{"id":"https://openalex.org/W3091769478","doi":"https://doi.org/10.1093/bioinformatics/btaa875","title":"QAlign: aligning nanopore reads accurately using current-level modeling","display_name":"QAlign: aligning nanopore reads accurately using current-level modeling","publication_year":2020,"publication_date":"2020-09-29","ids":{"openalex":"https://openalex.org/W3091769478","doi":"https://doi.org/10.1093/bioinformatics/btaa875","mag":"3091769478","pmid":"https://pubmed.ncbi.nlm.nih.gov/33051648"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa875","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa875","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/5/625/37808775/btaa875.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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/5/625/37808775/btaa875.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076585799","display_name":"Dhaivat Joshi","orcid":"https://orcid.org/0000-0001-9050-5931"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dhaivat Joshi","raw_affiliation_strings":["Electrical & Computer Engineering, University of California , Los Angeles, CA 90095, USA"],"affiliations":[{"raw_affiliation_string":"Electrical & Computer Engineering, University of California , Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019154579","display_name":"Shunfu Mao","orcid":"https://orcid.org/0000-0002-8203-0507"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shunfu Mao","raw_affiliation_strings":["Electrical & Computer Engineering, University of Washington , Seattle, WA 98195, USA"],"affiliations":[{"raw_affiliation_string":"Electrical & Computer Engineering, University of Washington , Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100722219","display_name":"Sreeram Kannan","orcid":"https://orcid.org/0000-0001-8843-2964"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sreeram Kannan","raw_affiliation_strings":["Electrical & Computer Engineering, University of Washington , Seattle, WA 98195, USA"],"affiliations":[{"raw_affiliation_string":"Electrical & Computer Engineering, University of Washington , Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083980887","display_name":"Suhas Diggavi","orcid":"https://orcid.org/0000-0001-7313-9861"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Suhas Diggavi","raw_affiliation_strings":["Electrical & Computer Engineering, University of California , Los Angeles, CA 90095, USA"],"affiliations":[{"raw_affiliation_string":"Electrical & Computer Engineering, University of California , Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5083980887","https://openalex.org/A5100722219"],"corresponding_institution_ids":["https://openalex.org/I161318765","https://openalex.org/I201448701"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6672,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.67909652,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"5","first_page":"625","last_page":"633"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9908000230789185,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.98580002784729,"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/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.8940218687057495},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7524661421775818},{"id":"https://openalex.org/keywords/nanopore","display_name":"Nanopore","score":0.670846700668335},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.664336621761322},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.6096013188362122},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5228774547576904},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5150980353355408},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.5040687322616577},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.494987428188324},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44818755984306335},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.44747987389564514},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.4294719099998474},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3965911269187927},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3888006806373596},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.33879587054252625},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.32997363805770874},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2720889449119568},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.20283594727516174},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1517651379108429},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1467723846435547},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14539504051208496}],"concepts":[{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.8940218687057495},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7524661421775818},{"id":"https://openalex.org/C141795571","wikidata":"https://www.wikidata.org/wiki/Q580942","display_name":"Nanopore","level":2,"score":0.670846700668335},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.664336621761322},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.6096013188362122},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5228774547576904},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5150980353355408},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.5040687322616577},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.494987428188324},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44818755984306335},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.44747987389564514},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.4294719099998474},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3965911269187927},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3888006806373596},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.33879587054252625},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.32997363805770874},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2720889449119568},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.20283594727516174},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1517651379108429},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1467723846435547},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14539504051208496},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa875","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa875","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/5/625/37808775/btaa875.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":"pmid:33051648","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33051648","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8097683","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8097683","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/btaa875","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa875","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/5/625/37808775/btaa875.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":[],"awards":[{"id":"https://openalex.org/G1856544841","display_name":null,"funder_award_id":"1651236","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2346146521","display_name":null,"funder_award_id":"1R01HG008164","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6803920600","display_name":null,"funder_award_id":"1703403","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"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3091769478.pdf"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1519765314","https://openalex.org/W1984812591","https://openalex.org/W2011657487","https://openalex.org/W2011993186","https://openalex.org/W2099809434","https://openalex.org/W2106678197","https://openalex.org/W2136651963","https://openalex.org/W2149573463","https://openalex.org/W2150131459","https://openalex.org/W2168133698","https://openalex.org/W2346680365","https://openalex.org/W2420913016","https://openalex.org/W2607027360","https://openalex.org/W2607669908","https://openalex.org/W2736859409","https://openalex.org/W2747406892","https://openalex.org/W2789843538","https://openalex.org/W2791982652","https://openalex.org/W2899616402","https://openalex.org/W2949395034","https://openalex.org/W2950609999","https://openalex.org/W2950827710","https://openalex.org/W2950891420","https://openalex.org/W2951149781","https://openalex.org/W2953020124","https://openalex.org/W3093111434","https://openalex.org/W6737143606"],"related_works":["https://openalex.org/W2962743744","https://openalex.org/W3009176350","https://openalex.org/W3021840362","https://openalex.org/W2951397007","https://openalex.org/W3022783334","https://openalex.org/W2580258113","https://openalex.org/W2763726643","https://openalex.org/W2952788979","https://openalex.org/W2607669908","https://openalex.org/W3090794301"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3}],"updated_date":"2026-03-17T09:09:15.849793","created_date":"2025-10-10T00:00:00"}