分子网络
Models of reaction networks within interacting compartments (RNIC) are a generalization of stochastic reaction networks. It is most natural to think of the interacting compartments as "cells" that can appear, degrade, split, and even merge,…
We prove that if a given reaction network $\mathcal{N}$ has a weakly reversible deficiency zero realization for all choice of rate constants, then there exists a $\textit{unique}$ weakly reversible deficiency zero network $\mathcal{N}'$…
Recurrent neural networks are frequently studied in terms of their information-processing capabilities. The structural properties of these networks are seldom considered, beyond those emerging from the connectivity tuning necessary for…
Interpreting biological networks becomes challenging when molecular components, such as genes or proteins, participate in numerous interactions, resulting in densely connected regions and overlapping interactions that obscure functional…
The body plan of the fruit fly is determined by the expression of just a handful of genes. We show that the spatial patterns of expression for several of these genes scale precisely with the size of the embryo. Concretely, discrete…
In a developing embryo, information about the position of cells is encoded in the concentrations of "morphogen" molecules. In the fruit fly, the local concentrations of just a handful of proteins encoded by the gap genes are sufficient to…
In genetic networks, information of relevance to the organism is represented by the concentrations of transcription factor molecules. In order to extract this information the cell must effectively "measure"' these concentrations, but there…
Long COVID is a multisystem condition characterized by persistent symptoms such as fatigue, cognitive impairment, and systemic inflammation, following COVID-19 infection, yet its mechanisms remain poorly understood. In this study, we…
What is the most crucial characteristic of a system with life activity? Currently, many theories have attempted to explain the most essential difference between living systems and general systems, such as the self-organization theory and…
Intracellular networks process cellular-level information and control cell fate. They can be computationally modeled using Boolean networks, which are implicit-time causal models of discrete binary events. These networks can be embedded in…
In the early 1970s, the Kacser/Burns and the Heinrich/Rapoport groups independently discovered the important summation and connectivity theorems in metabolic control analysis. These theorems were derived originally by using thought…
Cell polarization is a critical process that separates molecular species into two distinct regions in prokaryotic and eukaryotic cells, guiding biological processes such as cell division and cell differentiation. Although several underlying…
Advances in methods of biological data collection are driving the rapid growth of comprehensive datasets across clinical and research settings. These datasets provide the opportunity to monitor biological systems in greater depth and at…
$\beta$-arrestins play pivotal roles in seven transmembrane receptor (7TMR) signalling and trafficking. To study their functional role in the regulation of specific receptor systems, current research relies mainly on genetic tools, as few…
One central goal of systems biology is to infer biochemical regulations from large-scale OMICS data. Many aspects of cellular physiology and organism phenotypes could be understood as a result of the metabolic interaction network dynamics.…
Achaete-scute complex homolog 2 (ASCL2) codes a part of the basic helix-loop-helix (BHLH) transcription factor family. WNTs have been found to directly affect the stemness of the tumor cells via regulation of ASCL2. Switching off the ASCL2…
Modeling dynamical biological systems is key for understanding, predicting, and controlling complex biological behaviors. Traditional methods for identifying governing equations, such as ordinary differential equations (ODEs), typically…
The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of…
Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphorylation datasets…
In this paper, we propose a hypothesis regarding the travel and movement of chemicals between locations. We introduce six distinct methods to explain this process. The chemicals referred to in this article are those that we detect by the…