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Glioblastoma (GBM) is a highly morbid and lethal disease with poor prognosis. Their emergent properties such as cellular heterogeneity, therapy resistance, and self-renewal are largely attributed to the interactions between a subset of…
Phylogenetics is a widely used concept in evolutionary biology. It is the reconstruction of evolutionary history by building trees that represent branching patterns and sequences. These trees represent shared history, and it is our…
In agricultural landscapes, the composition and spatial configuration of cultivated and semi-natural elements strongly impact species dynamics, their interactions and habitat connectivity. To allow for landscape structural analysis and…
Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…
Gene Regulatory Network (GRN) plays an important role in knowing insight of cellular life cycle. It gives information about at which different environmental conditions genes of particular interest get over expressed or under expressed.…
Phyllotaxis describes the arrangement of florets, scales or leaves in composite flowers or plants (daisy, aster, sunflower, pinecone, pineapple). As a structure, it is a geometrical foam, the most homogeneous and densest covering of a large…
This paper deals with a model of cellular growth called "Epigenetic Tracking", whose key features are: i) distinction bewteen "normal" and "driver" cells; ii) presence in driver cells of an epigenetic memory, that holds the position of the…
Understanding which genes control which traits in an organism remains one of the central challenges in biology. Despite significant advances in data collection technology, our ability to map genes to traits is still limited. This…
Phyllotactic patterns, i.e. regular arrangements of leaves or seeds around a plant stem, are fascinating examples of complex structures encountered in Nature. In botany, their symmetries develop when a new primordium periodically grows in…
Constructing cell developmental trajectories is a critical task in single-cell RNA sequencing (scRNA-seq) analysis, enabling the inference of potential cellular progression paths. However, current automated methods are limited to…
Communicating cells can coordinate their gene expressions to form spatial patterns. 'Secrete-and-sense cells' secrete and sense the same molecule to do so and are ubiquitous. Here we address why and how these cells, from disordered…
Plant morphogenesis relies on dynamic growth deformations at the cell and tissue scales driven by osmotic fluxes. A mechanistic understanding of this phenomenon demands a physical framework that integrates cell imbibition, tissue mechanics,…
Predicting the responses of a cell under perturbations may bring important benefits to drug discovery and personalized therapeutics. In this work, we propose a novel graph variational Bayesian causal inference framework to predict a cell's…
Networks in machine learning offer examples of complex high-dimensional dynamical systems reminiscent of biological systems. Here, we study the learning dynamics of Generalized Hopfield networks, which permit a visualization of internal…
Genomics methods have uncovered patterns in a range of biological systems, but obscure important aspects of cell behavior: the shape, relative locations of, movement of, and interactions between cells in space. Spatial technologies that…
We analyse a large data set of genetic markers obtained from populations of Cymodocea nodosa, a marine plant occurring from the East Mediterranean to the Iberian-African coasts in the Atlantic Ocean. We fully develop and test a recently…
We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…
Mechanical interactions among cells in a growing microbial colony can significantly influence the colony's spatial genetic structure and, thus, evolutionary outcomes such as the fates of rare mutations. Here, we computationally investigate…
Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…
The delimitation of bioregions helps to understand historical and ecological drivers of species distribution. In this work, we performed a network analysis of the spatial distribution patterns of plants in south of France…