Computational approaches for circRNAs prediction and in silico characterization

A guide to naming eukaryotic circular RNAs

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

3dRNA: 3D Structure Prediction from Linear to Circular RNAs

(2022) Yi Zhang et al.   JOURNAL OF MOLECULAR BIOLOGY

circRIP: an accurate tool for identifying circRNA–RBP interactions

(2022) Xin Dong et al.   BRIEFINGS IN BIOINFORMATICS

Characterization of circular RNAs with advanced sequencing technologies in human complex diseases

(2022) Hang Ruan et al.   Wiley Interdisciplinary Reviews-RNA

StackCirRNAPred: computational classification of long circRNA from other lncRNA based on stacking strategy

(2022) Xin Wang et al.   BMC BIOINFORMATICS

CYCLeR—a novel tool for the full isoform assembly and quantification of circRNAs

(2022) Stefan R Stefanov et al.   NUCLEIC ACIDS RESEARCH

isoCirc catalogs full-length circular RNA isoforms in human transcriptomes

(2021) Ruijiao Xin et al.   Nature Communications

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

(2021) Jinyang Zhang et al.   NATURE BIOTECHNOLOGY

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

(2021) Jing Feng et al.   NUCLEIC ACIDS RESEARCH

catRAPID omics v2.0: going deeper and wider in the prediction of protein–RNA interactions

(2021) Alexandros Armaos et al.   NUCLEIC ACIDS RESEARCH

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

(2021) Karim Rahimi et al.   Nature Communications

Evolutionary dynamics of circular RNAs in primates

(2021) Gabriela Santos-Rodriguez et al.   eLife

Circular RNA repertoires are associated with evolutionarily young transposable elements

(2021) Franziska Gruhl et al.   eLife

Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data

(2021) Dat Thanh Nguyen et al.   BMC BIOINFORMATICS

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

(2021) Enrico Gaffo et al.   BRIEFINGS IN BIOINFORMATICS

Quantifying full-length circular RNAs in cancer

(2021) Ken Hung-On Yu et al.   GENOME RESEARCH

CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers

(2021) Yigang Chen et al.   NUCLEIC ACIDS RESEARCH

exoRBase 2.0: an atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids

(2021) Hongyan Lai et al.   NUCLEIC ACIDS RESEARCH

CircR2Disease v2.0: An Updated Web Server for Experimentally Validated circRNA–disease Associations and Its Application

(2021) Chunyan Fan et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Accurate quantification of circular RNAs identifies extensive circular isoform switching events

(2020) Jinyang Zhang et al.   Nature Communications

Autophagy-associated circRNA circCDYL augments autophagy and promotes breast cancer progression

(2020) Gehao Liang et al.   Molecular Cancer

Modulation of circRNA Metabolism by m6A Modification

(2020) Gaia Di Timoteo et al.   Cell Reports

Matrix factorization with neural network for predicting circRNA-RBP interactions

(2020) Zhengfeng Wang et al.   BMC BIOINFORMATICS

Circular RNA Signature in Lung Adenocarcinoma: A MiOncoCirc Database-Based Study and Literature Review

(2020) Shikang Zhao et al.   Frontiers in Oncology

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

(2019) Yi Zheng et al.   Genome Medicine

Computational approaches for circular RNA analysis

(2019) Tobias Jakobi et al.   Wiley Interdisciplinary Reviews-RNA

Circular exonic RNAs: When RNA structure meets topology

(2019) Dmitri D. Pervouchine   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Deep learning of the back-splicing code for circular RNA formation

(2019) Jun Wang et al.   BIOINFORMATICS

Differential expression and bioinformatics analysis of circRNA in osteosarcoma

(2019) Yizhe Xi et al.   BIOSCIENCE REPORTS

Using circular RNA SMARCA5 as a potential novel biomarker for hepatocellular carcinoma

(2019) Zuhua Li et al.   CLINICA CHIMICA ACTA

Inhibition of circHIPK3 prevents angiotensin II-induced cardiac fibrosis by sponging miR-29b-3p

