Related papers: Chromatin Structure Changes in Human Disease: A Mi…
The use of networks to integrate different genetic, proteomic, and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases. Here we introduce a new phenotypic database summarizing…
This paper generalizes a previously published differential equation that describes the relation between the age-specific incidence, remission, and mortality of a disease with its prevalence. The underlying model is a simple compartment…
Chromatin and associated proteins constitute the highly folded structure of chromosomes. We consider a self-avoiding polymer model of the chromatin, segments of which may get cross-linked via protein binders that repel each other. The…
Chromosomal crossovers play a crucial role in meiotic cell division, as they ensure proper chromosome segregation and increase genetic variability. Experiments have consistently revealed two key observations across species: (i) the number…
Gradual transformation of the epidermal stem cells to corneocytes involves a chain of chronologically well-arranged events that mostly stimulated locally by their neighbors. Cell diversity that observed during the differentiation through…
This review provides a perspective on recent developments and their implications for our understanding of novel quantum phenomena in the physics of two-dimensional organic solids. We concentrate on the phase transitions and collective…
This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene…
Despite differences in brain sizes and cognitive niches among mammals, their cerebral cortices posses many common features and regularities. These regularities have been a subject of experimental investigation in neuroanatomy for the last…
The problem of the structure of nucleons and their interaction in the concept of nonperturbative QCD is discussed as an approach to studying the transformation of current quarks into constituent ones and the search for the mechanism of such…
In population genetics, mutation rate is often treated as a homogeneous parameter across the genome. Empirical evidence, however, shows systematic variation across genomic contexts associated with chromatin organization and epigenomic…
Understanding the distinction between causation and correlation is critical in Alzheimer's disease (AD) research, as it impacts diagnosis, treatment, and the identification of true disease drivers. This experiment investigates the…
Tumors are defined by their intense proliferation, but sometimes cancer cells turn senescent and stop replicating. In the stochastic cancer model in which all cells are tumorigenic, senescence is seen as the result of random mutations,…
Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as…
Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…
Crystals are a state of matter characterised by periodic order. Yet crystalline materials can harbour disorder in many guises, such as non-repeating variations in composition, atom displacements, bonding arrangements, molecular…
This is an introduction to the special issue Genome organization: experiments and simulations, published in Chromosome Research, volume 25, issue 1 (2017).
The past decade has seen a revolution in genomic technologies that enable a flood of genome-wide profiling of chromatin marks. Recent literature tried to understand gene regulation by predicting gene expression from large-scale chromatin…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
Comorbidity networks, which capture disease-disease co-occurrence usually based on electronic health records, reveal structured patterns in how diseases cluster and progress across individuals. However, how these networks evolve across…
In the crowded eukaryotic nucleus, euchromatin and heterochromatin segregate into distinct compartments, a phenomenon often attributed to homotypic interactions mediated by liquid liquid phase separation of chromatin associated proteins.…