Related papers: Codon Bias Patterns of $E.coli$'s Interacting Prot…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
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…
The ratios of the codon usage in the quartets and sextets for the vertebrate series exhibit a correlated behaviour which fits naturally in the framework of the crystal basis model of the genetic code. Moreover the observed universal…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
Co-optimizing mRNA sequences for both codon optimality and secondary structure is crucial for producing stable and efficacious mRNA therapeutics. Codon optimization, which adjusts nucleotide sequences to enhance translational efficiency,…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…
Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use…
Background Synonymous codon choice is mainly affected by mutation and selection. For the majority of genes within a genome, mutational pressure is the major driving force, but selective strength can be strong and dominant for specific set…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…
Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational…
A survey of the patterns of synonymous codon preferences in the HIV env gene reveals a relation between the codon bias and the mutability requirements in different regions in the protein. At hypervariable regions in $gp120$, one finds a…
The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. It has long been suggested that the resulting correlations among amino acid compositions at different…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment,…
The presence of clusters of rare codons is known to negatively impact the efficiency and accuracy of protein production. In this paper, we demonstrate a statistical method of identifying such clusters in the coding sequence of a gene. Using…
Attributed network embedding (ANE) is to learn low-dimensional vectors so that not only the network structure but also node attributes can be preserved in the embedding space. Existing ANE models do not consider the specific combination…
The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…