{"id":"https://openalex.org/W2747029575","doi":"https://doi.org/10.1145/3107411.3108188","title":"Varsimlab","display_name":"Varsimlab","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2747029575","doi":"https://doi.org/10.1145/3107411.3108188","mag":"2747029575"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3108188","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3108188","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043383193","display_name":"Abdelrahman Hosny","orcid":"https://orcid.org/0000-0003-4020-7973"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Abdelrahman Hosny","raw_affiliation_strings":["University of Connecticut, Storrs, CT, USA"],"affiliations":[{"raw_affiliation_string":"University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075494433","display_name":"Fatima Zare","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fatima Zare","raw_affiliation_strings":["University of Connecticut, Storrs, CT, USA"],"affiliations":[{"raw_affiliation_string":"University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010254642","display_name":"Sheida Nabavi","orcid":"https://orcid.org/0000-0002-5996-1020"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sheida Nabavi","raw_affiliation_strings":["University of Connecticut, Storrs, CT, USA"],"affiliations":[{"raw_affiliation_string":"University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5043383193"],"corresponding_institution_ids":["https://openalex.org/I140172145"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12420742,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"581","last_page":"581"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9847000241279602,"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":0.9847000241279602,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9807999730110168,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9805999994277954,"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/indel","display_name":"Indel","score":0.6713407039642334},{"id":"https://openalex.org/keywords/structural-variation","display_name":"Structural variation","score":0.6608960032463074},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.6361041069030762},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5602319836616516},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5243849158287048},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5180254578590393},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.44876739382743835},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.4326293468475342},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4209856688976288},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.4081129729747772},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4020857810974121},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3509349524974823},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.12035974860191345}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.6713407039642334},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.6608960032463074},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.6361041069030762},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5602319836616516},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5243849158287048},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5180254578590393},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.44876739382743835},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4326293468475342},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4209856688976288},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.4081129729747772},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4020857810974121},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3509349524974823},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.12035974860191345}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3107411.3108188","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3108188","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3134412476","https://openalex.org/W2842676186","https://openalex.org/W2160911017","https://openalex.org/W2005276393","https://openalex.org/W2553356891","https://openalex.org/W2091911799","https://openalex.org/W3005131427","https://openalex.org/W2029233263","https://openalex.org/W2949103014","https://openalex.org/W2142819802"],"abstract_inverted_index":{"Individuals":[0],"of":[1,13,18,36,40,109,163,259,291,339],"a":[2,34,164,208,232,267,283,327,336],"species":[3],"have":[4,126,157,171,230],"similar":[5],"characteristics":[6],"but":[7],"they":[8,82,186],"are":[9,151,187,195],"rarely":[10],"identical":[11],"because":[12],"the":[14,19,107,148,161,225,260,289,311,314],"genomic":[15,21,41,130,205,344],"variations.":[16],"One":[17],"important":[20,51],"variations":[22,77,206,246],"is":[23,33,316,331],"structural":[24,110,245],"variation":[25,30,111,131],"(SV),":[26],"including":[27],"copy":[28],"number":[29],"(CNV),":[31],"which":[32,237],"result":[35,103],"amplifications":[37],"or":[38],"deletions":[39,73],"regions.":[42],"It":[43,256],"has":[44],"been":[45,127,158,172],"shown":[46],"that":[47,100,150],"SV":[48],"plays":[49],"an":[50,239,271],"role":[52],"in":[53,104,145],"phenotypic":[54,118],"diversity":[55],"and":[56,69,72,96,121,155,183,192,211,247,252,263,279,302,305,318],"evolution.":[57],"A":[58],"Genome":[59],"encompasses":[60],"other":[61,212],"aberrations":[62],"such":[63,180,215,295],"as":[64,181,216,296,335],"Single":[65],"Nucleotide":[66],"Polymorphism":[67],"(SNP)":[68],"small":[70],"insertions":[71],"(Indels).":[74],"Although":[75],"genetic":[76],"contribute":[78],"to":[79,89,190,197,207,220,223,243,249,276,310,324,333,342],"our":[80],"uniqueness,":[81],"can":[83],"comprise":[84],"critical":[85],"developmental":[86],"genes":[87,94],"leading":[88],"gene":[90,97],"dosage":[91],"imbalances,":[92],"new":[93],"creation,":[95],"structures":[98],"reshaping":[99],"ultimately":[101],"may":[102],"disease.":[105],"Understanding":[106],"mechanisms":[108],"formation":[112],"helps":[113],"us":[114],"better":[115],"understand":[116],"human":[117],"diversity,":[119],"evolution":[120],"diseases":[122],"susceptibility.":[123],"Computational":[124],"tools":[125,149,262,341],"developed":[128,173,231],"for":[129,153,174,321],"detection":[132,154],"using":[133],"next-generation":[134],"sequencing":[135,177],"(NGS)":[136],"data.":[137],"However,":[138,185],"with":[139],"no":[140],"prior":[141],"knowledge":[142],"about":[143],"variants":[144],"real":[146],"samples,":[147],"used":[152,222,275],"analysis":[156],"hindered":[159],"by":[160],"lack":[162],"gold":[165],"standard":[166,268],"benchmark.":[167],"Some":[168],"multi-variant":[169],"simulators":[170,202],"whole":[175],"genome":[176],"(WGS)":[178],"data":[179],"SInC":[182],"SCNVSim.":[184],"not":[188],"easy":[189,320],"use":[191,325],"technical":[193],"skills":[194],"required":[196],"run":[198],"them.":[199],"Moreover,":[200],"those":[201],"only":[203],"apply":[204],"reference":[209],"file;":[210],"software":[213,285],"tools,":[214],"ART":[217],"simulator,":[218],"need":[219],"be":[221],"generate":[224,250],"sequenced":[226],"short":[227,254,307],"reads.":[228,255,308],"We":[229],"user-friendly":[233],"automated":[234],"pipeline,":[235],"VarSimLab,":[236],"offers":[238],"integrated":[240,340],"web-based":[241],"suite":[242,338],"simulate":[244],"also":[248],"WGS":[251],"WES":[253],"utilizes":[257],"some":[258],"existing":[261],"packages":[264],"them":[265],"into":[266,282],"Docker":[269,312],"image;":[270],"open":[272],"source":[273],"technology":[274],"package":[277],"applications":[278],"their":[280],"dependencies":[281],"standardized":[284],"container.":[286],"VarSimLab":[287,330],"automates":[288],"process":[290],"simulating":[292],"tumor":[293,303],"genotypes":[294],"SNPs,":[297],"Indels,":[298],"CNVs,":[299],"transition/transversion,":[300],"ploidy":[301],"sub-clone":[304],"generating":[306],"Thanks":[309],"technology,":[313],"pipeline":[315],"platform-independent":[317],"super":[319],"non-technical":[322],"scientists":[323],"from":[326],"web":[328],"browser.":[329],"designed":[332],"grow":[334],"full":[337],"analyze":[343],"aberrations.":[345]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2017-08-31T00:00:00"}
