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In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
Genes are frequently regulated in complex manners, necessitating modelling approaches which go beyond simple (linear) gene-to-gene interactions and address the modularity of cis-regulatory regions and alternate transcription initiation…
N6-methyladenosine (m6A) is the most abundant mRNA modification within mammalian cells, holding pivotal significance in the regulation of mRNA stability, translation, and splicing. Furthermore, it plays a critical role in the regulation of…
While coding regions in the genome have a direct interpretation in terms of protein products, significant fractions are non-coding and yet control essential biological functions. Unlike the genetic code, there is no "lookup table" that…
In this paper, we propose a novel framework for modeling and analysis of networked discrete-event systems (DES). We assume that the plant is controlled by a feedback supervisor whose control decisions are subject to communication delays and…
Genetic circuits need a cellular environment to operate in, which naturally couples the circuit function with the overall functionality of gene regulatory network. To execute their functions all gene circuits draw resources in the form of…
The inclusion of the sensing functionality in the coming generations of cellular networks necessitates a rethink of dense cell deployments. In this paper, we analyze and optimize dense cell topologies for dual-functional radar-communication…
Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse…
Multisite protein modification is a ubiquitous mechanism utilized by cells to control protein functions. We have recently proposed a dynamical description of multisite protein modification which embodies all the essential features of the…
Recently, there has been a lot of effort in understanding sRNA mediated regulation of gene expression and how this mode of regulation differs from transcriptional regulation.In E.coli, in the presence of oxidative stress, the synthesis of…
Deciphering gene regulatory networks is a central problem in computational biology. Here, we explore the use of multi-modal neural networks to learn predictive models of gene expression that include cis and trans regulatory components. We…
With the explosion of distributed energy resources (DERs), voltage regulation in distribution networks has been facing a great challenge. This paper derives an asynchronous distributed voltage control strategy based on the partial…
The introduction of Renewable Energy Sources (RES) and Distributed Energy Resources (DERs) has led to the formulation of Microgrids (MGs) and Networks of MGs (NMGs). MGs and NMGs can operate in islanded mode, transforming the grid into a…
The increasing penetration of distributed energy resources (DERs) creates new voltage issues in distribution networks. This study proposes an algorithm that mitigates these issues, by actively managing the active and reactive power of those…
We report relaxation dynamics of glycerol-water mixtures as probed by megahertz-to-terahertz dielectric spectroscopy in a frequency range from 50 MHz to 0.5 THz at room temperature. The dielectric relaxation spectra reveal several…
This paper uses a recently presented abstract, tuneable Boolean regulatory network model extended to consider aspects of mobile DNA, such as transposons. The significant role of mobile DNA in the evolution of natural systems is becoming…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
We prove that complex networks of interactions have the capacity to regulate and buffer unpredictable fluctuations in production events. We show that non-bursty network-driven activation dynamics can effectively regulate the level of…
Gene regulation is an important fundamental biological process. The regulation of gene expression is managed through a variety of methods including epigenetic processes (e.g., DNA methylation). Understanding the role of epigenetic changes…
Modeling and simulation approaches for infectious disease dynamics have proven to be essential tools for effective control of the spread of epidemics in the population. Among these approaches, it is obvious that compartmental mathematical…