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Process Mining offers a powerful framework for uncovering, analyzing, and optimizing real-world business processes. Petri nets provide a versatile means of modeling process behavior. However, traditional methods often struggle to…
Blood coagulation is governed by tightly regulated reaction networks that unfold within a flowing, heterogeneous microvascular environment. Reduced kinetic models of the intrinsic and extrinsic pathways have seen limited in vitro…
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…
Cancer is a complex disease that is characterized by uncontrolled growth and division of cells. It involves a complex interplay between genetic and environmental factors that lead to the initiation and progression of tumors. Recent advances…
Positron Emission Tomography (PET) /Computed Tomography (CT) is crucial for diagnosing, managing, and planning treatment for various cancers. Developing reliable deep learning models for the segmentation of tumor lesions in PET/CT scans in…
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…
Angiogenesis is a key process in the tumoral growth which allows the cancerous tissue to impact on its vasculature in order to improve the nutrient's supply and the metastatic process. In this paper, we introduce a model for the density of…
In this work, we review previously developed coarse-grained (CG) particle models for biological membrane and red blood cells (RBCs) and discuss the advantages of the CG particle method over the continuum and atomic simulations on modeling…
The ability to locally degrade the extracellular matrix (ECM) and interact with the tumour microenvironment is a key process distinguishing cancer from normal cells, and is a critical step in the metastatic spread of the tumour. The…
The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is therefore of critical importance for gaining systems-level…
Cell spreading is investigated at various scales in order to understand motility of living cells which is essential for a range of physiological activities in higher organisms as well as in microbes. At a microscopic scale, it has been seen…
Carcinogenesis is a proteiform phenomenon, with tumors emerging in various locations and displaying complex, diverse shapes. At the crucial intersection of research and clinical practice, it demands precise and flexible assessment. However,…
The morphogenesis of cells and tissues involves an interplay between chemical signals and active forces on their surrounding surface layers. The complex interaction of hydrodynamics and material flows on such active surfaces leads to…
This study introduces an open-source computational framework for the generation and permeability evaluation of synthetic porous media. The proposed methodology integrates crystallographic and meshing tools to construct controlled…
Convergent extension of epithelial tissue is a key motif of animal morphogenesis. On a coarse scale, cell motion resembles laminar fluid flow; yet in contrast to a fluid, epithelial cells adhere to each other and maintain the tissue layer…
Oncolytic virotherapy is an experimental cancer treatment that uses genetically engineered viruses to target and kill cancer cells. One major limitation of this treatment is that virus particles are rapidly cleared by the immune system,…
Cell-penetrating peptides (CPPs) such as HIV's trans-activating transcriptional activator (TAT) and polyarginine rapidly pass through the plasma membranes of mammalian cells by an unknown mechanism called transduction. They may be medically…
We present a fully automated, anatomically guided deep learning pipeline for prostate cancer (PCa) risk stratification using routine MRI. The pipeline integrates three key components: an nnU-Net module for segmenting the prostate gland and…
Risk evaluation to identify individuals who are at greater risk of cancer as a result of heritable pathogenic variants is a valuable component of individualized clinical management. Using principles of Mendelian genetics, Bayesian…
We propose a multiscale model of the invasion of the extracellular matrix by two types of cancer cells, the differentiated cancer cells and the cancer stem cells. We assume that the epithelial mesenchymal-like transition between them is…