{"entity": "researcher", "timestamp": "2026-09-26T03:41:51.526Z", "family": "Ye", "given": "Chu-Yu", "initials": "CY", "orcid": "0000-0003-0903-0356", "affiliations": ["Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Zhejiang, China."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/513210186600438192897f04e20762fe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/513210186600438192897f04e20762fe"}}, "publications": [{"entity": "publication", "iuid": "640ec3393ec74ccfbe0c37823591e05a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/640ec3393ec74ccfbe0c37823591e05a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/640ec3393ec74ccfbe0c37823591e05a"}}, "title": "Author Correction: Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision.", "authors": [{"family": "Vromman", "given": "Marieke", "initials": "M", "orcid": "0000-0002-0163-0675", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f05bd8220f04108b1ad8f91f7ed7f2f.json"}}, {"family": "Anckaert", "given": "Jasper", "initials": "J", "orcid": "0000-0001-8144-4639", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8624905b13644c19adaa1fccdd4c060.json"}}, {"family": "Bortoluzzi", "given": "Stefania", "initials": "S"}, {"family": "Buratin", "given": "Alessia", "initials": "A"}, {"family": "Chen", "given": "Chia-Ying", "initials": "CY"}, {"family": "Chu", "given": "Qinjie", "initials": "Q"}, {"family": "Chuang", "given": "Trees-Juen", "initials": "TJ", "orcid": "0000-0002-9661-6672", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3cfb20fbe854dd68a23a566de81ea40.json"}}, {"family": "Dehghannasiri", "given": "Roozbeh", "initials": "R", "orcid": "0000-0001-7413-3437", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f9e46d425474636bbe163a61fdd9152.json"}}, {"family": "Dieterich", "given": "Christoph", "initials": "C", "orcid": "0000-0001-9468-6311", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a96a3cb9e094e478a88a3a212c34460.json"}}, {"family": "Dong", "given": "Xin", "initials": "X"}, {"family": "Flicek", "given": "Paul", "initials": "P", "orcid": "0000-0002-3897-7955", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82bb154b15a149a8b520e3943b3d5124.json"}}, {"family": "Gaffo", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6338-7677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a30412a5d86429d99d9ab62bf7be0b2.json"}}, {"family": "Gu", "given": "Wanjun", "initials": "W"}, {"family": "He", "given": "Chunjiang", "initials": "C", "orcid": "0000-0002-4868-331X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72c3c920875f480eb4a3d6aa4e06d43c.json"}}, {"family": "Hoffmann", "given": "Steve", "initials": "S"}, {"family": "Izuogu", "given": "Osagie", "initials": "O", "orcid": "0000-0003-3116-2558", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06413110cfef43ea92be50d369f69ed5.json"}}, {"family": "Jackson", "given": "Michael S", "initials": "MS"}, {"family": "Jakobi", "given": "Tobias", "initials": "T", "orcid": "0000-0002-3906-0401", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4361576ff7f944b1bd8708407f290405.json"}}, {"family": "Lai", "given": "Eric C", "initials": "EC", "orcid": "0000-0002-8432-5851", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0719ffef7c5d47bb8d0e66a14dfca2c3.json"}}, {"family": "Nuytens", "given": "Justine", "initials": "J", "orcid": "0000-0002-4878-1200", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4eaf70fb292f4b308815a9e0b39c586b.json"}}, {"family": "Salzman", "given": "Julia", "initials": "J"}, {"family": "Santibanez-Koref", "given": "Mauro", "initials": "M"}, {"family": "Stadler", "given": "Peter", "initials": "P", "orcid": "0000-0002-5016-5191", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40908f18c47c41f099937751e398b12b.json"}}, {"family": "Thas", "given": "Olivier", "initials": "O", "orcid": "0000-0001-6442-4089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a5739b9bb3247e38eb8168143b5d31b.json"}}, {"family": "Vanden