Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

(2021) Nicholas C. Huston et al.   MOLECULAR CELL

A Dengue Virus Serotype 1 mRNA-LNP Vaccine Elicits Protective Immune Responses

(2021) Clayton J. Wollner et al.   JOURNAL OF VIROLOGY

Theoretical basis for stabilizing messenger RNA through secondary structure design

(2021) Hannah K Wayment-Steele et al.   NUCLEIC ACIDS RESEARCH

High-throughput 5′ UTR engineering for enhanced protein production in non-viral gene therapies

(2021) Jicong Cao et al.   Nature Communications

The challenge and prospect of mRNA therapeutics landscape

(2020) Yuhua Weng et al.   BIOTECHNOLOGY ADVANCES

The Architecture of SARS-CoV-2 Transcriptome

(2020) Dongwan Kim et al.   CELL

Ribosome Collisions Trigger General Stress Responses to Regulate Cell Fate

(2020) Colin Chih-Chien Wu et al.   CELL

GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control

(2020) Kelsey L. Hickey et al.   MOLECULAR CELL

SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness

(2020) Kizzmekia S. Corbett et al.   NATURE

Decoding mRNA translatability and stability from the 5′ UTR

(2020) Longfei Jia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ribosome collisions trigger cis-acting feedback inhibition of translation initiation

(2020) Szymon Juszkiewicz et al.   eLife

Optimization of 5′ Untranslated Region of Modified mRNA for Use in Cardiac or Hepatic Ischemic Injury

(2020) Nishat Sultana et al.   Molecular Therapy-Methods & Clinical Development

Leveraging mRNA Sequences and Nanoparticles to Deliver SARS‐CoV‐2 Antigens In Vivo

(2020) Chunxi Zeng et al.   ADVANCED MATERIALS

Characteristics of SARS-CoV-2 and COVID-19

(2020) Ben Hu et al.   NATURE REVIEWS MICROBIOLOGY

Structure and regulation of coronavirus genomes: state-of-the-art and novel insights from SARS-CoV-2 studies

(2020) Ilaria Manfredonia et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Addressing the Cold Reality of mRNA Vaccine Stability

(2020) Daan J.A. Crommelin et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Gene- and Species-Specific Hox mRNA Translation by Ribosome Expansion Segments

(2020) Kathrin Leppek et al.   MOLECULAR CELL

Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine

(2020) Lindsey R. Baden et al.   NEW ENGLAND JOURNAL OF MEDICINE

Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine

(2020) Fernando P. Polack et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ciphers and Executioners: How 3′-Untranslated Regions Determine the Fate of Messenger RNAs

(2019) Vinay K. Mayya et al.   Frontiers in Genetics

Delivering the Messenger: Advances in Technologies for Therapeutic mRNA Delivery

(2019) Piotr S. Kowalski et al.   MOLECULAR THERAPY

Human 5′ UTR design and variant effect prediction from a massively parallel translation assay

(2019) Paul J. Sample et al.   NATURE BIOTECHNOLOGY

mRNA structure regulates protein expression through changes in functional half-life

(2019) David M. Mauger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers

(2019) Daniel Liu   PeerJ

mRNA vaccines — a new era in vaccinology

(2018) Norbert Pardi et al.   NATURE REVIEWS DRUG DISCOVERY

RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

(2018) Danny Incarnato et al.   NUCLEIC ACIDS RESEARCH

Arginase I mRNA therapy – A novel approach to rescue arginase 1 enzyme deficiency

(2018) Kirtika H. Asrani et al.   RNA Biology

What Are 3′ UTRs Doing?

(2018) Christine Mayr   Cold Spring Harbor Perspectives in Biology

Improving mRNA-Based Therapeutic Gene Delivery by Expression-Augmenting 3′ UTRs Identified by Cellular Library Screening

(2018) Alexandra G. Orlandini von Niessen et al.   MOLECULAR THERAPY

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

(2017) Ugur Sahin et al.   NATURE

Codon optimality, bias and usage in translation and mRNA decay

(2017) Gavin Hanson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

(2017) Kathrin Leppek et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Updates to the RNA mapping database (RMDB), version 2

(2017) Joseph D Yesselman et al.   NUCLEIC ACIDS RESEARCH

kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences

(2017) Xuebing Wu et al.   NUCLEIC ACIDS RESEARCH

In vitro analysis of RQC activities provides insights into the mechanism and function of CAT tailing

