{"id":"https://openalex.org/W3184635404","doi":"https://doi.org/10.1093/bib/bbab269","title":"Deep learning-based real-time detection of novel pathogens during sequencing","display_name":"Deep learning-based real-time detection of novel pathogens during sequencing","publication_year":2021,"publication_date":"2021-06-24","ids":{"openalex":"https://openalex.org/W3184635404","doi":"https://doi.org/10.1093/bib/bbab269","mag":"3184635404","pmid":"https://pubmed.ncbi.nlm.nih.gov/34297793"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab269","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab269","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"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/A5039532268","display_name":"Jakub M. Bartoszewicz","orcid":"https://orcid.org/0000-0001-6893-2371"},"institutions":[{"id":"https://openalex.org/I143288331","display_name":"Hasso Plattner Institute","ror":"https://ror.org/058rn5r42","country_code":"DE","type":"facility","lineage":["https://openalex.org/I143288331","https://openalex.org/I176453806"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jakub M Bartoszewicz","raw_affiliation_strings":["Digital Engineering Faculty, Hasso Plattner Institute, University of Postdam, Prof.-Dr.-Helmert-Stra\u00dfe 2-3, 14482 Brandenburg, Germany"],"affiliations":[{"raw_affiliation_string":"Digital Engineering Faculty, Hasso Plattner Institute, University of Postdam, Prof.-Dr.-Helmert-Stra\u00dfe 2-3, 14482 Brandenburg, Germany","institution_ids":["https://openalex.org/I143288331"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010414906","display_name":"Ulrich Genske","orcid":"https://orcid.org/0000-0003-2462-5163"},"institutions":[{"id":"https://openalex.org/I143288331","display_name":"Hasso Plattner Institute","ror":"https://ror.org/058rn5r42","country_code":"DE","type":"facility","lineage":["https://openalex.org/I143288331","https://openalex.org/I176453806"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ulrich Genske","raw_affiliation_strings":["Digital Engineering Faculty, Hasso Plattner Institute, University of Postdam, Prof.-Dr.-Helmert-Stra\u00dfe 2-3, 14482 Brandenburg, Germany"],"affiliations":[{"raw_affiliation_string":"Digital Engineering Faculty, Hasso Plattner Institute, University of Postdam, Prof.-Dr.-Helmert-Stra\u00dfe 2-3, 14482 Brandenburg, Germany","institution_ids":["https://openalex.org/I143288331"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005996110","display_name":"Bernhard Y. Renard","orcid":"https://orcid.org/0000-0003-4589-9809"},"institutions":[{"id":"https://openalex.org/I143288331","display_name":"Hasso Plattner Institute","ror":"https://ror.org/058rn5r42","country_code":"DE","type":"facility","lineage":["https://openalex.org/I143288331","https://openalex.org/I176453806"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Bernhard Y Renard","raw_affiliation_strings":["Digital Engineering Faculty, Hasso Plattner Institute, University of Postdam, Prof.-Dr.-Helmert-Stra\u00dfe 2-3, 14482 Brandenburg, Germany"],"affiliations":[{"raw_affiliation_string":"Digital Engineering Faculty, Hasso Plattner Institute, University of Postdam, Prof.-Dr.-Helmert-Stra\u00dfe 2-3, 14482 Brandenburg, Germany","institution_ids":["https://openalex.org/I143288331"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005996110","https://openalex.org/A5039532268"],"corresponding_institution_ids":["https://openalex.org/I143288331"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.8044,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.70769598,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"6","first_page":null,"last_page":null},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.988099992275238,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.983299970626831,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.8499630689620972},{"id":"https://openalex.org/keywords/minion","display_name":"Minion","score":0.7339475154876709},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.649486780166626},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5949893593788147},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5435783863067627},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.53324294090271},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5040961503982544},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.49870872497558594},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.47059357166290283},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.44657108187675476},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.435651570558548},{"id":"https://openalex.org/keywords/illumina-dye-sequencing","display_name":"Illumina dye sequencing","score":0.422454833984375},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39359283447265625},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38675034046173096},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2536906898021698},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.14618566632270813},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1288817822933197}],"concepts":[{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.8499630689620972},{"id":"https://openalex.org/C2779927696","wikidata":"https://www.wikidata.org/wiki/Q6865654","display_name":"Minion","level":5,"score":0.7339475154876709},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.649486780166626},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5949893593788147},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5435783863067627},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.53324294090271},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5040961503982544},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.49870872497558594},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.47059357166290283},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.44657108187675476},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.435651570558548},{"id":"https://openalex.org/C106337198","wikidata":"https://www.wikidata.org/wiki/Q13564012","display_name":"Illumina dye