Related papers: On three genetic repressilator topologies
The different cell types in a living organism acquire their identity through the process of cell differentiation in which the multipotent progenitor cells differentiate into distinct cell types. Experimental evidence and analysis of…
Recent experiments showed that multiple copies of the molecular machine RNA polymerase (RNAP) can efficiently synthesize mRNA collectively in the active state of the promoter. However, environmentally-induced promoter repression results in…
Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…
Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This `redundancy' of…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
Driven dissipative systems at ambient conditions typically exhibit continuous responses shaped by fluctuations and relaxation, with discrete macroscopic states arising only under specific dynamical constraints. Here, we report the emergence…
The problem of sample complexity of online reinforcement learning is often studied in the literature without taking into account any partial knowledge about the system dynamics that could potentially accelerate the learning process. In this…
Self-regulatory models are common in nature, as described e.g. in (\cite{mur}), (\cite{ha}) and (\cite{Gb}).\\ Let us consider a system made up of a number of glands as a motivation. Each gland secretes a hormone that allows secretion in…
We introduce a new Hopf algebra that operates on pairs of finite interval partitions and permutations of equal length. This algebra captures vincular patterns, which involve specifying both the permutation patterns and the consecutive…
Motivated by a certain type of unfolding of a Hopf-Hopf singularity, we consider a one-parameter family $(f_\gamma)_{\gamma\geq0}$ of $C^3$--vector fields in $\mathbb{R}^4$ whose flows exhibit a heteroclinic cycle associated to two periodic…
We bring together three key amplification mechanisms in linear dynamical systems: spectral criticality, resonance, and non-normality. We present a unified linear framework that both distinguishes and quantitatively links these effects…
When biological foundation models such as scGPT and Geneformer process single-cell gene expression, what geometric and topological structure forms in their internal representations? Is that structure biologically meaningful or a training…
Constructing gene regulatory networks is a fundamental task in systems biology. We introduce a Gaussian reciprocal graphical model for inference about gene regulatory relationships by integrating mRNA gene expression and DNA level…
Dynamical systems theory describes how interacting quantities change over time and space, from molecular oscillators to large-scale biological patterns. Such systems often involve nonlinear feedbacks, delays, and interactions across scales.…
The design of biological systems is hindered by uncertainty arising from both intrinsic stochasticity of biomolecular reactions and variability across laboratory or experimental conditions. In this work, we present a sequential framework to…
We present a novel analysis of the dynamics of tensor power iterations in the overcomplete regime where the tensor CP rank is larger than the input dimension. Finding the CP decomposition of an overcomplete tensor is NP-hard in general. We…
Traditional energy-based learning models associate a single energy metric to each configuration of variables involved in the underlying optimization process. Such models associate the lowest energy state to the optimal configuration of…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…
Our aim is to predict how often genic and non-genic promoters fire within a cell. We first review a parsimonious pan-genomic model for genome organization and gene regulation, where transcription rate is determined by proximity in 3D space…
A social choice procedure is modeled as a repeated Nash game between the social agents, who are communicating with each other through a social communication network modeled by an undirected graph. The agents' criteria for this game are…