(Q21284253)

18 August 2022

Alan Villalobos

1

Alan

Villalobos

1 reference

18 August 2022

Jon E Ness

series ordinal

2

author given names

Jon E

author last names

Ness

1 reference

18 August 2022

Jeremy Minshull

series ordinal

4

author given names

Jeremy

author last names

Minshull

1 reference

18 August 2022

Sridhar Govindarajan

series ordinal

5

author given names

Sridhar

author last names

Govindarajan

1 reference

JCat: a novel tool to adapt codon usage of a target gene to its potential expression host

18 August 2022

language of work or name

English

0 references

publication date

2006

0 references

published in

BMC Bioinformatics

0 references

volume

7

0 references

issue

1

0 references

page(s)

285

0 references

uses

Gene Designer

0 references

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

GeMS: an advanced software package for designing synthetic genes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Comparative context analysis of codon pairs on an ORFeome scale

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Mfold web server for nucleic acid folding and hybridization prediction

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Codon usage tabulated from international DNA sequence databases: status for the year 2000

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Accurate multiplex gene synthesis from programmable DNA microchips

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Influences on gene expression in vivo by a Shine-Dalgarno sequence.

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Overexpression of tnaC of Escherichia coli inhibits growth by depleting tRNA2Pro availability

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Initiation of protein synthesis in bacteria

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

mRNA helicase activity of the ribosome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Codon bias and heterologous protein expression

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Putting engineering back into protein engineering: bioinformatic approaches to catalyst design.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Stop codons preceded by rare arginine codons are efficient determinants of SsrA tagging in Escherichia coli

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Codon bias at the 3'-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

How translational accuracy influences reading frame maintenance

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

The downstream box: an efficient and independent translation initiation signal in Escherichia coli

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Codon usage in bacteria: correlation with gene expressivity

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Total synthesis and cloning of a gene coding for the ribonuclease S protein

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Influence of modification next to the anticodon in tRNA on codon context sensitivity of translational suppression and accuracy

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Nonrandom utilization of codon pairs in Escherichia coli

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Gene2Oligo: oligonucleotide design for in vitro gene synthesis.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

UpGene: Application of a web-based DNA codon optimization algorithm

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Hierarchy of sequence-dependent features associated with prokaryotic translation

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Novel in-frame two codon translational hop during synthesis of bovine placental lactogen in a recombinant strain of Escherichia coli

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Errors of heterologous protein expression

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Constraints on codon context in Escherichia coli genes. Their possible role in modulating the efficiency of translation

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Ribosomes and translation

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

GMAP: a multi-purpose computer program to aid synthetic gene design, cassette mutagenesis and the introduction of potential restriction sites into DNA sequences

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Codon pair utilization biases influence translational elongation step times

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Undermodification in the first position of the anticodon of supG-tRNA reduces translational efficiency

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

An effect of codon context on the mistranslation of UGU codons in vitro.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Influence of the codon following the AUG initiation codon on the expression of a modified lacZ gene in Escherichia coli

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Codon contexts in enterobacterial and coliphage genes.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

A set of Macintosh computer programs for the design and analysis of synthetic genes.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Mistranslational errors associated with the rare arginine codon CGG in Escherichia coli

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

MELTING, computing the melting temperature of nucleic acid duplex

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

Absence of effect of varying Thr-Leu codon pairs on protein synthesis in a T7 system

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

PCR-based gene synthesis as an efficient approach for expression of the A T-rich malaria genome.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1523223

The Synthetic Gene Designer: a flexible web platform to explore sequence manipulation for heterologous expression

29 November 2018

1 reference

12 December 2020

Abortive translation caused by peptidyl-tRNA drop-off at NGG codons in the early coding region of mRNA

1 reference

12 December 2020

Validation of RNAi silencing specificity using synthetic genes: salicylic acid-binding protein 2 is required for innate immunity in plants

1 reference

12 December 2020

Cooperative effects by the initiation codon and its flanking regions on translation initiation

1 reference

12 December 2020

Codon optimizer: a freeware tool for codon optimization

1 reference

12 December 2020

Total Synthesis of the Gene for an Alanine Transfer Ribonucleic Acid from Yeast

1 reference

12 December 2020

The influence of codon context on genetic code translation

1 reference

12 December 2020

Effects of surrounding sequence on the suppression of nonsense codons

1 reference

12 December 2020

Codon context effects in missense suppression

1 reference

12 December 2020

Codon usage determines translation rate in Escherichia coli

1 reference

12 December 2020

mRNAs can be stabilized by DEAD-box proteins

1 reference

12 December 2020

Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2105-7-285

1 reference

journals/bmcbi/VillalobosNGMG06

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

0 references

1 reference

1 reference

PubMed publication ID

16756672

1 reference