(2019) Huaner Ni et al.   INTERNATIONAL JOURNAL OF CARDIOLOGY

Circular RNAs open a new chapter in cardiovascular biology

(2019) Simona Aufiero et al.   Nature Reviews Cardiology

Circbank: a comprehensive database for circRNA with standard nomenclature

(2019) Ming Liu et al.   RNA Biology

Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model

(2019) Chengyu Liu et al.   BIOINFORMATICS

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

CRIP: predicting circRNA-RBP interaction sites using a codon-based encoding and hybrid deep neural networks

(2019) Kaiming Zhang et al.   RNA

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

(2019) Hang Ruan et al.   Genome Medicine

Methods for analysis of circular RNAs

(2019) Poonam R. Pandey et al.   Wiley Interdisciplinary Reviews-RNA

Integration of Bioinformatic Predictions and Experimental Data to Identify circRNA-miRNA Associations

(2019) Martina Dori et al.   Genes

The mechanism and function of circular RNAs in human diseases

(2018) Kexin Lei et al.   EXPERIMENTAL CELL RESEARCH

circRNA disease: a manually curated database of experimentally supported circRNA-disease associations

(2018) Zheng Zhao et al.   Cell Death & Disease

TRCirc: a resource for transcriptional regulation information of circRNAs

(2018) Zhidong Tang et al.   BRIEFINGS IN BIOINFORMATICS

The emerging landscape of circular RNA in cardiovascular diseases

(2018) Meng-yuan Zhou et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

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

(2018) Mette Dahl et al.   LABORATORY INVESTIGATION

Circ2Disease: a manually curated database of experimentally validated circRNAs in human disease

(2018) Dongxia Yao et al.   Scientific Reports

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

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

The interaction of circRNAs and RNA binding proteins: An important part of circRNA maintenance and function

(2018) Jiankun Zang et al.   JOURNAL OF NEUROSCIENCE RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Xiaoyong Pan et al.   Genes

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

Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1

(2017) Kotb Abdelmohsen et al.   RNA Biology

Circular RNA Expression Profiles Alter Significantly in Mouse Brain After Transient Focal Ischemia

(2017) Suresh L. Mehta et al.   STROKE

CircRNA_000203 enhances the expression of fibrosis-associated genes by derepressing targets of miR-26b-5p, Col1a2 and CTGF, in cardiac fibroblasts

(2017) Chun-Mei Tang et al.   Scientific Reports

A comprehensive overview and evaluation of circular RNA detection tools

(2017) Xiangxiang Zeng et al.   PLoS Computational Biology

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

(2016) Avi Srivastava et al.   BIOINFORMATICS

PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events

(2016) Osagie G. Izuogu et al.   BMC BIOINFORMATICS

A circular RNA protects the heart from pathological hypertrophy and heart failure by targeting miR-223

(2016) Kun Wang et al.   EUROPEAN HEART JOURNAL

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

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

Myocardial Infarction-Associated Circular RNA Predicting Left Ventricular Dysfunction

(2016) Melanie Vausort et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

RNAComposer and RNA 3D structure prediction for nanotechnology

(2016) Marcin Biesiada et al.   METHODS

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

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans

(2016) Lesca M. Holdt et al.   Nature Communications

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

(2016) Yuan Gao et al.   Nature Communications

circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations

(2016) Xiaoping Chen et al.   Scientific Reports

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

Circular RNA: A new star of noncoding RNAs

(2015) Shibin Qu et al.   CANCER LETTERS

Mechanisms of RNA loading into exosomes

(2015) Teresa Janas et al.   FEBS LETTERS

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

(2015) Xiaoyong Pan et al.   Molecular BioSystems

CircNet: a database of circular RNAs derived from transcriptome sequencing data

(2015) Yu-Chen Liu et al.   NUCLEIC ACIDS RESEARCH

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

CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs

(2015) Dawood B. Dudekula et al.   RNA Biology

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

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

CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains

(2014) Patrick R. Wright et al.   NUCLEIC ACIDS RESEARCH

circBase: a database for circular RNAs

(2014) Petar Glažar 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

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits

(2013) Suman Ghosal et al.   Frontiers in Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

(2012) W. R. Jeck et al.   RNA

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

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

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology