{"id":"https://openalex.org/W4310937878","doi":"https://doi.org/10.1093/bioinformatics/btac792","title":"Synggen: fast and data-driven generation of synthetic heterogeneous NGS cancer data","display_name":"Synggen: fast and data-driven generation of synthetic heterogeneous NGS cancer data","publication_year":2022,"publication_date":"2022-12-09","ids":{"openalex":"https://openalex.org/W4310937878","doi":"https://doi.org/10.1093/bioinformatics/btac792","pmid":"https://pubmed.ncbi.nlm.nih.gov/36484701"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac792","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac792","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"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":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btac792","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071707913","display_name":"Riccardo Scandino","orcid":"https://orcid.org/0000-0002-1640-5307"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Riccardo Scandino","raw_affiliation_strings":["Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento , Trento 38123, Italy"],"raw_orcid":"https://orcid.org/0000-0002-1640-5307","affiliations":[{"raw_affiliation_string":"Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento , Trento 38123, Italy","institution_ids":["https://openalex.org/I193223587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076394887","display_name":"Federico Calabrese","orcid":"https://orcid.org/0000-0002-2804-3235"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Federico Calabrese","raw_affiliation_strings":["Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento , Trento 38123, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento , Trento 38123, Italy","institution_ids":["https://openalex.org/I193223587"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045520201","display_name":"Alessandro Romanel","orcid":"https://orcid.org/0000-0003-4855-8620"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Alessandro Romanel","raw_affiliation_strings":["Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento , Trento 38123, Italy"],"raw_orcid":"https://orcid.org/0000-0003-4855-8620","affiliations":[{"raw_affiliation_string":"Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento , Trento 38123, Italy","institution_ids":["https://openalex.org/I193223587"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5045520201"],"corresponding_institution_ids":["https://openalex.org/I193223587"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5887,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.60960559,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.7588000297546387,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.7588000297546387,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.03629999980330467,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.029899999499320984,"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/exome","display_name":"Exome","score":0.6642370820045471},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5819586515426636},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.5709806680679321},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5701013803482056},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5332156419754028},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5008842945098877},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.47939395904541016},{"id":"https://openalex.org/keywords/germline","display_name":"Germline","score":0.462864488363266},{"id":"https://openalex.org/keywords/precision-medicine","display_name":"Precision medicine","score":0.441635400056839},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3228532075881958},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31711578369140625},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2999127507209778},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2290457785129547},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.12529677152633667},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.12412446737289429},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11483511328697205}],"concepts":[{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.6642370820045471},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5819586515426636},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.5709806680679321},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5701013803482056},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5332156419754028},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5008842945098877},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.47939395904541016},{"id":"https://openalex.org/C109825262","wikidata":"https://www.wikidata.org/wiki/Q1139164","display_name":"Germline","level":3,"score":0.462864488363266},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.441635400056839},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3228532075881958},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31711578369140625},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2999127507209778},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2290457785129547},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.12529677152633667},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.12412446737289429},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11483511328697205},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","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":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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059472","descriptor_name":"Exome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059472","descriptor_name":"Exome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059472","descriptor_name":"Exome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac792","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac792","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"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:36484701","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36484701","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:iris.unitn.it:11572/369948","is_oa":true,"landing_page_url":"https://academic.oup.com/bioinformatics/article/39/1/btac792/6885441?login=true","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac792/48520879/btac792.pdf","source":{"id":"https://openalex.org/S4306401913","display_name":"Institutional Research Information System (Universit\u00e0 degli Studi di Trento)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I193223587","host_organization_name":"University of Trento","host_organization_lineage":["https://openalex.org/I193223587"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9825741","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825741","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,"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/btac792","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac792","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"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":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W2520919442","https://openalex.org/W2558624268","https://openalex.org/W2796038592","https://openalex.org/W2887128493","https://openalex.org/W2906896602","https://openalex.org/W2996823610","https://openalex.org/W2999932323","https://openalex.org/W3176360473"],"related_works":["https://openalex.org/W2093932542","https://openalex.org/W2043256480","https://openalex.org/W2772505697","https://openalex.org/W3083501552","https://openalex.org/W2400191746","https://openalex.org/W1983406990","https://openalex.org/W2484239316","https://openalex.org/W3024198590","https://openalex.org/W4367844067","https://openalex.org/W2106924416"],"abstract_inverted_index":{"SUMMARY:":[0],"Whole-exome":[1],"and":[2,13,25,58,62,77,85,97],"targeted":[3,63],"sequencing":[4,64],"are":[5,28,92,117],"widely":[6],"utilized":[7],"both":[8],"in":[9,14,29,87],"translational":[10],"cancer":[11,60,90],"genomics":[12],"the":[15,35,52,69],"setting":[16],"of":[17,22,38,55,71],"precision":[18],"medicine.":[19],"The":[20],"benchmarking":[21],"computational":[23],"methods":[24],"tools":[26],"that":[27],"continuous":[30],"development":[31],"is":[32,108],"fundamental":[33],"for":[34,51],"correct":[36],"interpretation":[37],"somatic":[39,80],"genomic":[40,81],"profiling":[41],"results.":[42],"To":[43],"this":[44],"aim":[45],"we":[46],"developed":[47],"synggen,":[48],"a":[49],"tool":[50],"fast":[53],"generation":[54],"large-scale":[56],"realistic":[57],"heterogeneous":[59],"whole-exome":[61],"synthetic":[65,89],"datasets,":[66],"which":[67],"enables":[68],"incorporation":[70],"phased":[72],"germline":[73],"single":[74],"nucleotide":[75],"polymorphisms":[76],"complex":[78],"allele-specific":[79],"events.":[82],"Synggen":[83],"performances":[84],"effectiveness":[86],"generating":[88],"data":[91,116],"shown":[93],"across":[94],"different":[95,99],"scenarios":[96],"considering":[98],"platforms":[100],"with":[101],"distinct":[102],"characteristics.":[103],"AVAILABILITY":[104],"AND":[105],"IMPLEMENTATION:":[106],"synggen":[107],"freely":[109],"available":[110,118],"at":[111,119],"https://bitbucket.org/CibioBCG/synggen/.":[112],"SUPPLEMENTARY":[113],"INFORMATION:":[114],"Supplementary":[115],"Bioinformatics":[120],"online.":[121]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-26T07:53:14.480251","created_date":"2025-10-10T00:00:00"}
