Related papers: Transient crosslinking kinetics optimize gene clus…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
We showed in our previous studies that just $3\%$ cross-links, at special points along the contour of the bacterial DNA help the DNA-polymer to get organized at micron length scales \cite{jpcm,epl}. In this work, we investigate how does the…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
The last decades have not only been characterized by an explosive growth of data, but also an increasing appreciation of data as a valuable resource. Their value comes with the ability to extract meaningful patterns that are of economic,…
Network science has become an essential interdisciplinary tool for understanding complex biological systems. However, because these systems undergo continuous, often stimulus-driven changes in both structure and function, traditional static…
Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II Topoisomerase (TopoII) enzymes play an important role in…
Allostery refers to the puzzling phenomenon of long-range communication between distant sites in proteins. Despite its importance in biomolecular regulation and signal transduction, the underlying dynamical process is not well understood.…
Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus\textemdash some of those transiently link and pass two chromatin segments. Here we study how such an active…
Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a…
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…
The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the…
Increasing evidence has shown that gene-gene interactions have important effects on biological processes of human diseases. Due to the high dimensionality of genetic measurements, existing interaction analysis methods usually suffer from a…
High-density DNA arrays, used to monitor gene expression at a genomic scale, have produced vast amounts of information which require the development of efficient computational methods to analyze them. The important first step is to extract…
Understanding how transcription factors (TFs) regulate mammalian gene expression in space and time is a central topic in biology. To activate a gene, a TF has first to diffuse in the available space of the nucleus until it reaches a target…
Despite its high and direct impact on nearly all biological processes, the underlying structure of gene-gene interaction networks is investigated so far according to pair connections. To address this, we explore the gene interaction…
We review the mechanism and consequences of the "bridging-induced attraction", a generic biophysical principle which underpins some existing models for chromosome organisation in 3-D. This attraction, which was revealed in polymer…
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signaling molecules - morphogens - guide this process. The continuous positional information…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can…