{"id":"https://openalex.org/W3205889289","doi":"https://doi.org/10.1145/3466752.3480117","title":"SquiggleFilter: An Accelerator for Portable Virus Detection","display_name":"SquiggleFilter: An Accelerator for Portable Virus Detection","publication_year":2021,"publication_date":"2021-10-17","ids":{"openalex":"https://openalex.org/W3205889289","doi":"https://doi.org/10.1145/3466752.3480117","mag":"3205889289"},"language":"en","primary_location":{"id":"doi:10.1145/3466752.3480117","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3466752.3480117","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3466752.3480117","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"MICRO-54: 54th Annual IEEE/ACM International Symposium on Microarchitecture","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3466752.3480117","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032742203","display_name":"Tim Dunn","orcid":"https://orcid.org/0000-0003-3429-4329"},"institutions":[{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tim Dunn","raw_affiliation_strings":["University of Michigan, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067923579","display_name":"Harisankar Sadasivan","orcid":"https://orcid.org/0000-0002-2832-458X"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Harisankar Sadasivan","raw_affiliation_strings":["University of Michigan"],"affiliations":[{"raw_affiliation_string":"University of Michigan","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090783302","display_name":"Jack Wadden","orcid":"https://orcid.org/0000-0002-3055-3656"},"institutions":[{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jack Wadden","raw_affiliation_strings":["University of Michigan, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003185757","display_name":"Kush Goliya","orcid":null},"institutions":[{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kush Goliya","raw_affiliation_strings":["University of Michigan, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100714448","display_name":"Kuan-Yu Chen","orcid":"https://orcid.org/0000-0002-4168-6446"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kuan-Yu Chen","raw_affiliation_strings":["University of Michigan"],"affiliations":[{"raw_affiliation_string":"University of Michigan","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026311377","display_name":"David Blaauw","orcid":"https://orcid.org/0000-0001-6744-7075"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Blaauw","raw_affiliation_strings":["University of Michigan"],"affiliations":[{"raw_affiliation_string":"University of Michigan","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027544576","display_name":"Reetuparna Das","orcid":"https://orcid.org/0000-0002-5894-8342"},"institutions":[{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Reetuparna Das","raw_affiliation_strings":["University of Michigan, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075649670","display_name":"Satish Narayanasamy","orcid":"https://orcid.org/0000-0001-5016-1214"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Satish Narayanasamy","raw_affiliation_strings":["University of Michigan, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5032742203"],"corresponding_institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"],"apc_list":null,"apc_paid":null,"fwci":6.8832,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.97410479,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":null,"issue":null,"first_page":"535","last_page":"549"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9947999715805054,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/minion","display_name":"Minion","score":0.985493004322052},{"id":"https://openalex.org/keywords/software-portability","display_name":"Software portability","score":0.882148027420044},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.72132408618927},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.6724323034286499},{"id":"https://openalex.org/keywords/dna-sequencer","display_name":"DNA sequencer","score":0.5989881753921509},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.5761262774467468},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.3814704418182373},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3468916714191437},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2870680093765259},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.27778494358062744},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16793489456176758},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12134340405464172}],"concepts":[{"id":"https://openalex.org/C2779927696","wikidata":"https://www.wikidata.org/wiki/Q6865654","display_name":"Minion","level":5,"score":0.985493004322052},{"id":"https://openalex.org/C63000827","wikidata":"https://www.wikidata.org/wiki/Q3080428","display_name":"Software portability","level":2,"score":0.882148027420044},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.72132408618927},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.6724323034286499},{"id":"https://openalex.org/C70712619","wikidata":"https://www.wikidata.org/wiki/Q908889","display_name":"DNA sequencer","level":4,"score":0.5989881753921509},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.5761262774467468},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3814704418182373},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3468916714191437},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2870680093765259},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.27778494358062744},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16793489456176758},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12134340405464172},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3466752.3480117","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3466752.3480117","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3466752.3480117","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"MICRO-54: 54th Annual IEEE/ACM International Symposium on Microarchitecture","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3466752.3480117","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3466752.3480117","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3466752.3480117","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"MICRO-54: 54th Annual IEEE/ACM International Symposium on Microarchitecture","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G334983740","display_name":null,"funder_award_id":"2030454","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3205889289.pdf","grobid_xml":"https://content.openalex.org/works/W3205889289.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1853995153","https://openalex.org/W2145903120","https://openalex.org/W2150936443","https://openalex.org/W2161831889","https://openalex.org/W2582252439","https://openalex.org/W2605343262","https://openalex.org/W2789843538","https://openalex.org/W2795964999","https://openalex.org/W2883847355","https://openalex.org/W2891691532","https://openalex.org/W2898984509","https://openalex.org/W2923669172","https://openalex.org/W2928905502","https://openalex.org/W2952045272","https://openalex.org/W2966084642","https://openalex.org/W2979449748","https://openalex.org/W3041821205","https://openalex.org/W3042538963","https://openalex.org/W3083653247","https://openalex.org/W3086574032","https://openalex.org/W4251439545","https://openalex.org/W4254502766"],"related_works":["https://openalex.org/W2602845639","https://openalex.org/W2887783619","https://openalex.org/W2900530048","https://openalex.org/W4320503067","https://openalex.org/W4367176272","https://openalex.org/W3210632422","https://openalex.org/W2794729690","https://openalex.org/W3088570659","https://openalex.org/W2949940039","https://openalex.org/W2789689831"],"abstract_inverted_index":{"The":[0],"MinION":[1],"is":[2],"a":[3,18,22,34,50],"recent-to-market":[4],"handheld":[5],"nanopore":[6],"sequencer.":[7],"It":[8],"can":[9],"be":[10],"used":[11],"to":[12,31],"determine":[13],"the":[14],"whole":[15],"genome":[16],"of":[17,36,46],"target":[19],"virus":[20],"in":[21,49],"biological":[23],"sample.":[24,52],"Its":[25],"Read":[26],"Until":[27],"feature":[28],"allows":[29],"us":[30],"skip":[32],"sequencing":[33],"majority":[35],"non-target":[37],"reads":[38,48],"(DNA/RNA":[39],"fragments),":[40],"which":[41,61],"constitutes":[42],"more":[43],"than":[44],"99%":[45],"all":[47],"typical":[51],"However,":[53],"it":[54],"does":[55],"not":[56],"have":[57],"any":[58],"on-board":[59],"computing,":[60],"significantly":[62],"limits":[63],"its":[64],"portability.":[65]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":7}],"updated_date":"2026-03-06T13:50:29.536080","created_date":"2025-10-10T00:00:00"}
