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The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…
Affective computing plays a key role in human-computer interactions, entertainment, teaching, safe driving, and multimedia integration. Major breakthroughs have been made recently in the areas of affective computing (i.e., emotion…
A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…
The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological…
Cell state discovery is crucial for understanding biological systems and enhancing medical outcomes. A key aspect of this process is identifying distinct biomarkers that define specific cell states. However, difficulties arise from the…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
At present it is still quite difficult to match the vast knowledge on the behavior of individual tumor cells with macroscopic measurements on clinical tumors. On the modeling side, we already know how to deal with many molecular pathways…
The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, where a whole macromolecule is represented by a small number of particles, can be of…
For constructing neuronal network models computational neuroscientists have access to wide-ranging anatomical data that nevertheless tend to cover only a fraction of the parameters to be determined. Finding and interpreting the most…
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…
Living soft tissues appear to promote the development and maintenance of a preferred mechanical state within a defined tolerance around a so-called set-point. This phenomenon is often referred to as mechanical homeostasis. In contradiction…
It is important to understand the coordinated performance of cells in tissue. One possible mechanism in this coordination involves intracellular calcium signaling. The topology of intercellular connections in tissue should also play an…
Transcriptome foundation models TFMs hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling…
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…
Cell cell and cell matrix adhesions are fundamental in all multicellular organisms. They play a key role in cellular growth, differentiation, pattern formation and migration. Cell-cell adhesion is substantial in the immune response,…
Exploring the structural topology of genome-based large-scale metabolic network is essential for investigating possible relations between structure and functionality. Visualization would be helpful for obtaining immediate information about…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…
Feature selection techniques are essential for high-dimensional data analysis. In the last two decades, their popularity has been fuelled by the increasing availability of high-throughput biomolecular data where high-dimensionality is a…