Collective behaviour in living systems is observed across many scales, from bacteria to insects, to fish shoals. Zebrafish have emerged as a model system amenable to laboratory study. Here we report a three-dimensional study of the collective dynamics of fifty zebrafish. We observed the emergence of collective behaviour changing between \yy{ordered...
Published in PLoS Computational Biology
Genome-wide association studies, which study the association between genetic variants and various phenotypes, typically rely on genotyping arrays. Only a small proportion of genetic variants within the genome are typed on genotyping arrays. Untyped variants are statistically inferred through a process known as genotype imputation, where correlation...
Published in PLoS computational biology
Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families. Does successful inference mainly rely on correlations from structural contacts or from phylo...
Published in PLoS computational biology
Proteins are typically represented by discrete atomic coordinates providing an accessible framework to describe different conformations. However, in some fields proteins are more accurately represented as near-continuous surfaces, as these are imprinted with geometric (shape) and chemical (electrostatics) features of the underlying protein structur...
Published in PLoS computational biology
While campaigns of vaccination against SARS-CoV-2 are underway across the world, communities face the challenge of a fair and effective distribution of a limited supply of doses. Current vaccine allocation strategies are based on criteria such as age or risk. In the light of strong spatial heterogeneities in disease history and transmission, we exp...
Published in PLoS Computational Biology
The ability to form memories and recall them is one of the fascinating features of our brain. Working memory operates like a memory scratch pad storing ongoing information for further processing. Here, we present a computational model dissecting the influence of astrocytes on the stability and duration of working memories. We find that a long astro...
Published in PLoS Computational Biology
Published in PLoS computational biology
Neural circuits consist of many noisy, slow components, with individual neurons subject to ion channel noise, axonal propagation delays, and unreliable and slow synaptic transmission. This raises a fundamental question: how can reliable computation emerge from such unreliable components? A classic strategy is to simply average over a population of ...
Published in PLoS Computational Biology
How do animals see the world? This is particularly an interesting question when the animal’s eyes look very different from our own, or if they inhabit an environment that is visually very different from ours. Biologists approach this question by seeking to determine not only how animal eyes function but also what selective pressures led to the evol...
Published in PLoS computational biology
