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Cell counting is a ubiquitous, yet tedious task that would greatly benefit from automation. From basic biological questions to clinical trials, cell counts provide key quantitative feedback that drive research. Unfortunately, cell counting…
Unlike other tissue types, like epithelial tissue, which consist of cells with a much more homogeneous structure and function, the nervous tissue spans in a complex multilayer environment whose topographical features display a large…
A coupled cell network is a model for many situations such as food webs in ecosystems, cellular metabolism, economical networks... It consists in a directed graph $G$, each node (or cell) representing an agent of the network and each…
Ablation studies have been widely used in the field of neuroscience to tackle complex biological systems such as the extensively studied Drosophila central nervous system, the vertebrate brain and more interestingly and most delicately, the…
We address the problem of building theoretical models that help elucidate the function of the visual brain at computational/algorithmic and structural/mechanistic levels. We seek to understand how the receptive fields and topographic maps…
An important part of the analysis of bio-molecular networks is to detect different functional units. Different functions are reflected in a different evolutionary dynamics, and hence in different statistical characteristics of network…
During development, the mammalian brain differentiates into specialized regions with distinct functional abilities. While many factors contribute to functional specialization, we explore the effect of neuronal density on the development of…
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…
We study the problem of explaining a rich class of behavioral properties of deep neural networks. Distinctively, our influence-directed explanations approach this problem by peering inside the network to identify neurons with high influence…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
We investigate cortical learning from the perspective of mechanism design. First, we show that discretizing standard models of neurons and synaptic plasticity leads to rational agents maximizing simple scoring rules. Second, our main result…
This work considers the problem of finding analytical expressions for the expected values of dis- tributed computing performance metrics when the underlying communication network has a complex structure. Through active probing tests a real…
The study of thrombosis is crucial to understand and develop new therapies for diseases like deep vein thrombosis, diabetes related strokes, pulmonary embolism etc. The last two decades have seen an exponential growth in studies related to…
Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…
Network neuroscience is the emerging discipline concerned with investigating the complex patterns of interconnections found in neural systems, and to identify principles with which to understand them. Within this discipline, one…
Cortical networks, in-vitro as well as in-vivo, can spontaneously generate a variety of collective dynamical events such as network spikes, UP and DOWN states, global oscillations, and avalanches. Though each of them have been variously…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
This paper deals with the derivation of a collective model of cell populations out of an individual-based description of the underlying physical particle system. By looking at the spatial distribution of cells in terms of time-evolving…
Two computational models to be used as tools for experimental research on the retinal implant are presented. In the first model, the electric field produced by a multi-electrode array in a uniform retina is calculated. In the second model,…
An astonishingly diverse biomolecular circuitry orchestrates the functioning machinery underlying every living cell. These biomolecules and their circuits have been engineered not only for various industrial applications but also to perform…