Published in BMC Bioinformatics on June 06, 2006
Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet (2010) 5.37
Refinement of tools for targeted gene expression in Drosophila. Genetics (2010) 4.53
The APC/C maintains the spindle assembly checkpoint by targeting Cdc20 for destruction. Nat Cell Biol (2008) 4.08
Design parameters to control synthetic gene expression in Escherichia coli. PLoS One (2009) 3.38
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat Biotechnol (2014) 2.63
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res (2007) 2.63
Optimization in computational systems biology. BMC Syst Biol (2008) 2.50
Targeted development of registries of biological parts. PLoS One (2008) 2.33
Principles of genetic circuit design. Nat Methods (2014) 1.79
Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. Proc Natl Acad Sci U S A (2011) 1.75
Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucleic Acids Res (2009) 1.70
Industrial production of recombinant therapeutics in Escherichia coli and its recent advancements. J Ind Microbiol Biotechnol (2012) 1.67
Foundations for the design and implementation of synthetic genetic circuits. Nat Rev Genet (2012) 1.65
Writing DNA with GenoCAD. Nucleic Acids Res (2009) 1.60
Computational tools for the synthetic design of biochemical pathways. Nat Rev Microbiol (2012) 1.45
Gene composer: database software for protein construct design, codon engineering, and gene synthesis. BMC Biotechnol (2009) 1.43
Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer. BMC Biotechnol (2009) 1.40
You're one in a googol: optimizing genes for protein expression. J R Soc Interface (2009) 1.39
Codon usage: nature's roadmap to expression and folding of proteins. Biotechnol J (2011) 1.36
Monoclonal antibody produced in plants efficiently treats West Nile virus infection in mice. Proc Natl Acad Sci U S A (2010) 1.23
Deletion of the Pichia pastoris KU70 homologue facilitates platform strain generation for gene expression and synthetic biology. PLoS One (2012) 1.20
Programming cells: towards an automated 'Genetic Compiler'. Curr Opin Biotechnol (2010) 1.20
Comparison of two codon optimization strategies to enhance recombinant protein production in Escherichia coli. Microb Cell Fact (2011) 1.20
The GeneOptimizer Algorithm: using a sliding window approach to cope with the vast sequence space in multiparameter DNA sequence optimization. Syst Synth Biol (2010) 1.18
Dynamic imaging of the effector immune response to listeria infection in vivo. PLoS Pathog (2011) 1.16
Plasmid DNA vaccine vector design: impact on efficacy, safety and upstream production. Biotechnol Adv (2009) 1.12
Constitutive Activation of the PrfA regulon enhances the potency of vaccines based on live-attenuated and killed but metabolically active Listeria monocytogenes strains. Infect Immun (2008) 1.11
Concern Synthetic versions of firefly luciferase and Renilla luciferase reporter genes that resist transgene silencing in sugarcane. BMC Plant Biol (2014) 1.10
GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs. Nucleic Acids Res (2010) 1.10
Invasive extravillous trophoblasts restrict intracellular growth and spread of Listeria monocytogenes. PLoS Pathog (2011) 1.09
Heterologous expression and extracellular secretion of cellulolytic enzymes by Zymomonas mobilis. Appl Environ Microbiol (2010) 1.08
GeneDesign 3.0 is an updated synthetic biology toolkit. Nucleic Acids Res (2010) 1.05
Decoding mechanisms by which silent codon changes influence protein biogenesis and function. Int J Biochem Cell Biol (2015) 1.04
Protein engineering of improved prolyl endopeptidases for celiac sprue therapy. Protein Eng Des Sel (2008) 1.03
Optimal encoding rules for synthetic genes: the need for a community effort. Mol Syst Biol (2007) 1.01
SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains. ACS Synth Biol (2012) 1.01
Lumen Thiol Oxidoreductase1, a disulfide bond-forming catalyst, is required for the assembly of photosystem II in Arabidopsis. Plant Cell (2011) 1.00
A novel system for rapid and cost-effective production of detection and diagnostic reagents of West Nile virus in plants. J Biomed Biotechnol (2011) 0.98
Developments in the tools and methodologies of synthetic biology. Front Bioeng Biotechnol (2014) 0.97
GeneGenie: optimized oligomer design for directed evolution. Nucleic Acids Res (2014) 0.96
Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. J Mol Biol (2010) 0.94
Computational tools for metabolic engineering. Metab Eng (2012) 0.94
In situ overlap and sequence synthesis during DNA assembly. ACS Synth Biol (2013) 0.93
Engineering genes for predictable protein expression. Protein Expr Purif (2012) 0.93
