10/22/25 The article introducing CIRCpedia v3 has been published in Nucleic Acids Research.

07/01/25 CIRCpedia v3 is online.

07/07/18 circRNA identification based on human reference genome hg19 was added into the CIRCpedia.

06/29/18 Another 17 human samples and 27 mouse samples have been added into CIRCpedia.

05/18/18 Another 22 human samples and 12 fly samples have been added into CIRCpedia. In addition, 2 zebrafish samples and 6 rat samples have been added into CIRCpedia.

05/17/18 FPM was used to represent circRNA expression level.

05/18/18 CIRCpedia has updated to CIRCpedia v2, Six species were available in the new version.

09/15/17 CIRCexplorer2 releases version 2.3.0 on github

12/15/16 Another 8 human samples, 6 mouse samples, 30 fly samples and 12 worm samples have been added into CIRCpedia.

09/26/16 CIRCexplorer2 releases version 2.2.6 on github

08/16/16 Hs68 has been added into CIRCpedia.

07/26/16 Another 25 samples are added into CIRCpedia.

07/22/16 CIRCexplorer2 releases version 2.1.2 on github

04/05/16 CIRCexplorer2 releases version 2.0.0 on github

12/10/15 CIRCpedia is officially online and in beta version.

For CIRCpedia v3:

Zhai SN*, Zhang YY, Chen MH, Fu ZC, Chen LL, Yang L#. CIRCpedia v3: an interactive database for circular RNA characterization and functional exploration. Nucleic Acids Res, 2025, doi: 10.1093/nar/gkaf1039

For CIRCexplorer3/CLEAR:

Ma XK*, Wang MR, Liu CX, Dong R, Carmichael GG, Chen LL and Yang L#. A CLEAR pipeline for direct comparison of circular and linear RNA expression. Genomics Proteomics Bioinformatics, 2019, doi: 10.1016/j.gpb.2019.11.004

For CIRCpedia v2:

Dong R*, Ma XK*, Li GW, Yang L#. CIRCpedia v2: An Updated Database for Comprehensive CircRNA Annotation and Expression Comparison. Genomics Proteomics Bioinformatics, 2018, doi:10.1016/j.gpb.2018.08.001

For CIRCexplorer2 and CIRCpedia:

Zhang XO*, Dong R*, Zhang Y*, Zhang JL, Luo Z, Zhang J, Chen LL#, Yang L#. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res, 2016, 26(9): 1277-1287

For CIRCexplorer:

Zhang XO*, Wang HB*, Zhang Y, Lu X, Chen LL#, Yang L#. Complementary sequence-mediated exon circularization. Cell. 2014, 159: 134-147

CIRCexplorer: A combined strategy to identify junction reads from back spliced exons and intron lariats.

CIRCexplorer2: A comprehensive and integrative circular RNA analysis toolset.

CIRCexplorer3/CLEAR: A computational pipeline for Circular and Linear RNA Expression Analysis from Ribosomal-RNA depleted (Ribo–) RNA-seq.