A celebrated and controversial hypothesis suggests that some biological systems—parts,
aspects, or groups of them—may extract important functional benefits from operating at the …

Inverse problems in statistical physics are motivated by the challenges of 'big data'in
different fields, in particular high-throughput experiments in biology. In inverse problems, the …

Flocking is a typical example of emergent collective behavior, where interactions between
individuals produce collective patterns on the large scale. Here we show how a quantitative …

Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional
(3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse …

The problem of reconstructing nonlinear and complex dynamical systems from measured
data or time series is central to many scientific disciplines including physical, biological …

In the course of evolution, proteins undergo important changes in their amino acid
sequences, while their three-dimensional folded structure and their biological function …

Maximum entropy models are the least structured probability distributions that exactly
reproduce a chosen set of statistics measured in an interacting network. Here we use this …

Direct-coupling analysis is a group of methods to harvest information about coevolving
residues in a protein family by learning a generative model in an exponential family from …

HIV is a highly mutable virus, and over 30 years after its discovery, a vaccine or cure is still
not available. The isolation of broadly neutralizing antibodies (bnAbs) from HIV-infected …

Viral immune evasion by sequence variation is a major hindrance to HIV-1 vaccine design.
To address this challenge, our group has developed a computational model, rooted in …