Approaches and challenges in genome-wide circular RNA identification and quantification

A guide to naming eukaryotic circular RNAs

(2023) Ling-Ling Chen et al.   NATURE CELL BIOLOGY

Computational approaches for circRNAs prediction and in silico characterization

(2023) Camilo Rebolledo et al.   BRIEFINGS IN BIOINFORMATICS

Spatial Profiling of Circular RNAs in Cancer Reveals High Expression in Muscle and Stromal Cells

(2023) Juan L. García-Rodríguez et al.   CANCER RESEARCH

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

(2023) Marieke Vromman et al.   NATURE METHODS

Biogenesis and Regulatory Roles of Circular RNAs

(2022) Li Yang et al.   Annual Review of Cell and Developmental Biology

Circular RNAs: Characterization, cellular roles, and applications

(2022) Chu-Xiao Liu et al.   CELL

Best practice standards for circular RNA research

(2022) Anne F. Nielsen et al.   NATURE METHODS

Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing

(2022) Wanying Wu et al.   Nature Communications

isoCirc catalogs full-length circular RNA isoforms in human transcriptomes

(2021) Ruijiao Xin et al.   Nature Communications

Best practices to ensure robust investigation of circular RNAs: pitfalls and tips

(2021) Samantha Dodbele et al.   EMBO REPORTS

Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long

(2021) Jinyang Zhang et al.   NATURE BIOTECHNOLOGY

Structured elements drive extensive circular RNA translation

(2021) Chun-Kan Chen et al.   MOLECULAR CELL

CSCD2: an integrated interactional database of cancer-specific circular RNAs

(2021) Jing Feng et al.   NUCLEIC ACIDS RESEARCH

Linking circular intronic RNA degradation and function in transcription by RNase H1

(2021) Xiang Li et al.   Science China-Life Sciences

Nanopore sequencing of brain-derived full-length circRNAs reveals circRNA-specific exon usage, intron retention and microexons

(2021) Karim Rahimi et al.   Nature Communications

Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2

(2021) Enrico Gaffo et al.   BRIEFINGS IN BIOINFORMATICS

Nanopore long-read sequencing of circRNAs

(2021) Karim Rahimi et al.   METHODS

RNA circles with minimized immunogenicity as potent PKR inhibitors

(2021) Chu-Xiao Liu et al.   MOLECULAR CELL

circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing

(2021) Zelin Liu et al.   eLife

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

RNA Circularization Diminishes Immunogenicity and Can Extend Translation Duration In Vivo

(2019) R. Alexander Wesselhoeft et al.   MOLECULAR CELL

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

(2019) Chu-Xiao Liu et al.   CELL

Circ RNA wrap – a flexible pipeline for circ RNA identification, transcript prediction, and abundance estimation

(2019) Lin Li et al.   FEBS LETTERS

Circular RNA F-circSR derived from SLC34A2-ROS1 fusion gene promotes cell migration in non-small cell lung cancer

(2019) Ke Wu et al.   Molecular Cancer

SplintQuant: A method for accurately quantifying circular RNA transcript abundance without reverse transcription bias

(2019) Vanessa M. Conn et al.   RNA

The biogenesis, biology and characterization of circular RNAs

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

Comprehensive characterization of circular RNAs in ~ 1000 human cancer cell lines

(2019) Hang Ruan et al.   Genome Medicine

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

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

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

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

Enzyme-free digital counting of endogenous circular RNA molecules in B-cell malignancies

(2018) Mette Dahl et al.   LABORATORY INVESTIGATION

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

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

WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA

(2018) Xiaoyong Pan et al.   Genes

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

(2017) Xiang Li et al.   MOLECULAR CELL

CSCD: a database for cancer-specific circular RNAs

(2017) Siyu Xia et al.   NUCLEIC ACIDS RESEARCH

Circular RNAs are abundantly expressed and upregulated during human epidermal stem cell differentiation

(2017) Lasse Sommer Kristensen et al.   RNA Biology

Oncogenic Role of Fusion-circRNAs Derived from Cancer-Associated Chromosomal Translocations

(2016) Jlenia Guarnerio et al.   CELL

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

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 RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis

(2015) Yan Li et al.   CELL RESEARCH

Genome-wide discovery of human splicing branchpoints

(2015) Tim R. Mercer et al.   GENOME RESEARCH

PredcircRNA: computational classification of circular RNA from other long non-coding RNA using hybrid features

(2015) Xiaoyong Pan et al.   Molecular BioSystems

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

NCLscan: accurate identification of non-co-linear transcripts (fusion,trans-splicing and circular RNA) with a good balance between sensitivity and precision

(2015) Trees-Juen Chuang et al.   NUCLEIC ACIDS RESEARCH

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

Transcriptome-wide investigation of circular RNAs in rice

(2015) Tingting Lu et al.   RNA

Exon Circularization Requires Canonical Splice Signals

(2015) Stefan Starke et al.   Cell Reports

Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals

(2015) Andranik Ivanov et al.   Cell Reports

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

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

(2015) Xiaoying Fan et al.   GENOME BIOLOGY

Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood

(2015) Sebastian Memczak et al.   PLoS One

Complementary Sequence-Mediated Exon Circularization

(2014) Xiao-Ou Zhang et al.   CELL

circRNA Biogenesis Competes with Pre-mRNA Splicing

(2014) Reut Ashwal-Fluss et al.   MOLECULAR 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

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

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

(2013) Sebastian Memczak et al.   NATURE

Correction: Cell-Type Specific Features of Circular RNA Expression

(2013) Julia Salzman et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis

(2012) E. J. Gardner et al.   GENES & DEVELOPMENT

Long Noncoding RNAs with snoRNA Ends

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

(2012) Julia Salzman et al.   PLoS One

Circular RNAs are abundant, conserved, and associated with ALU repeats

(2012) W. R. Jeck et al.   RNA

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

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

(2010) Peng Cui et al.   GENOMICS

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

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Power sequencing

(2008) Brenton R. Graveley   NATURE

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE