{"id":"https://openalex.org/W4392515713","doi":"https://doi.org/10.1093/bioinformatics/btae129","title":"NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data","display_name":"NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data","publication_year":2024,"publication_date":"2024-03-01","ids":{"openalex":"https://openalex.org/W4392515713","doi":"https://doi.org/10.1093/bioinformatics/btae129","pmid":"https://pubmed.ncbi.nlm.nih.gov/38444093"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae129","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae129","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae129/56873975/btae129.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae129/56873975/btae129.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027174942","display_name":"Michael D. Linderman","orcid":"https://orcid.org/0000-0002-9643-7148"},"institutions":[{"id":"https://openalex.org/I195575238","display_name":"Middlebury College","ror":"https://ror.org/0217hb928","country_code":"US","type":"education","lineage":["https://openalex.org/I195575238"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael D Linderman","raw_affiliation_strings":["Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States"],"raw_orcid":"https://orcid.org/0000-0002-9643-7148","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States","institution_ids":["https://openalex.org/I195575238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103231251","display_name":"Jacob Wallace","orcid":"https://orcid.org/0009-0004-7136-5688"},"institutions":[{"id":"https://openalex.org/I195575238","display_name":"Middlebury College","ror":"https://ror.org/0217hb928","country_code":"US","type":"education","lineage":["https://openalex.org/I195575238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob Wallace","raw_affiliation_strings":["Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States"],"raw_orcid":"https://orcid.org/0009-0004-7136-5688","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States","institution_ids":["https://openalex.org/I195575238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094082678","display_name":"Alderik van der Heyde","orcid":null},"institutions":[{"id":"https://openalex.org/I195575238","display_name":"Middlebury College","ror":"https://ror.org/0217hb928","country_code":"US","type":"education","lineage":["https://openalex.org/I195575238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alderik van der Heyde","raw_affiliation_strings":["Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States","institution_ids":["https://openalex.org/I195575238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094082679","display_name":"Eliza Wieman","orcid":"https://orcid.org/0000-0002-6807-7632"},"institutions":[{"id":"https://openalex.org/I195575238","display_name":"Middlebury College","ror":"https://ror.org/0217hb928","country_code":"US","type":"education","lineage":["https://openalex.org/I195575238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eliza Wieman","raw_affiliation_strings":["Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States"],"raw_orcid":"https://orcid.org/0000-0002-6807-7632","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States","institution_ids":["https://openalex.org/I195575238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094082680","display_name":"Daniel Brey","orcid":null},"institutions":[{"id":"https://openalex.org/I195575238","display_name":"Middlebury College","ror":"https://ror.org/0217hb928","country_code":"US","type":"education","lineage":["https://openalex.org/I195575238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Brey","raw_affiliation_strings":["Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States","institution_ids":["https://openalex.org/I195575238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067924733","display_name":"Yiran Shi","orcid":"https://orcid.org/0000-0002-5311-3784"},"institutions":[{"id":"https://openalex.org/I195575238","display_name":"Middlebury College","ror":"https://ror.org/0217hb928","country_code":"US","type":"education","lineage":["https://openalex.org/I195575238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yiran Shi","raw_affiliation_strings":["Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States","institution_ids":["https://openalex.org/I195575238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028606515","display_name":"Peter J. Hansen","orcid":"https://orcid.org/0000-0003-3061-9333"},"institutions":[{"id":"https://openalex.org/I195575238","display_name":"Middlebury College","ror":"https://ror.org/0217hb928","country_code":"US","type":"education","lineage":["https://openalex.org/I195575238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter Hansen","raw_affiliation_strings":["Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Middlebury College , Middlebury, VT 05753, United States","institution_ids":["https://openalex.org/I195575238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003203969","display_name":"Zahra Shamsi","orcid":"https://orcid.org/0000-0002-9834-2978"},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zahra Shamsi","raw_affiliation_strings":["Google, Mountain View , CA 94043, United States"],"raw_orcid":"https://orcid.org/0000-0002-9834-2978","affiliations":[{"raw_affiliation_string":"Google, Mountain View , CA 94043, United States","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073573091","display_name":"Jeremiah Zhe Liu","orcid":"https://orcid.org/0000-0002-7410-4502"},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremiah Liu","raw_affiliation_strings":["Google, Mountain View , CA 94043, United States"],"raw_orcid":"https://orcid.org/0000-0002-7410-4502","affiliations":[{"raw_affiliation_string":"Google, Mountain View , CA 94043, United