Differential transit peptide recognition during preprotein binding and translocation into flowering plant plastids. Plant Cell (2012) 0.89
A critical analysis of codon optimization in human therapeutics. Trends Mol Med (2014) 0.88
Codon preference optimization increases prokaryotic cystatin C expression. J Biomed Biotechnol (2012) 0.86
An engineered split M.HhaI-zinc finger fusion lacks the intended methyltransferase specificity. Biochem Biophys Res Commun (2008) 0.86
H-NS silences gfp, the green fluorescent protein gene: gfpTCD is a genetically Remastered gfp gene with reduced susceptibility to H-NS-mediated transcription silencing and with enhanced translation. J Bacteriol (2010) 0.86
Engineering biological systems using automated biofoundries. Metab Eng (2017) 0.85
Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization. BMC Bioinformatics (2011) 0.85
Computational codon optimization of synthetic gene for protein expression. BMC Syst Biol (2012) 0.85
Advances and computational tools towards predictable design in biological engineering. Comput Math Methods Med (2014) 0.84
Real-time PCR assay and a synthetic positive control for the rapid and sensitive detection of the emerging resistance gene New Delhi Metallo-β-lactamase-1 (bla(NDM-1)). Med Microbiol Immunol (2011) 0.83
CCS5, a thioredoxin-like protein involved in the assembly of plastid c-type cytochromes. J Biol Chem (2010) 0.82
Modified 'one amino acid-one codon' engineering of high GC content TaqII-coding gene from thermophilic Thermus aquaticus results in radical expression increase. Microb Cell Fact (2014) 0.82
Computational tools and algorithms for designing customized synthetic genes. Front Bioeng Biotechnol (2014) 0.81
Analysis of the ketosynthase-chain length factor heterodimer from the fredericamycin polyketide synthase. Chem Biol (2011) 0.81
Efficient production of methionine from 2-amino-4-methylthiobutanenitrile by recombinant Escherichia coli harboring nitrilase. J Ind Microbiol Biotechnol (2014) 0.81
GenoLIB: a database of biological parts derived from a library of common plasmid features. Nucleic Acids Res (2015) 0.79
Molecular cloning and functional characterization of components of the capsule biosynthesis complex of Neisseria meningitidis serogroup A: toward in vitro vaccine production. J Biol Chem (2014) 0.79
Design and synthesis of a quintessential self-transmissible IncX1 plasmid, pX1.0. PLoS One (2011) 0.78
Parallel in vivo DNA assembly by recombination: experimental demonstration and theoretical approaches. PLoS One (2013) 0.78
Sequence similarity is more relevant than species specificity in probabilistic backtranslation. BMC Bioinformatics (2007) 0.78
Quantification of the physiochemical constraints on the export of spider silk proteins by Salmonella type III secretion. Microb Cell Fact (2010) 0.76
Characterization and application of a newly synthesized 2-deoxyribose-5-phosphate aldolase. J Ind Microbiol Biotechnol (2012) 0.76
Codon-Optimized NADH Oxidase Gene Expression and Gene Fusion with Glycerol Dehydrogenase for Bienzyme System with Cofactor Regeneration. PLoS One (2015) 0.76
Grand challenge commentary: Transforming biosynthesis into an information science. Nat Chem Biol (2010) 0.76
Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein. Sci Rep (2016) 0.75
Recombinant Lactococcus lactis fails to secrete bovine chymosine. Bioengineered (2014) 0.75
Heterologous expression of Aspergillus aculeatus endo-polygalacturonase in Pichia pastoris by high cell density fermentation and its application in textile scouring. BMC Biotechnol (2017) 0.75
Pushing the limits of automatic computational protein design: design, expression, and characterization of a large synthetic protein based on a fungal laccase scaffold. Syst Synth Biol (2011) 0.75
Pichia pastoris versus Saccharomyces cerevisiae: a case study on the recombinant production of human granulocyte-macrophage colony-stimulating factor. BMC Res Notes (2017) 0.75
Algorithms for optimizing cross-overs in DNA shuffling. BMC Bioinformatics (2012) 0.75
Engineering Translation in Mammalian Cell Factories to Increase Protein Yield: The Unexpected Use of Long Non-Coding SINEUP RNAs. Comput Struct Biotechnol J (2016) 0.75
Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli. BMC Bioinformatics (2017) 0.75
DNASynth: a computer program for assembly of artificial gene parts in decreasing temperature. Biomed Res Int (2015) 0.75
Directed evolution of a yeast-displayed HIV-1 SOSIP gp140 spike protein toward improved expression and affinity for conformational antibodies. PLoS One (2015) 0.75
PromoterCAD: Data-driven design of plant regulatory DNA. Nucleic Acids Res (2013) 0.75
Targeted DNA methylation in human cells using engineered dCas9-methyltransferases. Sci Rep (2017) 0.75
