{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T21:32:23Z","timestamp":1771018343053,"version":"3.50.1"},"reference-count":232,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","issue":"2","license":[{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/ieeexplore.ieee.org\/Xplorehelp\/downloads\/license-information\/IEEE.html"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["72293581"],"award-info":[{"award-number":["72293581"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["72274152"],"award-info":[{"award-number":["72274152"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62402376"],"award-info":[{"award-number":["62402376"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62572389"],"award-info":[{"award-number":["62572389"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IIEEE Trans. Software Eng."],"published-print":{"date-parts":[[2026,2]]},"DOI":"10.1109\/tse.2025.3641225","type":"journal-article","created":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T18:40:10Z","timestamp":1765219210000},"page":"595-617","source":"Crossref","is-referenced-by-count":0,"title":["Reaching Software Quality for Bioinformatics Applications: How Far Are We?"],"prefix":"10.1109","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7173-7793","authenticated-orcid":false,"given":"Xiaoyan","family":"Zhu","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0759-6866","authenticated-orcid":false,"given":"Tianxiang","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3850-5680","authenticated-orcid":false,"given":"Xin","family":"Lai","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-0425-3646","authenticated-orcid":false,"given":"Xin","family":"Lian","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-1680-5756","authenticated-orcid":false,"given":"Hangyu","family":"Cheng","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3862-6557","authenticated-orcid":false,"given":"Jiayin","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"263","reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbx100"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.59717\/j.xinn-life.2024.100083"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01891-9"},{"key":"ref4","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2016.10.019"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.7717\/peerj-cs.839"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2021.12.001"},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.1177\/00368504211010570"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005772"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005265"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.1109\/CSEET.2009.44"},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0224288"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1109\/ICECDS.2017.8389562"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1007\/s10664-025-10620-6"},{"key":"ref14","doi-asserted-by":"publisher","DOI":"10.1007\/s10664-022-10184-9"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1016\/b978-0-323-89775-4.00006-7"},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1016\/j.comtox.2022.100248"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1057\/s41599-022-01141-4"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1649-8"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1011920"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.1126\/science.314.5807.1856"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw139"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-024-03343-2"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1016\/j.eclinm.2021.100856"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqab019"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1715-2"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0881-8"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-91602-6_6"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1007\/s10664-020-09880-1"},{"key":"ref29","first-page":"27865","article-title":"Self-supervised bug detection and repair","volume-title":"Proc. Adv. Neural Inf. Process. Syst.","volume":"34","author":"Allamanis","year":"2021"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1145\/3597926.3598135"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1109\/ISSRE62328.2024.00022"},{"key":"ref32","doi-asserted-by":"publisher","DOI":"10.1109\/TSE.2024.3427815"},{"key":"ref33","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijsu.2021.105906"},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1109\/TSE.2024.3363611"},{"key":"ref35","article-title":"Empirical study on software and process quality in bioinformatics tools","author":"Ferenc","year":"2022","journal-title":"bioRxiv"},{"key":"ref36","article-title":"Coverity: Coverity Scan Static Analysis","year":"2025"},{"key":"ref37","article-title":"SonarQube","year":"2025"},{"key":"ref38","first-page":"385","article-title":"CoBOT: Static C\/C++ Bug detection in the presence of incomplete code","volume-title":"Proc. IEEE\/ACM 26th Int. Conf. Program Comprehension (ICPC)","author":"Gao","year":"2018"},{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.1109\/TSE.2020.3004525"},{"key":"ref40","article-title":"SonarQube C++ Community plugin","year":"2025"},{"key":"ref41","article-title":"LintR: A \u2018Linter\u2019 for R Code","author":"Hester","year":"2025"},{"key":"ref42","doi-asserted-by":"publisher","DOI":"10.1109\/APSEC.2012.93"},{"key":"ref43","doi-asserted-by":"publisher","DOI":"10.1109\/ICMLA.2018.00224"},{"key":"ref44","doi-asserted-by":"publisher","DOI":"10.1109\/ACCESS.2023.3339994"},{"key":"ref45","doi-asserted-by":"publisher","DOI":"10.1098\/rspl.1896.0076"},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.1002\/9780470479216.corpsy0491"},{"key":"ref47","doi-asserted-by":"publisher","DOI":"10.1080\/01621459.1952.10483441"},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.18653\/v1\/2024.acl-long.810"},{"key":"ref49","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-15-S16-S15"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1145\/3193977.3193981","article-title":"Quality assurance of bioinformatics software: A case study of testing a biomedical text processing tool using metamorphic testing","volume-title":"Proc. 3rd Int. Workshop Metamorphic Testing","author":"Srinivasan","year":"2018"},{"key":"ref51","doi-asserted-by":"publisher","DOI":"10.1109\/TSE.2022.3160155"},{"key":"ref52","doi-asserted-by":"publisher","DOI":"10.1109\/TSE.2022.3150302"},{"key":"ref53","article-title":"Xanitizer by rigs it - Because security matters","year":"2024"},{"key":"ref54","article-title":"Find security bugs","year":"2024"},{"key":"ref55","doi-asserted-by":"publisher","DOI":"10.1145\/3368308.3415419"},{"key":"ref56","doi-asserted-by":"publisher","DOI":"10.1145\/3319535.3345659"},{"key":"ref57","doi-asserted-by":"publisher","DOI":"10.1109\/ASE.2017.8115707"},{"key":"ref58","article-title":"Cryptoapi-bench","year":"2024"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1145\/2901739.2903506","article-title":"MUBench: A benchmark for API-misuse detectors","volume-title":"Proc. IEEE\/ACM 13th Work. Conf. Mining Softw. Repositories (MSR)","author":"Amann","year":"2016"},{"key":"ref60","article-title":"OWASP