Codon bias and heterologous protein expression.

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Trends in Biotechnology

• Publication date

  2004-07-01

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1016/J.TIBTECH.2004.04.006PMID 15245907
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Protein translocation through a tunnel induces changes in folding kinetics: A lattice model study

  2006cited by this paper
• The geometry of the ribosomal polypeptide exit tunnel.

  2006cited by this paper
• Modelling sequential protein folding under kinetic control

  2006cited by this paper
• Ribosome exit tunnel can entropically stabilize α-helices

  2005cited by this paper
• Folding zones inside the ribosomal exit tunnel

  2005cited by this paper
• The co‐translational folding and interactions of nascent protein chains: a new approach using fluorescence resonance energy transfer

  2005cited by this paper
• Ribosome exit tunnel can entropically stabilize alpha-helices.

  2005cited by this paper
• Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins.

  2004cited by this paper
• Three-dimensional structures of translating ribosomes by Cryo-EM.

  2004cited by this paper
• Driving change: the evolution of alternative genetic codes.

  2004cited by this paper
• Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli: RNA stability and secondary structure but not tRNA abundance.

  2004cited by this paper
• The protein folding 'speed limit'.

  2004cited by this paper
• Silent point mutation in DsRed resulting in enhanced relative fluorescence intensity.

  2004cited by this paper
• The role of cotranslation in protein folding: a lattice model study

  2004cited by this paper
• The dynamic tunnel

  2004cited by this paper
• Protein Expression A Practical Approach

  2004cited by this paper
• Codon optimization of the HPV-16 E5 gene enhances protein expression.

  2003cited by this paper
• A pattern matching algorithm for codon optimization and CpG motif-engineering in DNA expression vectors

  2003cited by this paper
• Codon adaptation index as a measure of dominating codon bias

  2003cited by this paper
• Effects of codon usage versus putative 5'-mRNA structure on the expression of Fusarium solani cutinase in the Escherichia coli cytoplasm.

  2003cited by this paper
• Codon Pairs in the Genome of Escherichia Coli

  2003cited by this paper
• Effect of Codon Optimization on Expression Levels of a Functionally Folded Malaria Vaccine Candidate in Prokaryotic and Eukaryotic Expression Systems

  2003cited by this paper
• A Synthetic E7 Gene of Human Papillomavirus Type 16 That Yields Enhanced Expression of the Protein in Mammalian Cells and Is Useful for DNA Immunization Studies

  2003cited by this paper
• The chemistry of protein synthesis and voyage through the ribosomal tunnel.

  2003cited by this paper
• Optimized gene synthesis and high expression of human interleukin-18.

  2003cited by this paper
• Comparative evolutionary genomics unveils the molecular mechanism of reassignment of the CTG codon in Candida spp.

  2003cited by this paper
• Hierarchy of sequence-dependent features associated with prokaryotic translation.

  2003cited by this paper
• Mfold web server for nucleic acid folding and hybridization prediction

  2003cited by this paper
• Effects of codon-optimization on protein expression by the human herpesvirus 6 and 7 U51 open reading frame.

  2003cited by this paper
• Codon Usage Optimization of HIV Type 1 Subtype C gag, pol, env, and nef Genes: In Vitro Expression and Immune Responses in DNA-Vaccinated Mice

  2003cited by this paper
• Codon optimization of Caenorhabditis elegans GluCl ion channel genes for mammalian cells dramatically improves expression levels.

  2003cited by this paper
• Coordinated Nonvectorial Folding in a Newly Synthesized Multidomain Protein

  2002cited by this paper
• Cloning and hemolysin-mediated secretory expression of a codon-optimized synthetic human interleukin-6 gene in Escherichia coli.

  2002cited by this paper
• Codon‐improved Cre recombinase (iCre) expression in the mouse

  2002cited by this paper
• Optimization of the expression of equistatin in Pichia pastoris.

  2002cited by this paper
• Gene optimization is necessary to express a bivalent anti-human anti-T cell immunotoxin in Pichia pastoris.

