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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: ye cy. 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.
Characteristics of plant circular RNAs.
Chu Q, Bai P, Zhu X, Zhang X, Mao L, Zhu QH, Fan L, Ye CY. Chu Q, et al. Among authors: ye cy. Brief Bioinform. 2020 Jan 17;21(1):135-143. doi: 10.1093/bib/bby111. Brief Bioinform. 2020. PMID: 30445438
Recent origination of circular RNAs in plants.
Chu Q, Ding Y, Xu X, Ye CY, Zhu QH, Guo L, Fan L. Chu Q, et al. Among authors: ye cy. New Phytol. 2022 Jan;233(1):515-525. doi: 10.1111/nph.17798. Epub 2021 Oct 29. New Phytol. 2022. PMID: 34643280 Free article.
PlantcircBase: A Database for Plant Circular RNAs.
Chu Q, Zhang X, Zhu X, Liu C, Mao L, Ye C, Zhu QH, Fan L. Chu Q, et al. Mol Plant. 2017 Aug 7;10(8):1126-1128. doi: 10.1016/j.molp.2017.03.003. Epub 2017 Mar 16. Mol Plant. 2017. PMID: 28315753 Free article. No abstract available.
Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed.
Guo L, Qiu J, Ye C, Jin G, Mao L, Zhang H, Yang X, Peng Q, Wang Y, Jia L, Lin Z, Li G, Fu F, Liu C, Chen L, Shen E, Wang W, Chu Q, Wu D, Wu S, Xia C, Zhang Y, Zhou X, Wang L, Wu L, Song W, Wang Y, Shu Q, Aoki D, Yumoto E, Yokota T, Miyamoto K, Okada K, Kim DS, Cai D, Zhang C, Lou Y, Qian Q, Yamaguchi H, Yamane H, Kong CH, Timko MP, Bai L, Fan L. Guo L, et al. Nat Commun. 2017 Oct 18;8(1):1031. doi: 10.1038/s41467-017-01067-5. Nat Commun. 2017. PMID: 29044108 Free PMC article.
The Circular RNA Profiles of Colorectal Tumor Metastatic Cells.
Jiang W, Zhang X, Chu Q, Lu S, Zhou L, Lu X, Liu C, Mao L, Ye C, Timko MP, Fan L, Ju H. Jiang W, et al. Front Genet. 2018 Feb 9;9:34. doi: 10.3389/fgene.2018.00034. eCollection 2018. Front Genet. 2018. PMID: 29479369 Free PMC article.
RiceRelativesGD: a genomic database of rice relatives for rice research.
Mao L, Chen M, Chu Q, Jia L, Sultana MH, Wu D, Kong X, Qiu J, Ye CY, Zhu QH, Chen X, Fan L. Mao L, et al. Among authors: ye cy. Database (Oxford). 2019 Jan 1;2019:baz110. doi: 10.1093/database/baz110. Database (Oxford). 2019. PMID: 31560050 Free PMC article.
The genome of Eucalyptus grandis.
Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan AR, Hussey SG, Pinard D, van der Merwe K, Singh P, van Jaarsveld I, Silva-Junior OB, Togawa RC, Pappas MR, Faria DA, Sansaloni CP, Petroli CD, Yang X, Ranjan P, Tschaplinski TJ, Ye CY, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente HS, Saidi N, Cassan-Wang H, Dunand C, Hefer CA, Bornberg-Bauer E, Kersting AR, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd AE, Liston A, Spatafora JW, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Külheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel SH, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones RC, Steane DA, Vaillancourt RE, Potts BM, Joubert F, Barry K, Pappas GJ, Strauss SH, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar DS, Schmutz J. Myburg AA, et al. Among authors: ye cy. Nature. 2014 Jun 19;510(7505):356-62. doi: 10.1038/nature13308. Epub 2014 Jun 11. Nature. 2014. PMID: 24919147
165 results