Matthew D. Berg

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.

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.

This study shows TUDCA reduces drug bioavailability, not directly aiding protein folding, and rescues yeast from ER stress by sequestering toxic compounds.

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

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

This study investigates the role of Tra1 in yeast chronological aging, finding it regulates stress response genes and mitochondrial function, impacting longevity.

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.

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.

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 genes with chemical-genetic interactions with AZC in yeast, revealing pathways involved in coping with amino acid mis-incorporation and proteotoxic stress.

The paper identifies a deleterious S213P mutation in the eco1-1 allele using mistranslating tRNA variants that suppress its temperature sensitivity.

The paper shows that Sfp1 regulates Tra1 expression in response to polyQ protein stress in yeast, linking TORC1 to SAGA complex function.