Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver
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Protein synthesis plays an important role in biological systems since its products, proteins and enzymes, constitute most of the molecular machinery required for cell regulation, growth and function in the tissue. Understanding the mechanisms of decoding a ...
Noise in genetic networks has been the subject of extensive experimental and computational studies. However, very few of these studies have considered noise properties using mechanistic models that account for the discrete movement of ribosomes and RNA pol ...
RNase E is an essential bacterial endoribonuclease involved in the turnover of messenger RNA and the maturation of structured RNA precursors in Escherichia coli. Here, we present the crystal structure of the E. coli RNase E catalytic domain in the apo-stat ...
We present and validate BlastR, a method for efficiently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded ...
Despite the establishment of design principles to optimize codon choice for heterologous expression vector design, the relationship between codon sequence and final protein yield remains poorly understood. In this work, we present a computational framework ...
RNA plays key roles in essential biological processes, such as protein synthesis, transcriptional regulation, splicing and retroviral replication. The structural diversity of RNA molecules and the lack of known RNA repair mechanisms make these biopolymers ...
More than 100 modified nucleosides have been found in naturally occurring RNA sequences. These modifications are involved in the correct folding, in the maintenance of the reading frame during translation and in the proper interaction with enzymes and prot ...
MicroRNAs (miRNAs) comprise a large set of short noncoding RNAs that bind to messenger RNAs (mRNAs) to reduce their translation into functional proteins. Computational prediction of miRNA targets is the first stage in the discovery and validation of new re ...
There has been much discussion in the literature regarding the determinants of ribosomal decoding speed during the mRNA translation process. Computational results based on mechanistic models for ribosomal kinetics have predicted a major role for near-cogna ...
Translation is a central cellular process and the complexity of its mechanism necessitates mathematical frameworks to better understand system properties and make quantitative predictions. We have developed a gene sequence-specific mechanistic model for tr ...