Related papers: Bridging physiological and evolutionary time scale…
Segmentation in arthropod embryogenesis represents a well-known example of body plan diversity. Striped patterns of gene expression that lead to the future body segments appear simultaneously or sequentially in long and short germ-band…
In the context of global warming, tree populations rely on two primary mechanisms of adaptation: phenotypic plasticity, which enables individuals to adjust their behavior in response to environmental stress, and genetic evolution, driven by…
Climate change is reshaping species interactions and movement across fragmented landscapes. Despite this, most mathematical models assume random diffusion, overlooking the influence of directed movement. Here, we develop a graph based…
Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in…
Gene regulation is central to understanding cellular processes and development, potentially leading to the discovery of new treatments for diseases and personalized medicine. Inferring gene regulatory networks (GRNs) from single-cell RNA…
We have introduced a novel multiplex recurrence network (MRN) approach by combining recurrence networks with the multiplex network approach in order to investigate multivariate time series. The potential use of this approach is demonstrated…
Random Boolean networks (RBNs) are frequently employed for modelling complex systems driven by information processing, e.g. for gene regulatory networks (GRNs). Here we propose a hierarchical adaptive RBN (HARBN) as a system consisting of…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
Positive selection drives the emergence of adaptive mutations in Mycobacterium tuberculosis, shaping drug resistance, transmissibility, and virulence. Phylogenetic trees capture evolutionary relationships among isolates and provide a…
In this research, we study biological networks at different scales: a gene autoregulatory network at the single-cell level and the gut microbiota at the population level. Proteins are the main actors in cells, they are the building blocks,…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. They also tend to have broad distributions for the out-degree. What mechanisms might be responsible for these…
Evolutionary algorithms (EAs) simulate natural selection but have two main limitations: (1) they rarely update individuals based on global correlations, limiting comprehensive learning; (2) they struggle with balancing exploration and…
The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics…
Tuning curves characterizing the response selectivities of biological neurons often exhibit large degrees of irregularity and diversity across neurons. Theoretical network models that feature heterogeneous cell populations or random…
The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
Understanding causal relationships within Gene Regulatory Networks (GRNs) is essential for unraveling the gene interactions in cellular processes. However, causal discovery in GRNs is a challenging problem for multiple reasons including the…
Correct inference of genetic regulations inside a cell is one of the greatest challenges in post genomic era for the biologist and researchers. Several intelligent techniques and models were already proposed to identify the regulatory…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
Modelling genetic phenomena affecting biological traits is important for the development of agriculture as it allows breeders to predict the potential of breeding for certain traits. One such phenomenon is heterosis or hybrid vigor:…