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Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision.
Vromman M, Anckaert J, Bortoluzzi S, Buratin A, Chen CY, Chu Q, Chuang TJ, Dehghannasiri R, Dieterich C, Dong X, Flicek P, Gaffo E, Gu W, He C, Hoffmann S, Izuogu O, Jackson MS, Jakobi T, Lai EC, Nuytens J, Salzman J, Santibanez-Koref M, Stadler P, Thas O, Vanden Eynde E, Verniers K, Wen G, Westholm J, Yang L, Ye CY, Yigit N, Yuan GH, Zhang J, Zhao F, Vandesompele J, Volders PJ. Vromman M, et al. Among authors: yang l. Nat Methods. 2023 Aug;20(8):1159-1169. doi: 10.1038/s41592-023-01944-6. Epub 2023 Jul 13. Nat Methods. 2023. PMID: 37443337 Free PMC article.
Comparative analysis of the transcriptome across distant species.
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Gerstein MB, et al. Among authors: yang l. Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424. Nature. 2014. PMID: 25164755 Free PMC article.
Screening for functional circular RNAs using the CRISPR-Cas13 system.
Li S, Li X, Xue W, Zhang L, Yang LZ, Cao SM, Lei YN, Liu CX, Guo SK, Shan L, Wu M, Tao X, Zhang JL, Gao X, Zhang J, Wei J, Li J, Yang L, Chen LL. Li S, et al. Among authors: yang lz, yang l. Nat Methods. 2021 Jan;18(1):51-59. doi: 10.1038/s41592-020-01011-4. Epub 2020 Dec 7. Nat Methods. 2021. PMID: 33288960
A guide to naming eukaryotic circular RNAs.
Chen LL, Bindereif A, Bozzoni I, Chang HY, Matera AG, Gorospe M, Hansen TB, Kjems J, Ma XK, Pek JW, Rajewsky N, Salzman J, Wilusz JE, Yang L, Zhao F. Chen LL, et al. Among authors: yang l. Nat Cell Biol. 2023 Jan;25(1):1-5. doi: 10.1038/s41556-022-01066-9. Nat Cell Biol. 2023. PMID: 36658223 Free PMC article.
Therapeutic application of circular RNA aptamers in a mouse model of psoriasis.
Guo SK, Liu CX, Xu YF, Wang X, Nan F, Huang Y, Li S, Nan S, Li L, Kon E, Li C, Wei MY, Su R, Wei J, Peng S, Ad-El N, Liu J, Peer D, Chen T, Yang L, Chen LL. Guo SK, et al. Among authors: yang l. Nat Biotechnol. 2024 Apr 23. doi: 10.1038/s41587-024-02204-4. Online ahead of print. Nat Biotechnol. 2024. PMID: 38653797
Regulation of circRNA biogenesis.
Chen LL, Yang L. Chen LL, et al. Among authors: yang l. RNA Biol. 2015;12(4):381-8. doi: 10.1080/15476286.2015.1020271. RNA Biol. 2015. PMID: 25746834 Free PMC article. Review.
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