811 citations · 7.3k across the 89 of their papers we have counts for
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Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies
Cosimo Lupo, Natanael Spisak, Aleksandra M. Walczak +1
Affinity maturation is crucial for improving the binding affinity of antibodies to antigens. This process is mainly driven by point substitutions caused by somatic hypermutations o…
Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints
Victor Chardès, Massimo Vergassola, Aleksandra M. Walczak +1
In order to target threatening pathogens, the adaptive immune system performs a continuous reorganization of its lymphocyte repertoire. Following an immune challenge, the B cell re…
MINIMALIST: Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories
Giulio Isacchini, Natanael Spisak, Armita Nourmohammad +2
Simulation-based inference enables learning the parameters of a model even when its likelihood cannot be computed in practice. One class of methods uses data simulated with differe…
Antigenic waves of virus-immune co-evolution
Jacopo Marchi, Michael Lässig, Aleksandra M. Walczak +1
The evolution of many microbes and pathogens, including circulating viruses such as seasonal influenza, is driven by immune pressure from the host population. In turn, the immune s…
NoisET: Noise learning and Expansion detection of T-cell receptors
Meriem Bensouda Koraichi, Maximilian Puelma Touzel, Andrea Mazzolini +2
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…
A Renormalization Group Approach to Connect Discrete- and Continuous-Time Descriptions of Gaussian Processes
Federica Ferretti, Victor Chardès, Thierry Mora +2
Discretization of continuous stochastic processes is needed to numerically simulate them or to infer models from experimental time series. However, depending on the nature of the p…