States","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086328119","display_name":"Bruce D. Gelb","orcid":"https://orcid.org/0000-0001-8527-5027"},"institutions":[{"id":"https://openalex.org/I4210111958","display_name":"Child Health and Development Institute","ror":"https://ror.org/02bns0488","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111958"]},{"id":"https://openalex.org/I4210147155","display_name":"Pediatrics and Genetics","ror":"https://ror.org/03t432d20","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210147155"]},{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bruce D Gelb","raw_affiliation_strings":["Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, NY 10029, United States"],"raw_orcid":"https://orcid.org/0000-0001-8527-5027","affiliations":[{"raw_affiliation_string":"Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, NY 10029, United States","institution_ids":["https://openalex.org/I4210111958","https://openalex.org/I98704320","https://openalex.org/I4210147155"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008757230","display_name":"Ali Bashir","orcid":"https://orcid.org/0000-0002-5240-9604"},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ali Bashir","raw_affiliation_strings":["Google, Mountain View , CA 94043, United States"],"raw_orcid":"https://orcid.org/0000-0002-5240-9604","affiliations":[{"raw_affiliation_string":"Google, Mountain View , CA 94043, United States","institution_ids":["https://openalex.org/I1291425158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5027174942"],"corresponding_institution_ids":["https://openalex.org/I195575238"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.0749,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.90846068,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"40","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.8285999894142151,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.8285999894142151,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.10109999775886536,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.030300000682473183,"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/genotyping","display_name":"Genotyping","score":0.8353370428085327},{"id":"https://openalex.org/keywords/concordance","display_name":"Concordance","score":0.5978692770004272},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5971523523330688},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.5911074876785278},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5807825922966003},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5180268883705139},{"id":"https://openalex.org/keywords/zygosity","display_name":"Zygosity","score":0.495538592338562},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4866707921028137},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4784564971923828},{"id":"https://openalex.org/keywords/structural-variation","display_name":"Structural variation","score":0.4648496210575104},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.42152926325798035},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4202900528907776},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.35160234570503235},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33341971039772034},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08960339426994324}],"concepts":[{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.8353370428085327},{"id":"https://openalex.org/C160798450","wikidata":"https://www.wikidata.org/wiki/Q4230870","display_name":"Concordance","level":2,"score":0.5978692770004272},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5971523523330688},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.5911074876785278},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5807825922966003},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5180268883705139},{"id":"https://openalex.org/C197845989","wikidata":"https://www.wikidata.org/wiki/Q13048280","display_name":"Zygosity","level":2,"score":0.495538592338562},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4866707921028137},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4784564971923828},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.4648496210575104},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.42152926325798035},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4202900528907776},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.35160234570503235},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33341971039772034},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08960339426994324},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","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":"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":"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":"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","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},{"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},{"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/bioinformatics/btae129","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae129","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae129/56873975/btae129.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38444093","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38444093","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:10955255","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10955255","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10955255/pdf/btae129.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae129","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae129","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae129/56873975/btae129.