D. Figeys

Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry

This study evaluates how different experimental workflows affect fecal metaproteomic results, showing that DIA-PASEF improves protein identification and small protein recovery compared to DDA.

Pairing Metagenomics and Metaproteomics to Characterize Ecological Niches and Metabolic Essentiality of gut microbiomes

This study develops a computational pipeline combining metagenomics and metaproteomics to identify proteins' metabolic and ecological roles in gut microbiomes using simulated and real data.

RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics

RapidAIM 2.0 evaluates gut microbiome functional responses to xenobiotics using high-throughput metaproteomics and in vitro culturing.

Comprehensive assessment of functional effects of commonly used sweeteners on ex vivo human gut microbiome

This study evaluates the functional effects of 21 common sweeteners on human gut microbiomes using metaproteomics, identifying potential prebiotic properties in certain sugar alcohols.

Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics

This study evaluates the cultivability and functional activity of biobanked microbiota using an ex vivo assay and metaproteomics, showing stability after long-term freezing.

Examining the effects of an anti-Salmonella bacteriophage preparation, BAFASAL, on ex vivo human gut microbiome composition and function using a multi-omics approach

This study evaluates the impact of BAFASAL, a bacteriophage preparation, on human gut microbiome composition and function using multi-omics analyses in an ex vivo setting.

Exploring the microbiome-wide lysine acetylation, succinylation and propionylation in human gut microbiota

The paper develops a method to analyze lysine acylations in the human gut microbiome, identifying thousands of modified peptides and showing differential distribution across microbial species.

Studying the dynamics of the gut microbiota using metabolically stable isotopic labeling and metaproteomics.

The paper develops a metaproteomic workflow and software tool to study gut microbiome functional dynamics using stable isotopic labeling and time series analysis.

Metaproteomic responses of in vitro gut microbiomes to resistant starches: the role of resistant starch type and inter-individual variations

This study examines how different types of resistant starches affect gut microbiome protein expression and functional pathways, revealing inter-individual variations in responses.

Growth phase-dependent responses of an in vitro gut microbiome to metformin

This study shows that metformin affects in vitro gut microbiota differently depending on when it is added during growth phases, with the log phase showing the strongest impact on growth and functional changes.

An in vitro model maintaining taxon-specific functional activities of the gut microbiome

The paper develops an in vitro model called Mipro that maintains gut microbiome functional and compositional profiles, showing strong correlation with in vivo responses to metformin.

RapidAIM: A culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

RapidAIM screens xenobiotics against individual microbiomes using metaproteomics, showing compound effects on abundance, composition, and functional pathways across individuals.

Therapeutic Targeting of Casein Kinase 1δ/ε in an Alzheimer's Disease Mouse Model

This study shows that inhibiting CK1δ/ε improves memory and circadian rhythms in Alzheimer's mice by reversing proteomic changes and synaptic plasticity.