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
Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the transcriptome using RNA-sequencing (RNA-seq). Paradoxically, these variants between the samples are usually ignor...
Published in PLoS Computational Biology
The development of vaccines has sparked high hopes towards the control of SARS-CoV-2 transmission without resorting to extensive community-wide restrictions. A fundamental unanswered question concerns the best possible allocation of a limited vaccine stock in space and time given a specific goal. We address this through an optimal control framework...
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
This work introduces a method that combines the singular value decomposition (SVD) with Archetypal Analysis to perform fast and accurate genetic clustering by first reducing the dimensionality of the space of genomic sequences. Each sequence is described as a convex combination (admixture) of archetypes (cluster representatives) in the reduced dime...
Published in PLoS Computational Biology
Published in PLoS Computational Biology
Remarkably, the brain can perform precise computations, despite being composed of noisy neurons with slow, unreliable synaptic connectivity. To understand how this is possible, we can imagine the classic strategy where neurons are grouped into weakly-coupled subpopulations, creating redundancy to achieve high precision. But interestingly, recent wo...
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
Published in PLoS Computational Biology