Upscale production of a recombinant cyclodextrin glycosyltransferase from Paenibacillus macerans in Escherichia coli. 3 Biotech (2017) 0.75
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res (1982) 12.99
Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science (2002) 9.50
Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res (2000) 7.88
Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry (1995) 6.40
DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic Acids Res (2002) 5.75
Codon bias and heterologous protein expression. Trends Biotechnol (2004) 5.20
Codon usage determines translation rate in Escherichia coli. J Mol Biol (1989) 5.07
mRNA helicase activity of the ribosome. Cell (2005) 4.72
Synthetic biology. Nat Rev Genet (2005) 4.67
Accurate multiplex gene synthesis from programmable DNA microchips. Nature (2004) 4.16
Effects of surrounding sequence on the suppression of nonsense codons. J Mol Biol (1983) 3.95
Ribosomes and translation. Annu Rev Biochem (1997) 3.87
Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev (2005) 3.78
Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc Natl Acad Sci U S A (2004) 2.84
Nonrandom utilization of codon pairs in Escherichia coli. Proc Natl Acad Sci U S A (1989) 2.81
The influence of codon context on genetic code translation. Nature (1980) 2.72
JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res (2005) 2.60
Total synthesis of the gene for an alanine transfer ribonucleic acid from yeast. Nature (1970) 2.51
Influence of the codon following the AUG initiation codon on the expression of a modified lacZ gene in Escherichia coli. EMBO J (1987) 2.46
Stop codons preceded by rare arginine codons are efficient determinants of SsrA tagging in Escherichia coli. Proc Natl Acad Sci U S A (2002) 2.02
Codon pair utilization biases influence translational elongation step times. J Biol Chem (1995) 2.00
MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics (2001) 2.00
How translational accuracy influences reading frame maintenance. EMBO J (1999) 1.96
Gene2Oligo: oligonucleotide design for in vitro gene synthesis. Nucleic Acids Res (2004) 1.92
Hierarchy of sequence-dependent features associated with prokaryotic translation. Genome Res (2003) 1.90
PCR-based gene synthesis as an efficient approach for expression of the A+T-rich malaria genome. Protein Eng (1999) 1.82
mRNAs can be stabilized by DEAD-box proteins. Nature (1994) 1.72
The downstream box: an efficient and independent translation initiation signal in Escherichia coli. EMBO J (1996) 1.70
Constraints on codon context in Escherichia coli genes. Their possible role in modulating the efficiency of translation. J Mol Biol (1986) 1.69
UpGene: Application of a web-based DNA codon optimization algorithm. Biotechnol Prog (2004) 1.67
Codon bias at the 3'-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli. Gene (2001) 1.65
Influence of modification next to the anticodon in tRNA on codon context sensitivity of translational suppression and accuracy. J Bacteriol (1986) 1.65
Codon context effects in missense suppression. J Mol Biol (1984) 1.52
Errors of heterologous protein expression. Curr Opin Biotechnol (1996) 1.48
Total synthesis and cloning of a gene coding for the ribonuclease S protein. Science (1984) 1.46
GeMS: an advanced software package for designing synthetic genes. Nucleic Acids Res (2005) 1.45
Codon optimizer: a freeware tool for codon optimization. Protein Expr Purif (2003) 1.35
Cooperative effects by the initiation codon and its flanking regions on translation initiation. Gene (2001) 1.33
Comparative context analysis of codon pairs on an ORFeome scale. Genome Biol (2005) 1.28
Mistranslational errors associated with the rare arginine codon CGG in Escherichia coli. Protein Expr Purif (2003) 1.21
Undermodification in the first position of the anticodon of supG-tRNA reduces translational efficiency. Mol Gen Genet (1984) 1.18
Codon contexts in enterobacterial and coliphage genes. Mol Biol Evol (1987) 1.16
Novel in-frame two codon translational hop during synthesis of bovine placental lactogen in a recombinant strain of Escherichia coli. Nucleic Acids Res (1992) 1.09
The Synthetic Gene Designer: a flexible web platform to explore sequence manipulation for heterologous expression. Protein Expr Purif (2005) 1.06
An effect of codon context on the mistranslation of UGU codons in vitro. J Mol Biol (1984) 1.01
Abortive translation caused by peptidyl-tRNA drop-off at NGG codons in the early coding region of mRNA. FEBS J (2005) 1.00
Overexpression of tnaC of Escherichia coli inhibits growth by depleting tRNA2Pro availability. J Bacteriol (2006) 1.00
Influences on gene expression in vivo by a Shine-Dalgarno sequence. Mol Microbiol (2006) 0.97
