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Precise molecular subtyping of gliomas, including isocitrate dehydrogenase (IDH) mutation and 1p/19q codeletion, directly guides surgical and therapeutic decisions, yet currently relies on invasive tissue sampling. Deep learning on…
In this paper, we investigate a mathematical model describing the interactions between effector cells (E), cancer cells (T), and the IL-2 compound (IL). The model considered here is a generalization, taking into account some cross-diffusion…
Background The epidermal growth factor receptor (EGFR) is frequently overexpressed in many cancers, including non-small cell lung cancer (NSCLC). In silcio modeling is considered to be an increasingly promising tool to add useful insights…
The interactions between tumor cells and the tumor microenvironment (TME) dictate therapeutic efficacy of radiation and many systemic therapies in breast cancer. However, to date, there is not a widely available method to reproducibly…
Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…
Using a novel modeling approach based on the so-called environmental stress level (ESL), we develop a mathematical model to describe systematically the collective influence of oxygen concentration and stiffness of the extracellular matrix…
Feedback is ubiquitous in both biological and engineered control systems. In biology, in addition to typical feedback between plant and controller, we observe feedback pathways within control systems, which we call internal feedback…
We study variants of hierarchical modular network models suggested by Kaiser and Hilgetag [Frontiers in Neuroinformatics, 4 (2010) 8] to model functional brain connectivity, using extensive simulations and quenched mean-field theory (QMF),…
Many kinase inhibitors have been approved as cancer therapies. Recently, libraries of kinase inhibitors have been extensively profiled, thus providing a map of the strength of action of each compound on a large number of its targets. These…
In this paper, we build a model for biological neural nets where the activity of the network is described by Hawkes processes having a variable length memory. The particularity of this paper is to deal with an infinite number of components.…
In cell proliferation, stem cell differentiation, chemoresistance and tissue organization, the ubiquitous role of YAP/TAZ continues to impact our fundamental understanding in numerous physiological and disease systems. YAP/TAZ is an…
In the study of therapeutic strategies for the treatment of cancer, eco-evolutionary dynamics are of particular interest, since characteristics of the tumour population, interaction with the environment and effects of the treatment,…
We propose a consistency model based on the optimal-transport flow. A physics-informed design of partially input-convex neural networks (PICNN) plays a central role in constructing the flow field that emulates the displacement…
We introduce a model of percolation induced by disorder, where an initially homogeneous network with links of equal weight is disordered by the introduction of heterogeneous weights for the links. We consider a pair of nodes i and j to be…
In a recent paper, Wilmes et al. demonstrated a qualitative integration of omics data streams to gain a mechanistic understanding of cyclosporine A toxicity. One of their major conclusions was that cyclosporine A strongly activates the…
Nonlinear systems driven by recurrent signals are known to exhibit complex dynamical responses which, in the physiological context, can have important functional consequences. One of the simplest biological systems that is exposed to such…
The network representation is becoming increasingly popular for the description of cardiovascular interactions based on the analysis of multiple simultaneously collected variables. However, the traditional methods to assess network links…
Cancer invasion and metastasis depend on angiogenesis. The cellular processes (growth, migration, and apoptosis) that occur during angiogenesis are tightly regulated by signaling molecules. Thus, understanding how cells synthesize multiple…
Tumors are extremely heterogeneous and comprise of a number of intratumor microenvironments or sub-regions. These tumor microenvironments may interact with eac based on complex high-level relationships, which could provide important insight…
Cellular signaling involves the transmission of environmental information through cascades of stochastic biochemical reactions, inevitably introducing noise that compromises signal fidelity. Each stage of the cascade often takes the form of…