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Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
Transforming Growth Factor-beta (TGF-beta) signalling is an important regulator of cellular growth and differentiation. The principal intracellular mediators of TGF-beta signalling are the Smad proteins, which upon TGF-beta stimulation…
Crohn's disease is an inflammatory bowel disease (IBD) that is not well understood. In particular, unlike other IBDs, the inflamed parts of the intestine compromise deep layers of the tissue and are not continuous but separated and…
Ligand-receptor interactions constitute a fundamental mechanism of cell-cell communication and signaling. NicheNet is a well-established computational tool that infers ligand-receptor interactions that potentially regulate gene expression…
The Turing pattern model is one type of reaction-diffusion (RD) model. The first identification of pattern formation by the Turing pattern model in an actual animal was made in the 1990s with the observation of patterns in the sea anemone.…
In early development, regulation of transcription results in precisely positioned and highly reproducible expression patterns that specify cellular identities. How transcription, a fundamentally noisy molecular process, is regulated to…
Budding allows virus replication and macromolecular secretion in cells. It involves the formation of a bud, i.e. an outgrowth from the cell membrane that evolves into an envelope. The largest energetic barrier to bud formation is membrane…
Gene regulatory networks (GRNs) play a crucial role in the control of cellular functions. Numerous methods have been developed to infer GRNs from gene expression data, including mechanism-based approaches, information-based approaches, and…
Membrane bending is an extensively studied problem from both modeling and experimental perspectives because of the wide implications of curvature generation in cell biology. Many of the curvature generating aspects in membranes can be…
A theory for qualitative models of gene regulatory networks has been developed over several decades, generally considering transcription factors to regulate directly the expression of other transcription factors, without any intermediate…
Brine channels are formed in sea ice under certain constraints and represent a habitat of different microorganisms. The complex system depends on a number of various quantities as salinity, density, pH-value or temperature. Each quantity…
Branching in vascular networks and in overall organismic form is one of the most common and ancient features of multicellular plants, fungi, and animals. By combining machine-learning techniques with new theory that relates vascular form to…
The dynamics of gene transcription is tightly regulated in eukaryotes. Recent experiments have revealed various kinds of transcriptional dynamics, such as RNA polymerase II pausing, that involves regulation at the transcription initiation…
Understanding biological phenomena requires a systemic approach that incorporates different mechanisms acting on different spatial and temporal scales, since in organisms the workings of all components, such as organelles, cells, and organs…
In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model was recently proposed to explain this scaling for metabolic enzymes and their…
Muscles sense internally generated and externally applied forces, responding to these in a coordinated hierarchical manner at different time scales. The center of the basic unit of the muscle, the sarcomeric M-band, is perfectly placed to…
Traditional top-down robotic design often lacks the adaptability needed to handle real-world complexities, prompting the need for more flexible approaches. Therefore, this study introduces a novel cellular plasticity model tailored for…
We consider here the morphogenesis (pattern formation) problem for some genetic network models. First, we show that any given spatio-temporal pattern can be generated by a genetic network involving a sufficiently large number of genes.…
To evaluate the translational capabilities of foundation models, we develop a pathological concept learning approach focused on kidney cancer. By leveraging TNM staging guidelines and pathology reports, we build comprehensive pathological…
The Gierer-Meinhardt system occurs in morphogenesis, where the development of an organism from a single cell is modelled. One of the steps in the development, is the formation of spatial patterns of the cell structure, starting from an…