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We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component systems which are well-studied experimentally as well…

Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology,…

We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current…

We develop a model-independent reduction method of chemical reaction systems based on the stoichiometry, which determines their network topology. A subnetwork can be eliminated systematically to give a reduced system with fewer degrees of…

The ability to detect weak distributed activation patterns in networks is critical to several applications, such as identifying the onset of anomalous activity or incipient congestion in the Internet, or faint traces of a biochemical spread…

Zero-one reaction networks are pivotal to cellular signaling, and establishing the equivalence of such networks represents a foundational computational challenge in the realm of chemical reaction network research. Herein, we propose a…

There is an intuitive analogy of an organic chemist's understanding of a compound and a language speaker's understanding of a word. Consequently, it is possible to introduce the basic concepts and analyze potential impacts of linguistic…

The problem of achieving consensus in a network of connected systems arises in many science and engineering applications. In contrast to previous works, we focus on the system reactivity, i.e., the initial amplification of the norm of the…

Neural networks have in recent years shown promise for helping software engineers write programs and even formally verify them. While semantic information plays a crucial part in these processes, it remains unclear to what degree popular…

Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about…

Various biological system models have been proposed in systems biology, which are based on the complex biological reactions kinetic of various components. These models are not practical because we lack of kinetic information. In this paper,…

The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the…

Embedding computation in biochemical environments incompatible with traditional electronics is expected to have wide-ranging impact in synthetic biology, medicine, nanofabrication and other fields. Natural biochemical systems are typically…

Given a dynamical system with polynomial right-hand side, can it be generated by a reaction network that possesses certain properties? This question is important because some network properties may guarantee specific dynamical properties,…

Given the ever-increasing computational costs of modern machine learning models, we need to find new ways to reuse such expert models and thus tap into the resources that have been invested in their creation. Recent work suggests that the…

We consider steady states of dynamics that have an underlying network structure. We study how a steady state responds to small perturbations in the network parameters and how this sensitivity is connected to the network structure. We…

Thermodynamics constrains the flow of matter in a reaction network to occur through routes along which the Gibbs energy decreases, implying that viable steady-state flux patterns should be void of closed reaction cycles. Identifying and…

Retrosynthesis is one of the fundamental problems in organic chemistry. The task is to identify reactants that can be used to synthesize a specified product molecule. Recently, computer-aided retrosynthesis is finding renewed interest from…

Reaction networks can display a wide array of dynamics. However, it is possible for different reaction networks to display the same dynamics. This phenomenon is called dynamical equivalence and makes network identification a hard problem to…

Steady states are frequently used to investigate the long-term behaviors of (bio)-chemical systems. Recently, there has been a growing interest in network-based approaches due to their efficiency in deriving parametrizations of positive…