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Learning causal relationships from time series data is an important but challenging problem. Existing synthetic datasets often contain hidden artifacts that can be exploited by causal discovery methods, reducing their usefulness for…
Omics technologies enable unbiased investigation of biological systems through massively parallel sequence acquisition or molecular measurements, bringing the life sciences into the era of Big Data. A central challenge posed by such omics…
Motor proteins are key players in intracellular transport processes and biological motion. Theoretical modeling of these systems has been achieved by the use of step processes on one-dimensional lattices. After a comprehensive introduction…
This review was written for the Encyclopedia of Complexity and System Science (Springer-Verlag, Berlin, 2008), and is intended as a guide to the growing literature which approaches the phenomena of cell biology from a more theoretical point…
Understanding large molecular networks consisting of entities such as genes, proteins or RNAs that interact in complex ways to drive the cellular machinery has been an active focus of systems biology. Computational approaches have played a…
The recent advances in cancer immunotherapy boosted the development of tumor-immune system models aiming to provide mechanistic understanding and indicate more efficient treatment regimes. However, the complexity of such models, their…
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…
Multicellular tissues are the building blocks of many biological systems and organs. These tissues are not static, but dynamically change over time. Even if the overall structure remains the same there is a turnover of cells within the…
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…
This thesis is a compendium of research which brings together ideas from the fields of Complex Networks and Computational Neuroscience to address two questions regarding neural systems: 1) How the activity of neurons, via synaptic changes,…
A small but growing number of people are finding interesting parallels between ecosystems as studied by ecologists (think of a Savanna or the Amazon rain forest or a Coral reef) and tumours1-3. The idea of viewing cancer from an ecological…
Cell migration is a fundamental process involved in physiological phenomena such as the immune response and morphogenesis, but also in pathological processes, such as the development of tumor metastasis. These functions are effectively…
The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput…
Phenotype variations define heterogeneity of biological and molecular systems, which play a crucial role in several mechanisms. Heterogeneity has been demonstrated in tumor cells. Here, samples from blood of patients affected from colon…
Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called ribosomes. Although the experimental investigation of protein synthesis has been a traditional area of research in molecular cell…
System dynamics is a popular approach in many fields of science and technology, but it has not been investigated for cell signaling pathways yet. It is a well formulated methodology used to analyze the components of a system considering the…
Background: Tumours are diverse ecosystems with persistent heterogeneity in various cancer hallmarks like self-sufficiency of growth factor production for angiogenesis and reprogramming of energy-metabolism for aerobic glycolysis. This…
The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or…
In this review, we discuss recent advances on the plasticity of cancer stem cells and highlight their relevance to understand the metastatic process and to guide therapeutic interventions. Recent results suggest that the strict hierarchical…
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of…