Eynde", "given": "Eveline", "initials": "E", "orcid": "0000-0003-0454-4171", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e3b146a5ecc4acfb1f9bc1ed2838f1b.json"}}, {"family": "Verniers", "given": "Kimberly", "initials": "K"}, {"family": "Wen", "given": "Guoxia", "initials": "G"}, {"family": "Westholm", "given": "Jakub", "initials": "J", "orcid": "0000-0002-6849-6220", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/966341b184974f0f81c34e36cadd74e0.json"}}, {"family": "Yang", "given": "Li", "initials": "L", "orcid": "0000-0001-8833-7473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0cc4bce4acf4608ae7858bf93ba8d3a.json"}}, {"family": "Ye", "given": "Chu-Yu", "initials": "CY", "orcid": "0000-0003-0903-0356", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/513210186600438192897f04e20762fe.json"}}, {"family": "Yigit", "given": "Nurten", "initials": "N", "orcid": "0000-0003-1183-8688", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e1ebd0c53504b298cf1084f9da6f436.json"}}, {"family": "Yuan", "given": "Guo-Hua", "initials": "GH", "orcid": "0000-0002-8459-3784", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2627d5ff5ae4a1eb318997c53a062a0.json"}}, {"family": "Zhang", "given": "Jinyang", "initials": "J", "orcid": "0000-0002-5163-894X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/214b44ef77db49808a472c46b7f28b41.json"}}, {"family": "Zhao", "given": "Fangqing", "initials": "F", "orcid": "0000-0002-6216-1235", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a68277cdcad3479fa10ca2ad1d756303.json"}}, {"family": "Vandesompele", "given": "Jo", "initials": "J", "orcid": "0000-0001-6274-0184", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bae7636507c4c7ebd2e51cb4c72af8c.json"}}, {"family": "Volders", "given": "Pieter-Jan", "initials": "PJ", "orcid": "0000-0002-2685-2637", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fac44563b164dae90052b9764a8f9ab.json"}}], "type": "published erratum", "published": "2025-02-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "22", "issue": "2", "pages": "448", "issn-l": "1548-7091"}, "abstract": null, "doi": "10.1038/s41592-024-02569-z", "pmid": "39825083", "labels": [], "xrefs": [{"db": "pii", "key": "10.1038/s41592-024-02569-z"}], "notes": [], "created": "2026-09-23T14:37:49.429Z", "modified": "2026-09-23T14:37:49.808Z"}, {"entity": "publication", "iuid": "3c850a13e5b34ee390d3b260eecb0af5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3c850a13e5b34ee390d3b260eecb0af5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3c850a13e5b34ee390d3b260eecb0af5"}}, "title": "Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision.", "authors": [{"family": "Vromman", "given": "Marieke", "initials": "M", "orcid": "0000-0002-0163-0675", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f05bd8220f04108b1ad8f91f7ed7f2f.json"}}, {"family": "Anckaert", "given": "Jasper", "initials": "J", "orcid": "0000-0001-8144-4639", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8624905b13644c19adaa1fccdd4c060.json"}}, {"family": "Bortoluzzi", "given": "Stefania", "initials": "S"}, {"family": "Buratin", "given": "Alessia", "initials": "A"}, {"family": "Chen", "given": "Chia-Ying", "initials": "CY"}, {"family": "Chu", "given": "Qinjie", "initials": "Q"}, {"family": "Chuang", "given": "Trees-Juen", "initials": "TJ", "orcid": "0000-0002-9661-6672", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3cfb20fbe854dd68a23a566de81ea40.json"}}, {"family": "Dehghannasiri", "given": "Roozbeh", "initials": "R", "orcid": "0000-0001-7413-3437", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f9e46d425474636bbe163a61fdd9152.json"}}, {"family": "Dieterich", "given": "Christoph", "initials": "C", "orcid": "0000-0001-9468-6311", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a96a3cb9e094e478a88a3a212c34460.json"}}, {"family": "Dong", "given": "Xin", "initials": "X"}, {"family": "Flicek", "given": "Paul", "initials": "P", "orcid": "0000-0002-3897-7955", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82bb154b15a149a8b520e3943b3d5124.json"}}, {"family": "Gaffo", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6338-7677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a30412a5d86429d99d9ab62bf7be0b2.json"}}, {"family": "Gu", "given": "Wanjun", "initials": "W"}, {"family": "He", "given": "Chunjiang", "initials": "C", "orcid": "0000-0002-4868-331X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72c3c920875f480eb4a3d6aa4e06d43c.json"}}, {"family": "Hoffmann", "given": "Steve", "initials": "S"}, {"family": "Izuogu", "given": "Osagie", "initials": "O", "orcid": "0000-0003-3116-2558", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06413110cfef43ea92be50d369f69ed5.json"}}, {"family": "Jackson", "given": "Michael