Phylogenetic and recombinant analyses of complete coding sequences of DENV-1 from field-caught mosquitoes in Thailand.
Sign Up to like & getrecommendations! Published in 2020 at "Virus research"
DOI: 10.1016/j.virusres.2020.198041
Abstract: Dengue diseases are a group of infectious diseases that have been widespread throughout the world for several decades. Dengue outbreaks have occurred in many parts of the world, including Southeast Asia. The outbreak and the… read more here.
Keywords: dengue; coding sequences; denv genotype; amino acid ... See more keywords
GC-rich coding sequences reduce transposon-like, small RNA-mediated transgene silencing
Sign Up to like & getrecommendations! Published in 2017 at "Nature Plants"
DOI: 10.1038/s41477-017-0040-6
Abstract: The molecular basis of transgene susceptibility to silencing is poorly characterized in plants; thus, we evaluated several transgene design parameters as means to reduce heritable transgene silencing. Analyses of Arabidopsis plants with transgenes encoding a… read more here.
Keywords: small rna; transgene silencing; transposon like; sequences reduce ... See more keywords
Analysis of selection in protein-coding sequences accounting for common biases
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbaa431
Abstract: The evolution of protein-coding genes is usually driven by selective processes, which favor some evolutionary trajectories over others, optimizing the subsequent protein stability and activity. The analysis of selection in this type of genetic data… read more here.
Keywords: selection protein; analysis selection; selection; protein coding ... See more keywords
Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps’ Genomes
Sign Up to like & getrecommendations! Published in 2022 at "Genome Biology and Evolution"
DOI: 10.1093/gbe/evac142
Abstract: Abstract Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription,… read more here.
Keywords: pseudogenes intergenic; intergenic protein; coding sequences; protein coding ... See more keywords
Readthrough errors purge deleterious cryptic sequences, facilitating the birth of coding sequences.
Sign Up to like & getrecommendations! Published in 2020 at "Molecular biology and evolution"
DOI: 10.1093/molbev/msaa046
Abstract: De novo protein-coding innovations sometimes emerge from ancestrally non-coding DNA, despite the expectation that translating random sequences is overwhelmingly likely to be deleterious. The "pre-adapting selection" hypothesis claims that emergence is facilitated by prior, low-level… read more here.
Keywords: readthrough errors; selection; non coding; cryptic sequences ... See more keywords
Kozak Sequence Acts as a Negative Regulator for De Novo Transcription Initiation of Newborn Coding Sequences in the Plant Genome
Sign Up to like & getrecommendations! Published in 2021 at "Molecular Biology and Evolution"
DOI: 10.1093/molbev/msab069
Abstract: Abstract The manner in which newborn coding sequences and their transcriptional competency emerge during the process of gene evolution remains unclear. Here, we experimentally simulated eukaryotic gene origination processes by mimicking horizontal gene transfer events… read more here.
Keywords: plant; newborn coding; plant genome; gene ... See more keywords
Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates
Sign Up to like & getrecommendations! Published in 2017 at "Molecular Biology and Evolution"
DOI: 10.1093/molbev/msx199
Abstract: Abstract The evolutionary history of vertebrates is marked by three ancient whole-genome duplications: two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched… read more here.
Keywords: whole genome; nervous system; duplicate; retention ... See more keywords
Conserved non-coding sequences and de novo Mutator insertion alleles are imprinted in maize.
Sign Up to like & getrecommendations! Published in 2022 at "Plant physiology"
DOI: 10.1093/plphys/kiac459
Abstract: Genomic imprinting is an epigenetic phenomenon in which differential allele expression occurs in a parent-of-origin dependent manner. Imprinting in plants is tightly linked to transposable elements (TEs), and it has been hypothesized that genomic imprinting… read more here.
Keywords: imprinting; coding sequences; conserved non; mutator ... See more keywords
Genomic diversity and functional insights of carbapenem-resistant Klebsiella pneumoniae revealed by centroid coding sequences analysis
Sign Up to like & getrecommendations! Published in 2025 at "Microbial Genomics"
DOI: 10.1099/mgen.0.001457
Abstract: Abstract Klebsiella pneumoniae is a primary bacterial pathogen responsible for various human infections with the emergence of carbapenem-resistant K. pneumoniae (CRKP) as a significant clinical challenge. Although previous studies have classified K. pneumoniae based on… read more here.
Keywords: genomic diversity; klebsiella pneumoniae; centroid coding; pneumoniae ... See more keywords
COATi: Statistical Pairwise Alignment of Protein-Coding Sequences
Sign Up to like & getrecommendations! Published in 2024 at "Molecular Biology and Evolution"
DOI: 10.1101/2023.05.22.541791
Abstract: Sequence alignment is an essential method in bioinformatics and the basis of many analyses, including phylogenetic inference, ancestral sequence reconstruction, and gene annotation. Sequence artifacts and errors made during alignment reconstruction can impact downstream analyses… read more here.
Keywords: protein coding; statistical pairwise; coding sequences; sequence ... See more keywords
Coding sequences of sarcoplasmic reticulum calcium ATPase regulatory peptides and expression of calcium regulatory genes in recurrent exertional rhabdomyolysis
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Veterinary Internal Medicine"
DOI: 10.1111/jvim.15425
Abstract: Background Sarcolipin (SLN), myoregulin (MRLN), and dwarf open reading frame (DWORF) are transmembrane regulators of the sarcoplasmic reticulum calcium transporting ATPase (SERCA) that we hypothesized played a role in recurrent exertional rhabdomyolysis (RER). Objectives Compare… read more here.
Keywords: rer; regulatory genes; control; expression ... See more keywords