Codon Usage Database
Other names: codon_usage_database
Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.
Description
More detailed information about this field from each metasource.
Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:08.869248
Webpage:
http://www.kazusa.or.jp/codon/Webpage
More detailed information about this field from each metasource.
http://www.kazusa.or.jp/codon/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:08.869248
Publications:
Publications
More detailed information about this field from each metasource.
Codon usage tabulated from international DNA sequence databases: status for the year 2000
PMID: 10592250
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:08.869248
Publications
More detailed information about this field from each metasource.
Codon usage tabulated from international DNA sequence databases: status for the year 2000
PMID: 10592250
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:08.869248
-
Codon usage tabulated from international DNA sequence databases: status for the year 2000
PubMed citations: 467.
467 articles citing: Codon usage tabulated from international DNA sequence databases: status for the year 2000
Ionizing radiation and chemical oxidant exposure impacts on Cryptococcus neoformans transfer RNAs. PMID:35349591
Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes? PMID:35330182
Mutation bias shapes the spectrum of adaptive substitutions. PMID:35145034
Screening of the Promising Direct Thrombin Inhibitors from Haematophagous Organisms. Part I: Recombinant Analogues and Their Antithrombotic Activity In Vitro. PMID:35052692
Toward efficient multiple-site incorporation of unnatural amino acids using cell-free translation system. PMID:35024479
Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance. PMID:35015630
Evolutionary Stability Optimizer (ESO): A Novel Approach to Identify and Avoid Mutational Hotspots in DNA Sequences While Maintaining High Expression Levels. PMID:34928133
Streptococcus pneumoniae: a Plethora of Temperate Bacteriophages With a Role in Host Genome Rearrangement. PMID:34869076
Glue Genes Are Subjected to Diverse Selective Forces during Drosophila Development. PMID:34788814
Histone H3K27 Methylation Perturbs Transcriptional Robustness and Underpins Dispensability of Highly Conserved Genes in Fungi. PMID:34751371
CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern. PMID:34738275
CompoDynamics: a comprehensive database for characterizing sequence composition dynamics. PMID:34718745
mRNA codon optimization with quantum computers. PMID:34714834
Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip. PMID:34530443
K-Mer Analyses Reveal Different Evolutionary Histories of Alpha, Beta, and Gamma Papillomaviruses. PMID:34502564
Construction of à la carte QconCAT protein standards for multiplexed quantification of user-specified target proteins. PMID:34496840
Human Codon Usage: The Genetic Basis of Pathogen Latency. PMID:34430963
Expression of a human cDNA in moss results in spliced mRNAs and fragmentary protein isoforms. PMID:34385580
Role of a cryptic tRNA gene operon in survival under translational stress. PMID:34379789
An inside look at a biofilm: Pseudomonas aeruginosa flagella biotracking. PMID:34117070
Consequences of Mixotrophy on Cell Energetic Metabolism in Microchloropsis gaditana Revealed by Genetic Engineering and Metabolic Approaches. PMID:34113360
Genetic changes and evolutionary analysis of canine circovirus. PMID:34104994
Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China. PMID:34072978
An Unsupervised Algorithm for Host Identification in Flaviviruses. PMID:34069049
Adaptation and Codon-Usage Preference of Apple and Pear-Infecting Apple Stem Grooving Viruses. PMID:34063757
Genetic code expansion enables visualization of Salmonella type three secretion system components and secreted effectors. PMID:34061032
Development of Clostridium saccharoperbutylacetonicum as a Whole Cell Biocatalyst for Production of Chirally Pure (R)-1,3-Butanediol. PMID:34055760
Nanoparticle-mediated tumor cell expression of mIL-12 via systemic gene delivery treats syngeneic models of murine lung cancers. PMID:33958660
L-Carnitine Production Through Biosensor-Guided Construction of the Neurospora crassa Biosynthesis Pathway in Escherichia coli. PMID:33937222
Association of whole mtDNA, an NADPH G11914A variant, and haplogroups with high physical performance in an elite military troop. PMID:33909855
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. PMID:33904398
Incorporating Machine Learning into Established Bioinformatics Frameworks. PMID:33809353
The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense. PMID:33801257
Designing and generating a mouse model: frequently asked questions. PMID:33797414
Luciferase-based reporter system for in vitro evaluation of elongation rate and processivity of ribosomes. PMID:33684199
Protein products of nonstop mRNA disrupt nucleolar homeostasis. PMID:33619693
Assessing optimal: inequalities in codon optimization algorithms. PMID:33607980
CRISPR-Cas9-Based Toolkit for Clostridium botulinum Group II Spore and Sporulation Research. PMID:33584620
Conversion of L-arabinose to L-ribose by genetically engineered Candida tropicalis. PMID:33559750
Exploiting genetic diversity and gene synthesis to identify superior nitrogenase NifH protein variants to engineer N2-fixation in plants. PMID:33398015
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Codon Usage and Replicative Fitness. PMID:33392612
Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. PMID:33377145
Elimination of Mutant mtDNA by an Optimized mpTALEN Restores Differentiation Capacities of Heteroplasmic MELAS-iPSCs. PMID:33376755
Expression of transgenes enriched in rare codons is enhanced by the MAPK pathway. PMID:33335127
Pseudouridine-mediated translation control of mRNA by methionine aminoacyl tRNA synthetase. PMID:33305314
Genomic and evolutionary comparison between SARS-CoV-2 and other human coronaviruses. PMID:33290786
Prediction of the incubation period for COVID-19 and future virus disease outbreaks. PMID:33256718
A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila. PMID:33203452
Improving the Expression of Human Granulocyte Colony Stimulating Factor in Escherichia coli by Reducing the GC-content and Increasing mRNA Folding Free Energy at 5'-Terminal End. PMID:33072539
Insights into Genomic Epidemiology, Evolution, and Transmission Dynamics of Genotype VII of Class II Newcastle Disease Virus in China. PMID:33066232
Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea. PMID:32994183
Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus. PMID:32992529
Biased Mutation and Selection in RNA Viruses. PMID:32986832
Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study. PMID:32776991
Effect of Mutations on mRNA and Globin Stability: The Cases of Hb Bernalda/Groene Hart and Hb Southern Italy. PMID:32751969
Selective translation by alternative bacterial ribosomes. PMID:32723820
Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis. PMID:32689943
Pathogenic Mechanisms of Somatic Mutation and Genome Mosaicism in Aging. PMID:32649873
Codon optimized Tol2 transposase results in increased transient expression of a crystallin-GFP transgene in zebrafish. PMID:32626847
Comparison of cell-based versus cell-free mammalian systems for the production of a recombinant human bone morphogenic growth factor. PMID:32624737
TLR7 dosage polymorphism shapes interferogenesis and HIV-1 acute viremia in women. PMID:32554924
Role of ultraviolet mutational signature versus tumor mutation burden in predicting response to immunotherapy. PMID:32530570
Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1. PMID:32511314
Transcriptional Activity and Protein Levels of Horizontally Acquired Genes in Yeast Reveal Hallmarks of Adaptation to Fermentative Environments. PMID:32425968
Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation. PMID:32395662
CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1. PMID:32334589
A Phosphite Dehydrogenase Variant with Promiscuous Access to Nicotinamide Cofactor Pools Sustains Fast Phosphite-Dependent Growth of Transplastomic Chlamydomonas reinhardtii. PMID:32276527
Presenting a codon-optimized palette of fluorescent proteins for use in Candida albicans. PMID:32273559
Development of a new oral poliovirus vaccine for the eradication end game using codon deoptimization. PMID:32218998
Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. PMID:32200634
mCherry Protein as an In Vivo Quantitative Reporter of Gene Expression in the Chloroplast of Chlamydomonas reinhardtii. PMID:32185599
From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes. PMID:32159237
Ornithine capture by a translating ribosome controls bacterial polyamine synthesis. PMID:32094585
Codon usage by chloroplast gene is bias in Hemiptelea davidii. PMID:32089527
Use of synthetic biology tools to optimize the production of active nitrogenase Fe protein in chloroplasts of tobacco leaf cells. PMID:31985876
Quantitative Analysis of Spatial Distributions of All tRNA Genes in Budding Yeast. PMID:31951810
Cas9/gRNA-mediated genome editing of yeast mitochondria and Chlamydomonas chloroplasts. PMID:31934513
Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design. PMID:31911390
[Synonymous Codon Usage-a Guide for Co-Translational Protein Folding in the Cell]. PMID:31876270
COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences. PMID:31800035
The effector GpRbp-1 of Globodera pallida targets a nuclear HECT E3 ubiquitin ligase to modulate gene expression in the host. PMID:31756029
Codon usage patterns of LT-Ag genes in polyomaviruses from different host species. PMID:31727090
mRNA structure regulates protein expression through changes in functional half-life. PMID:31712433
A plasmid vector that directs hyperproduction of recombinant proteins in the thermophiles Geobacillus species. PMID:31701242
Unraveling the Role of Silent Mutation in the ω-Subunit of Escherichia coli RNA Polymerase: Structure Transition Inhibits Transcription. PMID:31681877
Rare-variant pathogenicity triage and inclusion of synonymous variants improves analysis of disease associations of orphan G protein-coupled receptors. PMID:31628190
Computational design and interpretation of single-RNA translation experiments. PMID:31618265
Hippocampal Subregions Express Distinct Dendritic Transcriptomes that Reveal Differences in Mitochondrial Function in CA2. PMID:31597108
A photoactivatable crosslinking system reveals protein interactions in the Toxoplasma gondii inner membrane complex. PMID:31584943
Codon bias confers stability to human mRNAs. PMID:31482640
A tRNA-mimic Strategy to Explore the Role of G34 of tRNAGly in Translation and Codon Frameshifting. PMID:31405256
The Needs for Developing Experiments on Reservoirs in Hantavirus Research: Accomplishments, Challenges and Promises for the Future. PMID:31331096
Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions. PMID:31301672
Efficient biochemical production of acetoin from carbon dioxide using Cupriavidus necator H16. PMID:31297151
VEGAS as a Platform for Facile Directed Evolution in Mammalian Cells. PMID:31280962
Advances and Challenges in Cell-Free Incorporation of Unnatural Amino Acids Into Proteins. PMID:31191324
Developing a codon optimization method for improved expression of recombinant proteins in actinobacteria. PMID:31171855
Protocols for yTREX/Tn5-based gene cluster expression in Pseudomonas putida. PMID:31162833
Sequence and expression levels of circular RNAs in progenitor cell types during mouse corticogenesis. PMID:30926618
A synonymous germline variant in a gene encoding a cell adhesion molecule is associated with cutaneous mast cell tumour development in Labrador and Golden Retrievers. PMID:30901340
In-silico Evaluation of Rare Codons and their Positions in the Structure of ATP8b1 Gene. PMID:30881940
Gaussian-Distributed Codon Frequencies of Genomes. PMID:30808691
Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients. PMID:30804909
APOBEC-related mutagenesis and neo-peptide hydrophobicity: implications for response to immunotherapy. PMID:30723579
Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp. PMID:30651145
Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses. PMID:30587213
Combining near-infrared fluorescence with Brainbow to visualize expression of specific genes within a multicolor context. PMID:30586321
Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern. PMID:30475085
Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific. PMID:30388838
Fluorescent Proteins, Promoters, and Selectable Markers for Applications in the Lyme Disease Spirochete Borrelia burgdorferi. PMID:30315081
New tools for high-throughput expression of fungal secretory proteins in Saccharomyces cerevisiae and Pichia pastoris. PMID:30289201
Codon usage regulates human KRAS expression at both transcriptional and translational levels. PMID:30275015
Systematic Comparison of Strategies to Achieve Soluble Expression of Plasmodium falciparum Recombinant Proteins in E. coli. PMID:30259259
