Related papers: Complementing cell taxonomies with a multicellular…
In this paper, we derive an effective macroscale description suitable to describe the growth of biological tissue within a porous tissue-engineering scaffold. As in our recent work (Holden \textit{et al.} "A multiphase multiscale model for…
Xenium, a new spatial transcriptomics platform, enables subcellular-resolution profiling of complex tumor tissues. Despite the rich morphological information in histology images, extracting robust cell-level features and integrating them…
Heterogeneous, interconnected, systems-level, molecular data have become increasingly available and key in precision medicine. We need to utilize them to better stratify patients into risk groups, discover new biomarkers and targets,…
Tissue engineering aims to grow artificial tissues \emph{in vitro} to replace those in the body that have been damaged through age, trauma or disease. A recent approach to engineer artificial cartilage involves seeding cells within a…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
This paper deals with the derivation of a collective model of cell populations out of an individual-based description of the underlying physical particle system. By looking at the spatial distribution of cells in terms of time-evolving…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
Bio-digital systems that merge microbial life with technology promise new modes of computation, combining biological adaptability with digital precision. Yet realizing this potential symbiotically -- where biological and digital agents…
Biological systems across various length and time scales are noisy, including tissues. Why are biological tissues inherently chaotic? Does heterogeneity play a role in determining the physiology and pathology of tissues? How do physical and…
The tumor microenvironment (TME) is a spatially heterogeneous ecosystem where cellular interactions shape tumor progression and response to therapy. Multiplexed imaging technologies enable high-resolution spatial characterization of the…
This thesis (extended abstract) presents the software development efforts toward efficient exploitation of heterogeneity through intricate mapping of computational kernels, collaborative execution of multiple processing elements and…
We investigate the use of hybrid techniques in complex processes of infectious diseases. Since predictive disease models in biomedicine require a multiscale approach for understanding the molecule-cell-tissue-organ-body interactions,…
Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. Understanding the cybernetics of cancer requires…
For the first time the phenomenon of cellular structure coarsening are consistently analysed from the positions of kinetic, hydrodynamic and stochastodynamic theories of nonequilibrium statistical systems. Thereby micro-, meso- and…
Spatially-resolved omics-data enable researchers to precisely distinguish cell types in tissue and explore their spatial interactions, enabling deep understanding of tissue functionality. To understand what causes or deteriorates a disease…
Empirical studies of graphs have contributed enormously to our understanding of complex systems. Known today as network science, what was originally a theoretical study of graphs has grown into a more scientific exploration of communities…
There is an unmet need for artificial intelligence techniques that can speed up the design of growth strategies for cultured tissues. Cultured tissue is increasingly important for a range of applications such as cultivated meat,…
Determining the trajectories of cells and their lineages or ancestries in live-cell experiments are fundamental to the understanding of how cells behave and divide. This paper proposes novel online algorithms for jointly tracking and…
In this paper, we extend previous work on the mathematical modeling of oxygen transport in biological tissues (Matzavinos et al., 2009). Specifically, we include in the modeling process the arterial and venous microstructure within the…
Intracellular transport processes are essential to the healthy development of many organisms as well as more generally to healthy cellular function. The complex dynamics and interactions between protein molecules and filaments on different…