Related papers: Deciphering cell signaling rewiring in human disor…

Various biological phenomena, like cell differentiation and pattern formation in multicellular organisms, are explained using the bifurcation theory. Molecular network motifs like positive feedback and mutual repressor exhibit bifurcation…

In multicellular organisms, epithelial cells form layers separating compartments responsible for different physiological functions. At the early stage of epithelial layer formation, each cell of an aggregate defines an inner and an outer…

Due to structural and functional abnormalities or genetic variations and mutations, there may be dysfunctional molecules within an intracellular signaling network that do not allow the network to correctly regulate its output molecules,…

Cell tracking is a key computational task in live-cell microscopy, but fully automated analysis of high-throughput imaging requires reliable and, thus, uncertainty-aware data analysis tools, as the amount of data recorded within a single…

Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…

Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities encoded in patterns of association among microbial gene…

We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a…

Recent developments in synthetic biology, next-generation sequencing, and machine learning provide an unprecedented opportunity to rationally design new disease treatments based on measured responses to gene perturbations and drugs to…

Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multi-dimensional information from…

Collective oscillation of cells in a population has been reported under diverse biological contexts and with vastly different molecular constructs. Could there be common principles similar to those that govern spontaneous oscillation in…

This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…

Biological cells encode information about their environment through biochemical signaling networks that control their internal state and response. This information is often encoded in the dynamical patterns of the signaling molecules,…

The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and…

Signaling molecules play an important role for many cellular functions. We investigate here a general system of two membrane reaction-diffusion equations coupled to a diffusion equation inside the cell by a Robin-type boundary condition and…

A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…

A dynamic model for failures in biological organisms is proposed and studied both analytically and numerically. Each cell in the organism becomes dead under sufficiently strong stress, and is then allowed to be healed with some probability.…

Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…

Cancer is a complex disease driven by dynamic regulatory shifts that cannot be fully captured by individual molecular profiling. We employ a data-driven approach to construct a coarse-grained dynamic network model based on hallmark…

A coupled map is suggested to investigate various spatial or temporal designs in biology: Several cells (or tissues) in an organ are considered as connected to each other in terms of some molecular diffusions or electrical potential…

Recent advances in high-resolution experimental methods have highlighted the significance of cell signal pathway crosstalk and localised signalling activity in the development and disease of numerous biological systems. The investigation of…