O. Rivoire

Inference and design of antibody specificity: from experiments to models and back

This paper develops a multi-stage approach combining phage display experiments, machine learning, and biophysical modeling to design antibodies with customized specificity profiles.

A role for conformational changes in enzyme catalysis

This paper presents a model showing how conformational changes in enzymes break a trade-off between specificity for transition states and product release, using substrate handles and chemical similarities between reaction states.

Multilevel selection in the evolution of sexual dimorphism in phenotypic plasticity

The paper shows that sexual dimorphism in phenotypic plasticity can evolve and offset the twofold cost of males when mating occurs within related groups, but may be unstable in panmictic populations due to sexual selection.

Assessing in vivo the impact of gene context on transcription through DNA supercoiling

The paper assesses how gene context affects transcription in vivo by measuring gene expression in E. coli with varying distances to topological barriers and promoters.

Undersampling and the inference of coevolution in proteins

This paper shows that current methods for inferring protein coevolution are biased due to undersampling and scale mismatches in epistatic interactions.

Parameters and determinants of responses to selection in antibody libraries

The paper quantifies how scaffold evolutionary maturation affects antibody library response to selection, finding maturated scaffolds show lower response to arbitrary targets.