AboutSoftwares
- CIRI2 A de novo circular RNA identification tool
- CIRI-AS A de novo detection tool for circRNA internal components and alternative splicing events based on spliced junction signatures
- CIRI-full An accurate, high-throughput approach that uses both BSJ and reverse overlap (RO) features to reconstruct and quantify full-length circular RNAs
- CIRI-vis A tool for visualizing alignments of BSJ & RO merged reads and estimating the related abundance of isoforms
- CIRIquant A comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data
- CIRI-long Circular RNA Identification for Long-Reads Nanopore Sequencing Data
Databases
Articles
- Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing.
Nature Communications (2022), doi.org/10.1038/s41467-022-30963-8.
Wu Wanying^, Zhang Jinyang^, Cao Xiaofei, Cai Zhengyi, Zhao Fangqing - Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long.
Nature Biotechnology (2021), doi.org/10.1038/s41587-021-00842-6.
Zhang Jinyang^, Hou Linlin^, Zuo Zhengqiang^, Ji Peifeng, Zhang Xiaorong, Xue Yuanchao, Zhao Fangqing - Characterizing circular RNAs using nanopore sequencing.
Trends in Biochemical Sciences (2021).
Zhang Jinyang, Zhao Fangqing - Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets.
Methods (2021),doi.org/10.1016/j.ymeth.2021.03.017.
Zhang Jinyang, Zhao Fangqing - CircAltas: an integrated resource of one million highly confident circular RNAs from 1,070 vertebrate transcriptomes.
Genome Biology,2020 21:101.
Wu Wanying^, Ji Peifeng^ & Zhao Fangqing. - Accurate quantification of circular RNAs identifies extensive circular isoform switching events.
Nature Communications, 2020, 11:90.
Zhang Jinyang, Chen Shuai, Yang Jingwei & Zhao Fangqing. - Expanded expression landscape and prioritization of circular RNAs in mammals.
Cell Reports, 2019, 26:3444-3460.
Ji Peifeng^, Wu Wanying^, Chen Shuai^, Zheng Yi, Zhou Lin, Zhang Jinyang, Cheng Hao,Yan Jin, Zhang Shaogeng, Yang Penghui & Zhao Fangqing. - Reconstruction of full-length circular RNAs enables isoform-level quantification.
Genome Medicine, 2019, 11:2.
Zheng Yi^, Ji Peifeng^, Chen Shuai, Hou Linlin & Zhao Fangqing. - Circular RNA identification based on multiple seed matching.
Briefings in Bioinformatics,2017, DOI: 10.1093/bib/bbx014.
Gao Yuan^, Zhang Jinyang & Zhao Fangqing. - Comprehensive identification of internal structure and alternative splicing events in circular RNAs.
Nature Communications, 2016, 7:12060.
Gao Yuan^, Wang Jinfeng^, Zheng Yi^, Zhang Jinyang, Chen Shuai & Zhao Fangqing. - CIRI: an efficient and unbiased algorithm for de novo circular RNA identification.
Genome Biology, 2015, 16:4.
Gao Yuan^, Wang Jinfeng^ & Zhao Fangqing.
Concat us:
- Wu Wanying: wuwanying@biols.ac.cn
- Zhang Jinyang: zhangjinyang@biols.ac.cn