Whole-cell (+)-ambrein production in the yeast Pichia pastoris. PMID:30197866
The effects of codon usage on the formation of secondary structures of nucleocapsid protein of peste des petits ruminants virus. PMID:30155714
Discovery, characterization, and remediation of a C-terminal Fc-extension in proteins expressed in CHO cells. PMID:30148415
Queuosine-modified tRNAs confer nutritional control of protein translation. PMID:30093495
Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes. PMID:30026186
GPD1 and ADH3 Natural Variants Underlie Glycerol Yield Differences in Wine Fermentation. PMID:30018610
Codon usage clusters correlation: towards protein solubility prediction in heterologous expression systems in E. coli. PMID:30006617
Insights into the genetic and host adaptability of emerging porcine circovirus 3. PMID:29973122
Wild-type Kras expands and exhausts hematopoietic stem cells. PMID:29875320
Codon adaptation biases among sylvatic and urban genotypes of Dengue virus type 2. PMID:29792991
Selection and Neutral Mutations Drive Pervasive Mutability Losses in Long-Lived Anti-HIV B-Cell Lineages. PMID:29688540
A Multicolor Split-Fluorescent Protein Approach to Visualize Listeria Protein Secretion in Infection. PMID:29653838
Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias. PMID:29387823
Saturation mutagenesis reveals manifold determinants of exon definition. PMID:29242188
Multiplexed in vivo homology-directed repair and tumor barcoding enables parallel quantification of Kras variant oncogenicity. PMID:29233960
The Bacillus BioBrick Box 2.0: expanding the genetic toolbox for the standardized work with Bacillus subtilis. PMID:29118374
Generation of an arginine-tRNA-adapted Saccharomyces cerevisiae strain for effective heterologous protein expression. PMID:29098364
Net Evolutionary Loss of Residue Polarity in Drosophilid Protein Cores Indicates Ongoing Optimization of Amino Acid Composition. PMID:28985302
Role for ribosome-associated complex and stress-seventy subfamily B (RAC-Ssb) in integral membrane protein translation. PMID:28972146
A new and updated resource for codon usage tables. PMID:28865429
Rational identification of aggregation hotspots based on secondary structure and amino acid hydrophobicity. PMID:28842596
Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution. PMID:28830350
Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms. PMID:28754661
Metabolic engineering of Rhodopseudomonas palustris for the obligate reduction of n-butyrate to n-butanol. PMID:28702083
HIV Progression Depends on Codon and Amino Acid Usage Profile of Envelope Protein and Associated Host-Genetic Influence. PMID:28663742
RNA editing by the host ADAR system affects the molecular evolution of the Zika virus. PMID:28649357
Analysis of Newly Identified and Rare Synonymous Genetic Variants in the RET Gene in Patients with Medullary Thyroid Carcinoma in Polish Population. PMID:28647780
A Dual Luciferase Reporter System for B. burgdorferi Measures Transcriptional Activity during Tick-Pathogen Interactions. PMID:28620587
The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity. PMID:28601219
ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications. PMID:28419256
Evolutionary changes in transcription factor coding sequence quantitatively alter sensory organ development and function. PMID:28406397
Increased taxon sampling reveals thousands of hidden orthologs in flatworms. PMID:28400424
Mutational Pressure in Zika Virus: Local ADAR-Editing Areas Associated with Pauses in Translation and Replication. PMID:28275585
Standard Codon Substitution Models Overestimate Purifying Selection for Nonstationary Data. PMID:28175284
Synthesis of bacteriophage lytic proteins against Streptococcus pneumoniae in the chloroplast of Chlamydomonas reinhardtii. PMID:28160380
Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies. PMID:28053115
Secreted Proteins Defy the Expression Level-Evolutionary Rate Anticorrelation. PMID:28007979
Codon usage is less optimized in eukaryotic gene segments encoding intrinsically disordered regions than in those encoding structural domains. PMID:27915289
Bioinformatic Identification of Rare Codon Clusters (RCCs) in HBV Genome and Evaluation of RCCs in Proteins Structure of Hepatitis B Virus. PMID:27882067
Evolution of codon usage in Zika virus genomes is host and vector specific. PMID:27729643
Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins. PMID:27659324
Beyond Zipf's Law: The Lavalette Rank Function and Its Properties. PMID:27658296
Side effects of extra tRNA supplied in a typical bacterial protein production scenario. PMID:27515297
The DAU cluster: a comparative analysis of 18 RHD alleles, some forming partial D antigens. PMID:27480171
Codon Optimization to Enhance Expression Yields Insights into Chloroplast Translation. PMID:27465114
An integrated, structure- and energy-based view of the genetic code. PMID:27448410
Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti. PMID:27447951
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. PMID:27436286
The Yin and Yang of codon usage. PMID:27354349
Nucleotide composition of the Zika virus RNA genome and its codon usage. PMID:27278486
Mechanism and biological role of Dnmt2 in Nucleic Acid Methylation. PMID:27232191
DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea). PMID:27176219
Transgene Expression in Microalgae-From Tools to Applications. PMID:27148328
Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses. PMID:27119730
Development of phytase-expressing chlamydomonas reinhardtii for monogastric animal nutrition. PMID:26969115
A Heterologous Multiepitope DNA Prime/Recombinant Protein Boost Immunisation Strategy for the Development of an Antiserum against Micrurus corallinus (Coral Snake) Venom. PMID:26938217
Exploiting tRNAs to Boost Virulence. PMID:26797637
Chloramphenicol acetyltransferase-a new selectable marker in stable nuclear transformation of the red alga Cyanidioschyzon merolae. PMID:26715590
The Potential Mutation of GAK Gene in the Typical Sporadic Parkinson's Disease from the Han Population of Chinese Mainland. PMID:26676575
Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay. PMID:26637602
Zinc finger nuclease-based double-strand breaks attenuate malaria parasites and reveal rare microhomology-mediated end joining. PMID:26573820
The essential gene set of a photosynthetic organism. PMID:26508635
Acetylcholinesterases from the Disease Vectors Aedes aegypti and Anopheles gambiae: Functional Characterization and Comparisons with Vertebrate Orthologues. PMID:26447952
Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine. PMID:26424849
ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization. PMID:26391121
The many roles of glutamate in metabolism. PMID:26323613
Association of ADORA1 rs2228079 and ADORA2A rs5751876 Polymorphisms with Gilles de la Tourette Syndrome in the Polish Population. PMID:26317759
Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution. PMID:26306510
Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species. PMID:26271136
In Vitro Expansion of CAG, CAA, and Mixed CAG/CAA Repeats. PMID:26270660
Reassignment of a rare sense codon to a non-canonical amino acid in Escherichia coli. PMID:26240376
Nucleotide composition bias and codon usage trends of gene populations in Mycoplasma capricolum subsp. capricolum and M. Agalactiae. PMID:26174672
The UGG Isoacceptor of tRNAPro Is Naturally Prone to Frameshifts. PMID:26140378
Cancer, Warts, or Asymptomatic Infections: Clinical Presentation Matches Codon Usage Preferences in Human Papillomaviruses. PMID:26139833
Codon-optimized fluorescent mTFP and mCherry for microscopic visualization and genetic counterselection of streptococci and enterococci. PMID:26122309
Generating a Metal-responsive Transcriptional Regulator to Test What Confers Metal Sensing in Cells. PMID:26109070
A codon-optimized green fluorescent protein for live cell imaging in Zymoseptoria tritici. PMID:26092799
Engineering selection stringency on expression vector for the production of recombinant human alpha1-antitrypsin using Chinese Hamster ovary cells. PMID:26033090
Common synonymous variants in ABCA4 are protective for chloroquine induced maculopathy (toxic maculopathy). PMID:25884411
B cell variable genes have evolved their codon usage to focus the targeted patterns of somatic mutation on the complementarity determining regions. PMID:25660968
On the biased nucleotide composition of the human coronavirus RNA genome. PMID:25656063
Expression of fluorescent proteins in Branchiostoma lanceolatum by mRNA injection into unfertilized oocytes. PMID:25650764
Inducible suppression of global translation by overuse of rare codons. PMID:25636849
DNASynth: a computer program for assembly of artificial gene parts in decreasing temperature. PMID:25629047
Increased functional protein expression using nucleotide sequence features enriched in highly expressed genes in zebrafish. PMID:25628360
Engineering the genome of Thermus thermophilus using a counterselectable marker. PMID:25605305
Use of mCherry Red fluorescent protein for studies of protein localization and gene expression in Clostridium difficile. PMID:25527559
Genetic distance for a general non-stationary markov substitution process. PMID:25503772
Engineering β1,4-galactosyltransferase I to reduce secretion and enhance N-glycan elongation in insect cells. PMID:25462875
Rare codons capacitate Kras-driven de novo tumorigenesis. PMID:25437878
The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome. PMID:25350396
The characteristics of rare codon clusters in the genome and proteins of hepatitis C virus; a bioinformatics look. PMID:25349685
Computational tools and algorithms for designing customized synthetic genes. PMID:25340050
New developments of RNAi in Paracoccidioides brasiliensis: prospects for high-throughput, genome-wide, functional genomics. PMID:25275433
Refining the balance of attenuation and immunogenicity of respiratory syncytial virus by targeted codon deoptimization of virulence genes. PMID:25249281
Hsp90 promotes kinase evolution. PMID:25246701
Comprehensive analysis of stop codon usage in bacteria and its correlation with release factor abundance. PMID:25217634
A novel, live-attenuated vesicular stomatitis virus vector displaying conformationally intact, functional HIV-1 envelope trimers that elicits potent cellular and humoral responses in mice. PMID:25215861
Quantitative evaluation of E1 endoglucanase recovery from tobacco leaves using the vacuum infiltration-centrifugation method. PMID:24971334
Influenza A virus attenuation by codon deoptimization of the NS gene for vaccine development. PMID:24965472
Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa. PMID:24948679
Monitoring protein misfolding by site-specific labeling of proteins in vivo. PMID:24915041
Unnatural amino acid incorporation in E. coli: current and future applications in the design of therapeutic proteins. PMID:24790983
Transformable facultative thermophile Geobacillus stearothermophilus NUB3621 as a host strain for metabolic engineering. PMID:24788326
GeneGenie: optimized oligomer design for directed evolution. PMID:24782527
Synthetic versions of firefly luciferase and Renilla luciferase reporter genes that resist transgene silencing in sugarcane. PMID:24708613
Genetic code redundancy and its influence on the encoded polypeptides. PMID:24688635
Heterozygous de novo and inherited mutations in the smooth muscle actin (ACTG2) gene underlie megacystis-microcolon-intestinal hypoperistalsis syndrome. PMID:24676022
A condition-specific codon optimization approach for improved heterologous gene expression in Saccharomyces cerevisiae. PMID:24636000
Genome-wide analysis of codon usage and influencing factors in chikungunya viruses. PMID:24595095
Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes. PMID:24550280
Inclusion of the bovine neutrophil beta-defensin 3 with glycoprotein D of bovine herpesvirus 1 in a DNA vaccine modulates immune responses of mice and cattle. PMID:24451331
Sense codon emancipation for proteome-wide incorporation of noncanonical amino acids: rare isoleucine codon AUA as a target for genetic code expansion. PMID:24433543
Dependency of codon usage on protein sequence patterns: a statistical study. PMID:24410898
A Rev-Independent gag/pol Eliminates Detectable psi-gag Recombination in Lentiviral Vectors. PMID:24380052
The distribution of synonymous codon choice in the translation initiation region of dengue virus. PMID:24204777
Expression and purification of recombinant Saccharomyces cerevisiae mitochondrial carrier protein YGR257Cp (Mtm1p). PMID:24184947
Translational landscape of photomorphogenic Arabidopsis. PMID:24179124
Purifying selection in porcine reproductive and respiratory syndrome virus ORF5a protein influences variation in envelope glycoprotein 5 glycosylation. PMID:24084290
Accessibility of myofilament cysteines and effects on ATPase depend on the activation state during exposure to oxidants. PMID:23894416
