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We propose a novel computational framework leveraging hypergraph theory to analyse cancer stem cell markers (CSCMs) across multiple organs. Hypergraphs provide a robust representation of CSCM co-expression patterns, capturing their complex…
Mechanical cues from the extracellular microenvironment play a central role in regulating the structure, function and fate of living cells. Nevertheless, the precise nature of the mechanisms and processes underlying this crucial cellular…
Cancer cells possess a nearly universal set of characteristics termed the hallmarks of cancer, including replicative immortality and resisting cell death. Dysregulated differentiation is present in virtually all cancers yet has not yet been…
Identifying concentrations of components from an observed mixture is a fundamental problem in signal processing. It has diverse applications in fields ranging from hyperspectral imaging to denoising biomedical sensors. This paper focuses on…
Understanding the mechanisms by which cells coordinate their size with their ability to divide has long attracted the interest of biologists. The Target of Rapamycin (TOR) pathway is becoming increasingly recognized as a master regulator of…
Cell competition in multicellular organisms has been shown to play a critical role during the development of organisms, cancer progression, and in the establishment and maintenance of tissue homeostasis. Various mechanisms of cell…
Phase I dose-finding trials in oncology seek to find the maximum tolerated dose (MTD) of a drug under a specific schedule. Evaluating drug-schedules aims at improving treatment safety while maintaining efficacy. However, while we can…
Fission yeast G2/M transition is regulated by a biochemical reaction networks which contains four components: Cdc13, Cdc2, Wee1, and Cdc25. This circuit is characterized by the ultrasensitive responses of Wee1 or Cdc25 to Cdc13/Cdc2…
Biological systems perform an astonishing array of dynamical processes -- including development and repair, regulation, behavior and motor control, sensing and signaling, and adaptation, among others. Powered by the transduction of stored…
Cancer is a disease driven by random DNA mutations and the interaction of many complex phenomena. To improve the understanding and ultimately find more effective treatments, researchers leverage computer simulations mimicking the tumor…
Heteroclinic cycles are widely used in neuroscience in order to mathematically describe different mechanisms of functioning of the brain and nervous system. Heteroclinic cycles and interactions between them can be a source of different…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
An endogenous molecular-cellular network for both normal and abnormal functions is assumed to exist. This endogenous network forms a nonlinear stochastic dynamical system, with many stable attractors in its functional landscape. Normal or…
Biological organisms are simple at heart: cells, their basic units, perform a variety of behaviors by expressing proteins from DNA-encoded genes. Gene expression though depends on sets of often-convoluted regulatory interactions known as…
We study the role of active coupling on the transport properties of homogeneously charged macromolecules in an infinitely dilute solution. An enzyme becomes actively bound to a segment of the macromolecule, exerting an electrostatic force…
Cell neighbor exchanges are integral to tissue rearrangements in biology, including development and repair. Often these processes occur via topological T1 transitions analogous to those observed in foams, grains and colloids. However, in…
Cancer stem cells are controlled by developmental networks that are often topologically indistinguishable from normal, healthy stem cells. The question is why cancer stem cells can be both phenotypically distinct and have morphological…
Cancer research has traditionally focused on identifying driver genes, those with mutations that initiate tumorigenesis. The Cancer Driver Gene (CDG) paradigm, further supported by the observation of oncogene addiction in tumors, has…
The azide-alkyne Huisgen cycloaddition has a key role in click chemistry and configures as powerful tool in pharmaceutical and medicinal chemistry. Although this reaction has already been largely studied, there is an ongoing debate about…
Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukayotic cells,…