A5006952010- Advanced Proteomics Techniques and Applications
- Advanced Biosensing Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Liver Disease Diagnosis and Treatment
- Gene expression and cancer classification
- Gene Regulatory Network Analysis
- Fatigue and fracture mechanics
- Genetic and Kidney Cyst Diseases
- Probabilistic and Robust Engineering Design
- Machine Learning in Bioinformatics
- Structural Integrity and Reliability Analysis
- Endoplasmic Reticulum Stress and Disease
- Receptor Mechanisms and Signaling
Université Grenoble Alpes
2021-2024
Centre National de la Recherche Scientifique
2021-2024
CEA Grenoble
2021-2024
Inserm
2021-2024
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2021-2024
Institut polytechnique de Grenoble
2021-2024
Educational Department of Liaoning Province
2022
Translational Innovation in Medicine and Complexity
2021
Abstract Background Metabolic dysfunction-associated steatotic liver disease (MASLD) is estimated to affect 30% of the world’s population, and its prevalence increasing in line with obesity. Liver fibrosis closely related mortality, making it most important clinical parameter for MASLD. It currently assessed by biopsy – an invasive procedure that has some limitations. There thus urgent need a reliable non-invasive means diagnose earlier MASLD stages. Methods A discovery study was performed...
Abstract Label-free bottom-up proteomics using mass spectrometry and liquid chromatography has long established as one of the most popular high-throughput analysis workflow for proteome characterization. However, it produces data hindered by complex heterogeneous missing values, which imputation remained problematic. To cope with this, we introduce Pirat, an algorithm that harnesses this challenge following unprecedented approach. Notably, models instrument limit estimating a global...
Abstract In proteomic differential analysis, FDR control is often performed through a multiple test correction ( i . e ., the adjustment of original p-values). this protocol, we apply recent and alternative method, based on so-called knockoff filters. It shares interesting conceptual similarities with target-decoy competition procedure, classically used in proteomics for at peptide identification. To provide practitioners unified understanding proteomics, procedure real simulated...
SUMMARY Label-free bottom-up proteomics using mass spectrometry and liquid chromatography has long been established as one of the most popular high-throughput analysis workflows for proteome characterization. However, it produces data hindered by complex heterogeneous missing values, which imputation remained problematic. To cope with this, we introduce Pirat, an algorithm that harnesses this challenge original likelihood maximization strategy. Notably, models instrument limit learning a...
In their recent article, Madej et al. 1 proposed an original way to solve the recurrent issue of controlling for false discovery rate (FDR) in peptide-spectrum-match (PSM) validation. Briefly, they derive a single precise distribution decoy matches termed Common Decoy Distribution (CDD) and use it control FDR during target-only search. Conceptually, this approach is appealing as takes best two worlds, i.e., decoy-based approaches (which leverage large-scale collection empirical mismatches)...