  2002cited by this paper
• Influences on translation initiation and early elongation by the messenger RNA region flanking the initiation codon at the 3' side.

  2002cited by this paper
• Codon optimization improves heterologous expression of a Schistosoma mansoni cDNA in HEK293 cells

  2002cited by this paper
• Overexpression in Escherichia coli of the AT-rich trpA and trpB genes from the hyperthermophilic archaeon Pyrococcus furiosus.

  2002cited by this paper
• Synonymous codon usage bias and the expression of human glucocerebrosidase in the methylotrophic yeast, Pichia pastoris.

  2002cited by this paper
• Folding of a nascent peptide on the ribosome.

  2001cited by this paper
• Rewiring the keyboard: evolvability of the genetic code

  2001cited by this paper
• Contribution of molecular chaperones to protein folding in the cytoplasm of prokaryotic and eukaryotic cells.

  2001cited by this paper
• Folding of newly translated proteins in vivo: the role of molecular chaperones.

  2001cited by this paper
• Codon Optimization of Gene Fragments EncodingPlasmodium falciparum Merzoite Proteins Enhances DNA Vaccine Protein Expression and Immunogenicity in Mice

  2001cited by this paper
• Enhancement of Capsid Gene Expression: Preparing the Human Papillomavirus Type 16 Major Structural Gene L1 for DNA Vaccination Purposes

  2001cited by this paper
• Codon optimization markedly improves doxycycline regulated gene expression in the mouse heart

  2001cited by this paper
• High-Level Expression in Mammalian Cells of Recombinant House Dust Mite Allergen ProDer p 1 with Optimized Codon Usage

  2001cited by this paper
• Codon and base biases after the initiation codon of the open reading frames in the Escherichia coli genome and their influence on the translation efficiency.

  2001cited by this paper
• A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes

  2001cited by this paper
• Improvement of reading frame maintenance is a common function for several tRNA modifications

  2001cited by this paper
• Increasing expression of P450 and P450-reductase proteins from monocots in heterologous systems.

  2000cited by this paper
• Increased Expression and Immunogenicity of Sequence-Modified Human Immunodeficiency Virus Type 1 gag Gene

  2000cited by this paper
• Concerted Action of Multiple cis-Acting Sequences Is Required for Rev Dependence of Late Human Immunodeficiency Virus Type 1 Gene Expression

  2000cited by this paper
• High-level expression and mutagenesis of recombinant human phosphatidylcholine transfer protein using a synthetic gene: evidence for a C-terminal membrane binding domain.

  2000cited by this paper
• Optimizing heterologous expression in dictyostelium: importance of 5' codon adaptation.

  2000cited by this paper
• Folding and association of oligomeric and multimeric proteins.

  2000cited by this paper
• Use of silent mutations in cDNA encoding human glutathione transferase M2-2 for optimized expression in Escherichia coli.

  1999cited by this paper
• Papillomavirus Capsid Protein Expression Level Depends on the Match between Codon Usage and tRNA Availability

  1999cited by this paper
• Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation

  1999cited by this paper
• Gene synthesis, bacterial expression and purification of the Rickettsia prowazekii ATP/ADP translocase.

  1999cited by this paper
• Analysis and Predictions from Escherichia coli Sequences , or E . coli In Silico

  1999cited by this paper
• The reverse transcriptase component of the Tetrahymena telomerase ribonucleoprotein complex.

  1998cited by this paper
• Codon optimization of the gene encoding a domain from human type 1 neurofibromin protein results in a threefold improvement in expression level in Escherichia coli.

  1998cited by this paper
• Silent mutations in the Escherichia coli ompA leader peptide region strongly affect transcription and translation in vivo.

  1998cited by this paper
• An Extreme Codon Preference Strategy : Codon Reassignment

  1998cited by this paper
• Optimization of codon usage of plasmid DNA vaccine is required for the effective MHC class I-restricted T cell responses against an intracellular bacterium.

  1998cited by this paper
• Heelprinting analysis of in vivo ribosome pause sites.