(2017) Beatriz A Osuna et al.   eLife

NanoLuc: A Small Luciferase Is Brightening Up the Field of Bioluminescence

(2016) Christopher G. England et al.   BIOCONJUGATE CHEMISTRY

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

(2016) Meghan Zubradt et al.   NATURE METHODS

Human cellular CYBA UTR sequences increase mRNA translation without affecting the half-life of recombinant RNA transcripts

(2016) Mehrije Ferizi et al.   Scientific Reports

CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure

(2015) Goro Terai et al.   BIOINFORMATICS

Sequence-engineered mRNA Without Chemical Nucleoside Modifications Enables an Effective Protein Therapy in Large Animals

(2015) Andreas Thess et al.   MOLECULAR THERAPY

Consistent global structures of complex RNA states through multidimensional chemical mapping

(2015) Clarence Yu Cheng et al.   eLife

cocor: A Comprehensive Solution for the Statistical Comparison of Correlations

(2015) Birk Diedenhofen et al.   PLoS One

Standardization of RNA Chemical Mapping Experiments

(2014) Wipapat Kladwang et al.   BIOCHEMISTRY

RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation

(2014) Shifeng Xue et al.   NATURE

Massively parallel functional annotation of 3′ untranslated regions

(2014) Wenxue Zhao et al.   NATURE BIOTECHNOLOGY

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

mRNA-based therapeutics — developing a new class of drugs

(2014) Ugur Sahin et al.   NATURE REVIEWS DRUG DISCOVERY

Multiple roles of the coding sequence 5′ end in gene expression regulation

(2014) Tamir Tuller et al.   NUCLEIC ACIDS RESEARCH

RNA design rules from a massive open laboratory

(2014) Jeehyung Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

3′ Cap-Independent Translation Enhancers of Plant Viruses

(2013) Anne E. Simon et al.   Annual Review of Microbiology

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

Single-cell mRNA transfection studies: Delivery, kinetics and statistics by numbers

(2013) Carolin Leonhardt et al.   Nanomedicine-Nanotechnology Biology and Medicine

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis

(2013) Hanjoo Kim et al.   NUCLEIC ACIDS RESEARCH

The contribution of pseudouridine to stabilities and structure of RNAs

(2013) Elzbieta Kierzek et al.   NUCLEIC ACIDS RESEARCH

Engineered Luciferase Reporter from a Deep Sea Shrimp Utilizing a Novel Imidazopyrazinone Substrate

(2012) Mary P. Hall et al.   ACS Chemical Biology

A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails

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

A unifying model for mTORC1-mediated regulation of mRNA translation

(2012) Carson C. Thoreen et al.   NATURE

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The 3′ Untranslated Region of the Rabies Virus Glycoprotein mRNA Specifically Interacts with Cellular PCBP2 Protein and Promotes Transcript Stability

(2012) Saiprasad Palusa et al.   PLoS One

The role of the 3' untranslated region in post-transcriptional regulation of protein expression in mammalian cells.

(2012) Eva Matoulkova et al.   RNA Biology

ViennaRNA Package 2.0

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

The ribosome uses two active mechanisms to unwind messenger RNA during translation

(2011) Xiaohui Qu et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

From unwinding to clamping — the DEAD box RNA helicase family

(2011) Patrick Linder et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

3′ Cap-independent translation enhancers of positive-strand RNA plant viruses

(2011) Beth L Nicholson et al.   Current Opinion in Virology

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Sindbis Virus Usurps the Cellular HuR Protein to Stabilize Its Transcripts and Promote Productive Infections in Mammalian and Mosquito Cells

(2010) Kevin J. Sokoloski et al.   Cell Host & Microbe

Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation

(2010) Bart R. Anderson et al.   NUCLEIC ACIDS RESEARCH

Penalized Regression with Ordinal Predictors

(2009) Jan Gertheiss et al.   INTERNATIONAL STATISTICAL REVIEW

Incorporation of Pseudouridine Into mRNA Yields Superior Nonimmunogenic Vector With Increased Translational Capacity and Biological Stability

(2008) Katalin Karikó et al.   MOLECULAR THERAPY

Poly(A) leader of eukaryotic mRNA bypasses the dependence of translation on initiation factors

(2008) N. E. Shirokikh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting the sizes of large RNA molecules

(2008) A. M. Yoffe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure-specific manner

(2008) S. R. Nallagatla et al.   RNA