S", "initials": "MS"}, {"family": "Jakobi", "given": "Tobias", "initials": "T", "orcid": "0000-0002-3906-0401", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4361576ff7f944b1bd8708407f290405.json"}}, {"family": "Lai", "given": "Eric C", "initials": "EC", "orcid": "0000-0002-8432-5851", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0719ffef7c5d47bb8d0e66a14dfca2c3.json"}}, {"family": "Nuytens", "given": "Justine", "initials": "J", "orcid": "0000-0002-4878-1200", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4eaf70fb292f4b308815a9e0b39c586b.json"}}, {"family": "Salzman", "given": "Julia", "initials": "J"}, {"family": "Santibanez-Koref", "given": "Mauro", "initials": "M"}, {"family": "Stadler", "given": "Peter", "initials": "P", "orcid": "0000-0002-5016-5191", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40908f18c47c41f099937751e398b12b.json"}}, {"family": "Thas", "given": "Olivier", "initials": "O", "orcid": "0000-0001-6442-4089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a5739b9bb3247e38eb8168143b5d31b.json"}}, {"family": "Vanden Eynde", "given": "Eveline", "initials": "E", "orcid": "0000-0003-0454-4171", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e3b146a5ecc4acfb1f9bc1ed2838f1b.json"}}, {"family": "Verniers", "given": "Kimberly", "initials": "K"}, {"family": "Wen", "given": "Guoxia", "initials": "G"}, {"family": "Westholm", "given": "Jakub", "initials": "J", "orcid": "0000-0002-6849-6220", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/966341b184974f0f81c34e36cadd74e0.json"}}, {"family": "Yang", "given": "Li", "initials": "L", "orcid": "0000-0001-8833-7473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0cc4bce4acf4608ae7858bf93ba8d3a.json"}}, {"family": "Ye", "given": "Chu-Yu", "initials": "CY", "orcid": "0000-0003-0903-0356", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/513210186600438192897f04e20762fe.json"}}, {"family": "Yigit", "given": "Nurten", "initials": "N", "orcid": "0000-0003-1183-8688", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e1ebd0c53504b298cf1084f9da6f436.json"}}, {"family": "Yuan", "given": "Guo-Hua", "initials": "GH", "orcid": "0000-0002-8459-3784", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2627d5ff5ae4a1eb318997c53a062a0.json"}}, {"family": "Zhang", "given": "Jinyang", "initials": "J", "orcid": "0000-0002-5163-894X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/214b44ef77db49808a472c46b7f28b41.json"}}, {"family": "Zhao", "given": "Fangqing", "initials": "F", "orcid": "0000-0002-6216-1235", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a68277cdcad3479fa10ca2ad1d756303.json"}}, {"family": "Vandesompele", "given": "Jo", "initials": "J", "orcid": "0000-0001-6274-0184", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bae7636507c4c7ebd2e51cb4c72af8c.json"}}, {"family": "Volders", "given": "Pieter-Jan", "initials": "PJ", "orcid": "0000-0002-2685-2637", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fac44563b164dae90052b9764a8f9ab.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "20", "issue": "8", "pages": "1159-1169", "issn-l": "1548-7091"}, "abstract": "The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed using computational tools. Numerous such tools have been developed, but a systematic comparison with orthogonal validation is missing. Here, we set up a circRNA detection tool benchmarking study, in which 16 tools detected more than 315,000 unique circRNAs in three deeply sequenced human cell types. Next, 1,516 predicted circRNAs were validated using three orthogonal methods. Generally, tool-specific precision is high and similar (median of 98.8%, 96.3% and 95.5% for qPCR, RNase R and amplicon sequencing, respectively) whereas the sensitivity and number of predicted circRNAs (ranging from 1,372 to 58,032) are the most significant differentiators. Of note, precision values are lower when evaluating low-abundance circRNAs. We also show that the tools can be used complementarily to increase detection sensitivity. Finally, we offer recommendations for future circRNA detection and validation.", "doi": "10.1038/s41592-023-01944-6", "pmid": "37443337", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1960069"}, {"db": "pmc", "key": "PMC10870000"}, {"db": "pii", "key": "10.1038/s41592-023-01944-6"}], "notes": [], "created": "2026-09-23T07:39:36.960Z", "modified": "2026-09-23T07:39:37.901Z"}]}