Marc G. Chevrette

Integrating targeted genome mining and structure-guided modeling reveals unexplored 7-deazapurine-containing pathways

The paper integrates genome mining and structure-guided modeling to discover new 7-deazapurine-containing biosynthetic gene clusters and their chemical functions.

PARAS: high-accuracy machine-learning of substrate specificities in nonribosomal peptide synthetases

Random forest predictors PARAS and PARASECT, trained on 3,653 curated adenylation domains, outperform earlier NRPS substrate predictors and correctly assigned L-Trp to an unusual tryptopeptin synthetase domain.

Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data

The paper introduces a collaborative platform for curating microbial metabolite knowledge to enhance metabolomics data interpretation.

Nematicidal indole oxazoles and chemoattractants from soil bacteria

This study identifies labradorin 1, an indole compound from Pseudomonas sp. TE4607, as a nematicidal agent effective against both free-living and parasitic nematodes.

Using cross-species co-expression to predict metabolic interactions in microbiomes.

This paper predicts microbial metabolic interactions using cross-species co-expression analysis of RNA-sequencing data from microbiome datasets.

Skin lipid chemistry influences host-microbiome-pathogen interactions in snake fungal disease (ophidiomycosis)

The paper investigates how snake skin lipid chemistry and the microbiome influence the growth of Ophidiomyces ophidiicola, revealing antifungal lipids and bacterial-fungal interactions that shape the skin microbiome.

Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity

The paper introduces GATOR-GC, a genome mining tool that identifies diverse gene clusters and maps their evolutionary patterns, revealing previously uncharacterized biosynthetic functions.

Learning gene interactions and functional landscapes from entire bacterial proteomes

This paper introduces a whole bacterial proteome foundation model trained on ESM embeddings to capture gene interactions and genomic integrity, achieving state-of-the-art results in operon identification and genotype-phenotype mapping.

Convergent Evolution of the Antimycobacterial Lasso Peptide Triculamin

This study identifies the biosynthesis of triculamin, a lasso peptide with antimycobacterial activity, and shows its convergent evolution across bacterial phyla.

Characterizing constitutive promoters across the Proteobacteria

The paper identifies and characterizes constitutive promoters across three Proteobacteria classes, showing their expression range and portability between hosts.