Steven P. Gygi

This study shows that fission yeast CK1 orthologues Hhp1 and Hhp2 promote DNA double-strand break repair through both homologous recombination and non-homologous end joining by phosphorylating substrates like Arp8.

This study uses transdifferentiated neurons to show lysosomal deficits are an early event in aging and Alzheimer's disease, leading to proteotoxic deposits and cell death.

This study integrates multi-omics data from mouse embryonic stem cells to identify genetic drivers of proteome variability and uncover regulatory mechanisms in pluripotency.

This study uses patient-derived neurons to show that PGRN deficiency causes proteostasis breakdown and TDP-43 aggregation in FTD.

DAGBagM learns DAGs with mixed continuous and binary variables to identify prognostic protein biomarkers in ovarian cancer.

The paper identifies genetic drivers of protein phosphorylation using multi-omics data from mouse tissues, revealing novel interactions and targets of PDK1 in obesity and diabetes.

The paper uses proximity labeling and mass spectrometry to identify proteins associated with internalized EGFR, revealing TFG's role in endosomal sorting.

The paper shows that ALS genes FUS, TAF15, and MATR3 regulate the MHC II antigen presentation pathway by downregulating HLA-DR and CD74 through loss of CIITA, with implications for immune system failure in ALS.

The paper analyzes transcriptome and proteome data from aged mouse hearts to identify molecular changes associated with aging, revealing distinct biological processes and genetic loci influencing age-related changes.

The paper integrates protein imaging and interaction data to create a unified map of eukaryotic cell structure, revealing new subcellular systems and protein associations.

The paper analyzes liver proteomes across three genetically diverse mouse populations to understand how genetic variation influences protein abundance and its relationship to phenotypes.

The paper identifies Pdzrn3 as a target of Wnt5a-Ror signaling through proteomic analysis and shows its degradation is essential for cell migration.

The paper creates two large-scale cell-line-specific human interactomes using affinity-purification mass spectrometry and identifies shared and cell-specific protein interactions.

This study profiles mRNA and protein levels in aging kidneys, finding that protein changes reveal more extensive and functionally significant aging-related alterations than mRNA.

The paper identifies enriched neurodegenerative microglia signatures in EVs from Alzheimer's disease mouse models using proteomic analysis.

The paper introduces Monocle, an algorithm that improves monoisotopic mass estimation in proteomics, increasing peptide identifications by up to two-fold.

The paper identifies the rixosome, an RNA degradation complex, as essential for heterochromatin spreading and epigenetic inheritance by degrading heterochromatic RNAs.

This paper provides a guide to the quantitative proteomic data from the Cancer Cell Line Encyclopedia, explaining normalization methods and data interpretation.

The paper shows the rixosome, an RNA degradation complex, associates with human PRC complexes and is required for silencing Polycomb target genes.

The paper introduces AID, a shape-independent method for analyzing thermal proteome profiles, and identifies panobinostat targets in a TPP dataset.

The paper identifies PCIF1 as the first human m6Am methyltransferase and shows it regulates gene expression by suppressing cap-dependent translation through m6Am methylation.

The paper quantifies protein and phospho-site dynamics during fertilization and meiotic exit in Xenopus eggs using mass spectrometry-based proteomics, revealing limited degradation and extensive dephosphorylation.