Structured elements drive extensive circular RNA translation

Ribosome states signal RNA quality control

(2021) Karole N. D’Orazio et al.   MOLECULAR CELL

When Long Noncoding Becomes Protein Coding

(2020) Corrine Corrina R. Hartford et al.   MOLECULAR AND CELLULAR BIOLOGY

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

(2020) Birkir Reynisson et al.   NUCLEIC ACIDS RESEARCH

A Quantitative Proteome Map of the Human Body

(2020) Lihua Jiang et al.   CELL

Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

(2020) Trine Line Hauge Okholm et al.   Genome Medicine

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization

(2019) Lukas Minus Orre et al.   MOLECULAR CELL

Insights into the biogenesis and potential functions of exonic circular RNA

(2019) Chikako Ragan et al.   Scientific Reports

A novel protein encoded by a circular RNA circPPP1R12A promotes tumor pathogenesis and metastasis of colon cancer via Hippo-YAP signaling

(2019) Xiao Zheng et al.   Molecular Cancer

The Landscape of Circular RNA in Cancer

(2019) Josh N. Vo 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

N6-Methyladenosine Modification Controls Circular RNA Immunity

(2019) Y. Grace Chen et al.   MOLECULAR CELL

A length-dependent evolutionarily conserved pathway controls nuclear export of circular RNAs

(2018) Chuan Huang et al.   GENES & DEVELOPMENT

A novel protein encoded by the circular form of the SHPRH gene suppresses glioma tumorigenesis

(2018) Maolei Zhang et al.   ONCOGENE

Signature of circular RNAs in human induced pluripotent stem cells and derived cardiomyocytes

(2018) Wei Lei et al.   Stem Cell Research & Therapy

A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma

(2018) Maolei Zhang et al.   Nature Communications

Translation of noncoding RNAs: Focus on lncRNAs, pri-miRNAs, and circRNAs

(2017) Lian-Ju Li et al.   EXPERIMENTAL CELL RESEARCH

Novel Role of FBXW7 Circular RNA in Repressing Glioma Tumorigenesis

(2017) Yibing Yang et al.   JNCI-Journal of the National Cancer Institute

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

Sensing Self and Foreign Circular RNAs by Intron Identity

(2017) Y. Grace Chen et al.   MOLECULAR CELL

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

(2017) Xiang Li et al.   MOLECULAR CELL

An update on sORFs.org: a repository of small ORFs identified by ribosome profiling

(2017) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

CSCD: a database for cancer-specific circular RNAs

(2017) Siyu Xia et al.   NUCLEIC ACIDS RESEARCH

RNA structure inference through chemical mapping after accidental or intentional mutations

(2017) Clarence Y. Cheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel Role of FBXW7 Circular RNA in Repressing Glioma Tumorigenesis

(2017) Yibing Yang et al.   JNCI-Journal of the National Cancer Institute

The complexity of the translation ability of circRNAs

(2016) Javier T. Granados-Riveron et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Circular RNAs are miRNA sponges and can be used as a new class of biomarker

(2016) Franceli Rodrigues Kulcheski et al.   JOURNAL OF BIOTECHNOLOGY

Comprehensive Circular RNA Profiling Reveals That hsa_circ_0005075, a New Circular RNA Biomarker, Is Involved in Hepatocellular Crcinoma Development

(2016) Xingchen Shang et al.   MEDICINE

Nonsense-Mediated Decay Restricts LncRNA Levels in Yeast Unless Blocked by Double-Stranded RNA Structure

(2016) Maxime Wery et al.   MOLECULAR CELL

A human microprotein that interacts with the mRNA decapping complex

(2016) Nadia G D'Lima et al.   Nature Chemical Biology

Identification of senescence-associated circular RNAs (SAC-RNAs) reveals senescence suppressor CircPVT1

(2016) Amaresh C. Panda et al.   NUCLEIC ACIDS RESEARCH

Cyclin B Translation Depends on mTOR Activity after Fertilization in Sea Urchin Embryos

(2016) Héloïse Chassé et al.   PLoS One

Systematic discovery of cap-independent translation sequences in human and viral genomes

(2016) Shira Weingarten-Gabbay et al.   SCIENCE

Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs

(2016) Qiupeng Zheng et al.   Nature Communications

Circular RNAs and their associations with breast cancer subtypes

(2016) Asha A. Nair et al.   Oncotarget

Screening differential circular RNA expression profiles reveals the regulatory role of circTCF25-miR-103a-3p/miR-107-CDK6 pathway in bladder carcinoma

