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In many fields, researchers are interested in large and complex biological processes. Two important examples are gene expression and DNA methylation in genetics. One key problem is to identify aberrant patterns of these processes and…
A recently formulated description of homogeneous nucleation for Brownian particles in the over-damped limit based on fluctuating hydrodynamics is used to determine the nucleation pathway, characterized as the most likely path (MLP), for the…
Directed polymers on 1+1 dimensional lattices coupled to a heat bath at temperature $T$ are studied numerically for three ensembles of the site disorder. In particular correlations of the disorder as well as fractal patterning are…
Motivated by differential co-expression analysis in genomics, we consider in this paper estimation and testing of high-dimensional differential correlation matrices. An adaptive thresholding procedure is introduced and theoretical…
We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbour calculations. Within this model, the finiteness of stacking enthalpies is shown…
DNA methylation is an epigenetic mechanism that regulates gene expression by adding methyl groups to DNA. Abnormal methylation patterns can disrupt gene expression and have been linked to cancer development. To quantify DNA methylation,…
The role of thermal pressure fluctuation excited within tightly packaged DNA prior to ejection from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Biological organisms exhibit diverse strategies for adapting to varying environments. For example, a population of organisms may express the same phenotype in all environments (`unvarying strategy'), or follow environmental cues and express…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
Elements of nuclear symmetry energy evaluated from different energy density functionals parametrized by fitting selective bulk properties of few representative nuclei are seen to vary widely. Those obtained from experimental data on nuclear…
Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
In both criminal cases and civil cases there is an increasing demand for the analysis of DNA mixtures involving relationships. The goal might be, for example, to identify the contributors to a DNA mixture where the donors may be related, or…
The expression levels of many thousands of genes can be measured simultaneously by DNA microarrays (chips). This novel experimental tool has revolutionized research in molecular biology and generated considerable excitement. A typical…
Probability modelling for DNA sequence evolution is well established and provides a rich framework for understanding genetic variation between samples of individuals from one or more populations. We show that both classical and more recent…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
Background: Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features for association with disease. We propose a new approach,…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…