Characterisation of the Mycobacterium tuberculosis alternative sigma factor SigG: its operon and regulon. PMID:23871545
Ambushing the Ambush Hypothesis: predicting and evaluating off-frame codon frequencies in prokaryotic genomes. PMID:23799949
Expanded use of sense codons is regulated by modified cytidines in tRNA. PMID:23781103
The effects of the codon usage and translation speed on protein folding of 3D(pol) of foot-and-mouth disease virus. PMID:23715863
RanBP2/Nup358 potentiates the translation of a subset of mRNAs encoding secretory proteins. PMID:23630457
Sequence and structure-specific elements of HERG mRNA determine channel synthesis and trafficking efficiency. PMID:23608144
The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome. PMID:23542153
Next-generation site-directed transgenesis in the malaria vector mosquito Anopheles gambiae: self-docking strains expressing germline-specific phiC31 integrase. PMID:23516619
Single nucleotide polymorphisms in the Wilms' tumour gene 1 in clear cell renal cell carcinoma. PMID:23484026
Causes and implications of codon usage bias in RNA viruses. PMID:23451064
Functional analysis of the murine coronavirus genomic RNA packaging signal. PMID:23449786
Germline and somatic KLLN alterations in breast cancer dysregulate G2 arrest. PMID:23446638
Evaluation of the food grade expression systems NICE and pSIP for the production of 2,5-diketo-D-gluconic acid reductase from Corynebacterium glutamicum. PMID:23356419
Analysis of ER resident proteins in Saccharomyces cerevisiae: implementation of H/KDEL retrieval sequences. PMID:23324027
Novel fusion protein derived from vasostatin 30 and vasoinhibin II-14.1 potently inhibits coronary endothelial cell proliferation. PMID:23315240
Codon usage frequency of RNA virus genomes from high-temperature acidic-environment metagenomes. PMID:23308027
Rare codons regulate KRas oncogenesis. PMID:23246410
Structure and evolution of barley powdery mildew effector candidates. PMID:23231440
Two doses of bovine viral diarrhea virus DNA vaccine delivered by electroporation induce long-term protective immune responses. PMID:23220999
Patterns of synonymous codon usage on human metapneumovirus and its influencing factors. PMID:23193361
A comparative analysis on the synonymous codon usage pattern in viral functional genes and their translational initiation region of ASFV. PMID:23161403
Ribosomal frameshifting used in influenza A virus expression occurs within the sequence UCC_UUU_CGU and is in the +1 direction. PMID:23155484
Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development. PMID:23134595
Computational codon optimization of synthetic gene for protein expression. PMID:23083100
KIR2DL5: An Orphan Inhibitory Receptor Displaying Complex Patterns of Polymorphism and Expression. PMID:23060877
Application of synthetic biology in cyanobacteria and algae. PMID:23049529
Efficient expression systems for cysteine proteases of malaria parasites: too good to be true? PMID:23018863
Smelt was the likely beneficiary of an antifreeze gene laterally transferred between fishes. PMID:23009612
Most Used Codons per Amino Acid and per Genome in the Code of Man Compared to Other Organisms According to the Rotating Circular Genetic Code. PMID:22997484
Expression of recombinant human mutant granulocyte colony stimulating factor (Nartograstim) in Escherichia coli. PMID:22806165
Characterization of coding synonymous and non-synonymous variants in ADAMTS13 using ex vivo and in silico approaches. PMID:22768050
High codon adaptation in citrus tristeza virus to its citrus host. PMID:22698086
Release factor one is nonessential in Escherichia coli. PMID:22662873
Large-scale experimental studies show unexpected amino acid effects on protein expression and solubility in vivo in E. coli. PMID:22587847
Human POLB gene is mutated in high percentage of colorectal tumors. PMID:22577134
Algorithms for optimizing cross-overs in DNA shuffling. PMID:22536901
CBDB: the codon bias database. PMID:22536831
Cassette series designed for live-cell imaging of proteins and high-resolution techniques in yeast. PMID:22473760
Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. PMID:22467916
Comparative [corrected] codon usage between the three main viruses in pestivirus genus and their natural susceptible livestock. PMID:22395914
The Quantum Workings of the Rotating 64-Grid Genetic Code. PMID:22308074
Expression of a soluble form of iodotyrosine deiodinase for active site characterization by engineering the native membrane protein from Mus musculus. PMID:22238141
Differential trends in the codon usage patterns in HIV-1 genes. PMID:22216135
Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase. PMID:22158897
Overlapping photoprotective function of vitamin E and carotenoids in Chlamydomonas. PMID:22080601
Complete genomic sequence of bacteriophage felix o1. PMID:21994654
RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. PMID:21926996
Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach. PMID:21926196
Pervasive recombination and sympatric genome diversification driven by frequency-dependent selection in Borrelia burgdorferi, the Lyme disease bacterium. PMID:21890743
Microalgae as platforms for production of recombinant proteins and valuable compounds: progress and prospects. PMID:21882013
Tyrosine phosphorylation enhances RAD52-mediated annealing by modulating its DNA binding. PMID:21804533
Domain-domain interactions underlying herpesvirus-human protein-protein interaction networks. PMID:21760902
A ribosomal misincorporation of Lys for Arg in human triosephosphate isomerase expressed in Escherichia coli gives rise to two protein populations. PMID:21738601
Comparison of transgene expression in Aedes aegypti generated by mariner Mos1 transposition and ΦC31 site-directed recombination. PMID:21699593
In vivo functional analysis of the Dicistroviridae intergenic region internal ribosome entry sites. PMID:21646337
Determination of the molecular basis for a limited dimorphism, N417K, in the Plasmodium vivax Duffy-binding protein. PMID:21629662
Engineered resistance to Plasmodium falciparum development in transgenic Anopheles stephensi. PMID:21533066
Parallel on-chip gene synthesis and application to optimization of protein expression. PMID:21516083
8-Oxo-7,8-dihydroguanine in DNA does not constitute a barrier to transcription, but is converted into transcription-blocking damage by OGG1. PMID:21441539
Relationship between amino acid composition and gene expression in the mouse genome. PMID:21272306
Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations. PMID:21258063
Ancient gene duplication provided a key molecular step for anaerobic growth of Baker's yeast. PMID:21245414
HIV-1 modulates the tRNA pool to improve translation efficiency. PMID:21216840
The GeneOptimizer Algorithm: using a sliding window approach to cope with the vast sequence space in multiparameter DNA sequence optimization. PMID:21189842
The human mitochondrial tRNAMet: structure/function relationship of a unique modification in the decoding of unconventional codons. PMID:21168417
Introns form compositional clusters in parallel with the compositional clusters of the coding sequences to which they pertain. PMID:21132282
Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization. PMID:21122120
Synonymous but not the same: the causes and consequences of codon bias. PMID:21102527
Modeling compositional dynamics based on GC and purine contents of protein-coding sequences. PMID:21059261
A general model of codon bias due to GC mutational bias. PMID:21048949
Substrates of the Arabidopsis thaliana protein isoaspartyl methyltransferase 1 identified using phage display and biopanning. PMID:20870712
Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus. PMID:20723216
A synthetic three-color scaffold for monitoring genetic regulation and noise. PMID:20646328
Features of recent codon evolution: a comparative polymorphism-fixation study. PMID:20622912
Conservation of genomic localization and sequence content of Sau3AI-like restriction-modification gene cassettes among Listeria monocytogenes epidemic clone I and selected strains of serotype 1/2a. PMID:20581194
Micro-algae come of age as a platform for recombinant protein production. PMID:20556634
Phosphorylation and dephosphorylation among Dif chemosensory proteins essential for exopolysaccharide regulation in Myxococcus xanthus. PMID:20543066
Gene optimization mechanisms: a multi-gene study reveals a high success rate of full-length human proteins expressed in Escherichia coli. PMID:20506237
Study of completed archaeal genomes and proteomes: hypothesis of strong mutational AT pressure existed in their common predecessor. PMID:20451159
Expression and immunogenicity of the mycobacterial Ag85B/ESAT-6 antigens produced in transgenic plants by elastin-like peptide fusion strategy. PMID:20414351
The rules of variation: amino acid exchange according to the rotating circular genetic code. PMID:20371250
RCDI/eRCDI: a web-server to estimate codon usage deoptimization. PMID:20356391
Coevolution of DNA uptake sequences and bacterial proteomes. PMID:20333176
The human lysyl oxidase-like 2 protein functions as an amine oxidase toward collagen and elastin. PMID:20306300
Production of therapeutic proteins in algae, analysis of expression of seven human proteins in the chloroplast of Chlamydomonas reinhardtii. PMID:20230484
Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages. PMID:20097653
Profiling non-lysyl tRNAs in HIV-1. PMID:20007329
European wild boars and domestic pigs display different polymorphic patterns in the Toll-like receptor (TLR) 1, TLR2, and TLR6 genes. PMID:19953243
Engineering an efficient secretion of leech carboxypeptidase inhibitor in Escherichia coli. PMID:19874597
High-level expression of Camelid nanobodies in Nicotiana benthamiana. PMID:19862637
Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage. PMID:19745054
A mammalianized synthetic nitroreductase gene for high-level expression. PMID:19712451
Genetic inactivation of poliovirus infectivity by increasing the frequencies of CpG and UpA dinucleotides within and across synonymous capsid region codons. PMID:19605476
primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. PMID:19465390
Gene composer: database software for protein construct design, codon engineering, and gene synthesis. PMID:19383142
Prediction of disease-related mutations affecting protein localization. PMID:19309509
Live-Cell imaging and measurement of intracellular pH in filamentous fungi using a genetically encoded ratiometric probe. PMID:19286983
The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus. PMID:19216739
ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family. PMID:19102758
GtRNAdb: a database of transfer RNA genes detected in genomic sequence. PMID:18984615
Rare codons cluster. PMID:18923675
Identification and characterization of multiple Spidroin 1 genes encoding major ampullate silk proteins in Nephila clavipes. PMID:18828837
CAIcal: a combined set of tools to assess codon usage adaptation. PMID:18796141
The capsid-coding region hairpin element (cHP) is a critical determinant of dengue virus and West Nile virus RNA synthesis. PMID:18676000
New DNA polymerase from the hyperthermophilic marine archaeon Thermococcus thioreducens. PMID:18670731
Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. PMID:18655731
On the extent and origins of genic novelty in the phylum Nematoda. PMID:18596977
The molecular basis for relative physiological functionality of the ADP/ATP carrier isoforms in Saccharomyces cerevisiae. PMID:18562646
High-level expression, single-step immunoaffinity purification and characterization of human tetraspanin membrane protein CD81. PMID:18523555
Multiple factors contribute to keeping levels of the symbiosis regulator RscS low. PMID:18510559
Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: identifying genes associated with callogenesis and embryogenesis. PMID:18507865
Analysis of the distribution of functionally relevant rare codons. PMID:18457591
Hidden layers of human small RNAs. PMID:18402656
RNA landscape of evolution for optimal exon and intron discrimination. PMID:18391195
tRNA's modifications bring order to gene expression. PMID:18378185
Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts. PMID:18325113
UTILLdb, a Pisum sativum in silico forward and reverse genetics tool. PMID:18302733
A novel chromate reductase from Thermus scotoductus SA-01 related to old yellow enzyme. PMID:18263719
E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). PMID:18230160
Analysis of the codon use frequency of AMPK family genes from different species. PMID:18188681
Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum. PMID:18096748
On the correlation between the synonymy of codon usage and taxonomy. PMID:18064822
Biochemical characterization of DNA-binding proteins from Pyrobaculum aerophilum and Aeropyrum pernix. PMID:18064401
Complete genome sequence and analysis of the Streptomyces aureofaciens phage mu1/6. PMID:18062183