  1998cited by this paper
• Cotranslational Protein Folding*

  1997cited by this paper
• Cotranslational Folding of Globin*

  1997cited by this paper
• Yeast-enhanced green fluorescent protein (yEGFP): a reporter of gene expression in Candida albicans.

  1997cited by this paper
• Effects of codon usage and vector-host combinations on the expression of spinach plastocyanin in Escherichia coli.

  1997cited by this paper
• Bacterial expression and purification of biologically active mouse c‐Fos proteins by selective codon optimization

  1997cited by this paper
• Errors of heterologous protein expression.

  1996cited by this paper
• Transgenic barley expressing a protein-engineered, thermostable (1,3-1,4)-beta-glucanase during germination.

  1996cited by this paper
• Specific replacement of consecutive AGG codons results in high-level expression of human cardiac troponin T in Escherichia coli.

  1996cited by this paper
• A "humanized" green fluorescent protein cDNA adapted for high-level expression in mammalian cells

  1996cited by this paper
• Enzymatic activity of the ribosome‐bound nascent polypeptide

  1996cited by this paper
• Codon usage limitation in the expression of HIV-1 envelope glycoprotein.

  1996cited by this paper
• 1-Methylguanosine deficiency of tRNA influences cognate codon interaction and metabolism in Salmonella typhimurium

  1995cited by this paper
• Revisiting the Anfinsen cage.

  1995cited by this paper
• Circular permutation of polypeptide chains: implications for protein folding and stability.

  1995cited by this paper
• Folding of an enzyme into an active conformation while bound as peptidyl-tRNA to the ribosome.

  1995cited by this paper
• Kinetics of translation of γB crystallin and its circularly permutated variant in an in vitro cell‐free system: possible relations to codon distribution and protein folding

  1995cited by this paper
• Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli.

  1995cited by this paper
• Effects of tRNALeu1 overproduction in Escherichia coli

  1993cited by this paper
• Modification of the coding sequence enhances plant expression of insect control protein genes.

  1991cited by this paper
• Nonuniform size distribution of nascent globin peptides, evidence for pause localization sites, and a cotranslational protein-folding model

  1991cited by this paper
• Efficient expression of the Paramecium calmodulin gene in Escherichia coli after four TAA-to-CAA changes through a series of polymerase chain reactions.

  1991cited by this paper
• Protein folding: local structures, domains, subunits, and assemblies.

  1991cited by this paper
• An extreme codon preference strategy: codon reassignment.

  1991cited by this paper
• Evaluation of Foreign Gene Codon Optimization in Yeast: Expression of a Mouse IG Kappa Chain

  1991cited by this paper
• Basic local alignment search tool.

  1990cited by this paper
• Presence of the hypermodified nucleotide N6-(delta 2-isopentenyl)-2-methylthioadenosine prevents codon misreading by Escherichia coli phenylalanyl-transfer RNA.

  1989cited by this paper
• Expression of tetanus toxin fragment C in E. coli: high level expression by removing rare codons.

  1989cited by this paper
• Design, synthesis and expression of a human interleukin-2 gene incorporating the codon usage bias found in highly expressed Escherichia coli genes.

  1988cited by this paper
• Ribosome pausing and stacking during translation of a eukaryotic mRNA.

  1988cited by this paper
• Coevolution of codon usage and transfer RNA abundance

  1987cited by this paper
• The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

  1987cited by this paper
• Escherichia Coli and Salmonella: Typhimurium Cellular and Molecular Biology

  1987cited by this paper

• Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications

  2026cites this paper
• The first complete mitochondrial genome characterization of Lutjanus fulvus (Perciformes: Lutjanidae) and phylogenetic analysis within the Lutjanidae family

  2026cites this paper
• Current Landscape and Domestic Breakthroughs: A Comprehensive Review of Pet Vaccines in China

  2026cites this paper
• Characteristics of cold-adapted arylesterase and low-temperature efficient PBAT degradation via cell surface display technology.

