{"id":"https://openalex.org/W1976710643","doi":"https://doi.org/10.1371/journal.pone.0083356","title":"SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations","display_name":"SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations","publication_year":2013,"publication_date":"2013-12-16","ids":{"openalex":"https://openalex.org/W1976710643","doi":"https://doi.org/10.1371/journal.pone.0083356","mag":"1976710643","pmid":"https://pubmed.ncbi.nlm.nih.gov/24358278","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3865185"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pone.0083356","doi":"https://doi.org/10.1371/journal.pone.0083356","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0083356","pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0083356&type=printable","source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","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 ONE","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/plosone/article/file?id=10.1371/journal.pone.0083356&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085507659","display_name":"Steven N. Hart","orcid":"https://orcid.org/0000-0001-7714-2734","observed_orcids":["https://orcid.org/0000-0001-7714-2734"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven N. Hart","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016663287","display_name":"Vivekananda Sarangi","orcid":"https://orcid.org/0000-0002-3070-8582","observed_orcids":["https://orcid.org/0000-0002-3070-8582"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vivekananda Sarangi","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004159840","display_name":"Raymond M. Moore","orcid":"https://orcid.org/0000-0003-4196-1804","observed_orcids":["https://orcid.org/0000-0003-4196-1804"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Raymond Moore","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111996562","display_name":"Saurabh Baheti","orcid":"https://orcid.org/0000-0002-3564-7627","observed_orcids":["https://orcid.org/0000-0002-3564-7627"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Saurabh Baheti","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066150572","display_name":"Jaysheel Bhavsar","orcid":"https://orcid.org/0009-0003-6174-4329","observed_orcids":["https://orcid.org/0009-0003-6174-4329"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jaysheel D. Bhavsar","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016908886","display_name":"Fergus J. Couch","orcid":"https://orcid.org/0000-0001-9417-9985","observed_orcids":["https://orcid.org/0000-0001-9417-9985"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fergus J. Couch","raw_affiliation_strings":["Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110176668","display_name":"Jean-Pierre A. Kocher","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jean-Pierre A. Kocher","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America","institution_ids":["https://openalex.org/I1330342723"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5110176668"],"corresponding_institution_ids":["https://openalex.org/I1330342723"],"apc_list":{"value":2382,"currency":"USD","value_usd":2382},"apc_paid":{"value":2382,"currency":"USD","value_usd":2382},"fwci":4.8528,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.95313631,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"8","issue":"12","first_page":"e83356","last_page":"e83356"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9692000150680542,"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":0.9692000150680542,"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":0.020999999716877937,"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":0.0034000000450760126,"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-variants","display_name":"structural variants","score":0.8899999856948853},{"id":"https://openalex.org/keywords/change-point-detection","display_name":"change point detection","score":0.8289999961853027},{"id":"https://openalex.org/keywords/split-reads","display_name":"split reads","score":0.7749999761581421},{"id":"https://openalex.org/keywords/paired-end-sequencing","display_name":"paired-end sequencing","score":0.828000009059906},{"id":"https://openalex.org/keywords/variant-calling","display_name":"variant calling","score":0.515999972820282},{"id":"https://openalex.org/keywords/brca2","display_name":"BRCA2","score":0.8960000276565552}],"concepts":[{"id":"https://openalex.org/C206936463","wikidata":"https://www.wikidata.org/wiki/Q634179","display_name":"Breakpoint","level":4,"score":0.7505675554275513},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.6828216314315796},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6316011548042297},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.6137600541114807},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.587099552154541},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5657891631126404},{"id":"https://openalex.org/C63000827","wikidata":"https://www.wikidata.org/wiki/Q3080428","display_name":"Software portability","level":2,"score":0.5545222759246826},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5266516208648682},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5201714038848877},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.4896469712257385},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.4448956549167633},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4039537310600281},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3769491910934448},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.373159259557724},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.35231298208236694},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34810522198677063},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.33641940355300903},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.2194155752658844},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1640392243862152},{"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/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","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}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019457","descriptor_name":"Chromosome