Molecular Networks
We discuss in this survey several network modeling methods and their applicability to precision medicine. We review several network centrality methods (degree centrality, closeness centrality, eccentricity centrality, betweenness…
Data-driven dynamic models of cell biology can be used to predict cell response to unseen perturbations. Recent work (CellBox) had demonstrated the derivation of interpretable models with explicit interaction terms, in which the parameters…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
This study focuses on the task of supervised prediction of aging-related genes from -omics data. Unlike gene expression methods for this task that capture aging-specific information but ignore interactions between genes (i.e., their protein…
Feed-forward loops (FFLs) are among the most ubiquitously found motifs of reaction networks in nature. However, little is known about their stochastic behavior and the variety of network phenotypes they can exhibit. In this study, we…
Living cells sense their environment through the binding of extra-cellular molecular ligands to cell surface receptors. Puzzlingly, vast numbers of signaling pathways exhibit a high degree of cross talk between different signals whereby…
Objective: Human-curated disease ontologies are widely used for diagnostic evaluation, treatment and data comparisons over time, and clinical decision support. The classification principles underlying these ontologies are guided by the…
In this paper we show how inter-cellular molecular communication may change the overall levels of photosynthesis in plants. Individual plant cells respond to external stimuli, such as illumination levels, to regulate their photosynthetic…
Detecting cancers at early stages can dramatically reduce mortality rates. Therefore, practical cancer screening at the population level is needed. Here, we develop a comprehensive detection system to classify all common cancer types. By…
Energy-based modelling brings engineering insight to the understanding of biomolecular systems. It is shown how well-established control engineering concepts, such as loop-gain, arise from energy feedback loops and are therefore amenable to…
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
The statistical analysis of enzyme kinetic reactions usually involves models of the response functions which are well defined on the basis of Michaelis-Menten type equations. The error structure however is often without good reason assumed…
This paper is concerned with a novel method allowing communication between FRET nanonetworks and nerve cells. It is focused on two system components: fluorophores and channelrhodopsins which serve as transmitters and receivers,…
CoV2019 has evolved to be much more dangerous than CoV2003. Experiments suggest that structural rearrangements dramatically enhance CoV2019 activity. We identify a new first stage of infection that precedes structural rearrangements by…
Processing time-dependent information requires cells to quantify the duration of past regulatory events and program the time span of future signals. At the single-cell level, timer mechanisms can be implemented with genetic circuits: sets…
The widespread of Coronavirus has led to a worldwide pandemic with a high mortality rate. Currently, the knowledge accumulated from different studies about this virus is very limited. Leveraging a wide-range of biological knowledge, such as…
We present a symbolic algorithmic approach that allows to compute invariant manifolds and corresponding reduced systems for differential equations modeling biological networks which comprise chemical reaction networks for cellular…
eQuilibrator (equilibrator.weizmann.ac.il) is a calculator for biochemical equilibrium constants and Gibbs free energies, originally designed as a web-based interface. While the website now counts ${\sim}1000$ distinct monthly users, its…
In this study, we have developed a parallel version of the random time simulation algorithm. Firstly, we gave a rigorous basis of the random time description of the stochastic process of chemical reaction network time evolution. And then we…
We consider chemical reaction networks modeled by a discrete state and continuous in time Markov process for the vector copy number of the species and provide a novel particle filter method for state and parameter estimation based on exact…