  2026cites this paper
• Design, Construction, and Efficacy of a Novel Multiepitope Chimeric Vaccine Against Lumpfish (Cyclopterus lumpus) Infection

  2026cites this paper
• Computational optimization of DEK1 calpain domain solubility through integrated structural modelling and data-driven targeted mutagenesis

  2026cites this paper
• Codon Bias and Phylogenesis Analysis of Chloroplast Genome in Medicinal Plants of Elsholtzia

  2026cites this paper
• From Design to Clinical Use: mRNA Vaccines for Infectious Diseases and Cancer

  2026cites this paper
• GC-Biased Codon Usage and Dinucleotide Signatures Reveal Selection on Pi-ta Blast Resistance Gene Alleles in Oryza spp.

  2026cites this paper
• Cross-species gene redesign leveraging ortholog information and generative modeling

  2026influential citation
• Novel genomically engineered antibiotic-free whole-cell biocatalysts for PET hydrolysis and waste remediation.

  2026cites this paper
• Pichia-CLM: A language model-based codon optimization pipeline for Komagataella phaffii.

  2026cites this paper
• Large mRNA language foundation modeling with NUWA for unified sequence perception and generation

  2026cites this paper
• Considerations of Bacterial Robustness and Stability to Improve Bioprocess Design

  2026cites this paper
• Codon usage biases in the chloroplast genomes of 27 Ardisia species

  2026cites this paper
• The Tor pathway, ribosome concentration, and wobble decoding mediate inhibitory effects of the Leu-Pro CUC-CCG codon pair in Saccharomyces cerevisiae

  2026cites this paper
• CodonRL: Multi-Objective Codon Sequence Optimization Using Demonstration-Guided Reinforcement Learning

  2026cites this paper
• Computational and deep learning-assisted multi-epitope vaccine design targeting the RNA-dependent RNA polymerase of Nipah virus

  2026cites this paper
• Validation of cold shock-based technique for purification of recombinant C. elegans Phosphodiesterase 3 protein expressed in E. coli.

  2025cites this paper
• Shared regulatory factors influencing mRNA translation rate and half-life in yeast.

  2025cites this paper
• Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events

  2025cites this paper
• A multi-epitope vaccine targeting a key virulence factor ClfA: An In-silico approach to combat Staphylococcus aureus infections

  2025cites this paper
• Effective Gene Expression Prediction and Optimization from Protein Sequences

  2025cites this paper
• Exploring antibiotic resistance in diverse homologs of the dihydrofolate reductase protein family through broad mutational scanning

  2025cites this paper
• Optimizated Prolyl‐4‐Hydroxylase Expression in Komagataella phaffii Enables Efficient Triple‐Helix Formation of Recombinant Human Collagen

  2025cites this paper
• Curriculum-Augmented GFlowNets For mRNA Sequence Generation

  2025cites this paper
• Neighboring codon adjacent nucleotides have a conserved influence on mRNA decay

  2025cites this paper
• ColiFormer: A Transformer-Based Codon Optimization Model Balancing Multiple Objectives for Enhanced E. coli Gene Expression

  2025cites this paper
• Enhanced immunogenicity and protective efficacy of a novel bacillus Calmette-Guérin/Mycobacterium tuberculosis H37Ra fusion vaccine expressing codon-optimized culture filtrate protein 10 in a mouse model.

  2025cites this paper
• GC3 codons enhance protein production in diverse GC- and AT-rich plant species

  2025cites this paper
• Harnessing mRNA-lipid nanoparticles as innovative therapies for autoimmune diseases

  2025cites this paper
• Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution

  2025cites this paper
• Identifying new targets for improving terpenoid biosynthesis in Yarrowia lipolytica through random genomic cytosine base editing

  2025cites this paper
• Chemically modified tRNA enhances the translation capacity of mRNA rich in cognate codons

  2025cites this paper
• Harnessing mRNA for heart health: a new era in cardiovascular treatment

  2025cites this paper
• Enhancing mRNA translation efficiency with discriminative and generative artificial intelligence by optimizing 5′ UTR sequences

  2025cites this paper
• Availability of Charged tRNAs Drives Maximal Protein Synthesis at Intermediate Levels of Codon Usage Bias

  2025cites this paper
• Biochemical and functional analysis of a thermostable, xylose-tolerant glycoside hydrolase 43 β-xylosidase from Thermothelomyces thermophilus.

