Related papers: A Dynamical Model Reveals Gene Co-Localizations in…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
Brownian motion is a universal characteristic of colloidal particles embedded in a host medium, and it is the fingerprint of molecular transport or diffusion, a generic feature of relevance not only in Physics but also in several branches…
Finding coarse-grained, low-dimensional descriptions is an important task in the analysis of complex, stochastic models of gene regulatory networks. This task involves (a) identifying observables that best describe the state of these…
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…
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.…
The precise layout of gene expression patterns is a crucial step in development. Formation of a sharp boundary between high and low expression domains requires a genetic mechanism which is both sensitive and robust to fluctuations, a demand…
The ability of eukaryotic cells to squeeze through constrictions is limited by the stiffness of their large and rigid nucleus. However, migrating cells are often able to overcome this limitation and pass through constrictions much smaller…
Motivated by subdiffusive motion of bio-molecules observed in living cells we study the stochastic properties of a non-Brownian particle whose motion is governed by either fractional Brownian motion or the fractional Langevin equation and…
Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal…
Much of the genome is expressed in the vertebrate brain, with individual genes exhibiting different spatially-varying patterns of expression. These variations are not independent, with pairs of genes exhibiting complex patterns of…
The neutral mutation rate is known to vary widely along human chromosomes, leading to mutational hot and cold regions. We provide evidence that categories of functionally-related genes reside preferentially in mutationally hot or cold…
The predominant success of diffusion models in generative modeling has spurred significant interest in understanding their theoretical foundations. In this work, we propose a feature learning framework aimed at analyzing and comparing the…
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated…
Phase transformations ruled by non-simultaneous nucleation and growth do not lead to random distribution of nuclei. Since nucleation is only allowed in the untransformed portion of space, positions of nuclei are correlated. In this article…
Complex gene interactions play a significant role in cancer progression, driving cellular behaviors that contribute to tumor growth, invasion, and metastasis. Gene co-expression networks model the functional connectivity between genes under…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
Transcription factor (TF) molecules translocate by facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA). Despite the attention this mechanism received in the last 40 years, only a few studies…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
Dynamic models are widely used to mathematically describe biological phenomena that evolve over time. One important area of application is leukaemia research, where leukaemia cells are genetically modified in preclinical studies to explore…