Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies

Protein-Engineered Coagulation Factors for Hemophilia Gene Therapy

(2019) Benjamin J. Samelson-Jones et al.   Molecular Therapy-Methods & Clinical Development

Aptamers as quality control tool for production, storage and biosimilarity of the anti-CD20 biopharmaceutical rituximab

(2019) Sabrina Wildner et al.   Scientific Reports

Cycloheximide can distort measurements of mRNA levels and translation efficiency

(2019) Daniel A Santos et al.   NUCLEIC ACIDS RESEARCH

Translational and transcriptional responses in human primary hepatocytes under hypoxia

(2019) Gaya K Hettiarachchi et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Clinical Pharmacology Review of Plasma‐derived and Recombinant Protein Products: CBER Experience and Perspectives on Model‐Informed Drug Development

(2019) Million A. Tegenge et al.   HAEMOPHILIA

Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design

(2019) Aikaterini Alexaki et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein Quality Control in the Endoplasmic Reticulum

(2019) Benjamin M. Adams et al.   PROTEIN JOURNAL

A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data

(2019) Ajeet K. Sharma et al.   PLoS Computational Biology

Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants

(2019) Upendra K. Katneni et al.   Molecular Genetics & Genomic Medicine

Codon Optimization in the Production of Recombinant Biotherapeutics: Potential Risks and Considerations

(2018) Vincent P. Mauro   BIODRUGS

New Therapies for hemophilia

(2018) Angela C. Weyand et al.   BLOOD

Transcriptome-wide measurement of translation by ribosome profiling

(2017) Nicholas J. McGlincy et al.   METHODS

Codon-Resolution Analysis Reveals a Direct and Context-Dependent Impact of Individual Synonymous Mutations on mRNA Level

(2017) Siyu Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences

(2017) Amin Espah Borujeni et al.   NUCLEIC ACIDS RESEARCH

Ribosome dynamics during decoding

(2017) Marina V. Rodnina et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination

(2017) Arjun Prabhakar et al.   PROTEIN SCIENCE

Alteration of protein function by a silent polymorphism linked to tRNA abundance

(2017) Sebastian Kirchner et al.   PLOS BIOLOGY

Differential bicodon usage in lowly and highly abundant proteins

(2017) Luis A. Diambra   PeerJ

Analysis of Ribosome Stalling and Translation Elongation Dynamics by Deep Learning

(2017) Sai Zhang et al.   Cell Systems

The importance of mRNA structure in determining the pathogenicity of synonymous and non-synonymous mutations in haemophilia

(2016) N. Hamasaki-Katagiri et al.   HAEMOPHILIA

Single synonymous mutation in factor IX alters protein properties and underlies haemophilia B

(2016) Vijaya L Simhadri et al.   JOURNAL OF MEDICAL GENETICS

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations

(2016) Florian Buhr et al.   MOLECULAR CELL

Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9

(2016) Zachary R. Newman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Roles for Synonymous Codon Usage in Protein Biogenesis

(2015) Julie L. Chaney et al.   Annual Review of Biophysics

Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity

(2015) Danny D. Nedialkova et al.   CELL

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Decoding mechanisms by which silent codon changes influence protein biogenesis and function

(2015) Vedrana Bali et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding

(2015) Chien-Hung Yu et al.   MOLECULAR CELL

Efficient and quantitative high-throughput tRNA sequencing

(2015) Guanqun Zheng et al.   NATURE METHODS

Translational tuning optimizes nascent protein folding in cells

(2015) S. J. Kim et al.   SCIENCE

Exposing synonymous mutations

(2014) Ryan C. Hunt et al.   TRENDS IN GENETICS

A critical analysis of codon optimization in human therapeutics

(2014) Vincent P. Mauro et al.   TRENDS IN MOLECULAR MEDICINE

Measurement of average decoding rates of the 61 sense codons in vivo

(2014) Justin Gardin et al.   eLife

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

(2014) Liana F Lareau et al.   eLife

Integration-deficient Lentiviral Vectors Expressing Codon-optimized R338L Human FIX Restore Normal Hemostasis in Hemophilia B Mice

(2013) Thipparat Suwanmanee et al.   MOLECULAR THERAPY

A Visual Dual-Aptamer Logic Gate for Sensitive Discrimination of Prion Diseases-Associated Isoform with Reusable Magnetic Microparticles and Fluorescence Quantum Dots

(2013) Sai Jin Xiao et al.   PLoS One

Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma

(2013) J. J. Gartner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Further Characterization of the Target of a Potential Aptamer Biomarker for Pancreatic Cancer: Cyclophilin B and Its Posttranslational Modifications

(2013) Partha Ray et al.   Nucleic Acid Therapeutics

Aptamers as a Sensitive Tool to Detect Subtle Modifications in Therapeutic Proteins

(2012) Ran Zichel et al.   PLoS One

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

(2011) Nicholas T. Ingolia et al.   CELL

A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease

(2011) Patrick Brest et al.   NATURE GENETICS

Aptamer-Based Multiplexed Proteomic Technology for Biomarker Discovery

(2011) Larry Gold et al.   PLoS One

Multiparameter RNA and Codon Optimization: A Standardized Tool to Assess and Enhance Autologous Mammalian Gene Expression

(2011) Stephan Fath et al.   PLoS One

A Synonymous Single Nucleotide Polymorphism in ΔF508CFTRAlters the Secondary Structure of the mRNA and the Expression of the Mutant Protein

(2010) Rafal A. Bartoszewski et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

NUPACK: Analysis and design of nucleic acid systems

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The impact of intragenic CpG content on gene expression

(2010) Asli Petra Bauer 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