相关论文: On the clustering of rare codons and its effect on…
Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how…
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…
In the process of translation, ribosomes read the genetic code on an mRNA and assemble the corresponding polypeptide chain. The ribosomes perform discrete directed motion which is well modeled by a totally asymmetric simple exclusion…
Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…
Transcription factor concentrations provide signals to cells that allow them to regulate gene expression to make correct cell fate decisions. Calculations for noise bounds in gene regulation suggest that clustering or cooperative binding of…
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide…
A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…
The genetic code underlying protein synthesis is a canonical example of a degenerate biological system. Degeneracies in physical and biological systems can be lifted by external perturbations thus allowing degenerate systems to exhibit a…
We examine fluctuation effects due to the low copy number of proteins involved in pattern-forming dynamics within a bacterium. We focus on a stochastic model of the oscillating MinCDE protein system regulating accurate cell division in E.…
Deprivation of essential nutrients can have stark consequences for many processes in a cell. We consider amino acid starvation, which can result in bottlenecks in mRNA translation when ribosomes stall due to lack of resources, i.e. tRNAs…
Generating protein sequences conditioned on protein structures is an impactful technique for protein engineering. When synthesizing engineered proteins, they are commonly translated into DNA and expressed in an organism such as yeast. One…
Statistical language models frequently suffer from a lack of training data. This problem can be alleviated by clustering, because it reduces the number of free parameters that need to be trained. However, clustered models have the following…
Efficient protein synthesis depends on the availability of charged tRNA molecules. With 61 different codons, shifting the balance among the tRNA abundances can lead to large changes in the protein synthesis rate. Previous theoretical work…
The performance (accuracy and robustness) of several clustering algorithms is studied for linearly dependent random variables in the presence of noise. It turns out that the error percentage quickly increases when the number of observations…
How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same…
The percolation properties of clustered networks are analyzed in detail. In the case of weak clustering, we present an analytical approach that allows to find the critical threshold and the size of the giant component. Numerical simulations…
Text Clustering is a text mining technique which divides the given set of text documents into significant clusters. It is used for organizing a huge number of text documents into a well-organized form. In the majority of the clustering…
We consider the problem of clustering data that reside on discrete, low dimensional lattices. Canonical examples for this setting are found in image segmentation and key point extraction. Our solution is based on a recent approach to…
Motivated by recent experiments on an antibiotic resistance gene, we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation. We show that the range of possible interactions is…
One of the greatest challenges in biophysical models of translation is to identify coding sequences features that affect the rate of translation and therefore the overall protein production in the cell. We propose an analytic method to…