Complete genomic sequence of bacteriophage phiEcoM-GJ1, a novel phage that has myovirus morphology and a podovirus-like RNA polymerase. PMID:18039824
The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons. PMID:17942742
Rational design of a multiepitope vaccine encoding T-lymphocyte epitopes for treatment of chronic hepatitis B virus infections. PMID:17942551
Production of active eukaryotic proteins through bacterial expression systems: a review of the existing biotechnology strategies. PMID:17874175
Fully codon-optimized luciferase uncovers novel temperature characteristics of the Neurospora clock. PMID:17766461
BCoR-L1 variation and breast cancer. PMID:17697391
Identification, molecular characterization and subcellular localization of a Theileria annulata parasite protein secreted into the host cell cytoplasm. PMID:17659384
The selection of acceptable protein mutations. PMID:17540730
Translational control of recombinant human acetylcholinesterase accumulation in plants. PMID:17537261
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. PMID:17439967
Efficient target-selected mutagenesis in Caenorhabditis elegans: toward a knockout for every gene. PMID:17416746
Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS. PMID:17331558
Kinetic quality control of anticodon recognition by a eukaryotic aminoacyl-tRNA synthetase. PMID:17303165
Purifying selection in mitochondria, free-living and obligate intracellular proteobacteria. PMID:17295908
Detecting non-coding selective pressure in coding regions. PMID:17288582
pORE: a modular binary vector series suited for both monocot and dicot plant transformation. PMID:17273915
Sequencing and analysis of the biosynthetic gene cluster of the lipopeptide antibiotic Friulimicin in Actinoplanes friuliensis. PMID:17220414
Adaptation of a luciferase gene reporter and lac expression system to Borrelia burgdorferi. PMID:17220265
Host-related nucleotide composition and codon usage as driving forces in the recent evolution of the Astroviridae. PMID:17188318
Optimized FaeG expression and a thermolabile enterotoxin DNA adjuvant enhance priming of an intestinal immune response by an FaeG DNA vaccine in pigs. PMID:17108289
Using the nucleotide substitution rate matrix to detect horizontal gene transfer. PMID:17067382
Colocation of genes encoding a tRNA-mRNA hybrid and a putative signaling peptide on complementary strands in the genome of the hyperthermophilic bacterium Thermotoga maritima. PMID:16980482
Prokaryotes that grow optimally in acid have purine-poor codons in long open reading frames. PMID:16957882
EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot. PMID:16915518
Plant coenzyme A biosynthesis: characterization of two pantothenate kinases from Arabidopsis. PMID:16897480
Targeted expression of redesigned and codon optimised synthetic gene leads to recrystallisation inhibition and reduced electrolyte leakage in spring wheat at sub-zero temperatures. PMID:16847628
Insulated piggyBac vectors for insect transgenesis. PMID:16776846
Gene Designer: a synthetic biology tool for constructing artificial DNA segments. PMID:16756672
The synthesis and high-level expression of a beta2-adrenergic receptor gene in a tetracycline-inducible stable mammalian cell line. PMID:16731977
In vivo incorporation of multiple unnatural amino acids through nonsense and frameshift suppression. PMID:16728509
Translation of 'rare' codons in a cell-free protein synthesis system from Escherichia coli. PMID:16703415
High guanine and cytosine content increases mRNA levels in mammalian cells. PMID:16700628
Isolation and sequencing of a temperate transducing phage for Pasteurella multocida. PMID:16672452
Analyses of expressed sequence tags from apple. PMID:16531485
Determination of essential and variable residues in pediocin PA-1 by NNK scanning. PMID:16461660
Real-time monitoring of chloroplast gene expression by a luciferase reporter: evidence for nuclear regulation of chloroplast circadian period. PMID:16428442
Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples. PMID:16391035
Estimating diversifying selection and functional constraint in the presence of recombination. PMID:16387887
Single-channel properties of human NaV1.1 and mechanism of channel dysfunction in SCN1A-associated epilepsy. PMID:16380441
Do universal codon-usage patterns minimize the effects of mutation and translation error? PMID:16277746
Design, validation, and application of a seven-strain Staphylococcus aureus PCR product microarray for comparative genomics. PMID:16269792
New findings on evolution of metal homeostasis genes: evidence from comparative genome analysis of bacteria and archaea. PMID:16269744
Are stop codons recognized by base triplets in the large ribosomal RNA subunit? PMID:16199759
Optimization of codon usage enhances the immunogenicity of a DNA vaccine encoding mycobacterial antigen Ag85B. PMID:16113284
Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope. PMID:16103173
DNA sequence representation by trianders and determinative degree of nucleotides. PMID:16052707
A-tract clusters may facilitate DNA packaging in bacterial nucleoid. PMID:16024741
Gene algebra from a genetic code algebraic structure. PMID:16012800
Mycobacterial codon optimization enhances antigen expression and virus-specific immune responses in recombinant Mycobacterium bovis bacille Calmette-Guérin expressing human immunodeficiency virus type 1 Gag. PMID:15994765
A T-stem slip in human mitochondrial tRNALeu(CUN) governs its charging capacity. PMID:15972857
A general method for greatly improving the affinity of antibodies by using combinatorial libraries. PMID:15939870
Compositional properties of green-plant plastid genomes. PMID:15883877
Cloning and expression of the VHDL receptor from fat body of the corn ear worm, Helicoverpa zea. PMID:15861222
A reduced level of charged tRNAArgmnm5UCU triggers the wild-type peptidyl-tRNA to frameshift. PMID:15840821
Host-derived pathogenicity islands in poxviruses. PMID:15823205
cse, a Chimeric and variable gene, encodes an extracellular protein involved in cellular segregation in Streptococcus thermophilus. PMID:15805520
Molecular and genetic characterization of propionicin F, a bacteriocin from Propionibacterium freudenreichii. PMID:15574930
prot4EST: translating expressed sequence tags from neglected genomes. PMID:15571632
Selection on codon usage for error minimization at the protein level. PMID:15553093
Genome structure and transcriptional regulation of human coronavirus NL63. PMID:15548333
Convergent evolution of chromosomal sex-determining regions in the animal and fungal kingdoms. PMID:15538538