  2025cites this paper
• Systematic Evaluation of Vector Sequence Elements in Isogenic CHO Cells for Improved Antibody Production

  2025cites this paper
• Recombinant DNA the Bio-Revolution, Between Promise, Hurdles, and Achievements

  2025cites this paper
• In silico analysis of VEGFR2 and c-MET in consideration with immunologic facts: Implications for mRNA vaccine design against breast cancer.

  2025cites this paper
• A More Efficient Dynamic Programming Algorithm for Designing a Coding Sequence by Jointly Optimizing Its Structural Stability and Codon Usage

  2025cites this paper
• Chloroplast Genome Evolution and Codon Usage In the Medicinal Plant Pothos chinensis (Araceae)

  2025cites this paper
• Deep generative models design mRNA sequences with enhanced translational capacity and stability.

  2025cites this paper
• The role of neoantigens and tumor mutational burden in cancer immunotherapy: advances, mechanisms, and perspectives

  2025cites this paper
• Codon-deoptimized single-round infectious virus for therapeutic and vaccine applications

  2025cites this paper
• Negative epistasis limits current codon optimization approaches

  2025influential citation
• Geoengineering potential of marine bacterial carbonic anhydrases for long-term carbon storage

  2025cites this paper
• Two-stage process and strain engineering for continuous bioconversion of CO2 to butanol.

  2025cites this paper
• Advances and Challenges in mRNA Vaccine Technology

  2025cites this paper
• Genetic characterization of four bacteriophages of Salmonella enterica derived from different geographic regions in China via genomic comparison.

  2025cites this paper
• Opportunities in Therapeutic mRNA Stabilization: Sequence, Structure, Adjuvants and Vectors

  2025cites this paper
• Ribo-seq guided design of enhanced protein secretion in Komagataella phaffii

  2025cites this paper
• Design and preparation of artificial heme-copper enzymes.

  2025cites this paper
• Impact of different synonymous codon substitution strategies on SARS-CoV-2 nucleocapsid protein expression in Escherichia coli

  2025cites this paper
• Mitochondrial codon usage bias and novel phylogenetic insights: implications for taxonomic reevaluation of seven Xylotini species (Diptera, Syrphidae, Eristalinae)

  2025cites this paper
• HyperBind2: Multi-Shot Learning Enables Progressive Improvement in Computational Antibody Discovery

  2025cites this paper
• TOM: Transformer Neural Network Optimization of mRNA initiator region

  2025cites this paper
• Role of nucleotide pair frequency and synonymous codon usage in the evolution of bovine viral diarrhea virus

  2025cites this paper
• CloneFast: A simple plasmid design and construction guide for labs venturing into synthetic biology

  2025cites this paper
• Effective alternative strategies to combat challenges associated with MDR bacterial infections: Drug repurposing, role of artificial intelligence, and novel therapeutic options.

  2025cites this paper
• Characterization of oligosaccharides produced by a truncated dextransucrase from Weissella confusa Wcp3a isolated from pozol, a traditional fermented corn beverage.

  2025cites this paper
• From genetic code to global health: the impact of nucleic acid vaccines on disease prevention and treatment.

  2025cites this paper
• Targeted Expression and Purification of Elastin-Like Polypeptide-Fused Abrin: A Potential Strategy for Cancer Therapy

  2025cites this paper
• Exploring Antibiotic Resistance in Diverse Homologs of the Dihydrofolate Reductase Protein Family through Broad Mutational Scanning

  2025cites this paper
• Phylogenetic and Functional Diversity of Soluble Di‐Iron Monooxygenases

  2025cites this paper
• Decoding codon usage in human papillomavirus type 59

  2025cites this paper
• Technological breakthroughs and advancements in the application of mRNA vaccines: a comprehensive exploration and future prospects

  2025cites this paper
• The curious case of AAV immunology.

