{"id":"https://openalex.org/W4409261246","doi":"https://doi.org/10.1109/jssc.2025.3554616","title":"A 28-nm 239-bp/\u03bcJ Agile Pangenome Analysis Accelerator for Multi-Scheme Read Mapping","display_name":"A 28-nm 239-bp/\u03bcJ Agile Pangenome Analysis Accelerator for Multi-Scheme Read Mapping","publication_year":2025,"publication_date":"2025-04-08","ids":{"openalex":"https://openalex.org/W4409261246","doi":"https://doi.org/10.1109/jssc.2025.3554616"},"language":"en","primary_location":{"id":"doi:10.1109/jssc.2025.3554616","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jssc.2025.3554616","pdf_url":null,"source":{"id":"https://openalex.org/S83637746","display_name":"IEEE Journal of Solid-State Circuits","issn_l":"0018-9200","issn":["0018-9200","1558-173X"],"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 Journal of Solid-State Circuits","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/A5101810165","display_name":"Yichi Zhang","orcid":"https://orcid.org/0000-0002-3867-4698"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yichi Zhang","raw_affiliation_strings":["School of Integrated Circuits, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-3867-4698","affiliations":[{"raw_affiliation_string":"School of Integrated Circuits, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102891205","display_name":"Jianfeng Zhu","orcid":"https://orcid.org/0000-0002-0485-8034"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianfeng Zhu","raw_affiliation_strings":["School of Integrated Circuits, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-0485-8034","affiliations":[{"raw_affiliation_string":"School of Integrated Circuits, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077772195","display_name":"Liangwei Li","orcid":"https://orcid.org/0000-0002-9315-4353"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liangwei Li","raw_affiliation_strings":["School of Integrated Circuits, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Integrated Circuits, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001388330","display_name":"Gang Zeng","orcid":null},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gang Zeng","raw_affiliation_strings":["School of Integrated Circuits, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Integrated Circuits, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001177550","display_name":"Dibei Chen","orcid":"https://orcid.org/0000-0002-5507-5056"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dibei Chen","raw_affiliation_strings":["School of Integrated Circuits, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Integrated Circuits, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101107964","display_name":"Tairan Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tairan Zhang","raw_affiliation_strings":["School of Integrated Circuits, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Integrated Circuits, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026251774","display_name":"Yuhang Deng","orcid":"https://orcid.org/0000-0002-2937-0609"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yeyang Deng","raw_affiliation_strings":["School of Integrated Circuits, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Integrated Circuits, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028813107","display_name":"Zhicheng Gong","orcid":"https://orcid.org/0000-0002-2404-0942"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhicheng Gong","raw_affiliation_strings":["School of Integrated Circuits, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Integrated Circuits, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083014834","display_name":"Aoyang Zhang","orcid":"https://orcid.org/0000-0002-2128-5274"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Aoyang Zhang","raw_affiliation_strings":["School of Integrated Circuits, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-2128-5274","affiliations":[{"raw_affiliation_string":"School of Integrated Circuits, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100356161","display_name":"Yang Liu","orcid":"https://orcid.org/0000-0003-3800-3533"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Liu","raw_affiliation_strings":["School of Integrated Circuits, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Integrated Circuits, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036023084","display_name":"Shaojun Wei","orcid":"https://orcid.org/0000-0001-5117-7920"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaojun Wei","raw_affiliation_strings":["School of Integrated Circuits, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0001-5117-7920","affiliations":[{"raw_affiliation_string":"School of Integrated Circuits, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100358856","display_name":"Leibo Liu","orcid":"https://orcid.org/0000-0001-7548-4116"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Leibo Liu","raw_affiliation_strings":["School of Integrated Circuits, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0001-7548-4116","affiliations":[{"raw_affiliation_string":"School of Integrated Circuits, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I99065089"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.05444758,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"60","issue":"10","first_page":"3779","last_page":"3789"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9797000288963318,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9797000288963318,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9265999794006348,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.9120000004768372,"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/scheme","display_name":"Scheme (mathematics)","score":0.577409029006958},{"id":"https://openalex.org/keywords/agile-software-development","display_name":"Agile