Molecular Networks
Arabidopsis root hair patterning is controlled by a complex transcription factor network containing positive and negative feedback loops, epidermal cell-cell signalling, and positional signalling from underlying tissue. Recently, several…
Growth and decay are system-level properties of chemical reaction networks (CRNs) relevant from prebiotic chemistry to cellular metabolism. Their properties are typically analyzed through the kinetics of particular models, which requires…
Boolean networks are a widely used modeling framework in systems biology for studying gene regulation, signal transduction, and cellular decision-making. Empirical studies indicate that biological Boolean networks exhibit a high degree of…
Understanding mechanistic relationships among genes and their impacts on biological pathways is essential for elucidating disease mechanisms and advancing precision medicine. Despite the availability of extensive molecular interaction and…
Biochemical and environmental modeling typically relies on reaction networks to represent complex transformations. While the Linkage Class Decomposition (LCD) partitions networks based on visual standard connectivity, it often misaligns…
We present BSTModelKit.jl, an open-source Julia package for constructing, solving, and analyzing Biochemical Systems Theory (BST) models of biochemical networks. The package implements S-system representations, a canonical power-law…
Morphogenesis is the biological process that causes the emergence and changes of patterns (tissues and organs) in living organisms. It is a robust, self-organising mechanism, governed by Genetic Regulatory Networks (GRN), that hasn't been…
Trigger waves are self-regenerating propagating fronts that emerge from the coupling of nonlinear reaction kinetics and diffusion. In cells, trigger waves coordinate large-scale processes such as mitotic entry and stress responses. Although…
Homeostasis is widely observed in biological systems and refers to their ability to maintain an output quantity approximately constant despite variations in external disturbances. Mathematically, homeostasis can be formulated through an…
Mass-action networks are special cases of chemical reaction networks. For these systems, we argue that conserved quantities are dual to internal cycles. We introduce maximal invariant polyhedral supports, and we conjecture that there is a…
Building on the phenomenological and microscopic models reviewed in Part I, this second part focuses on network-level mechanisms that generate emergent temperature response curves. We review deterministic models in which temperature…
Genetic interactions and protein co-dependencies shape cellular fitness, buffering capacity, and disease vulnerability. However, systematic integration of co-dependency relationships across heterogeneous datasets remains limited. Here, we…
Benchmark rankings are routinely used to justify scientific claims about method quality in gene regulatory network (GRN) inference, yet the stability of these rankings under plausible evaluation protocol choices is rarely examined. We…
Biological systems operate under persistent noise, which can alter system states and induce transitions between attractors. Here, we study the attractor dynamics of Boolean networks focusing on the transitions between attractors induced by…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
In this Master's thesis, the graph properties of a multi-level drug-protein network are studied, as well as how the network's shape has informed discoveries over the years, identifying primarily crawling discoveries and a smaller number of…
We have developed URDME, a general software for simulation of stochastic reaction-diffusion processes on unstructured meshes. This allows for a more flexible handling of complicated geometries and curved boundaries compared to simulations…
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
We obtain bounds on the Kullback--Leibler divergence to equilibrium for mass-action chemical reaction networks (CRNs) with equilibrium. The associated decay rates are characterized in terms of the singular values of the stoichiometric…
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…