(2016) Zhenyu Zhong et al.   Scientific Reports

CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs

(2016) Tim Schneider et al.   Scientific Reports

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

(2016) Xiaoping Chen et al.   Scientific Reports

Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes

(2016) Yongchao Dou et al.   Scientific Reports

Nonsense-mediated RNA decay - a switch and dial for regulating gene expression

(2015) Jenna E. Smith et al.   BIOESSAYS

5′ UTR m6A Promotes Cap-Independent Translation

(2015) Kate D. Meyer et al.   CELL

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

(2015) Michal Bassani-Sternberg et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

The beta hairpin structure within ribosomal protein S5 mediates interplay between domains II and IV and regulates HCV IRES function

(2015) Prasanna Bhat et al.   NUCLEIC ACIDS RESEARCH

Inhibition of HCV translation by disrupting the structure and interactions of the viral CRE and 3′ X-tail

(2015) Andrew Tuplin et al.   NUCLEIC ACIDS RESEARCH

Circular RNAs remain peculiarly unclear in biogenesis and function

(2015) Liang Chen et al.   Science China-Life Sciences

Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution

(2015) Nick Quade et al.   Nature Communications

Rolling Circle Translation of Circular RNA in Living Human Cells

(2015) Naoko Abe et al.   Scientific Reports

Biogenesis, identification, and function of exonic circular RNAs

(2015) Iju Chen et al.   Wiley Interdisciplinary Reviews-RNA

Correlation of circular RNA abundance with proliferation – exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis and normal human tissues

(2015) Anna Bachmayr-Heyda et al.   Scientific Reports

The circular RNA Cdr1as, via miR-7 and its targets, regulates insulin transcription and secretion in islet cells

(2015) Huanyu Xu et al.   Scientific Reports

Biogenesis of Circular RNAs

(2014) Quentin Vicens et al.   CELL

Short intronic repeat sequences facilitate circular RNA production

(2014) Dongming Liang et al.   GENES & DEVELOPMENT

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

Quantitative profiling of initiating ribosomes in vivo

(2014) Xiangwei Gao et al.   NATURE METHODS

circBase: a database for circular RNAs

(2014) Petar Glažar et al.   RNA

Efficient backsplicing produces translatable circular mRNAs

(2014) Yang Wang et al.   RNA

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

Widespread Changes in the Posttranscriptional Landscape at the Drosophila Oocyte-to-Embryo Transition

(2014) Iva Kronja et al.   Cell Reports

Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine

(2014) Wilson Wong et al.   eLife

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   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

HCV IRES interacts with the 18S rRNA to activate the 40S ribosome for subsequent steps of translation initiation

(2013) A. A. Malygin et al.   NUCLEIC ACIDS RESEARCH

Cell-Type Specific Features of Circular RNA Expression

(2013) Julia Salzman et al.   PLoS Genetics

Translation regulation gets its ‘omics’ moment

(2013) Scott Kuersten et al.   Wiley Interdisciplinary Reviews-RNA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Circular RNA (circRNA) in Alzheimer's disease (AD)

(2013) Walter J. Lukiw   Frontiers in Genetics

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

A mechanistic overview of translation initiation in eukaryotes

(2012) Colin Echeverría Aitken et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Toward a Genome-Wide Landscape of Translational Control

(2012) O. Larsson et al.   Cold Spring Harbor Perspectives in Biology

Principles of Translational Control: An Overview

(2012) J. W. B. Hershey et al.   Cold Spring Harbor Perspectives in Biology

ViennaRNA Package 2.0

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

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Genome-wide analysis of translation reveals a critical role for deleted in azoospermia-like (Dazl) at the oocyte-to-zygote transition

(2011) J. Chen et al.   GENES & DEVELOPMENT

Punctuated cyclin synthesis drives early embryonic cell cycle oscillations

(2011) Qing Kang et al.   MOLECULAR BIOLOGY OF THE CELL

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction

(2011) Qiang Xie et al.   Protein & Cell

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Endoplasmic Reticulum Stress Induces G2 Cell-Cycle Arrest via mRNA Translation of the p53 Isoform p53/47

(2010) Karima Bourougaa et al.   MOLECULAR CELL

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution

(2010) J.-P. Armache et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IRESite—a tool for the examination of viral and cellular internal ribosome entry sites

(2009) Martin Mokrejš et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes

(2008) Andrey V Pisarev et al.   EMBO JOURNAL

DAP5 Promotes Cap-Independent Translation of Bcl-2 and CDK1 to Facilitate Cell Survival during Mitosis

(2008) Lea Marash et al.   MOLECULAR CELL

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

Splicing mediates the activity of four putative cellular internal ribosome entry sites

(2008) B. T. Baranick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the Mammalian 80S Ribosome at 8.7 Å Resolution

(2008) Preethi Chandramouli et al.   STRUCTURE

Structure and function of HCV IRES domains

(2008) Peter J. Lukavsky   VIRUS RESEARCH