Benchmark","year":"2024"},{"key":"ref61","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-22333-4_17"},{"key":"ref62","article-title":"JLint","year":"2024"},{"key":"ref63","doi-asserted-by":"publisher","DOI":"10.1145\/1052883.1052895"},{"key":"ref64","article-title":"NIST SAMATE: Static analysis tool exposition (SATE) IV","year":"2024"},{"key":"ref65","article-title":"PMD: An extensible cross-language static code analyzer","year":"2024"},{"key":"ref66","doi-asserted-by":"publisher","DOI":"10.1109\/TSMCA.2005.853493"},{"key":"ref67","doi-asserted-by":"publisher","DOI":"10.1145\/3359061.3361079"},{"key":"ref68","doi-asserted-by":"publisher","DOI":"10.1109\/SANER.2016.105"},{"key":"refb1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-017-1469-3"},{"key":"refb2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2227-7"},{"key":"refb3","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2017.06.003"},{"key":"refb4","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giz087"},{"key":"refb5","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000685"},{"key":"refb6","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3407"},{"key":"refb7","doi-asserted-by":"publisher","DOI":"10.1038\/s43018-022-00356-3"},{"key":"refb8","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"refb9","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts277"},{"key":"refb10","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"refb11","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt547"},{"key":"refb12","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz716"},{"key":"refb13","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"refb14","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbw054"},{"key":"refb15","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-00870-2"},{"key":"refb16","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013"},{"key":"refb17","doi-asserted-by":"publisher","DOI":"10.1109\/IPDPS.2019.00041"},{"key":"refb18","doi-asserted-by":"publisher","DOI":"10.1038\/srep33892"},{"key":"refb19","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqac066"},{"key":"refb20","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-17281-7"},{"key":"refb21","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14825"},{"key":"refb22","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-1175-6"},{"key":"refb23","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4401"},{"key":"refb24","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1645-z"},{"key":"refb25","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006378"},{"key":"refb26","doi-asserted-by":"publisher","DOI":"10.1038\/sdata.2017.151"},{"key":"refb27","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004873"},{"key":"refb28","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1006599"},{"key":"refb29","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx631"},{"key":"refb30","doi-asserted-by":"publisher","DOI":"10.1002\/ijc.33749"},{"key":"refb31","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt534"},{"key":"refb32","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2450"},{"key":"refb33","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15295-9"},{"key":"refb34","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx057"},{"key":"refb35","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0893-4"},{"key":"refb36","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1189-z"},{"key":"refb37","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4235"},{"key":"refb38","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts378"},{"key":"refb39","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw372"},{"key":"refb40","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1721085115"},{"key":"refb41","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.4958"},{"key":"refb42","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01101-x"},{"key":"refb43","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa1011"},{"key":"refb44","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1449-6"},{"key":"refb45","doi-asserted-by":"publisher","DOI":"10.1101\/gr.271908.120"},{"key":"refb46","article-title":"Robust foreground detection in somatic copy number data","author":"Deshpande","year":"2019","journal-title":"bioRxiv"},{"key":"refb47","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.12.045"},{"key":"refb48","article-title":"Laplacian eigenmaps and principal curves for high resolution pseudotemporal ordering of single-cell RNA-seq profiles","author":"Campbell","year":"2015","journal-title":"bioRxiv"},{"key":"refb49","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-25131-3"},{"key":"refb50","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw732"},{"key":"refb51","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.107"},{"key":"refb52","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-1176-5"},{"key":"refb53","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07234-6"},{"key":"refb54","article-title":"Haplotype-based variant detection from short-read sequencing","author":"Garrison","year":"2012"},{"key":"refb55","doi-asserted-by":"publisher","DOI":"10.1038\/gim.2017.26"},{"key":"refb56","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa1081"},{"key":"refb57","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.aal2192"},{"key":"refb58","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02423-x"},{"key":"refb59","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac757"},{"key":"refb60","doi-asserted-by":"publisher","DOI":"10.1101\/gr.263566.120"},{"key":"refb61","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02269-8"},{"key":"refb62","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4267"},{"key":"refb63","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac166"},{"key":"refb64","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-35365-9"},{"key":"refb65","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-45301-0"},{"key":"refb66","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3519"},{"key":"refb67","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-024-01057-0"},{"key":"refb68","article-title":"K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data","author":"Wagner","year":"2018","journal-title":"bioRxiv"},{"key":"refb69","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa888"},{"key":"refb70","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv803"},{"key":"refb71","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-6-r84"},{"key":"refb72","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty1044"},{"key":"refb73","doi-asserted-by":"publisher","DOI":"10.1101\/gr.239244.118"},{"key":"refb74","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv710"},{"key":"refb75","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1812-2"},{"key":"refb76","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-00971-x"},{"key":"refb77","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.11087.1"},{"key":"refb78","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.11.038"},{"key":"refb79","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02168-z"},{"key":"refb80","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btab705"},{"key":"refb81","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3988"},{"key":"refb82","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-0969-x"},{"key":"refb83","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3835"},{"key":"refb84","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw354"},{"key":"refb85","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005944"},{"key":"refb86","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19894-4"},{"key":"refb87","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-022-08357-3"},{"key":"refb88","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqaa021"},{"key":"refb89","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.13511.3"},{"issue":"null","key":"refb90","first-page":"849","article-title":"NIMFA: A python library for nonnegative matrix factorization","volume":"13","author":"\u017ditnik","year":"2012","journal-title":"J. Mach. Learn. Res."