分子网络
Perturbations are ubiquitous in metabolism. A central tool to understand and control their influence on metabolic networks is sensitivity analysis, which investigates how the network responds to external perturbations. We follow here a…
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…
Analysis of the structure of biological networks often uses statistical tests to establish the over-representation of motifs, which are thought to be important building blocks of such networks, related to their biological functions.…
Background: Network propagation has been widely used for nearly 20 years to predict gene functions and phenotypes. Despite the popularity of this approach, little attention has been paid to the question of provenance tracing in this…
While the analytical solution for the marginal distribution of a stochastic chemical reaction network has been extensively studied, its joint distribution, i.e. the solution of a high-dimensional chemical master equation, has received much…
The 2019 coronavirus disease (COVID-19) became a worldwide pandemic with currently no effective antiviral drug except treatments for symptomatic therapy. Flux balance analysis is an efficient method to analyze metabolic networks. It allows…
Genetic circuit design is a well-studied problem in synthetic biology. Ever since the first genetic circuits -- the repressilator and the toggle switch -- were designed and implemented, many advances have been made in this area of research.…
Stability is a key ingredient of protein fitness and its modification through targeted mutations has applications in various fields such as protein engineering, drug design and deleterious variant interpretation. Many studies have been…
Background:Gene regulations often change over time rather than being constant. But many of gene regulatory networks extracted from databases are static. The tumor suppressor gene $P53$ is involved in the pathogenesis of many tumors, and its…
Causal gene networks model the flow of information within a cell, but reconstructing them from omics data is challenging because correlation does not imply causation. Combining genomics and transcriptomics data from a segregating population…
Magombedze and Mulder (2013) studied the gene regulatory system of \textit{Mycobacterium Tuberculosis} (\textit{Mtb}) by partitioning this into three subsystems based on putative gene function and role in dormancy/latency development. Each…
The automated assembly and extension of dynamic network models using information extracted from literature are challenging due to the amount and inconsistency in published literature. Recently, efforts have been made to automatically and…
Models of transcriptional regulation that assume equilibrium binding of transcription factors have been very successful at predicting gene expression from sequence in bacteria. However, analogous equilibrium models do not perform as well in…
Gene expression is a fundamental process in a living system. The small RNAs (sRNAs) is widely observed as a global regulator in gene expression. The inherent nonlinearity in this regulatory process together with the bursty production of…
COPASI is a popular application for simulation and analysis of biochemical networks and their dynamics. While this software is widely used, it works as a standalone application and until now it was not possible for users to interact with…
The well-known issue of reconstructing regulatory networks from gene expression measurements has been somewhat disrupted by the emergence and rapid development of single-cell data. Indeed, the traditional way of seeing a gene regulatory…
We present an information-theoretic formalism to study signal transduction in four architectural variants of a model two-step cascade with increasing input population. Our results categorize these four types into two classes depending upon…
Drug resistance and metastasis - the major complications in cancer - both entail adaptation of cancer cells to stress, whether a drug or a lethal new environment. Intriguingly, these adaptive processes share similar features that cannot be…
The vulnerability of networks to targeted attacks is an issue of widespread interest for policymakers, military strategists, network engineers and systems biologists alike. Current approaches to circumvent targeted attacks seek to increase…
Network alignment aims to uncover topologically similar regions in the protein-protein interaction (PPI) networks of two or more species under the assumption that topologically similar regions tend to perform similar functions. Although…