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The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
We study causal inference in a multi-environment setting, in which the functional relations for producing the variables from their direct causes remain the same across environments, while the distribution of exogenous noises may vary. We…
We study the exponential stability of evolutionary equations. The focus is laid on second order problems and we provide a way to rewrite them as a suitable first order evolutionary equation, for which the stability can be proved by using…
Albanese varieties provide a standard tool in algebraic geometry for converting questions about varieties in general, to questions about Abelian varieties. A result of Serre provides the existence of an Albanese variety for any…
We consider character sequences evolving on a phylogenetic tree under the TKF91 model. We show that as the sequence lengths tend to infinity the the topology of the phylogenetic tree and the edge lengths are determined by any one of (a) the…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
Supergenes are genomic regions containing sets of tightly linked loci that control multi-trait phenotypic polymorphisms under balancing selection. Recent advances in genomics have uncovered significant variation in both the genomic…
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…
We answer two questions raised by Bryant, Francis and Steel in their work on consensus methods in phylogenetics. Consensus methods apply to every practical instance where it is desired to aggregate a set of given phylogenetic trees (say,…
We study evolution algebras of arbitrary dimension. We analyze in deep the notions of evolution subalgebras, ideals and non-degeneracy and describe the ideals generated by one element and characterize the simple evolution algebras. We also…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
Biases in molecular evolution can significantly influence evolutionary trajectories. They have been described in a variety of contexts such as development and mutation, but not for acquiring new functions (i.e. emergence). Here, we…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs.…
This is a survey on the finite basis problem for varieties of algebraic systems. Our exposition is in two directions: (i) We give numerous examples of varieties which are not finitely based. (ii) We give examples of important varieties with…
In this expository article, we provide a self-contained overview of the notion of convolution embedded in different theories: from the classical Fourier theory to the theory of algebraic signal processing. We discuss their relations and…