},{"key":"refb91","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-021-00573-7"},{"key":"refb92","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-00861-3"},{"key":"refb93","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw004"},{"key":"refb94","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0929-9"},{"key":"refb95","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-0930-z"},{"key":"refb96","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giaa145"},{"key":"refb97","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-0984-y"},{"key":"refb98","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx817"},{"key":"refb99","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2017.01.017"},{"key":"refb100","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02737-4"},{"key":"refb101","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-017-1621-0"},{"key":"refb102","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0602-8"},{"key":"refb103","doi-asserted-by":"publisher","DOI":"10.1155\/2015\/621690"},{"key":"refb104","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-023-00944-2"},{"key":"refb105","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2019.10.131"},{"key":"refb106","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-323"},{"key":"refb107","doi-asserted-by":"publisher","DOI":"10.1101\/gr.234062.117"},{"key":"refb108","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-021-04174-9"},{"key":"refb109","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-018-0033-z"},{"key":"refb110","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1200-8"},{"key":"refb111","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa1039"},{"key":"refb112","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1382-0"},{"key":"refb113","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae053"},{"key":"refb114","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-0825-9"},{"key":"refb115","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-021-04489-7"},{"key":"refb116","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003665"},{"key":"refb117","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaf072"},{"key":"refb118","doi-asserted-by":"publisher","DOI":"10.3390\/genes10070531"},{"key":"refb119","doi-asserted-by":"publisher","DOI":"10.1016\/j.gpb.2020.09.002"},{"key":"refb120","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3102"},{"key":"refb121","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx194"},{"key":"refb122","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab366"},{"key":"refb123","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-1109-3"},{"key":"refb124","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-13665-w"},{"key":"refb125","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0947-7"},{"key":"refb126","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx315"},{"key":"refb127","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-019-2797-2"},{"key":"refb128","article-title":"scSVA: An interactive tool for big data visualization and exploration in single-cell omics","author":"Tabaka","year":"2019","journal-title":"bioRxiv"},{"key":"refb129","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-016-0335-7"},{"key":"refb130","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3854"},{"key":"refb131","doi-asserted-by":"publisher","DOI":"10.1242\/dev.201873"},{"key":"refb132","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01206-w"},{"key":"refb133","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01767-y"},{"key":"refb134","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw572"},{"key":"refb135","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4207"},{"key":"refb136","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv368"},{"key":"refb137","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004575"},{"key":"refb138","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-018-0276-y"},{"key":"refb139","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1525"},{"key":"refb140","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1540-z"},{"key":"refb141","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-02024-y"},{"key":"refb142","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giaa151"},{"key":"refb143","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.102"},{"key":"refb144","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty807"},{"key":"refb145","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"refb146","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-018-0051-x"},{"key":"refb147","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-022-05008-y"},{"key":"refb148","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv751"},{"key":"refb149","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz492"},{"key":"refb150","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx754"},{"key":"refb151","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku181"},{"key":"refb152","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4634"},{"key":"refb153","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.11997.1"},{"key":"refb154","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw111"},{"key":"refb155","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw797"},{"key":"refb156","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1009123"},{"key":"refb157","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12549"},{"key":"refb158","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"refb159","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1575-1"},{"key":"refb160","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2016.05.007"},{"key":"refb161","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad074"},{"key":"refb162","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004572"},{"key":"refb163","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0669-3"},{"key":"refb164","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giy059"}],"container-title":["IEEE Transactions on Software Engineering"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx8\/32\/11395383\/11281877.pdf?arnumber=11281877","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T20:49:51Z","timestamp":1771015791000},"score":1,"resource":{"primary":{"URL":"https:\/\/ieeexplore.ieee.org\/document\/11281877\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2]]},"references-count":232,"journal-issue":{"issue":"2"},"URL":"https:\/\/doi.org\/10.1109\/tse.2025.3641225","relation":{},"ISSN":["0098-5589","1939-3520","2326-3881"],"issn-type":[{"value":"0098-5589","type":"print"},{"value":"1939-3520","type":"electronic"},{"value":"2326-3881","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2]]}}}