{"id":"https://openalex.org/W2978221280","doi":"https://doi.org/10.1093/bioinformatics/btz713","title":"SCSsim: an integrated tool for simulating single-cell genome sequencing data","display_name":"SCSsim: an integrated tool for simulating single-cell genome sequencing data","publication_year":2019,"publication_date":"2019-09-15","ids":{"openalex":"https://openalex.org/W2978221280","doi":"https://doi.org/10.1093/bioinformatics/btz713","mag":"2978221280","pmid":"https://pubmed.ncbi.nlm.nih.gov/31584615"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz713","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz713","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/btz713","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000095054","display_name":"Zhenhua Yu","orcid":"https://orcid.org/0000-0001-6526-6991"},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhenhua Yu","raw_affiliation_strings":["Department of Software Engineering, Ningxia University , Yinchuan 750021, China"],"raw_orcid":"https://orcid.org/0000-0001-6526-6991","affiliations":[{"raw_affiliation_string":"Department of Software Engineering, Ningxia University , Yinchuan 750021, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041329635","display_name":"Fang Du","orcid":"https://orcid.org/0000-0002-7377-5259"},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fang Du","raw_affiliation_strings":["Department of Software Engineering, Ningxia University , Yinchuan 750021, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Software Engineering, Ningxia University , Yinchuan 750021, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103823718","display_name":"Xuehong Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuehong Sun","raw_affiliation_strings":["Department of Software Engineering, Ningxia University , Yinchuan 750021, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Software Engineering, Ningxia University , Yinchuan 750021, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100359729","display_name":"Ao Li","orcid":"https://orcid.org/0000-0001-9910-8967"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ao Li","raw_affiliation_strings":["Department of Electronic Science and Technology, University of Science and Technology of China , Hefei 230027, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electronic Science and Technology, University of Science and Technology of China , Hefei 230027, China","institution_ids":["https://openalex.org/I126520041"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5000095054","https://openalex.org/A5100359729"],"corresponding_institution_ids":["https://openalex.org/I126520041","https://openalex.org/I21642278"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7457,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.70517241,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"36","issue":"4","first_page":"1281","last_page":"1282"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9854000210762024,"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"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9854000210762024,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.006899999920278788,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.0007999999797903001,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6851196885108948},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.6496875286102295},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5754269957542419},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5691156387329102},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5611191987991333},{"id":"https://openalex.org/keywords/single-cell-sequencing","display_name":"Single cell sequencing","score":0.5104948282241821},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.432364821434021},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.4318581819534302},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4115094542503357},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.253823459148407},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22548124194145203},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18348640203475952},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10295060276985168},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08343526721000671},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.08214488625526428}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6851196885108948},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.6496875286102295},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5754269957542419},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5691156387329102},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5611191987991333},{"id":"https://openalex.org/C174749747","wikidata":"https://www.wikidata.org/wiki/Q15917269","display_name":"Single cell sequencing","level":5,"score":0.5104948282241821},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.432364821434021},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4318581819534302},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4115094542503357},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.253823459148407},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22548124194145203},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18348640203475952},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10295060276985168},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08343526721000671},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.08214488625526428},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","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":"D017422","descriptor_name":"Sequence Analysis, DNA","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz713","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz713","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31584615","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31584615","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:pubmedcentral.nih.gov:7703785","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7703785","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz713","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz713","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1463133177","display_name":null,"funder_award_id":"61901238","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4199516844","display_name":"\u9762\u5411\u65b0\u4e00\u4ee3\u6d4b\u5e8f\u7684\u764c\u75c7\u62f7\u8d1d\u6570\u5f02\u5e38\u68c0\u6d4b\u53ca\u5176\u5173\u952e\u53d8\u5f02\u7684\u8ba1\u7b97\u53d1\u73b0\u7814\u7a76","funder_award_id":"61571414","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7094097324","display_name":"\u8054\u5408\u57fa\u56e0\u7ec4\u53d8\u5f02\u4e0e\u6570\u5b57\u75c5\u7406\u56fe\u50cf\u7684\u764c\u75c7\u591a\u6a21\u6001\u9884\u540e\u9884\u6d4b\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61971393","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2064977507","https://openalex.org/W2108234281","https://openalex.org/W2119180969","https://openalex.org/W2338882301","https://openalex.org/W2340974016","https://openalex.org/W2343469482","https://openalex.org/W2467325308","https://openalex.org/W2754025713","https://openalex.org/W2783079483","https://openalex.org/W2903388206","https://openalex.org/W2952415324"],"related_works":["https://openalex.org/W2582968398","https://openalex.org/W2099851046","https://openalex.org/W4210751097","https://openalex.org/W3035610982","https://openalex.org/W4211093350","https://openalex.org/W3198690628","https://openalex.org/W3121387483","https://openalex.org/W2951181326","https://openalex.org/W3208139257","https://openalex.org/W1978137972"],"abstract_inverted_index":{"MOTIVATION:":[0],"Allele":[1],"dropout":[2],"(ADO)":[3],"and":[4,17,44,92,101,125],"unbalanced":[5],"amplification":[6,39],"of":[7,13,37,79,86],"alleles":[8],"are":[9,35,157],"main":[10],"technical":[11],"issues":[12,21],"single-cell":[14,138],"sequencing":[15,33,104,113,139],"(SCS),":[16],"effectively":[18],"emulating":[19],"these":[20],"is":[22,131,148],"necessary":[23],"for":[24,48],"reliably":[25],"benchmarking":[26],"SCS-based":[27],"bioinformatics":[28],"tools.":[29],"Unfortunately,":[30],"currently":[31],"available":[32,150,158],"simulators":[34],"free":[36],"whole-genome":[38],"involved":[40],"in":[41,65,117,136],"SCS":[42,50,63],"technique":[43,100],"therefore":[45],"not":[46],"suited":[47],"generating":[49],"datasets.":[51],"We":[52],"develop":[53],"a":[54,66,84,132],"new":[55],"software":[56],"package":[57],"(SCSsim)":[58],"that":[59,129],"can":[60],"efficiently":[61],"simulate":[62],"datasets":[64],"parallel":[67],"fashion":[68],"with":[69,141],"minimal":[70],"user":[71],"intervention.":[72],"SCSsim":[73,130,147],"first":[74],"constructs":[75],"the":[76,95,107],"genome":[77,96,126],"sequence":[78],"single":[80],"cell":[81],"by":[82],"mimicking":[83,137],"complement":[85],"genomic":[87],"variations":[88],"under":[89],"user-controlled":[90],"manner,":[91],"then":[93],"amplifies":[94],"according":[97],"to":[98],"MALBAC":[99],"finally":[102],"yields":[103],"reads":[105],"from":[106],"amplified":[108],"products":[109],"based":[110],"on":[111],"inferred":[112],"profiles.":[114],"Comprehensive":[115],"evaluation":[116],"simulating":[118],"different":[119],"ADO":[120],"rates,":[121],"variation":[122],"detection":[123],"efficiency":[124],"coverage":[127],"demonstrates":[128],"very":[133],"useful":[134],"tool":[135],"data":[140,156],"high":[142],"efficiency.":[143],"AVAILABILITY":[144],"AND":[145],"IMPLEMENTATION:":[146],"freely":[149],"at":[151,159],"https://github.com/qasimyu/scssim.":[152],"SUPPLEMENTARY":[153],"INFORMATION:":[154],"Supplementary":[155],"Bioinformatics":[160],"online.":[161]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2}],"updated_date":"2026-06-18T08:10:14.011955","created_date":"2025-10-10T00:00:00"}