Benefits of being biased! PMID:15536251
Inactivation of an ABC transporter gene, mcyH, results in loss of microcystin production in the cyanobacterium Microcystis aeruginosa PCC 7806. PMID:15528494
Molecular genetic characterization and subcellular localization of a putative Theileria annulata membrane protein. PMID:15490238
The Escherichia coli argU10(Ts) phenotype is caused by a reduction in the cellular level of the argU tRNA for the rare codons AGA and AGG. PMID:15317795
Comparative genetic diversity of Pseudomonas stutzeri genomovars, clonal structure, and phylogeny of the species. PMID:15292125
Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project. PMID:15258807
Novel type V staphylococcal cassette chromosome mec driven by a novel cassette chromosome recombinase, ccrC. PMID:15215121
A conserved upstream open reading frame mediates sucrose-induced repression of translation. PMID:15208401
Heterologous expression and purification of active divercin V41, a class IIa bacteriocin encoded by a synthetic gene in Escherichia coli. PMID:15205430
An exposed domain in the severe acute respiratory syndrome coronavirus spike protein induces neutralizing antibodies. PMID:15194798
Cryptococcus neoformans virulence gene discovery through insertional mutagenesis. PMID:15075272
Translational accuracy during exponential, postdiauxic, and stationary growth phases in Saccharomyces cerevisiae. PMID:15075263
Root nodule Bradyrhizobium spp. harbor tfdAalpha and cadA, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins. PMID:15066803
Linkage of amino acid variation and evolution of human immunodeficiency virus type 1 gp120 envelope glycoprotein (subtype B) with usage of the second receptor. PMID:15045488
The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer. PMID:15040816
Molecular evidence for the evolution of metal homeostasis genes by lateral gene transfer in bacteria from the deep terrestrial subsurface. PMID:15006795
Complete sequence and evolutionary genomic analysis of the Pseudomonas aeruginosa transposable bacteriophage D3112. PMID:14702309
Optimum growth temperature and the base composition of open reading frames in prokaryotes. PMID:14666404
Hierarchy of sequence-dependent features associated with prokaryotic translation. PMID:14656971
Efficient target-selected mutagenesis in zebrafish. PMID:14613981
Ancient origin of the tryptophan operon and the dynamics of evolutionary change. PMID:12966138
Production of human papillomavirus type 16 virus-like particles in transgenic plants. PMID:12915537
Evolutionary patterns of codon usage in the chloroplast gene rbcL. PMID:12911031
Mechanisms of activation of phosphoenolpyruvate carboxykinase from Escherichia coli by Ca2+ and of desensitization by trypsin. PMID:12837799
Ribosomes stalling on uORF1 in the Xenopus Cx41 5' UTR inhibit downstream translation initiation. PMID:12799445
PF-IND: probability algorithm and software for separation of plant and fungal sequences. PMID:12719882
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. PMID:12663798
Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria. PMID:12620124
In vivo introduction of unpreferred synonymous codons into the Drosophila Adh gene results in reduced levels of ADH protein. PMID:12586711
OGRe: a relational database for comparative analysis of mitochondrial genomes. PMID:12519982
Enhanced heterologous expression of two Streptomyces griseolus cytochrome P450s and Streptomyces coelicolor ferredoxin reductase as potentially efficient hydroxylation catalysts. PMID:12514018
Gene structure, organization, expression, and potential regulatory mechanisms of arginine catabolism in Enterococcus faecalis. PMID:12399499
Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set. PMID:12361984
Complete sequence and organization of pBtoxis, the toxin-coding plasmid of Bacillus thuringiensis subsp. israelensis. PMID:12324359
Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. PMID:12176923
PrpE, a PPP protein phosphatase from Bacillus subtilis with unusual substrate specificity. PMID:12059787
Tandem repeats in protein coding regions of primate genes. PMID:12045144
eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments. PMID:12034828
Activation and evasion of the antiviral 2'-5' oligoadenylate synthetase/ribonuclease L pathway by hepatitis C virus mRNA. PMID:11991644
Structural, functional, and evolutionary analysis of moeZ, a gene encoding an enzyme required for the synthesis of the Pseudomonas metabolite, pyridine-2,6-bis(thiocarboxylic acid). PMID:11972321
Gene expression analysis with universal n-mer arrays. PMID:11779839
The intein of the Thermoplasma A-ATPase A subunit: structure, evolution and expression in E. coli. PMID:11722801
The BioTools Suite. A comprehensive suite of platform-independent bioinformatics tools. PMID:11697221
Biosynthesis of a fluorescent cyanobacterial C-phycocyanin holo-alpha subunit in a heterologous host. PMID:11553806
Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift. PMID:11544186
Enhancement of capsid gene expression: preparing the human papillomavirus type 16 major structural gene L1 for DNA vaccination purposes. PMID:11533183
Isolation and characterization of the Xanthine dehydrogenase gene of the Mediterranean fruit fly, Ceratitis capitata. PMID:11514452
A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. PMID:11305938
NmeSI restriction-modification system identified by representational difference analysis of a hypervirulent Neisseria meningitidis strain. PMID:11179359
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gene expression
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model organisms
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sequence analysis
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version: extracted_at: 2022-11-04T11:36:08.869248
experimental design and studies
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More detailed information about this field from each metasource.
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:08.869248
model organisms
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:08.869248
database management
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:08.869248
sequence analysis
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experimental design and studies
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gene expression model organisms data management sequence analysis experimental design and studies
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