Özge Karayel

The paper identifies urinary protein signatures linked to LRRK2 dysfunction in Parkinson's disease using multi-cohort proteomics and machine learning, showing cross-species relevance and potential as pharmacodynamic markers.

This study investigates how the LRRK2-N2081D variant increases Crohn's disease risk by showing it causes more severe colitis and distinct RAB substrate phosphorylation compared to LRRK2-G2019S.

MSstats+ improves differential protein analysis in proteomic experiments by incorporating longitudinal quality metrics to reduce false positives from poor-quality measurements.

The paper uses Perturb-seq to systematically study 1,130 E3 ligases and their roles in inflammatory responses in dendritic cells, revealing co-functional modules and genetic interactions.

This study identifies McIdas as a regulator of centriole numbers through PLK4-dependent phosphorylation, linking its role in cell cycle control to centriole duplication.

The paper uses proteomics and machine learning to identify potential biomarkers in cerebrospinal fluid for Parkinson's disease, showing altered protein levels and neuroinflammation signatures.

The paper determines the structural context of PTMs across the human proteome and identifies regulatory sites by analyzing their distribution in folded and disordered regions.

Concurrent multi-omics of SARS-CoV-2 and SARS-CoV in A549 cells, integrated by network diffusion, maps shared and virus-specific host perturbations and nominates antiviral drug hotspots.

This study uses urinary proteomics and machine learning to identify biomarkers for stratifying Parkinson's disease patients and LRRK2 mutation carriers.

The paper develops a DIA-based workflow for ubiquitinome analysis, revealing circadian regulation through novel ubiquitination sites and clusters.

The paper introduces a DIA-based systems biology workflow for high-throughput proteome analysis in yeast, revealing novel E3 ligase responses to metabolic shifts.

This study uses proteomics to analyze dynamic phospho-signaling networks in human erythropoiesis, identifying key regulatory mechanisms and markers across differentiation stages.

The paper reveals how environmental changes trigger structural transitions in GID E3 ubiquitin ligase complexes, enabling substrate recognition and degradation.