I. Andre

Accurate prediction of site- and amino-acid substitution rates with a mutation-selection model

This study introduces a mutation-selection model to predict site- and amino-acid substitution rates from amino acid sequences, showing it outperforms standard phylogenetic methods and correlates with empirical Bayes estimates.

Improved prediction of site-rates from structure with averaging across homologs

The paper shows that averaging site-specific mutation rates across homologous protein structures improves predictions of site-rates from structure.

Engineering multivalent Fc display for FcγR blockade

This study engineers multivalent Fc-displaying virus-like particles to block FcγR activation, showing that higher valency reduces receptor activation and enhances inhibition of immune complex-mediated phagocytosis.

DnaK response to expression of protein mutants is dependent on translation rate and stability

The paper investigates how DnaK response to protein mutants depends on translation rate and stability, finding initial response correlates with synthesis rate and later with stability.

A thermodynamic model of protein structure evolution explains empirical amino acid rate matrices

The paper develops a thermodynamic model to explain amino acid substitution rates by integrating protein stability and genetic code constraints, accurately replicating empirical rate matrices.

CD28 costimulatory domain protects against tonic signaling-induced functional impairment in CAR-Tregs

This study compares CD28 and 4-1BB costimulatory domains in CAR-Tregs, finding CD28 better preserves function and survival under tonic signaling.

Single cell analysis of FOXP3 deficiencies in humans and mice unmasks intrinsic and extrinsic CD4+ T cell perturbations

The paper analyzes FOXP3 deficiencies in humans and mice using single-cell RNA-seq and flow cytometry to uncover intrinsic and extrinsic CD4+ T cell perturbations in IPEX syndrome.

DNA-mediated self-assembly of gold nanoparticles on protein superhelix

This paper demonstrates a DNA-mediated method to conjugate gold nanoparticles to protein structures, enabling site-specific binding and stable assembly.