Breakage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pone.0083356","doi":"https://doi.org/10.1371/journal.pone.0083356","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0083356","pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0083356&type=printable","source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","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 ONE","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2851599","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3865185","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3865185","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3865185","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 One","raw_type":"Text"},{"id":"pmid:24358278","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24358278","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 one","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.799.5231","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.799.5231","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/73/fd/pone.0083356.PMC3865185.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:15e3a2cf33274b24aa741291a8b1456b","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/15e3a2cf33274b24aa741291a8b1456b","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 ONE, Vol 8, Iss 12, p e83356 (2013)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/879049","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_SoftSearch_Integration_of_Multiple_Sequence_Features_to_Identify_Breakpoints_of_Structural_Variations_/879049","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.pone.0083356","doi":"https://doi.org/10.1371/journal.pone.0083356","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0083356","pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0083356&type=printable","source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","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 ONE","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.428600013256073}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1976710643.pdf","grobid_xml":"https://content.openalex.org/works/W1976710643.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W2049997041","https://openalex.org/W2065817684","https://openalex.org/W2098652713","https://openalex.org/W2102619694","https://openalex.org/W2103011829","https://openalex.org/W2103970959","https://openalex.org/W2108234281","https://openalex.org/W2116126626","https://openalex.org/W2123690878","https://openalex.org/W2132037594","https://openalex.org/W2138044148","https://openalex.org/W2139993758","https://openalex.org/W2146005104","https://openalex.org/W2146112295","https://openalex.org/W2150506261","https://openalex.org/W2151413771","https://openalex.org/W2163066822","https://openalex.org/W2169145121"],"related_works":["https://openalex.org/W2287411355","https://openalex.org/W2111350087","https://openalex.org/W7096450334","https://openalex.org/W4317034776","https://openalex.org/W2884263788","https://openalex.org/W2735337817","https://openalex.org/W2159603617","https://openalex.org/W3012127159","https://openalex.org/W2170855681","https://openalex.org/W2787286508"],"abstract_inverted_index":{"BACKGROUND:":[0],"Structural":[1],"variation":[2],"(SV)":[3],"represents":[4],"a":[5,37,137,147],"significant,":[6],"yet":[7],"poorly":[8],"understood":[9],"contribution":[10],"to":[11,23,43,85,122,159,182],"an":[12,41,49,161],"individual's":[13],"genetic":[14],"makeup.":[15],"Advanced":[16],"next-generation":[17,60],"sequencing":[18,61,116],"technologies":[19],"are":[20,83,103],"widely":[21],"used":[22,84],"discover":[24],"such":[25],"variations,":[26],"but":[27],"there":[28],"is":[29,35,120],"no":[30],"single":[31],"detection":[32],"tool":[33],"that":[34,167],"considered":[36],"community":[38],"standard.":[39],"In":[40],"attempt":[42],"fulfil":[44],"this":[45],"need,":[46],"we":[47],"developed":[48,91],"algorithm,":[50],"SoftSearch,":[51],"for":[52,67],"discovering":[53],"structural":[54],"variant":[55],"breakpoints":[56,135],"in":[57,187],"Illumina":[58],"paired-end":[59],"data.":[62],"SoftSearch":[63,94,133,168,179],"combines":[64],"multiple":[65,176],"strategies":[66],"detecting":[68],"SV":[69,162],"including":[70],"split-read,":[71],"discordant":[72,80,149],"read-pair,":[73],"and":[74,79,92,97,118,146],"unmated":[75],"pairs.":[76],"Co-localized":[77],"split-reads":[78],"read":[81],"pairs":[82],"refine":[86],"the":[87,188],"breakpoints.":[88],"RESULTS:":[89],"We":[90,165],"validated":[93],"using":[95],"real":[96],"synthetic":[98],"datasets.":[99],"SoftSearch's":[100],"key":[101],"features":[102],"1)":[104],"not":[105,156,191],"requiring":[106],"secondary":[107],"(or":[108],"exhaustive":[109],"primary)":[110],"alignment,":[111],"2)":[112],"portability":[113],"into":[114],"established":[115],"workflows,":[117],"3)":[119],"applicable":[121],"any":[123],"DNA-sequencing":[124],"experiment":[125],"(e.g.":[126],"whole":[127],"genome,":[128],"exome,":[129],"custom":[130],"capture,":[131],"etc.).":[132],"identifies":[134],"from":[136,143],"small":[138],"number":[139],"of":[140],"soft-clipped":[141],"bases":[142],"split":[144],"reads":[145],"few":[148],"read-pairs":[150],"which":[151],"on":[152],"their":[153],"own":[154],"would":[155],"be":[157],"sufficient":[158],"make":[160],"call.":[163],"CONCLUSIONS:":[164],"show":[166],"can":[169],"identify":[170],"more":[171],"true":[172],"SVs":[173,186],"by":[174,193],"combining":[175],"sequence":[177],"features.":[178],"was":[180],"able":[181],"call":[183],"clinically":[184],"relevant":[185],"BRCA2":[189],"gene":[190],"reported":[192],"other":[194],"tools":[195],"while":[196],"offering":[197],"significantly":[198],"improved":[199],"overall":[200],"performance.":[201]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":12},{"year":2014,"cited_by_count":7}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}