Publications by authors named "D A VanderWall"
Article Synopsis
- - The study analyzes age-dependent changes in the brain proteins and their modifications in several mouse models of Alzheimer's disease (AD), focusing on how these models represent human AD complexities.
- - Results showed that commonly used mouse models only replicate about 30% of the protein changes seen in humans, but adding more genetic factors can increase this to 42%.
- - The research highlights inconsistencies between protein and gene expression in the 5xFAD model, indicating that amyloid plaque environments affect protein turnover, which could lead to new targets for AD treatment.
We present a standardized metadata template for assays used in pharmaceutical drug discovery research, according to the FAIR principles. We also describe the use of an automated tool for annotating assays from a variety of sources, including PubChem, commercial assay providers, and the peer-reviewed literature, to this metadata template. Adoption of a standardized metadata template will allow drug discovery scientists to better understand and compare the increasing amounts of assay data becoming available, and will facilitate the use of artificial intelligence tools and other computational methods for analysis and prediction.
View Article and Find Full Text PDFEpstein-Barr virus (EBV) causes infectious mononucleosis, triggers multiple sclerosis, and is associated with 200,000 cancers/year. EBV colonizes the human B cell compartment and periodically reactivates, inducing expression of 80 viral proteins. However, much remains unknown about how EBV remodels host cells and dismantles key antiviral responses.
View Article and Find Full Text PDFArticle Synopsis
- * Tspan8 is downregulated in ulcerative colitis in mice, which disrupts cell junctions and increases epithelial permeability, thereby upregulating Stat1 signaling.
- * Tspan8 is linked to lipid rafts and influences the endocytosis route of the IFN-γ receptor, which helps maintain intestinal epithelial integrity and minimizes inflammation.
Background: Mass spectrometry (MS)-based proteomic analysis of posttranslational modifications (PTMs) usually requires the pre-enrichment of modified proteins or peptides. However, recent ultra-deep whole proteome profiling generates millions of spectra in a single experiment, leaving many unassigned spectra, some of which may be derived from PTM peptides.
Methods: Here we present JUMPptm, an integrative computational pipeline, to extract PTMs from unenriched whole proteome.