Kris Gevaert

Functional diversification of UBP6 in plant immunity through N-degron pathway regulation

The paper shows that UBP6 cleavage generates a proteoform that stabilizes NPR1 and enhances plant immunity through the N-degron pathway.

TRMT10A deficiency and tRNA fragmentation disrupt human pancreatic β-cell identity and insulin maturation

This study shows TRMT10A deficiency causes β-cell dysfunction by promoting tRNA fragmentation and disrupting PCSK1 expression, leading to impaired insulin maturation and glucose-stimulated insulin secretion.

MLMarker: A machine learning framework for tissue inference and biomarker discovery

MLMarker computes tissue similarity scores for proteomics data, identifies tissue origins in biofluids, and provides interpretable predictions using a Random Forest model.

DiaReport: Reproducible Workflow for Differential Expression Analysis and Interactive Reporting in DIA-based Proteomics

DiaReport provides a reproducible workflow for differential expression analysis and interactive reporting in DIA-based proteomics, demonstrating its utility with an extracellular vesicle dataset.

Conditional stability of HY5 through the ATE N-degron pathway regulates environmental responses in Arabidopsis thaliana

Experimental mismatch in benchmarking PELSA and LiP-MS

The paper reanalyzes datasets comparing PELSA and LiP-MS, finding that reported differences arise from experimental mismatches and data imputation, cautioning against conclusions of quantitative superiority.

Advancing DIA-based Limited Proteolysis Workflows: introducing DIA-LiPA

The paper evaluates library-free DIA workflows for LiP-MS and introduces DIA-LiPA, a pipeline that improves structural interpretation of limited proteolysis data.

Exhaled breath condensate proteomics using amphipols improves protein detection but reveals statistical challenges in respiratory disease biomarker discovery

This study uses amphipols to improve protein detection in exhaled breath condensate but finds high variability and missing data hinder reliable biomarker discovery.

Collisional cross-section prediction for multiconformational peptide ions with IM2Deep

The paper improves IM2Deep to predict collisional cross-sections for peptides with multiple conformations, using a comprehensive dataset and tailored architecture.

A 96well ultrafiltration approach for the high-throughput proteome analysis of extracellular vesicles isolated from conditioned medium

This paper introduces a 96-well ultrafiltration method for isolating extracellular vesicles from conditioned medium, improving purity and reproducibility for proteomic analysis.

Biases in the Parsortix system observed with pancreatic cancer cell lines

This study evaluates the Parsortix system's bias in capturing pancreatic cancer cells with different epithelial-mesenchymal transition (EMT) phenotypes, finding lower recovery rates for mesenchymal-like cells.

Lack of AtMC1 catalytic activity triggers autoimmunity dependent on NLR stability

This study shows that lack of AtMC1 catalytic activity causes autoimmunity in Arabidopsis, which depends on NLR stability and can be reversed by overexpressing SNIPER1.

Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment

The paper assesses MS-based identifications of unannotated human microproteins, finding large variation in reported proteins and PSM quality across studies.

Olduvai domains downregulate mitochondrial pathways to promote human brain evolution and neoteny

This study shows Olduvai domains suppress mitochondrial pathways, delaying cellular maturation and promoting brain size increase in humans.

N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity

The paper shows that N-terminal acetylation by NatC protects proteins from degradation, enhancing longevity and motility, and that UBR4-KCMF1 targets unacetylated N-terminal Met followed by hydrophobic residues.

CysQuant: simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry

CysQuant quantifies cysteine oxidation and protein abundance using DDA or DIA-MS, revealing redox changes in Arabidopsis exposed to light.

N-terminal proteoforms may engage in different protein complexes

The paper investigates N-terminal proteoforms and finds they can engage in different protein complexes compared to their canonical counterparts.

Antagonism and selective modulation of the human glucocorticoid receptor both reduce recruitment of p300/CBP and the Mediator complex

The paper investigates how different GR ligands affect coregulator recruitment, finding that antagonists and selective modulators reduce interactions with p300/CBP and the Mediator complex compared to full agonists.

Machine learning on large-scale proteomics data identifies tissue- and cell type-specific proteins

A machine learning model trained on proteomics data from 183 human datasets identifies tissue and cell-type specific proteins with high accuracy.

Limited, but potentially functional translation of non-coding transcripts in the HEK293T cellular cytosol

The paper investigates non-coding transcript translation in HEK293T cells, finding limited but potentially functional translation products using ribosome profiling and mass spectrometry.

MSqRob takes the missing hurdle: uniting intensity- and count-based proteomics

The paper introduces a hurdle model to address missing values in proteomics by combining binomial count and intensity-based components, showing improved performance over existing methods.

The Plant PTM Viewer, a central resource exploring plant protein modifications. From site-seeing to protein function.

The paper introduces the Plant PTM Viewer, a database integrating over 200,000 PTM sites across five plant species to explore protein modifications and their functional implications.

FIGL1 and its novel partner FLIP form a conserved complex that regulates homologous recombination.

The paper identifies FLIP as a novel partner of FIGL1 that forms a conserved complex regulating meiotic homologous recombination in Arabidopsis and humans.

The expa1-1 mutant reveals a new biophysical lateral root organogenesis checkpoint

The study identifies a cell width checkpoint in pericycle cells that regulates asymmetric divisions during lateral root formation in plants.

The Proteolytic Landscape Of An Arabidopsis Separase-Deficient Mutant Reveals Novel Substrates Associated With Plant Development

The paper identifies novel substrates of separase in Arabidopsis by analyzing proteolytic changes in wild-type and separase mutant root tip cells, revealing roles in pH homeostasis, lipid signaling, and proteolytic network interactions.