Mathieu Lavallée‐Adam

The paper introduces iDMS, a neural network that predicts optimal separation and compensation voltages for DMS, improving glycosphingolipid analysis.

The paper introduces iDMS, a deep neural network that predicts optimal ion mobility parameters for resolving monoglycosphingolipid stereoisomers, improving the efficiency of DMS-based assays.

The paper identifies 7 novel polyP-binding proteins in E. coli linked to translation control and ribosome biogenesis, with specific roles for YihI and Rnr.

The paper uses proteomics to show that E. coli polyphosphate kinase (PPK) regulates lipid A modifications and polymyxin resistance during starvation by affecting the BasS/BasR two-component system.

META-BOA provides a web tool to balance metabolomics data using over-sampling algorithms and evaluates their impact through visualization and classification.

The paper investigates how Ddp1 and Ppx1 counter polyphosphate toxicity in yeast by analyzing stress responses and enzyme functions.

PIGNON detects differentially expressed functional annotations by mapping protein expression onto a protein-protein interaction network, identifying 168, 203, and 19 breast cancer pathways between and within breast cancer subtypes.

MetaProClust-MS1 rapidly clusters metaproteomes using short MS1 profiles, showing robust microbiome shifts and correlated cluster topologies compared to traditional tandem mass spectrometry.

The paper identifies human biological processes and protein sequence motifs potentially targeted by SARS-CoV-2 using PPI networks and computational methods.

This study shows that internally produced polyP in human cells activates signaling pathways and alters gene and protein expression through ectopic expression of a bacterial polyP synthetase.

MealTime-MS improves protein identification in mass spectrometry by using real-time supervised learning to reduce redundant data collection and enhance detection of low-abundance proteins.

pepFunk improves functional analysis of metaproteomic gut microbiome data by focusing on peptides rather than proteins, identifying more enriched KEGG pathways.

TargetSeeker-MS identifies drug targets on a proteome scale using EBPS-MS data, showing reproducibility in C. elegans and HEK293 samples treated with benomyl.

The paper identifies proteome-wide changes in mouse models of Alzheimer's disease, highlighting ApoE dysregulation and synaptic protein loss.