https://openalex.org/W1556957983","https://openalex.org/W1965849649","https://openalex.org/W1978815495","https://openalex.org/W1981804598","https://openalex.org/W1982420044","https://openalex.org/W1985108724","https://openalex.org/W2011502349","https://openalex.org/W2011652244","https://openalex.org/W2023843553","https://openalex.org/W2060465989","https://openalex.org/W2074373096","https://openalex.org/W2082346787","https://openalex.org/W2084594458","https://openalex.org/W2103441770","https://openalex.org/W2105011467","https://openalex.org/W2106062486","https://openalex.org/W2107275725","https://openalex.org/W2114296561","https://openalex.org/W2115775347","https://openalex.org/W2127380362","https://openalex.org/W2132549764","https://openalex.org/W2146496959","https://openalex.org/W2147228424","https://openalex.org/W2154826966","https://openalex.org/W2166621589","https://openalex.org/W2168196511","https://openalex.org/W2168707717","https://openalex.org/W2295862081","https://openalex.org/W2368900259","https://openalex.org/W2556885733","https://openalex.org/W2963482904","https://openalex.org/W4206262605","https://openalex.org/W4241632897","https://openalex.org/W4250981202","https://openalex.org/W4285719527","https://openalex.org/W6697732928","https://openalex.org/W6730224002"],"related_works":["https://openalex.org/W4390643767","https://openalex.org/W2150210843","https://openalex.org/W2532502681","https://openalex.org/W2518118925","https://openalex.org/W3159273459","https://openalex.org/W4319952061","https://openalex.org/W4280636456","https://openalex.org/W4388913998","https://openalex.org/W4310584535","https://openalex.org/W4295935044"],"abstract_inverted_index":{"Genome":[0],"sequencing":[1,55],"is":[2,63,128,149],"one":[3],"of":[4,27,31,34,46,53,92,109,130,155],"the":[5,18,25,28,51,57,89,95,153,156,166,173],"most":[6],"challenging":[7],"problems":[8],"in":[9,81,94],"computational":[10,85],"biology":[11],"and":[12,56,69,84,102,194],"bioinformatics.":[13],"As":[14,65],"a":[15,22,43,60,66,106,117,136,161,187],"traditional":[16],"algorithm,":[17,74],"string":[19],"match":[20],"meets":[21],"challenge":[23],"with":[24,88,142,190],"development":[26],"massive":[29],"volume":[30],"data":[32,93],"because":[33],"gene":[35,54],"sequencing.":[36],"Surveys":[37],"show":[38,179],"that":[39,180],"there":[40],"will":[41],"be":[42],"huge":[44],"amount":[45,91],"short":[47],"read":[48],"segments":[49],"during":[50],"process":[52],"need":[58],"for":[59,139,165],"highly":[61],"efficient":[62],"urgent.":[64],"classic":[67],"fast":[68],"exact":[70],"single":[71],"pattern":[72],"matching":[73],"Knuth-Morris-Pratt":[75],"(KMP)":[76],"algorithm":[77,164],"has":[78],"been":[79],"demonstrated":[80],"network":[82],"security":[83],"biology.":[86],"However,":[87],"increasing":[90],"modern":[96],"society,":[97],"it":[98],"becomes":[99],"increasingly":[100],"important":[101],"essential":[103],"to":[104,134,151,186],"provide":[105,160],"High-performance":[107],"implementation":[108],"KMP":[110,119],"algorithm.":[111],"In":[112],"this":[113],"article,":[114],"we":[115],"implement":[116],"scalable":[118],"accelerator":[120,127,182],"based":[121],"on":[122,172],"FPGA,":[123],"named":[124],"GeneKMP.":[125],"The":[126],"composed":[129],"different":[131],"computing":[132],"units":[133],"achieve":[135,184],"pipelined":[137],"organization":[138],"higher":[140],"throughput":[141],"satisfying":[143],"scalability.":[144],"A":[145],"novel":[146],"programming":[147],"model":[148],"provided":[150],"alleviate":[152],"burden":[154],"high-level":[157],"programmers.":[158],"We":[159],"greedy-based":[162],"partitioning":[163],"software/hardware":[167],"design":[168],"paradigms.":[169],"Experimental":[170],"results":[171],"state-of-the-art":[174],"Xilinx":[175],"FPGA":[176],"hardware":[177,192],"prototype":[178],"our":[181],"can":[183],"up":[185],"promising":[188],"speedup":[189],"insignificant":[191],"cost":[193],"power":[195],"consumption.":[196]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
