Related papers: Synonymous codon usage and selection on proteins

Filtered Poisson processes are often used as reference models for intermittent fluc- tuations in physical systems. Such a process is here extended by adding a noise term, either as a purely additive term to the process or as a dynamical…

Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than…

Feature extraction is an unavoidable task, especially in the critical step of preprocessing biological sequences. This step consists for example in transforming the biological sequences into vectors of motifs where each motif is a…

Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our…

Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…

We present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of…

It has been established that Terahertz (THz) band signals can interact with biomolecules through resonant modes. Specifically, of interest here, protein activation. Our research goal is to show how directing the mechanical signaling inside…

A steadily increasing body of evidence suggests that the brain performs probabilistic inference to interpret and respond to sensory input and that trial-to-trial variability in neural activity plays an important role. The neural sampling…

We develop a new technique for proving distribution testing lower bounds for properties defined by inequalities involving the bin probabilities of the distribution in question. Using this technique we obtain new lower bounds for…

Voting algorithms have been widely used as consensus protocols in the realization of fault-tolerant systems. These algorithms are best suited for distributed systems of nodes with low computational power or heterogeneous networks, where…

We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wildtype structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of…

The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…

Co-citation measurements can reveal the extent to which a concept representing a novel combination of existing ideas evolves towards a specialty. The strength of co-citation is represented by its frequency, which accumulates over time. Of…

Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base…

Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…

The equivalence of the characteristic function approach and the probabilistic approach to monotone and boolean convolutions is proven for non-compactly supported probability measures. A probabilistically motivated definition of the…

It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…

We propose a cautious Bayesian variable selection routine by investigating the sensitivity of a hierarchical model, where the regression coefficients are specified by spike and slab priors. We exploit the use of latent variables to…

The behavioural comparison of systems is an important concern of software engineering research. For example, the areas of specification discovery and specification mining are concerned with measuring the consistency between a collection of…

Naturally evolving proteins gradually accumulate mutations while continuing to fold to thermodynamically stable native structures. This process of neutral protein evolution is an important mode of genetic change, and forms the basis for the…