  2025cites this paper
• A deep learning model trained on expressed transcripts across different tissue types reveals cell-type codon-optimization preferences

  2025cites this paper
• Enhanced production of C50 carotenoid bacterioruberin by metabolically engineered Corynebacterium glutamicum.

  2025cites this paper
• Bioluminescent imaging of an oomycete pathogen empowers chemical selections and rational fungicide applications

  2025cites this paper
• Catch & Release—rapid cost‐effective protein purification from plants using a DIY GFP‐Trap‐protease approach

  2025cites this paper
• Generative AI-driven artificial DNA design for enhancing inter-species gene activation and enzymatic degradation of PET

  2025cites this paper
• Advancing mRNA vaccines: A comprehensive review of design, delivery, and efficacy in infectious diseases.

  2025cites this paper
• Uncovering evolutionary and phylogenetic relationships in Glyptothorax species through comparative mitochondrial genomics

  2025cites this paper
• Expanding fluorescence imaging tools in Staphylococcus aureus: Optimized expression of red fluorescent proteins.

  2025cites this paper
• Expression and purification of bacterial dye-decolorizing peroxidases using Escherichia coli.

  2025cites this paper
• Essential Logic and Facts Behind the Expansion of the Genetic Code: A Critical Assessment

  2025cites this paper
• Scaled codon usage similarity index: A comprehensive resource for crop plants

  2024influential citation
• From Sequence to System: Enhancing IVT mRNA Vaccine Effectiveness through Cutting-Edge Technologies.

  2024cites this paper
• Advancing novel veterinary vaccines: From comprehensive antigen and adjuvant design to preparation process optimization.

  2024cites this paper
• Metabolic engineering of Mucor circinelloides to improve astaxanthin production

  2024cites this paper
• Current Non-Viral-Based Strategies to Manufacture CAR-T Cells

  2024cites this paper
• Codon Optimization is Required to Express Fluorogenic Reporter Proteins in Lactococcus lactis

  2024cites this paper
• Newly developed mRNA vaccines induce immune responses in Litopenaeus vannamei shrimps during primary vaccination.

  2024cites this paper
• Deterministic Techniques for K-Mer Frequency Counting

  2024cites this paper
• Application of immunoinformatics to develop a novel and effective multiepitope chimeric vaccine against Variovorax durovernensis

  2024cites this paper
• Comparative Analysis of Codon Usage Bias in Six Eimeria Genomes

  2024cites this paper
• Strategies to overcome the challenges of low or no expression of heterologous proteins in Escherichia coli.

  2024cites this paper
• Transcriptional Dynamics of NRF2 Overexpression and KEAP1-NRF2 Inhibitors in Human Cell Line and Primary Lung Cells

  2024cites this paper
• Recent advancements in flavonoid production through engineering microbial systems

  2024cites this paper
• Comparative Analysis of Complete Mitochondrial Genomes of Five Chromodorididae Species (Nudibranchia:Doridina)

  2024cites this paper
• Deep generative models generate mRNA sequences with enhanced translation capacity and stability

  2024cites this paper
• mRNA medicine: Recent progresses in chemical modification, design, and engineering

  2024cites this paper
• Discovery and investigation of the truncation of the (GGGGS)n linker and its effect on the productivity of bispecific antibodies expressed in mammalian cells

  2024cites this paper
• Development of recombinant proteins for vaccine candidates against serotypes O and A of Foot-and-Mouth Disease virus in Bangladesh

  2024cites this paper
• Expression and Subcellular Localization of Lanthipeptides in Human Cells

  2024cites this paper
• mRNA vaccine development and applications: A special focus on tumors (Review)

  2024cites this paper
• Non-viral vectors for chimeric antigen receptor immunotherapy

  2024cites this paper