R. Bonneau

Rapid generation of antibody conformational ensembles using machine learning

This paper introduces Cadense, a machine learning framework that generates antibody conformational ensembles from sequence, capturing dynamic properties and improving docking accuracy.

Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases

This study performs a meta-analysis of gut microbiome data across 11 diseases, identifying shared and distinct microbial signatures using machine learning and differential abundance analysis.

Multi-omic analysis along the gut-brain axis points to a functional architecture of autism

The paper identifies a functional architecture of autism along the gut-brain axis using multi-omic data, revealing microbial and metabolic profiles linked to autism symptoms.

Specificities of modeling membrane proteins using multi-template homology modeling

The paper describes a protocol for multi-template homology modeling of membrane proteins using Rosetta, improving accuracy by integrating multiple templates.

Designing Peptides on a Quantum Computer

This paper maps protein design to a quantum annealer, demonstrating real-world applicability of quantum computing in designing peptides comparable to classical methods.

Distinct polysaccharide growth profiles of human intestinal Prevotella copri isolates

This study examines polysaccharide growth profiles of 83 P. copri isolates from 11 donors, revealing genomic and functional differences in polysaccharide utilization.

The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations

The study identifies four distinct clades within the Prevotella copri complex, showing reduced prevalence in Westernised populations compared to non-Westernised ones.

Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints

RosettaNMR improves protein structure prediction by integrating paramagnetic NMR restraints with chemical shifts and NOE data, achieving high accuracy in 50% of benchmark cases.

A comprehensive map of the dendritic cell transcriptional network engaged upon innate sensing of HIV

This study maps the transcriptional network in HIV-1 infected dendritic cells, identifying key regulators of interferon response and maturation.

Transcriptional regulatory networks that promote and restrict identities and functions of intestinal innate lymphoid cells

This study identifies transcriptional regulatory networks in intestinal ILC subsets, revealing key transcription factors and their roles in lineage identity and plasticity.

A novel domain assembly routine for creating full-length models of membrane proteins from known domain structures

This paper introduces a domain assembly protocol for membrane proteins that constructs full-length models without requiring domain interfaces or orientation knowledge.

c-Maf-dependent regulatory T cells mediate immunological tolerance to intestinal microbiota

This study identifies c-Maf-dependent regulatory T cells that suppress inflammation caused by the pathobiont Helicobacter hepaticus, preventing colitis in mice.

The Rosetta all-atom energy function for macromolecular modeling and design

The paper explains the Rosetta all-atom energy function, its mathematical models, and its application to biomolecular modeling and design, including new capabilities for membrane proteins and other macromolecules.

An Adaptive Geometric Search Algorithm for Macromolecular Scaffold Selection

This paper introduces an adaptive geometric search algorithm for macromolecular scaffold selection, improving efficiency in matching functional motifs to protein surfaces.

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP

The paper introduces mp_lipid_acc, a tool to predict lipid accessibility in membrane proteins using structural data, achieving 90% accuracy on a curated benchmark dataset.