{"id":"https://openalex.org/W2792398545","doi":"https://doi.org/10.1093/bioinformatics/bty167","title":"Arioc: GPU-accelerated alignment of short bisulfite-treated reads","display_name":"Arioc: GPU-accelerated alignment of short bisulfite-treated reads","publication_year":2018,"publication_date":"2018-03-15","ids":{"openalex":"https://openalex.org/W2792398545","doi":"https://doi.org/10.1093/bioinformatics/bty167","mag":"2792398545"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty167","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty167","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2673/25230719/bty167.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2673/25230719/bty167.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055200839","display_name":"Richard Wilton","orcid":"https://orcid.org/0000-0003-1263-5532"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Richard Wilton","raw_affiliation_strings":["Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100353748","display_name":"Xin Li","orcid":"https://orcid.org/0000-0001-8328-4894"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Li","raw_affiliation_strings":["School of Medicine, Sun Yat-sen University, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"School of Medicine, Sun Yat-sen University, Guangdong, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074378026","display_name":"Andrew P. Feinberg","orcid":"https://orcid.org/0000-0002-8364-1991"},"institutions":[{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]},{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew P Feinberg","raw_affiliation_strings":["Department of Biomedical Engineering, Johns Hopkins Whitehead School of Engineering, Baltimore, MD, USA","Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA","Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Johns Hopkins Whitehead School of Engineering, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019891335","display_name":"Alexander S. Szalay","orcid":"https://orcid.org/0000-0002-4108-3282"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander S Szalay","raw_affiliation_strings":["Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA","Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5055200839"],"corresponding_institution_ids":["https://openalex.org/I145311948"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2869,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.79592827,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"34","issue":"15","first_page":"2673","last_page":"2675"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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/T11482","display_name":"RNA modifications and cancer","score":0.9901999831199646,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9751999974250793,"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/computer-science","display_name":"Computer science","score":0.8614864349365234},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.6935702562332153},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.62452232837677},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5844601988792419},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5810468196868896},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.5214073657989502},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.4604871869087219},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.41173672676086426},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.21596083045005798},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18276143074035645},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14638370275497437}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8614864349365234},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.6935702562332153},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.62452232837677},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5844601988792419},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5810468196868896},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.5214073657989502},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.4604871869087219},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.41173672676086426},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.21596083045005798},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18276143074035645},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14638370275497437},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty167","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty167","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2673/25230719/bty167.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6061805","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6061805","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty167","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty167","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2673/25230719/bty167.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.41999998688697815,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2792398545.pdf","grobid_xml":"https://content.openalex.org/works/W2792398545.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2015831381","https://openalex.org/W2040507896","https://openalex.org/W2068448872","https://openalex.org/W2070102345","https://openalex.org/W2083084802","https://openalex.org/W2087064593","https://openalex.org/W2103810926","https://openalex.org/W2112113834","https://openalex.org/W2115872073","https://openalex.org/W2122686130","https://openalex.org/W2131374955","https://openalex.org/W2170551349","https://openalex.org/W2520810509"],"related_works":["https://openalex.org/W2075046026","https://openalex.org/W2142485291","https://openalex.org/W2320652536","https://openalex.org/W4210849164","https://openalex.org/W2161462353","https://openalex.org/W84129006","https://openalex.org/W2319727539","https://openalex.org/W2009169896","https://openalex.org/W189420351","https://openalex.org/W67367039"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"The":[2,192],"alignment":[3],"of":[4,29,68,135,186],"bisulfite-treated":[5],"DNA":[6],"sequences":[7],"(BS-seq":[8],"reads)":[9],"to":[10,22,52,62,74,78,107,156],"a":[11,15,96,132,183,205],"large":[12],"genome":[13],"involves":[14],"significant":[16],"computational":[17,116],"burden":[18],"beyond":[19],"that":[20,39,76,99],"required":[21],"align":[23],"non-bisulfite-treated":[24],"reads.":[25],"In":[26],"the":[27,54,59,66,70,114,125,140,160],"analysis":[28],"BS-seq":[30,63,115,146,180],"data,":[31],"this":[32,92],"can":[33,40],"present":[34],"an":[35],"important":[36],"performance":[37],"bottleneck":[38],"be":[41,87],"mitigated":[42],"by":[43,57,143],"appropriate":[44],"algorithmic":[45],"and":[46,81,121,190],"software-engineering":[47],"improvements.":[48],"One":[49],"strategy":[50,93],"is":[51,154,172,195,202],"modify":[53],"read-alignment":[55],"algorithms":[56],"integrating":[58],"logic":[60,117],"related":[61],"alignment,":[64],"with":[65,139],"goal":[67],"making":[69],"software":[71,194],"implementation":[72,191],"amenable":[73],"optimizations":[75],"lead":[77],"higher":[79],"speed":[80],"greater":[82],"sensitivity":[83,187],"than":[84,159,178],"might":[85],"otherwise":[86],"attainable.":[88],"Results":[89],"We":[90,112,128],"evaluated":[91],"using":[94],"Arioc,":[95],"short-read":[97],"aligner":[98],"uses":[100],"GPU":[101,120],"(general-purpose":[102],"graphics":[103],"processing":[104],"unit)":[105],"hardware":[106],"accelerate":[108],"computationally-expensive":[109],"programming":[110],"logic.":[111],"integrated":[113],"into":[118],"both":[119],"CPU":[122],"code":[123],"throughout":[124],"Arioc":[126,193],"implementation.":[127],"then":[129],"carried":[130],"out":[131],"read-by-read":[133],"comparison":[134],"Arioc's":[136,152,170],"reported":[137,142],"alignments":[138,141],"well-known":[144],"CPU-based":[145],"read":[147,162],"aligners.":[148],"With":[149,166],"simulated":[150],"reads,":[151,169],"accuracy":[153],"equal":[155],"or":[157],"better":[158],"other":[161],"aligners":[163,181],"we":[164],"evaluated.":[165],"human":[167],"sequencing":[168],"throughput":[171],"at":[173,199,215],"least":[174],"10":[175],"times":[176],"faster":[177],"existing":[179],"across":[182],"wide":[184],"range":[185],"settings.":[188],"Availability":[189],"available":[196,214],"for":[197],"download":[198],"https://github.com/RWilton/Arioc.":[200],"It":[201],"released":[203],"under":[204],"BSD":[206],"open-source":[207],"license.":[208],"Supplementary":[209,211],"information":[210],"data":[212],"are":[213],"Bioinformatics":[216],"online.":[217]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2025-10-10T00:00:00"}
