{"id":"https://openalex.org/W3012127159","doi":"https://doi.org/10.1371/journal.pcbi.1007737","title":"SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures","display_name":"SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures","publication_year":2020,"publication_date":"2020-03-17","ids":{"openalex":"https://openalex.org/W3012127159","doi":"https://doi.org/10.1371/journal.pcbi.1007737","mag":"3012127159","pmid":"https://pubmed.ncbi.nlm.nih.gov/32182236","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/7100977"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007737","doi":"https://doi.org/10.1371/journal.pcbi.1007737","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007737","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007737&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007737&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018068219","display_name":"Kunal Kathuria","orcid":"https://orcid.org/0000-0003-1898-8769","observed_orcids":["https://orcid.org/0000-0003-1898-8769"]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kunal Kathuria","raw_affiliation_strings":["Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA","Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006718448","display_name":"Aakrosh Ratan","orcid":"https://orcid.org/0000-0002-0782-3056","observed_orcids":["https://orcid.org/0000-0002-0782-3056"]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Aakrosh Ratan","raw_affiliation_strings":["Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA","Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA","Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America","Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-0782-3056","affiliations":[{"raw_affiliation_string":"Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5006718448"],"corresponding_institution_ids":["https://openalex.org/I51556381"],"apc_list":{"value":2500,"currency":"USD","value_usd":2500},"apc_paid":{"value":2500,"currency":"USD","value_usd":2500},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.02433778,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"16","issue":"3","first_page":"e1007737","last_page":"e1007737"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9643999934196472,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9643999934196472,"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":0.021400000900030136,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.01080000028014183,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/structural-variant-calling","display_name":"structural variant calling","score":0.777999997138977},{"id":"https://openalex.org/keywords/split-reads","display_name":"split reads","score":0.6190000176429749},{"id":"https://openalex.org/keywords/sequencing-depth","display_name":"sequencing depth","score":0.7929999828338623},{"id":"https://openalex.org/keywords/graph-clustering","display_name":"graph clustering","score":0.8450000286102295},{"id":"https://openalex.org/keywords/deletion","display_name":"deletion","score":0.6740000247955322},{"id":"https://openalex.org/keywords/duplication","display_name":"duplication","score":0.9990000128746033}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.7142674922943115},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6552132368087769},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.592078685760498},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5859729647636414},{"id":"https://openalex.org/C206936463","wikidata":"https://www.wikidata.org/wiki/Q634179","display_name":"Breakpoint","level":4,"score":0.4982945919036865},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4656684398651123},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44608843326568604},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.4301723837852478},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2985321283340454},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28948819637298584},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27989673614501953},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.18854358792304993},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10004547238349915},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C138626823","wikidata":"https://www.wikidata.org/wiki/Q916504","display_name":"Chromosomal translocation","level":3,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1007737","doi":"https://doi.org/10.1371/journal.pcbi.1007737","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007737","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007737&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"doi:10.1101/469981","doi":"https://doi.org/10.1101/469981","is_oa":true,"landing_page_url":"https://doi.org/10.1101/469981","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2018/11/16/469981.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:7100977","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7100977","pdf_url":null,"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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmid:32182236","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32182236","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,"listed_in":[],"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":"PLoS computational biology","raw_type":"Journal Article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1007737","doi":null,"is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007737","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:9d3e8ec6463a43bbaf10484a1501d236","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/9d3e8ec6463a43bbaf10484a1501d236","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 16, Iss 3, p e1007737 (2020)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/11995986","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/SVXplorer_Three-tier_approach_to_identification_of_structural_variants_via_sequential_recombination_of_discordant_cluster_signatures/11995986","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007737","doi":"https://doi.org/10.1371/journal.pcbi.1007737","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007737","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007737&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1080307856","display_name":null,"funder_award_id":"P30 CA044579","funder_id":"https://openalex.org/F4320317351","funder_display_name":"UVA Cancer Center"},{"id":"https://openalex.org/G9000901327","display_name":"University of Virginia Cancer Center Support Grant","funder_award_id":"P30CA044579","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320317351","display_name":"UVA Cancer Center","ror":"https://ror.org/04w75nz84"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3012127159.pdf","grobid_xml":"https://content.openalex.org/works/W3012127159.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1584799426","https://openalex.org/W1912672559","https://openalex.org/W1967448179","https://openalex.org/W1973067702","https://openalex.org/W1980099549","https://openalex.org/W1991333931","https://openalex.org/W2002438422","https://openalex.org/W2018742603","https://openalex.org/W2042838021","https://openalex.org/W2075331845","https://openalex.org/W2095680943","https://openalex.org/W2099910424","https://openalex.org/W2102619694","https://openalex.org/W2107830007","https://openalex.org/W2111350087","https://openalex.org/W2132022337","https://openalex.org/W2140869203","https://openalex.org/W2146005104","https://openalex.org/W2150264767","https://openalex.org/W2152956782","https://openalex.org/W2159091117","https://openalex.org/W2159640103","https://openalex.org/W2160429376","https://openalex.org/W2206844597","https://openalex.org/W2235737683","https://openalex.org/W2263137078","https://openalex.org/W2620600112","https://openalex.org/W2807304153","https://openalex.org/W2951745476","https://openalex.org/W2963186762","https://openalex.org/W4255949184"],"related_works":["https://openalex.org/W2170855681","https://openalex.org/W7213594874","https://openalex.org/W2892248322","https://openalex.org/W2166359802","https://openalex.org/W2951764279","https://openalex.org/W6917440025","https://openalex.org/W4362588107","https://openalex.org/W2101724808","https://openalex.org/W2949779661","https://openalex.org/W4285239178"],"abstract_inverted_index":{"The":[0],"identification":[1,46],"of":[2,47,71],"structural":[3,51],"variants":[4,22,52],"using":[5],"short-read":[6],"data":[7],"remains":[8],"challenging.":[9],"Most":[10],"approaches":[11,101],"that":[12,90],"use":[13],"discordant":[14,75],"paired-end":[15,76],"sequences":[16],"ignore":[17],"non-trivial":[18,72],"signatures":[19,73],"presented":[20],"by":[21,30,68],"containing":[23],"3":[24],"breakpoints,":[25],"such":[26,53],"as":[27,54],"those":[28],"generated":[29],"various":[31],"copy-paste":[32],"and":[33,42,56,79,95,105],"cut-paste":[34],"mechanisms.":[35],"This":[36],"can":[37],"result":[38],"in":[39,44],"lower":[40],"precision":[41],"sensitivity":[43],"the":[45,48,69],"more":[49,93],"common":[50],"deletions":[55],"duplications.":[57],"We":[58,88],"present":[59],"SVXplorer,":[60],"which":[61],"uses":[62],"a":[63],"graph-based":[64],"clustering":[65],"approach":[66],"streamlined":[67],"integration":[70],"from":[74],"alignments,":[77],"split-reads":[78],"read":[80],"depth":[81],"information":[82],"to":[83,98],"improve":[84],"upon":[85],"existing":[86,100],"methods.":[87],"show":[89],"SVXplorer":[91,108],"is":[92,109],"sensitive":[94],"precise":[96],"compared":[97],"several":[99],"on":[102],"multiple":[103],"real":[104],"simulated":[106],"datasets.":[107],"available":[110],"for":[111],"download":[112],"at":[113],"https://github.com/kunalkathuria/SVXplorer.":[114]},"counts_by_year":[],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2020-03-23T00:00:00"}
