Judit Villén

Carafe2 generates high-quality in silico spectral libraries for timsTOF DIA proteomics by fine-tuning deep learning models on DIA data, outperforming DDA-trained models in multiple applications.

This paper characterizes IDH+ glioma stem cell cultures to model GBM biology and therapeutic response, showing reproducible survival curves and methods to track cellular heterogeneity.

The paper profiles the proteome and phosphoproteome of yeast expressing three mistranslating tRNA variants, showing varied growth defects and impacts on cellular processes.

Carafe generates high-quality in silico spectral libraries for DIA proteomics by training deep learning models directly on DIA data, improving fragment ion intensity prediction and peptide detection.

The paper introduces a rapid and cost-effective method for phosphotyrosine peptide enrichment, enabling sensitive detection of phosphotyrosine sites in biological samples.

The paper identifies a toggle-switch mechanism in the ERECTA receptor that prevents inappropriate signaling by autoinhibition and rapid degradation after activation.

This study examines the effects of two mistranslating tRNA variants in Drosophila melanogaster, showing sex-specific impacts on development, lifespan, and locomotion.

The paper quantifies the fitness cost of spurious phosphorylation in yeast by expressing tyrosine kinases and analyzing phosphoproteomes, finding a strong correlation between spurious phosphorylation and decreased growth.

The paper compares the transcriptional response of male and female Drosophila melanogaster to proline-to-serine mistranslation, identifying sex-specific gene expression changes and their implications for disease and tRNA therapeutics.

The paper identifies TPL's role in nucleating the transcriptional preinitiation complex in yeast and plants through genetic and physical interaction studies.

The paper develops a microscale ex vivo cancer model using tumor cuboids that retain a complex tumor microenvironment, enabling drug and immunotherapy testing.

The paper maps the yeast phosphoproteome under 101 perturbations, identifying 25,000 regulated phosphosites and revealing stress response programs and regulatory networks.

The paper investigates how anticodon mutations in tRNAAla affect yeast growth and mistranslation, finding that anticodon sequence influences mistranslation extent and growth impact.

The paper introduces R2-pY, a robotic method for phosphotyrosine enrichment in proteomics, achieving high efficiency and reproducibility with 96 samples processed in parallel.

This study uses multidimensional proteomics to analyze age-related changes in yeast cells, identifying molecular trajectories of aging and rejuvenation.

The paper introduces pyAscore, a Python package for scoring PTM localization in mass spectrometry data, enhancing workflow integration and versatility.

The paper introduces a method to coisolate and fragment SILAC peptide pairs for improved identification and quantification in MS/MS-based proteomics.

This study shows that the impact of a mistranslating tRNA variant depends on genetic background and mistranslation frequency in yeast, with implications for understanding tRNA variants in human disease.

The paper introduces a proteomic technology called Miro to identify amino acid substitutions that affect protein function by using mistranslation and mass spectrometry.

This paper introduces a Drosophila melanogaster model with a mistranslating tRNA variant, showing it causes developmental delays, reduced adult viability, and sexually dimorphic morphological and behavioral effects.

This paper develops an inducible tRNA system to study mistranslation effects in yeast by regulating tRNA expression through RNA polymerase II promoters.

The paper identifies altered protein networks in the cerebellum of schizophrenia patients and validates findings in murine models of early postnatal stress.

This study compares the effects of two tRNA variants causing different amino acid substitutions in yeast, showing distinct impacts on growth, heat shock response, and transcriptome changes.

The paper identifies phosphosites that affect protein thermal stability by measuring stability differences between proteins and their phosphorylated forms at a proteomic scale.

DIAmeter is a library-free search engine for analyzing DIA mass spectrometry data using peptide sequences, supporting various isolation windows and post-translational modifications.

The paper identifies PKC as a therapeutic target for treating mitochondrial disease by analyzing proteomic and phosphoproteomic changes in a mouse model of Leigh syndrome.

The paper identifies altered calcium-binding proteins in the cerebellum of schizophrenia patients, linking them to synaptic dysfunction and suicide behaviors.

The paper introduces R2-P2, an automated phosphoproteomics method, and applies it to study MAPK pathway signaling in yeast, revealing phosphorylation events across multiple pathways.

Thesaurus identifies phosphoprotein positional isomers by analyzing fragment ions from mass spectrometry data, revealing kinase-specific regulation in the PI3K/AKT pathway.

The paper identifies proteomic and metabolic changes in brown fat tissue in response to cold exposure, highlighting increased acetylation and lipid synthesis.