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1497838195","display_name":null,"funder_award_id":"P20 GM103449","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1767215720","display_name":null,"funder_award_id":"UM1 HL098123","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G2265344572","display_name":"MRI: Acquisition of High Performance Computing Equipment for Research and Teaching at an Undergraduate Liberal Arts College","funder_award_id":"1827373","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2469982867","display_name":null,"funder_award_id":"U01HL153009","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G3425802160","display_name":null,"funder_award_id":"P20GM103449","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4680525519","display_name":null,"funder_award_id":"U01 HL153009","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G4771767919","display_name":null,"funder_award_id":"P20GM103449","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4806302692","display_name":null,"funder_award_id":"UM1HL098123","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5664770372","display_name":null,"funder_award_id":"OAC-1827314","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5855963385","display_name":null,"funder_award_id":"P20GM103449","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6111489155","display_name":"MRI: Acquisition of a GPU Accelerated Vermont Advanced Computing Core","funder_award_id":"1827314","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6751645197","display_name":null,"funder_award_id":"UM1HL098123","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G6937812294","display_name":null,"funder_award_id":"U01HL153009","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7389774262","display_name":null,"funder_award_id":"OAC-1827314","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"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392515713.pdf"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1973067702","https://openalex.org/W2007100755","https://openalex.org/W2083870688","https://openalex.org/W2100684179","https://openalex.org/W2111350087","https://openalex.org/W2111377561","https://openalex.org/W2146005104","https://openalex.org/W2152956782","https://openalex.org/W2157539385","https://openalex.org/W2235737683","https://openalex.org/W2263137078","https://openalex.org/W2396849069","https://openalex.org/W2779603631","https://openalex.org/W2889664156","https://openalex.org/W2908721251","https://openalex.org/W2948024819","https://openalex.org/W2951529834","https://openalex.org/W2963186762","https://openalex.org/W2972274962","https://openalex.org/W2989658460","https://openalex.org/W2990344913","https://openalex.org/W2996021891","https://openalex.org/W2997001777","https://openalex.org/W3007365321","https://openalex.org/W3034581902","https://openalex.org/W3034942609","https://openalex.org/W3109931242","https://openalex.org/W3130788486","https://openalex.org/W3165023362","https://openalex.org/W3175673060","https://openalex.org/W4223416923","https://openalex.org/W4294012180","https://openalex.org/W4313250582","https://openalex.org/W4317502116","https://openalex.org/W4360612418","https://openalex.org/W4376133202","https://openalex.org/W6779930420"],"related_works":["https://openalex.org/W2396356509","https://openalex.org/W2127983802","https://openalex.org/W2275643840","https://openalex.org/W4239979837","https://openalex.org/W2098209746","https://openalex.org/W2266101617","https://openalex.org/W1887805119","https://openalex.org/W2078949856","https://openalex.org/W565708011","https://openalex.org/W1973652618"],"abstract_inverted_index":{"MOTIVATION:":[0],"Structural":[1],"variants":[2],"(SVs)":[3],"play":[4],"a":[5,55,123,149],"causal":[6],"role":[7],"in":[8,32,126],"numerous":[9],"diseases":[10],"but":[11],"can":[12],"be":[13],"difficult":[14],"to":[15,139],"detect":[16],"and":[17,64,94,119,170],"accurately":[18],"genotype":[19,80],"(determine":[20],"zygosity)":[21],"with":[22,42],"short-read":[23],"genome":[24],"sequencing":[25],"data":[26,93],"(SRS).":[27],"Improving":[28],"SV":[29,79,110,115],"genotyping":[30,60,111,127,147],"accuracy":[31,112],"SRS":[33,92,96],"data,":[34],"particularly":[35],"for":[36,59,109,129,154],"the":[37,78,83,90,107,130,140],"many":[38],"SVs":[39,66,141,156],"first":[40],"detected":[41],"long-read":[43],"sequencing,":[44],"will":[45],"improve":[46],"our":[47],"understanding":[48],"of":[49],"genetic":[50],"variation.":[51],"RESULTS:":[52],"NPSV-deep":[53,76,101,135],"is":[54,136],"deep":[56],"learning-based":[57],"approach":[58],"previously":[61],"reported":[62],"insertion":[63],"deletion":[65,146],"that":[67,100],"recasts":[68],"this":[69],"task":[70],"as":[71,142],"an":[72],"image":[73],"similarity":[74,84],"problem.":[75],"predicts":[77],"based":[81],"on":[82],"between":[85],"pileup":[86],"images":[87],"generated":[88],"from":[89],"actual":[91],"matching":[95],"simulations.":[97],"We":[98],"show":[99],"consistently":[102],"matches":[103],"or":[104],"improves":[105,145],"upon":[106],"state-of-the-art":[108],"across":[113],"different":[114],"call":[116],"sets,":[117],"samples":[118],"variant":[120],"types,":[121],"including":[122],"25%":[124],"reduction":[125],"errors":[128],"Genome-in-a-Bottle":[131],"(GIAB)":[132],"high-confidence":[133],"SVs.":[134,163],"not":[137],"limited":[138],"described;":[143],"it":[144],"concordance":[148],"further":[150],"1.5":[151],"percentage":[152],"points":[153],"GIAB":[155],"(92%)":[157],"by":[158],"automatically":[159],"correcting":[160],"imprecise/incorrectly":[161],"described":[162],"AVAILABILITY":[164],"AND":[165],"IMPLEMENTATION:":[166],"Python/C++":[167],"source":[168],"code":[169],"pre-trained":[171],"models":[172],"freely":[173],"available":[174],"at":[175],"https://github.com/mlinderm/npsv2.":[176]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-07T14:30:12.667765","created_date":"2025-10-10T00:00:00"}