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Allostery commonly refers to the mechanism that regulates protein activity through the binding of a molecule at a different, usually distal, site from the orthosteric site. The omnipresence of allosteric regulation in nature and its…

This paper presents an intracellular feedback control strategy, to regulate the gene expression process dynamics. For this purpose, two types of genetic circuits are designed in order to compare concentrations of the input transcription…

In a modern recommender system, it is important to understand how products relate to each other. For example, while a user is looking for mobile phones, it might make sense to recommend other phones, but once they buy a phone, we might…

Inferring the structure and dynamics of network models is critical to understanding the functionality and control of complex systems, such as metabolic and regulatory biological networks. The increasing quality and quantity of experimental…

Many recent generative models make use of neural networks to transform the probability distribution of a simple low-dimensional noise process into the complex distribution of the data. This raises the question of whether biological networks…

Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…

In systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular…

Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the last few years fold-change detecting mechanisms, based on transcriptional networks, have been…

Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…

Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…

The relationship between the design and functionality of molecular networks is now a key issue in biology. Comparison of regulatory networks performing similar tasks can give insights into how network architecture is constrained by the…

In this report a systematic approach is used to determine the approximate genetic network and robust dependencies underlying differentiation. The data considered is in the form of a binary matrix and represent the expression of the nine…

Boolean networks are powerful mathematical tools for modeling the qualitative dynamics of genetic regulation. Yet inferred models often generate spurious attractors that lack biological viability. In this paper, we propose a parsimonious…

Rapid advances in high-throughput technologies have led to considerable interest in analyzing genome-scale data in the context of biological pathways, with the goal of identifying functional systems that are involved in a given phenotype.…

Network theory has proven invaluable in unraveling complex protein interactions. Previous studies have employed statistical methods rooted in network theory, including the Gaussian graphical model, to infer networks among proteins,…

An important challenge in cancer systems biology is to uncover the complex network of interactions between genes (tumor suppressor genes and oncogenes) implicated in cancer. Next generation sequencing provides unparalleled ability to probe…

Regulation of intrinsic noise in gene expression is essential for many cellular functions. Correspondingly, there is considerable interest in understanding how different molecular mechanisms of gene expression impact variations in protein…

Components of biological systems interact with each other in order to carry out vital cell functions. Such information can be used to improve estimation and inference, and to obtain better insights into the underlying cellular mechanisms.…

The interactions between proteins, DNA, and RNA in living cells constitute molecular networks that govern various cellular functions. To investigate the global dynamical properties and stabilities of such networks, we studied the cell-cycle…

Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a…