Molecular Networks
This review examines current and potential applications of DTs in healthcare, focusing on the integration of multi-omics data using multilayer network approaches in cancer research. We discuss methodologies, tools and platforms commonly…
The parameter region of multistationarity of a reaction network contains all the parameters for which the associated dynamical system exhibits multiple steady states. Describing this region is challenging and remains an active area of…
Previous work in Boolean dynamical networks has suggested that the number of components that must be controlled to select an existing attractor is typically set by the number of attractors admitted by the dynamics, with no dependence on the…
Asynchronous Boolean networks are a type of discrete dynamical system in which each variable can take one of two states, and a single variable state is updated in each time step according to pre-selected rules. Boolean networks are popular…
Identifying driver genes is crucial for understanding oncogenesis and developing targeted cancer therapies. Driver discovery methods using protein or pathway networks rely on traditional network science measures, focusing on nodes, edges,…
The equilibration of enzyme and complex concentrations in deterministic Michaelis-Menten reaction networks underlies the hyperbolic dependence between the input (substrates) and output (products). This relationship was first obtained by…
Irreversibility, in which a transient perturbation leaves a system in a new state, is an emergent property in systems of interacting entities. This property has well-established implications in statistical physics but remains underexplored…
Incomplete knowledge of metabolic processes hinders the accuracy of GEnome-scale Metabolic models (GEMs), which in turn impedes advancements in systems biology and metabolic engineering. Existing gap-filling methods typically rely on…
The in vivo circadian clock in single cyanobacteria is studied here by time-lapse fluorescence microscopy when the temperature is lowered below 25{\deg}C . We first disentangle the circadian clock behavior from the bacterial cold shock…
Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field…
Molecular communication (MC) within the synaptic cleft is vital for neurotransmitter diffusion, a process critical to cognitive functions. In Alzheimer's Disease (AD), beta-amyloid oligomers (A$\beta$os) disrupt this communication, leading…
The first passage time (FPT) is a generic measure that quantifies when a random quantity reaches a specific state. We consider the FTP distribution in nonlinear stochastic biochemical networks, where obtaining exact solutions of the…
The Hill function is relevant for describing enzyme binding and other processes in gene regulatory networks. Despite its theoretical foundation, it is often empirically used as a useful fitting function. Theoretical predictions suggest that…
Motif discovery is a powerful and insightful method to quantify network structures and explore their function. As a case study, we present a comprehensive analysis of regulatory motifs in the connectome of the model organism Caenorhabditis…
Recent studies suggest that drug-drug interaction (DDI) prediction via computational approaches has significant importance for understanding the functions and co-prescriptions of multiple drugs. However, the existing silico DDI prediction…
Steady state nonmonotonic ("biphasic") dose responses are often observed in experimental biology, which raises the control-theoretic question of identifying which possible mechanisms might underlie such behaviors. It is well known that the…
Fluctuations are inherent to biological systems, arising from the stochastic nature of molecular interactions, and influence various aspects of system behavior, stability, and robustness. These fluctuations can be categorized as intrinsic,…
Describing reaction rates in stochastic bio-circuits is commonly done by directly introducing the deterministically deduced Hill function into the master equation. However, when fluctuations in enzymatic reaction rates are not neglectable,…
The biological targets of traditional Chinese medicine (TCM) are the core effectors mediating the interaction between TCM and the human body. Identification of TCM targets is essential to elucidate the chemical basis and mechanisms of TCM…
Gene expression prediction plays a vital role in transcriptome-wide association studies (TWAS), which seek to establish associations between tissue gene expression and complex traits. Traditional models rely on genetic variants in close…