Evolutionary stability of antigenically escaping viruses.

Antigenic variation is the main immune escape mechanism for RNA viruses like influenza or SARS-CoV-2. While high mutation rates promote antigenic escape, they also induce large mutational loads and reduced fitness. It remains unclear how this cost-benefit trade-off selects the mutation rate of viruses.

Universality of evolutionary trajectories under arbitrary forms of self-limitation and competition.

The assumption of constant population size is central in population genetics. It led to a large body of results that is robust to modeling choices and that has proven successful to understand evolutionary dynamics. In reality, allele frequencies and population size are both determined by the interaction between a population and the environment.

Emergent statistical laws in single-cell transcriptomic data.

Large-scale data on single-cell gene expression have the potential to unravel the specific transcriptional programs of different cell types. The structure of these expression datasets suggests a similarity with several other complex systems that can be analogously described through the statistics of their basic building blocks. Transcriptomes of single cells are collections of messenger RNA abundances transcribed from a common set of genes just as books are different collections of words from a shared vocabulary, genomes of different species are specific compositions of genes belonging to evolutionary families, and ecological niches can be described by their species abundances.

Inspecting the interaction between human immunodeficiency virus and the immune system through genetic turnover.

Chronic infections of the human immunodeficiency virus (HIV) create a very complex coevolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely unknown and could help in disease treatment and vaccine development. Here we study a longitudinal dataset of ten HIV-infected people, where both the B-cell receptors and the virus are deeply sequenced.

NoisET: Noise Learning and Expansion Detection of T-Cell Receptors.

High-throughput sequencing of T- and B-cell receptors makes it possible to track immune repertoires across time, in different tissues, in acute and chronic diseases and in healthy individuals. However, quantitative comparison between repertoires is confounded by variability in the read count of each receptor clonotype due to sampling, library preparation, and expression noise. We review methods for accounting for both biological and experimental noise and present an easy-to-use python package that implements and generalizes a previously developed Bayesian method.

Generosity, selfishness and exploitation as optimal greedy strategies for resource sharing.

Resource sharing outside the kinship bonds is rare. Besides humans, it occurs in chimpanzee, wild dogs and hyenas, as well as in vampire bats. Resource sharing is an instance of animal cooperation, where an animal gives away part of the resources that it owns for the benefit of a recipient.

Zipf and Heaps laws from dependency structures in component systems.

Complex natural and technological systems can be considered, on a coarse-grained level, as assemblies of elementary components: for example, genomes as sets of genes or texts as sets of words. On one hand, the joint occurrence of components emerges from architectural and specific constraints in such systems. On the other hand, general regularities may unify different systems, such as the broadly studied Zipf and Heaps laws, respectively concerning the distribution of component frequencies and their number as a function of system size.