software development","score":0.5376428961753845},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48133644461631775},{"id":"https://openalex.org/keywords/nuclear-engineering","display_name":"Nuclear engineering","score":0.33022794127464294},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.23133432865142822},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21520301699638367},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.17925843596458435},{"id":"https://openalex.org/keywords/mathematical-analysis","display_name":"Mathematical analysis","score":0.07343491911888123}],"concepts":[{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.577409029006958},{"id":"https://openalex.org/C14185376","wikidata":"https://www.wikidata.org/wiki/Q30232","display_name":"Agile software development","level":2,"score":0.5376428961753845},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48133644461631775},{"id":"https://openalex.org/C116915560","wikidata":"https://www.wikidata.org/wiki/Q83504","display_name":"Nuclear engineering","level":1,"score":0.33022794127464294},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.23133432865142822},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21520301699638367},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.17925843596458435},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.07343491911888123}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/jssc.2025.3554616","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jssc.2025.3554616","pdf_url":null,"source":{"id":"https://openalex.org/S83637746","display_name":"IEEE Journal of Solid-State Circuits","issn_l":"0018-9200","issn":["0018-9200","1558-173X"],"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 Journal of Solid-State Circuits","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Climate action","score":0.47999998927116394,"id":"https://metadata.un.org/sdg/13"}],"awards":[{"id":"https://openalex.org/G254238106","display_name":null,"funder_award_id":"31513010104","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5221310371","display_name":null,"funder_award_id":"62204139","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8750436974","display_name":null,"funder_award_id":"U22B2024","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W2087064593","https://openalex.org/W2100751585","https://openalex.org/W2118526609","https://openalex.org/W2132341951","https://openalex.org/W2142113273","https://openalex.org/W2144560237","https://openalex.org/W2159647614","https://openalex.org/W2172230191","https://openalex.org/W2513408092","https://openalex.org/W2789843538","https://openalex.org/W2888300707","https://openalex.org/W2929354011","https://openalex.org/W2951331911","https://openalex.org/W2971559821","https://openalex.org/W3005228641","https://openalex.org/W3015825547","https://openalex.org/W3087961332","https://openalex.org/W3088400220","https://openalex.org/W3092652421","https://openalex.org/W3097807831","https://openalex.org/W3137352713","https://openalex.org/W3213101281","https://openalex.org/W4200597270","https://openalex.org/W4254502766","https://openalex.org/W4281647104","https://openalex.org/W4283210431","https://openalex.org/W4292240213","https://openalex.org/W4360605848","https://openalex.org/W4365513261","https://openalex.org/W4376133202","https://openalex.org/W4379054112","https://openalex.org/W4388469945","https://openalex.org/W4393406995","https://openalex.org/W4395106450"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2656997359","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890"],"abstract_inverted_index":{"Recent":[0],"advancements":[1],"in":[2,14,102],"deoxyribonucleic":[3],"acid":[4],"(DNA)":[5],"sequencing":[6],"have":[7],"brought":[8],"about":[9],"a":[10,75,90],"significant":[11],"paradigm":[12],"shift":[13],"genome":[15],"analysis,":[16],"moving":[17],"from":[18],"linear":[19],"approaches":[20],"to":[21,30,45,47,85,117,120,139,148],"pangenome":[22,61,103],"graphs.":[23],"Pangenome":[24],"analysis":[25],"demands":[26],"powerful":[27],"computation":[28],"capabilities":[29],"handle":[31],"graph":[32,77],"data":[33,51],"structures,":[34],"which":[35],"are":[36],"irregular":[37],"and":[38,50,95,110,136,143],"complex,":[39],"as":[40,42],"well":[41],"the":[43,56],"flexibility":[44],"adapt":[46,119],"various":[48],"algorithms":[49],"types.":[52],"This":[53],"article":[54],"presents":[55],"first":[57],"silicon":[58,152],"accelerator":[59,73],"for":[60],"read":[62,104],"mapping.":[63,105],"The":[64],"5.9-mm<sup":[65],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[66],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">2</sup>":[67],"822-mW":[68],"application-specific":[69],"integrated":[70],"circuit":[71],"(ASIC)":[72],"includes":[74],"dedicated":[76],"mapping":[78,122,135,151],"engine":[79],"(GME)":[80],"that":[81],"leverages":[82],"domain-specific":[83],"characteristics":[84],"parallelize":[86],"computations.":[87],"It":[88,128],"achieves":[89],"throughput":[91],"of":[92,99],"151.8":[93],"Mbp/s":[94],"an":[96,156],"energy":[97,145],"efficiency":[98,142,146],"239":[100],"bp/\u03bcJ":[101],"Moreover,":[106],"its":[107],"dynamic":[108],"reconfigurability":[109],"pipeline":[111],"bubble":[112],"hiding":[113],"technique":[114],"allow":[115],"it":[116],"efficiently":[118],"multiple":[121],"schemes":[123],"with":[124,132,159],"improved":[125],"hardware":[126],"utilization.":[127],"is":[129],"backward":[130],"compatible":[131],"conventional":[133],"short-read":[134,150],"offers":[137],"up":[138],"2.24\u00d7":[140],"area":[141],"3.65\u00d7":[144],"compared":[147],"state-of-the-art":[149],"accelerators":[153],"while":[154],"maintaining":[155],"accuracy":[157],"comparable":[158],"standard":[160],"software":[161],"packages.":[162]},"counts_by_year":[],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}