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. Protein Expr Purif (1998) 0.96
Validation of RNAi silencing specificity using synthetic genes: salicylic acid-binding protein 2 is required for innate immunity in plants. Plant J (2006) 0.91
GMAP: a multi-purpose computer program to aid synthetic gene design, cassette mutagenesis and the introduction of potential restriction sites into DNA sequences. Biotechniques (1994) 0.85
Absence of effect of varying Thr-Leu codon pairs on protein synthesis in a T7 system. Biochemistry (2001) 0.82
Putting engineering back into protein engineering: bioinformatic approaches to catalyst design. Curr Opin Biotechnol (2003) 0.81
A set of Macintosh computer programs for the design and analysis of synthetic genes. Comput Appl Biosci (1989) 0.80
Codon bias and heterologous protein expression. Trends Biotechnol (2004) 5.20
The APC/C maintains the spindle assembly checkpoint by targeting Cdc20 for destruction. Nat Cell Biol (2008) 4.08
Design parameters to control synthetic gene expression in Escherichia coli. PLoS One (2009) 3.38
Palaeotemperature trend for Precambrian life inferred from resurrected proteins. Nature (2008) 2.99
Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently. Nat Biotechnol (2002) 1.81
A family of thermostable fungal cellulases created by structure-guided recombination. Proc Natl Acad Sci U S A (2009) 1.50
[Emergency medical services require stronger resources when it comes to internal medicine]. Lakartidningen (2002) 1.39
You're one in a googol: optimizing genes for protein expression. J R Soc Interface (2009) 1.39
A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics (2007) 1.38
Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily. Biochemistry (2003) 1.36
Engineering the Salmonella type III secretion system to export spider silk monomers. Mol Syst Biol (2009) 1.26
Identification of likely orthologs of tobacco salicylic acid-binding protein 2 and their role in systemic acquired resistance in Arabidopsis thaliana. Plant J (2008) 1.25
Engineering proteinase K using machine learning and synthetic genes. BMC Biotechnol (2007) 1.17
SCHEMA recombination of a fungal cellulase uncovers a single mutation that contributes markedly to stability. J Biol Chem (2009) 1.11
Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection. Proc Natl Acad Sci U S A (2010) 1.09
Systematic variation of amino acid substitutions for stringent assessment of pairwise covariation. J Mol Biol (2003) 1.07
Protein engineering of improved prolyl endopeptidases for celiac sprue therapy. Protein Eng Des Sel (2008) 1.03
Designing genes for successful protein expression. Methods Enzymol (2011) 0.99
Engineering genes for predictable protein expression. Protein Expr Purif (2012) 0.93
Validation of RNAi silencing specificity using synthetic genes: salicylic acid-binding protein 2 is required for innate immunity in plants. Plant J (2006) 0.91
Biosynthesis of monomers for plastics from renewable oils. J Am Chem Soc (2010) 0.91
Semi-synthetic DNA shuffling of aveC leads to improved industrial scale production of doramectin by Streptomyces avermitilis. Metab Eng (2005) 0.91
Redesigning and characterizing the substrate specificity and activity of Vibrio fluvialis aminotransferase for the synthesis of imagabalin. Protein Eng Des Sel (2012) 0.90
Predicting enzyme function from protein sequence. Curr Opin Chem Biol (2005) 0.90
Improved biocatalysts from a synthetic circular permutation library of the flavin-dependent oxidoreductase old yellow enzyme. J Am Chem Soc (2013) 0.86
Engineered protein function by selective amino acid diversification. Methods (2004) 0.85
Engineering the aveC gene to enhance the ratio of doramectin to its CHC-B2 analogue produced in Streptomyces avermitilis. Biotechnol Bioeng (2003) 0.81
Analysis of the ketosynthase-chain length factor heterodimer from the fredericamycin polyketide synthase. Chem Biol (2011) 0.81
Putting engineering back into protein engineering: bioinformatic approaches to catalyst design. Curr Opin Biotechnol (2003) 0.81
Optimizing the search algorithm for protein engineering by directed evolution. Protein Eng (2003) 0.80
Directed evolution of gene-shuffled IFN-alpha molecules with activity profiles tailored for treatment of chronic viral diseases. Proc Natl Acad Sci U S A (2007) 0.80
The clinical consequences of a pre-hospital diagnosis of stroke by the emergency medical service system. A pilot study. Scand J Trauma Resusc Emerg Med (2012) 0.78
In silico design of functional DNA constructs. Methods Mol Biol (2012) 0.78
Preventing the misuse of gene synthesis. Nat Biotechnol (2009) 0.75
Patterning of antibodies using flexographic printing. Langmuir (2012) 0.75