{"id":"https://openalex.org/W4377245027","doi":"https://doi.org/10.1145/3595297","title":"An FPGA Accelerator for Genome Variant Calling","display_name":"An FPGA Accelerator for Genome Variant Calling","publication_year":2023,"publication_date":"2023-05-22","ids":{"openalex":"https://openalex.org/W4377245027","doi":"https://doi.org/10.1145/3595297"},"language":"en","primary_location":{"id":"doi:10.1145/3595297","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3595297","pdf_url":null,"source":{"id":"https://openalex.org/S112809824","display_name":"ACM Transactions on Reconfigurable Technology and Systems","issn_l":"1936-7406","issn":["1936-7406","1936-7414"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Reconfigurable Technology and 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/A5000224913","display_name":"Tiancheng Xu","orcid":"https://orcid.org/0000-0001-8817-7094"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tiancheng Xu","raw_affiliation_strings":["Rice University, USA"],"raw_orcid":"https://orcid.org/0000-0001-8817-7094","affiliations":[{"raw_affiliation_string":"Rice University, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011664674","display_name":"Scott Rixner","orcid":"https://orcid.org/0009-0005-5204-742X"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott Rixner","raw_affiliation_strings":["Rice University, USA"],"raw_orcid":"https://orcid.org/0009-0005-5204-742X","affiliations":[{"raw_affiliation_string":"Rice University, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034020280","display_name":"Alan L. Cox","orcid":"https://orcid.org/0009-0005-4904-9600"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alan L. Cox","raw_affiliation_strings":["Rice University, USA"],"raw_orcid":"https://orcid.org/0009-0005-4904-9600","affiliations":[{"raw_affiliation_string":"Rice University, USA","institution_ids":["https://openalex.org/I74775410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5000224913"],"corresponding_institution_ids":["https://openalex.org/I74775410"],"apc_list":null,"apc_paid":null,"fwci":1.5465,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.86007098,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"16","issue":"4","first_page":"1","last_page":"29"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10494","display_name":"Plant Virus Research Studies","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10494","display_name":"Plant Virus Research Studies","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9954000115394592,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9894999861717224,"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":0.8284280300140381},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6303489804267883},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.608854353427887},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5500685572624207},{"id":"https://openalex.org/keywords/hardware-acceleration","display_name":"Hardware acceleration","score":0.45178186893463135},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.19200527667999268},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11279061436653137},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09971863031387329},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09812429547309875},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08417266607284546}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8284280300140381},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6303489804267883},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.608854353427887},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5500685572624207},{"id":"https://openalex.org/C13164978","wikidata":"https://www.wikidata.org/wiki/Q600158","display_name":"Hardware acceleration","level":3,"score":0.45178186893463135},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.19200527667999268},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11279061436653137},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09971863031387329},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09812429547309875},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08417266607284546}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3595297","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3595297","pdf_url":null,"source":{"id":"https://openalex.org/S112809824","display_name":"ACM Transactions on Reconfigurable Technology and Systems","issn_l":"1936-7406","issn":["1936-7406","1936-7414"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Reconfigurable Technology and Systems","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"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":31,"referenced_works":["https://openalex.org/W1573552135","https://openalex.org/W1964807436","https://openalex.org/W2119180969","https://openalex.org/W2146496959","https://openalex.org/W2330100020","https://openalex.org/W2515042543","https://openalex.org/W2762861845","https://openalex.org/W2770095154","https://openalex.org/W2792407191","https://openalex.org/W2883847355","https://openalex.org/W2889448554","https://openalex.org/W2928905502","https://openalex.org/W2950629094","https://openalex.org/W2952946229","https://openalex.org/W2971157487","https://openalex.org/W3004059350","https://openalex.org/W3035066704","https://openalex.org/W3044547892","https://openalex.org/W3099458570","https://openalex.org/W3111187134","https://openalex.org/W3130281579","https://openalex.org/W3133845106","https://openalex.org/W3163764838","https://openalex.org/W3177399774","https://openalex.org/W3189987728","https://openalex.org/W3198434009","https://openalex.org/W4241365061","https://openalex.org/W4252658811","https://openalex.org/W4254502766","https://openalex.org/W4360806537","https://openalex.org/W6841465588"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2111241003","https://openalex.org/W2390279801","https://openalex.org/W4200391368","https://openalex.org/W2358668433","https://openalex.org/W2210979487","https://openalex.org/W2376932109","https://openalex.org/W2074043759","https://openalex.org/W2518118925","https://openalex.org/W3159273459"],"abstract_inverted_index":{"In":[0,59],"genome":[1,75],"analysis,":[2,67,76],"it":[3,26],"is":[4,27,35,41,63,69],"often":[5],"important":[6],"to":[7,30,73,83,98,111],"identify":[8],"variants":[9,16],"from":[10],"a":[11,36,50],"reference":[12],"genome.":[13],"However,":[14],"identifying":[15,44],"that":[17,40],"occur":[18],"with":[19],"low":[20],"frequency":[21],"can":[22,95],"be":[23,84],"challenging,":[24,71],"as":[25,77],"computationally":[28],"intensive":[29],"do":[31],"so":[32],"accurately.":[33],"LoFreq":[34,106],"widely":[37],"used":[38],"program":[39],"adept":[42],"at":[43,65],"low-frequency":[45],"variants.":[46],"This":[47],"article":[48],"presents":[49],"design":[51,91],"framework":[52],"for":[53,57],"an":[54],"FPGA-based":[55],"accelerator":[56,62,94],"LoFreq.":[58],"particular,":[60],"this":[61,93],"targeted":[64],"virus":[66],"which":[68],"particularly":[70],"compared":[72],"human":[74],"the":[78,81,90,102,114],"characteristics":[79],"of":[80,105,109],"data":[82],"analyzed":[85],"are":[86],"fundamentally":[87],"different.":[88],"Across":[89],"space,":[92],"achieve":[96],"up":[97,110],"120\u00d7":[99],"speedups":[100,108],"on":[101],"core":[103],"computation":[104],"and":[107],"51.7\u00d7":[112],"across":[113],"entire":[115],"program.":[116]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
