Related papers: DNA sequence correlations shape nonspecific transc…
Evolution of the amino acid sequences of transthyretin (TTR) can provide additional information about its dynamics that both complements and extends the already extensive static structural data. Protein dynamics is largely driven by…
Recent works on localized charge transport along DNA, based on a three--dimensional, tight--binding model (Eur. Phys. J. B 30:211, 2002; Phys. D 180:256, 2003), suggest that charge transport is mediated by the coupling of the radial and…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
The single nucleotide polymorphism (SNP) rs7903146 in the TCF7L2 gene has been determined as one of the strongest common genetic risk factors for Type 2 Diabetes (T2D). The location of the SNP in a non-coding region suggests a regulatory…
The sequence of amino acids in a protein is believed to determine its native state structure, which in turn is related to the functionality of the protein. In addition, information pertaining to evolutionary relationships is contained in…
More than any other species, humans form social ties to individuals who are neither kin nor mates, and these ties tend to be with similar people. Here, we show that this similarity extends to genotypes. Across the whole genome, friends'…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
Epigenetic modifications of histones crucially affect the eukaryotic gene activity, while the epigenetic histone state is largely determined by the binding of specific factors such as the transcription factors (TFs) to DNA. Here, the way…
Non-coding RNA are functional molecules that are not translated into proteins. Their function comes as important regulators of biological function. Because they are not translated, they need not be as stable as other types of RNA. The TKF91…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
Gene regulation in higher eukaryotes involves a complex interplay between the gene proximal promoter and distal genomic elements (such as enhancers) which work in concert to drive spatio-temporal expression. The experimental…
Site-specific recombination on supercoiled circular DNA molecules can yield a variety of knots and catenanes. Twist knots are some of the most common conformations of these products and they can act as substrates for further rounds of…
The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression…
Mutational neighbourhoods in genotype-phenotype (GP) maps are widely believed to be more likely to share characteristics than expected from random chance. Such genetic correlations should, as John Maynard Smith famously pointed out,…
Prediction of binding sites for transcription factors is important to understand how they regulate gene expression and how this regulation can be modulated for therapeutic purposes. Although in the past few years there are significant works…
We study the target searching on the DNA for proteins in the presence of non-constant drift and non-Gaussian $\alpha$-stable L\'evy fluctuations. The target searching is realized by the facilitated diffusion process. The existing works are…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
Positioning of nucleosomes along eukaryotic genomes plays an important role in their organization and regulation. There are many different factors affecting the location of nucleosomes. Some can be viewed as preferential binding of a single…
The first step in drug discovery is finding drug molecule moieties with medicinal activity against specific targets. Therefore, it is crucial to investigate the interaction between drug-target proteins and small chemical molecules. However,…
In recent years, significant progress in understanding the properties of supercoiled DNA has been obtained due to nanotechniques that made stretching and twisting of single molecules possible. Quantitative interpretation of such experiments…