{"id":"https://openalex.org/W4415757188","doi":"https://doi.org/10.1093/bioinformatics/btaf594","title":"insilicoSV: a flexible grammar-based framework for structural variant simulation and placement","display_name":"insilicoSV: a flexible grammar-based framework for structural variant simulation and placement","publication_year":2025,"publication_date":"2025-10-28","ids":{"openalex":"https://openalex.org/W4415757188","doi":"https://doi.org/10.1093/bioinformatics/btaf594","pmid":"https://pubmed.ncbi.nlm.nih.gov/41172269"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf594","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf594","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf594/65050239/btaf594.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/article-pdf/41/11/btaf594/65050239/btaf594.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070081715","display_name":"Enzo Battistella","orcid":"https://orcid.org/0000-0001-7053-5666"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Enzo Battistella","raw_affiliation_strings":["Broad Clinical Labs , Cambridge, MA 02142,","Broad Institute of MIT and Harvard , Cambridge, MA 02142,","Broad Institute of MIT and Harvard , Cambridge, MA"],"affiliations":[{"raw_affiliation_string":"Broad Clinical Labs , Cambridge, MA 02142,","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA 02142,","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101654008","display_name":"Ning Jiang","orcid":"https://orcid.org/0000-0003-4549-6372"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nick Jiang","raw_affiliation_strings":["Broad Institute of MIT and Harvard , Cambridge, MA 02142,","University of California, Berkeley , Berkeley, CA 94720,","University of California, Berkeley , Berkeley, CA","Broad Institute of MIT and Harvard , Cambridge, MA"],"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA 02142,","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"University of California, Berkeley , Berkeley, CA 94720,","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"University of California, Berkeley , Berkeley, CA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039579590","display_name":"Chris Rohlicek","orcid":null},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Rohlicek","raw_affiliation_strings":["Broad Institute of MIT and Harvard , Cambridge, MA 02142,","Broad Institute of MIT and Harvard , Cambridge, MA"],"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA 02142,","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091394580","display_name":"Ilya Shlyakhter","orcid":"https://orcid.org/0000-0002-9854-5118"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ilya Shlyakhter","raw_affiliation_strings":["Broad Institute of MIT and Harvard , Cambridge, MA 02142,","Broad Institute of MIT and Harvard , Cambridge, MA"],"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA 02142,","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014836509","display_name":"Victoria Popic","orcid":"https://orcid.org/0000-0003-3181-5432"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Victoria Popic","raw_affiliation_strings":["Broad Clinical Labs , Cambridge, MA 02142,","Broad Institute of MIT and Harvard , Cambridge, MA 02142,","Broad Institute of MIT and Harvard , Cambridge, MA"],"affiliations":[{"raw_affiliation_string":"Broad Clinical Labs , Cambridge, MA 02142,","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA 02142,","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA","institution_ids":["https://openalex.org/I107606265"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5070081715"],"corresponding_institution_ids":["https://openalex.org/I107606265"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.3367,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.9080271,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"41","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11450","display_name":"Model-Driven Software Engineering Techniques","score":0.3046000003814697,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11450","display_name":"Model-Driven Software Engineering Techniques","score":0.3046000003814697,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10639","display_name":"Advanced Software Engineering Methodologies","score":0.15469999611377716,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12127","display_name":"Software System Performance and Reliability","score":0.0885000005364418,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4916999936103821},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.4377000033855438},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.31630000472068787},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.23190000653266907}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7376000285148621},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4916999936103821},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.4377000033855438},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36579999327659607},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.31630000472068787},{"id":"https://openalex.org/C199639397","wikidata":"https://www.wikidata.org/wiki/Q1788588","display_name":"Engineering drawing","level":1,"score":0.2980000078678131},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2937999963760376},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.2705000042915344},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25290000438690186},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.23190000653266907}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","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},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf594","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf594","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf594/65050239/btaf594.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:41172269","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41172269","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:europepmc.org:11411691","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12603351","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,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf594","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf594","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf594/65050239/btaf594.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":[],"funders":[{"id":"https://openalex.org/F4320314070","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4415757188.pdf"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1973067702","https://openalex.org/W2002190096","https://openalex.org/W2117047421","https://openalex.org/W2117131162","https://openalex.org/W2120762351","https://openalex.org/W2146005104","https://openalex.org/W2150264767","https://openalex.org/W2165765309","https://openalex.org/W2235737683","https://openalex.org/W2582800429","https://openalex.org/W2682773473","https://openalex.org/W2789843538","https://openalex.org/W2905517925","https://openalex.org/W2944720959","https://openalex.org/W2949376507","https://openalex.org/W2951764279","https://openalex.org/W2963186762","https://openalex.org/W2980310926","https://openalex.org/W3004584205","https://openalex.org/W3032034316","https://openalex.org/W3034581902","https://openalex.org/W3162917414","https://openalex.org/W3165023362","https://openalex.org/W4211115630","https://openalex.org/W4225624933","https://openalex.org/W4234344490","https://openalex.org/W4295896785","https://openalex.org/W4310786235","https://openalex.org/W4313250582","https://openalex.org/W4360612418","https://openalex.org/W4382537978","https://openalex.org/W4390500910","https://openalex.org/W4403526343","https://openalex.org/W4411088098"],"related_works":[],"abstract_inverted_index":{"insilicoSV":[0],"is":[1],"available":[2],"under":[3],"the":[4],"MIT":[5],"license":[6],"at":[7],"https://github.com/PopicLab/insilicoSV":[8],"and":[9],"https://doi.org/10.5281/zenodo.17402009.":[10]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-11-01T00:00:00"}