CIRCexplorer pipelines for circRNA annotation and quantification from non-polyadenylated RNA-seq datasets

isoCirc catalogs full-length circular RNA isoforms in human transcriptomes

(2021) Ruijiao Xin et al.   Nature Communications

Fast and furious: insights of back splicing regulation during nascent RNA synthesis

(2021) Wei Xue et al.   Science China-Life Sciences

Biogenesis and Functions of Circular RNAs Come into Focus

(2020) Mei-Sheng Xiao et al.   TRENDS IN CELL BIOLOGY

Accurate quantification of circular RNAs identifies extensive circular isoform switching events

(2020) Jinyang Zhang et al.   Nature Communications

The expanding regulatory mechanisms and cellular functions of circular RNAs

(2020) Ling-Ling Chen   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Screening for functional circular RNAs using the CRISPR–Cas13 system

(2020) Siqi Li et al.   NATURE METHODS

Reconstruction of full-length circular RNAs enables isoform-level quantification

(2019) Yi Zheng et al.   Genome Medicine

Expanded Expression Landscape and Prioritization of Circular RNAs in Mammals

(2019) Peifeng Ji et al.   Cell Reports

Genome-wide identification of cancer-specific alternative splicing in circRNA

(2019) Jing Feng et al.   Molecular Cancer

Widespread and Functional RNA Circularization in Localized Prostate Cancer

(2019) Sujun Chen et al.   CELL

Structure and Degradation of Circular RNAs Regulate PKR Activation in Innate Immunity

(2019) Chu-Xiao Liu et al.   CELL

An improved method for circular RNA purification using RNase R that efficiently removes linear RNAs containing G-quadruplexes or structured 3′ ends

(2019) Mei-Sheng Xiao et al.   NUCLEIC ACIDS RESEARCH

The biogenesis, biology and characterization of circular RNAs

(2019) Lasse S. Kristensen et al.   NATURE REVIEWS GENETICS

Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells

(2018) Trees-Juen Chuang et al.   NUCLEIC ACIDS RESEARCH

Computational Strategies for Exploring Circular RNAs

(2018) Yuan Gao et al.   TRENDS IN GENETICS

A 360° view of circular RNAs: From biogenesis to functions

(2018) Jeremy E. Wilusz   Wiley Interdisciplinary Reviews-RNA

The Biogenesis, Functions, and Challenges of Circular RNAs

(2018) Xiang Li et al.   MOLECULAR CELL

CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison

(2018) Rui Dong et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Coordinated circRNA Biogenesis and Function with NF90/NF110 in Viral Infection

(2017) Xiang Li et al.   MOLECULAR CELL

Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function

(2017) Monika Piwecka et al.   SCIENCE

The Diversity of Long Noncoding RNAs and Their Generation

(2017) Huang Wu et al.   TRENDS IN GENETICS

Diverse alternative back-splicing and alternative splicing landscape of circular RNAs

(2016) Xiao-Ou Zhang et al.   GENOME RESEARCH

Detecting circular RNAs: bioinformatic and experimental challenges

(2016) Linda Szabo et al.   NATURE REVIEWS GENETICS

The biogenesis and emerging roles of circular RNAs

(2016) Ling-Ling Chen   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Circular RNA profile in gliomas revealed by identification tool UROBORUS

(2016) Xiaofeng Song et al.   NUCLEIC ACIDS RESEARCH

Comprehensive identification of internal structure and alternative splicing events in circular RNAs

(2016) Yuan Gao et al.   Nature Communications

The Biogenesis of Nascent Circular RNAs

(2016) Yang Zhang et al.   Cell Reports

Specific identification and quantification of circular RNAs from sequencing data

(2015) Jun Cheng et al.   BIOINFORMATICS

Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed

(2015) Agnieszka Rybak-Wolf et al.   MOLECULAR CELL

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity

(2015) Xintian You et al.   NATURE NEUROSCIENCE

Comparison of circular RNA prediction tools

(2015) Thomas B. Hansen et al.   NUCLEIC ACIDS RESEARCH

Regulation of circRNA biogenesis

(2015) Ling-Ling Chen et al.   RNA Biology

Splicing noncoding RNAs from the inside out

(2015) Li Yang   Wiley Interdisciplinary Reviews-RNA

Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development

(2015) Linda Szabo et al.   GENOME BIOLOGY

CIRI: an efficient and unbiased algorithm for de novo circular RNA identification

(2015) Yuan Gao et al.   GENOME BIOLOGY

Complementary Sequence-Mediated Exon Circularization

(2014) Xiao-Ou Zhang et al.   CELL

Detecting and characterizing circular RNAs

(2014) William R Jeck et al.   NATURE BIOTECHNOLOGY

Is an observed non-co-linear RNA product spliced intrans, incisor justin vitro?

(2014) Chun-Ying Yu et al.   NUCLEIC ACIDS RESEARCH

Circular RNAs: diversity of form and function

(2014) Erika Lasda et al.   RNA

Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation

(2014) Jakub O. Westholm et al.   Cell Reports

Circular Intronic Long Noncoding RNAs

(2013) Yang Zhang et al.   MOLECULAR CELL

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Long Noncoding RNAs with snoRNA Ends

(2012) Qing-Fei Yin et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

(2012) Julia Salzman et al.   PLoS One

Transcriptome-wide discovery of circular RNAs in Archaea

(2011) Miri Danan et al.   NUCLEIC ACIDS RESEARCH

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Power sequencing

(2008) Brenton R. Graveley   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS