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Bayesian network models are finding success in characterizing enzyme-catalyzed reactions, slow conformational changes, predicting enzyme inhibition, and genomics. In this work, we apply them to statistical modeling of peptides by…
Understanding the reasons for the success of deep neural networks trained using stochastic gradient-based methods is a key open problem for the nascent theory of deep learning. The types of data where these networks are most successful,…
DNA methylation is a well-studied genetic modification that regulates gene transcription of Eukaryotes. Its alternations have been recognized as a significant component of cancer development. In this study, we use the DNA methylation 450k…
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…
Background: Biomedical data are usually collections of longitudinal data assessed at certain points in time. Clinical observations assess the presences and severity of symptoms, which are the basis for description and modeling of disease…
Active (catalysed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eucaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, convergence of distributions from unbiased simulation is slow, limiting applications…
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…
Many biological processes have been the source of inspiration for heuristic methods that generate high-quality solutions to solve optimization and search problems. This thesis presents an epigenetic technique for Evolutionary Algorithms,…
Generation of molecules with desired chemical and biological properties such as high drug-likeness, high binding affinity to target proteins, is critical for drug discovery. In this paper, we propose a probabilistic generative model to…
Predicting protein secondary structure is a fundamental problem in protein structure prediction. Here we present a new supervised generative stochastic network (GSN) based method to predict local secondary structure with deep hierarchical…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
Tuberculosis is one of the most lethal contagious diseases caused by Mycobacterium tuberculosis (MTB), in many cases, the infected did not show any symptoms, because the bacilli entered the dormant stage in granulomas. The dormant stage of…
The eukaryotic Cys2His2 zinc finger proteins bind to DNA ubiquitously at highly conserved domains, responsible for gene regulation and the spatial organization of DNA. To study and understand the zinc finger DNA-protein interaction, we use…
Ecological systems can often be characterised by changes among a finite set of underlying states pertaining to individuals, populations, communities, or entire ecosystems through time. Owing to the inherent difficulty of empirical field…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…