Related papers: Modeling the dynamics of bivalent histone modifica…
As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our…
Interlayer rotation and stacking were recently demonstrated as effective strategies for tuning physical properties of various two-dimensional materials. The latter strategy was mostly realized in hetero-structures with continuously varied…
Cells coordinate adjustments in genome expression to accommodate changes in their environment. A drug in culture media for in vitro preclinical testing sometimes cause drastic regime shifting of genome expression system depending on the…
Deciphering regulatory events that drive malignant transformation represents a major challenge for systems biology. Here we analyzed genome-wide transcription profiling of an in-vitro transformation process. We focused on a cluster of genes…
Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…
Epigenetic inheritance during cell division is essential for preserving cell identity by stabilizing the overall chromatin organisation. Heterochromatin,the condensed and transcriptionally silent fraction of chromatin,is marked by specific…
Many genes have been identified as driving cellular differentiation, but because of their complex interactions, the understanding of their collective behaviour requires mathematical modelling. Intriguingly, it has been observed in numerous…
We study, by means of the periodic unfolding technique, the homogenization of a modified bidomain model, which describes the propagation of the action potential in the cardiac electrophysiology. Such a model, allowing the presence of…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
In StyleGAN, convolution kernels are shaped by both static parameters shared across images and dynamic modulation factors $w^+\in\mathcal{W}^+$ specific to each image. Therefore, $\mathcal{W}^+$ space is often used for image inversion and…
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help coordinate these cascades by attracting regulatory proteins to enhance…
In this thesis, we consider some spin effects in QCD and recurrence lattices with multi-site exchanges. Main topic of our manuscript are critical phenomena in spin systems defined on the recurrence lattices. Main tool of our approach is the…
Dominance is usually considered a constant value that describes the relative difference in fitness or phenotype between heterozygotes and the average of homozygotes at a focal polymorphic locus. However, the observed dominance can vary with…
Understanding the interplay among processes that occur over different timescales is a challenging issue in the physics of systems regulation. In gene regulation, the timescales for changes in chromatin states can differ from those for…
Epitaxial growth has become a promising route to achieve highly crystalline continuous two-dimensional layers. However, high-quality layer production with expected electrical properties is still challenging due to the defects induced by the…
We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA…
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially…
In two-dimensional nearly commensurate heterostructures, strain plays a critical role in shaping electronic behavior. While previous studies have focused on random strain introduced during fabrication, achieving controlled structural design…
In many transcriptomic studies, the correlation of genes might fluctuate with quantitative factors such as genetic ancestry. We propose a method that models the covariance between two variables to vary against a continuous covariate. For…
Gene duplication is believed to play a major role in the evolution of genomic complexity. The presence of a duplicate removes the constraint of natural selection upon the gene, leading to its likely loss of function or, occasionally, the…