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Identifying driver genes is crucial for understanding oncogenesis and developing targeted cancer therapies. Driver discovery methods using protein or pathway networks rely on traditional network science measures, focusing on nodes, edges,…
The genomic evolution inherent to cancer relates directly to a renewed focus on the voluminous next generation sequencing (NGS) data, and machine learning for the inference of explanatory models of how the (epi)genomic events are…
The influence of nitrogen incorporation on the energy distribution of interface states in the (100)Si/HfO2 system and their passivation by hydrogen have been studied. The results are compared to those of nominally N-free samples. The…
Predicting user influence in social networks is a critical problem, and hypergraphs, as a prevalent higher-order modeling approach, provide new perspectives for this task. However, the absence of explicit cascade or infection probability…
Compartmental epidemic models, grounded in mass-action kinetics, often assume homogeneous mixing. Although this neglects network structure, recent results show that for Poisson random graphs, the classical SIR model, especially the…
Cancer is a highly heterogeneous disease with significant variability in molecular features and clinical outcomes, making diagnosis and treatment challenging. In recent years, high-throughput omic technologies have facilitated the discovery…
Real-world systems, ranging from social and biological to infrastructural, can be modeled by multilayer networks. Promoting spreading dynamics in multilayer networks may significantly facilitate electronic advertising and predicting popular…
We formulate the dynamical model for the anti-tumor immune response based on intercellular cytokine-mediated interactions with the interleukin-2 (IL-2) taken into account. The analysis shows that the expression level of tumor antigens on…
Integrin signaling regulates cell migration and plays a pivotal role in developmental processes and cancer metastasis. Integrin signaling has been studied extensively and much data is available on pathway components and interactions. Yet…
Ionic liquid (IL) gating has emerged as a powerful tool to control the structural, electronic, optical, and magnetic properties of materials by driving ion motion at solid interfaces. In magneto-ionic systems, electric fields are used to…
Artificial neural networks (ANNs) have been extensively used for the description of problems arising from biological systems and for constructing neuromorphic computing models. The third generation of ANNs, namely, spiking neural networks…
Notch signaling is an evolutionary conserved cell-cell communication pathway. Besides regulating cell-fate decisions at an individual cell level, Notch signaling coordinates the emergent spatiotemporal patterning in a tissue through…
We consider the criticality for firing structures of a simplified integrate-and-fire neural model on the regular network, small-world network, and random networks. We simplify an integrate-and-fire model suggested by Levina, Herrmann and…
We propose and study a strongly coupled PDE-ODE system with tissue-dependent degenerate diffusion and haptotaxis that can serve as a model prototype for cancer cell invasion through the extracellular matrix. We prove the global existence of…
The classical Hodgkin--Huxley (HH) model neglects the time-dependence of ion concentrations in spiking dynamics. The dynamics is therefore limited to a time scale of milliseconds, which is determined by the membrane capacitance multiplied…
Cold atmospheric plasma (CAP) and plasma-treated liquids (PTLs) have recently become a promising option for cancer treatment, but the underlying mechanisms of the anti-cancer effect are still to a large extent unknown. Although hydrogen…
Intracellular networks process cellular-level information and control cell fate. They can be computationally modeled using Boolean networks, which are implicit-time causal models of discrete binary events. These networks can be embedded in…
Signaling networks are designed to sense an environmental stimulus and adapt to it. We propose and study a minimal model of signaling network that can sense and respond to external stimuli of varying strength in an adaptive manner. The…
Tumor angiogenesis concerns the development of new blood vessels supplying the necessary nutrients for the further development of existing tumor cells. The entire process is complex, involving the production and consumption of chemicals,…
Low-energy light ion beams are an essential resource in lithography for nanopatterning magnetic materials and interfaces due to their ability to modify the structure and properties of metamaterials. Here we create…