… information gain of these predictions compared to a null model of neutral evolution 13 (M.
Łuksza and M. Lässig, manuscript in preparation). As shown by the time-dependence of the …

Evolution is a quest for innovation. Organisms adapt to changing natural selection by evolving
new phenotypes. Can we read this dynamics in their genomes? Not every mutation under …

A fraction of COVID-19 convalescent individuals mount a potent antibody response to SARS-CoV-2
with cross-reactivity to SARS-CoV-1. To uncover their humoral response in detail, we …

Seasonal influenza is controlled through vaccination campaigns. Evolution of influenza
virus antigens means that vaccines must be updated to match novel strains, and vaccine …

… Each strain has a multiplicity m i in our data set, which counts the number of sequences
with HA genotype a i and season of observation t i (sequences observed in the same season …

… r m gives the point where the binding probability reaches a maximum (crater landscape),
or else values close to 1 (mesa landscape). r s approximately indicates the onset of selection, …

… , samples were crosslinked in 1% HCHO (prepared in 1× DPBS) at room temperature for 10
min, and HCHO was quenched by the addition of glycine at a final concentration of 0.125 M. …

… The probability p for observing for each pair k ≤ k' m kk' interactions in n kk' pairs of duplicates
is then given by . Symmetric and asymmetric attachment differ in how the probability of a …

… Next we evaluate the internal link numbers L α = L(c α ) and the pairwise mismatches M
αβ , defined as the minimum of M(c α , c β ) over all pairwise alignments of the subgraphs G α …

Natural selection favors fitter variants in a population, but actual evolutionary processes may
decrease fitness by mutations and genetic drift. How is the stochastic evolution of molecular …