sequencing","level":4,"score":0.422454833984375},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39359283447265625},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38675034046173096},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2536906898021698},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.14618566632270813},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1288817822933197},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","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":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbab269","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab269","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34297793","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34297793","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:kobv.de-opus4-uni-potsdam:67318","is_oa":false,"landing_page_url":"https://publishup.uni-potsdam.de/frontdoor/index/index/docId/67318","pdf_url":null,"source":{"id":"https://openalex.org/S4377196346","display_name":"publish.UP (University of Potsdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I176453806","host_organization_name":"University of Potsdam","host_organization_lineage":["https://openalex.org/I176453806"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"doc-type:article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8299999833106995,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G338375665","display_name":null,"funder_award_id":"031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"}],"funders":[{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1893970331","https://openalex.org/W2055043387","https://openalex.org/W2082741630","https://openalex.org/W2101305463","https://openalex.org/W2103441770","https://openalex.org/W2106533426","https://openalex.org/W2106797018","https://openalex.org/W2112170460","https://openalex.org/W2122598316","https://openalex.org/W2126526203","https://openalex.org/W2128124531","https://openalex.org/W2142678478","https://openalex.org/W2143280034","https://openalex.org/W2152984807","https://openalex.org/W2158112812","https://openalex.org/W2159954944","https://openalex.org/W2170551349","https://openalex.org/W2198606573","https://openalex.org/W2291003811","https://openalex.org/W2332582324","https://openalex.org/W2503273054","https://openalex.org/W2511039129","https://openalex.org/W2543454659","https://openalex.org/W2570535773","https://openalex.org/W2765745983","https://openalex.org/W2782702360","https://openalex.org/W2789843538","https://openalex.org/W2805852073","https://openalex.org/W2808755256","https://openalex.org/W2883511460","https://openalex.org/W2887837536","https://openalex.org/W2889412200","https://openalex.org/W2891521255","https://openalex.org/W2894555395","https://openalex.org/W2895532240","https://openalex.org/W2900501296","https://openalex.org/W2935703330","https://openalex.org/W2941591629","https://openalex.org/W2950964375","https://openalex.org/W2961729414","https://openalex.org/W2965629790","https://openalex.org/W2970675229","https://openalex.org/W2983282754","https://openalex.org/W2996727916","https://openalex.org/W2999719567","https://openalex.org/W3001171417","https://openalex.org/W3003110834","https://openalex.org/W3004280078","https://openalex.org/W3011874820","https://openalex.org/W3048846953","https://openalex.org/W3128792544","https://openalex.org/W3158986422","https://openalex.org/W3177525997","https://openalex.org/W4247053599","https://openalex.org/W6682562841","https://openalex.org/W6754628202","https://openalex.org/W6773651162","https://openalex.org/W6782325559"],"related_works":["https://openalex.org/W3210632422","https://openalex.org/W4308654983","https://openalex.org/W3007601977","https://openalex.org/W2605553322","https://openalex.org/W4280510551","https://openalex.org/W2809937935","https://openalex.org/W2953078967","https://openalex.org/W4390989074","https://openalex.org/W3132843139","https://openalex.org/W2950891420"],"abstract_inverted_index":{"Novel":[0],"pathogens":[1,73,93],"evolve":[2],"quickly":[3],"and":[4,27,74,100,120,147,150,168,173],"may":[5],"emerge":[6],"rapidly,":[7],"causing":[8],"dangerous":[9],"outbreaks":[10],"or":[11],"even":[12,41],"global":[13],"pandemics.":[14],"Next-generation":[15],"sequencing":[16,106,118,178,207],"is":[17,46,54],"the":[18,21,30,35,43,49,52,59,152,218],"state":[19],"of":[20,29,38,71,199,206],"art":[22],"in":[23],"open-view":[24],"pathogen":[25],"detection,":[26],"one":[28],"few":[31],"methods":[32],"available":[33],"at":[34],"earliest":[36],"stages":[37],"an":[39,187],"epidemic,":[40],"when":[42],"biological":[44],"threat":[45],"unknown.":[47],"Analyzing":[48],"samples":[50],"as":[51],"sequencer":[53],"running":[55],"can":[56,83],"greatly":[57],"reduce":[58],"turnaround":[60],"time,":[61,208],"but":[62,94],"existing":[63],"tools":[64],"rely":[65],"on":[66,77,165,171],"close":[67],"matches":[68],"to":[69,114,144,192,203,211],"lists":[70],"known":[72],"perform":[75],"poorly":[76],"novel":[78],"species.":[79],"Machine":[80],"learning":[81,167],"approaches":[82],"predict":[84],"if":[85],"single":[86],"reads":[87,149],"originate":[88],"from":[89,103],"more":[90,214],"distant,":[91],"unknown":[92],"require":[95],"relatively":[96],"long":[97,220],"input":[98],"sequences":[99,109,231],"processed":[101],"data":[102],"a":[104,115,124,156],"finished":[105,219],"run.":[107],"Incomplete":[108],"contain":[110],"less":[111],"information,":[112],"leading":[113],"trade-off":[116],"between":[117],"time":[119],"detection":[121],"accuracy.":[122],"Using":[123],"workflow":[125],"for":[126,228],"real-time":[127,157,193],"pathogenic":[128],"potential":[129],"prediction,":[130],"we":[131,185],"investigate":[132],"which":[133],"subsequences":[134],"already":[135],"allow":[136],"accurate":[137,215],"inference.":[138],"We":[139],"train":[140],"deep":[141],"neural":[142],"networks":[143],"classify":[145],"Illumina":[146,158,183],"Nanopore":[148,200],"integrate":[151],"models":[153],"with":[154],"HiLive2,":[155],"mapper.":[159],"This":[160],"approach":[161,223],"outperforms":[162],"alternatives":[163],"based":[164],"machine":[166],"sequence":[169],"alignment":[170],"simulated":[172],"real":[174],"data,":[175],"including":[176],"SARS-CoV-2":[177],"runs.":[179],"After":[180],"just":[181],"50":[182],"cycles,":[184],"observe":[186],"80-fold":[188],"sensitivity":[189],"increase":[190],"compared":[191],"mapping.":[194],"The":[195,222],"first":[196],"250":[197],"bp":[198],"reads,":[201],"corresponding":[202],"0.5":[204],"s":[205],"are":[209],"enough":[210],"yield":[212],"predictions":[213],"than":[216],"mapping":[217],"reads.":[221],"could":[224],"also":[225],"be":[226],"used":[227],"screening":[229],"synthetic":[230],"against":[232],"biosecurity":[233],"threats.":[234]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2025-10-10T00:00:00"}