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

Comprehensive analysis of circRNA expression profiles in humans by RAISE

(2017) Lin Li et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

Translation of CircRNAs

(2017) Nagarjuna Reddy Pamudurti et al.   MOLECULAR CELL

Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis

(2017) Ivano Legnini et al.   MOLECULAR CELL

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

(2017) Sayed Mohammad Ebrahim Sahraeian et al.   Nature Communications

A comprehensive overview and evaluation of circular RNA detection tools

(2017) Xiangxiang Zeng et al.   PLoS Computational Biology

FUCHS—towards full circular RNA characterization using RNAseq

(2017) Franziska Metge et al.   PeerJ

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

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

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Detecting circular RNAs: bioinformatic and experimental challenges

(2016) Linda Szabo et al.   NATURE REVIEWS GENETICS

Foxo3 circular RNA retards cell cycle progression via forming ternary complexes with p21 and CDK2

(2016) William W. Du et al.   NUCLEIC ACIDS RESEARCH

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

Acfs: accurate circRNA identification and quantification from RNA-Seq data

(2016) Xintian You et al.   Scientific Reports

Specific identification and quantification of circular RNAs from sequencing data

(2015) Jun Cheng et al.   BIOINFORMATICS

The RNA Binding Protein Quaking Regulates Formation of circRNAs

(2015) Simon J. Conn et al.   CELL

Genome-wide discovery of human splicing branchpoints

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

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

Exon-intron circular RNAs regulate transcription in the nucleus

(2015) Zhaoyong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Exon-intron circular RNAs regulate transcription in the nucleus

(2015) Zhaoyong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

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

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

(2014) Steve Hoffmann et al.   GENOME BIOLOGY

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

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

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

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

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

(2011) Daehwan Kim et al.   GENOME BIOLOGY

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