Related papers: Synonymous codon usage and selection on proteins
The ratio of non-synonymous to synonymous substitutions $\omega(=d_{N}/d_{S})$ has been widely used as a measure of adaptive evolution in protein coding genes. Omega can be defined in terms of population genetics parameters as the fixation…
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…
One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active…
We investigate an application in the automatic tuning of computer codes, an area of research that has come to prominence alongside the recent rise of distributed scientific processing and heterogeneity in high-performance computing…
Recent studies have shown that single-stranded viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison it has been suggested that wild-type…
Boolean formulae compactly encode huge, constrained search spaces. Thus, variability-intensive systems are often encoded with Boolean formulae. The search space of a variability-intensive system is usually too large to explore without…
Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases,…
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
Econophysics and econometrics agree that there is a correlation between volume and volatility in a time series. Using empirical data and their distributions, we further investigate this correlation and discover new ways that volatility and…
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…
Evolutionary dynamics and patterns of molecular evolution are strongly influenced by selection on linked regions of the genome, but our quantitative understanding of these effects remains incomplete. Recent work has focused on predicting…
Language change is a cultural evolutionary process in which variants of linguistic variables change in frequency through processes analogous to mutation, selection and genetic drift. In this work, we apply a recently-introduced method to…
Pierons and Chocholles seminal psychophysical work predicts that human response time to information relative to visual contrast and sound frequency decreases when contrast intensity or sound frequency increases. The goal of this study is to…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Coupling the control of expression stochasticity (noise) to the ability of expression change (plasticity) can alter gene function and influence adaptation. A number of factors, such as transcription re-initiation, strong chromatin…
In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial…
The paper considers variable selection in linear regression models where the number of covariates is possibly much larger than the number of observations. High dimensionality of the data brings in many complications, such as (possibly…
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,…
Even when driven by the same stimulus, neuronal responses are well-known to exhibit a striking level of spiking variability. In-vivo electrophysiological recordings also reveal a surprisingly large degree of variability at the subthreshold…