John R. Yates

The paper identifies phosphorylated pyruvate dehydrogenase (pPDH) as an in vivo marker for neuronal inhibition, correlating with reduced action potential firing and detectable across various inhibitory conditions.

The paper analyzes B cell responses to a germline-targeting immunogen in human Ig loci transgenic mice, finding diverse non-VRC01-class B cells and competitor B cells recognizing epitopes near the VRC01 epitope.

This study shows that WASP regulates nucleolar structure and function, affecting rRNA transcription and inflammatory cytokine response in macrophages.

The paper uses in vivo protein footprinting to study dynamic conformational changes in the proteome across multiple tissues in Alzheimer's disease progression, finding that structural changes precede expression changes in key pathways.

This study compares N-glycan processing in SARS-CoV-2 spike-proteins across variants to understand immune evasion mechanisms.

This study identifies a reduction in ER chaperones in PWS β-cells, leading to impaired insulin secretion and ER stress.

The paper shows that arginine depletion during inflammation reduces nuclear ArgRS, which interacts with SRRM2, altering splicing and metabolic outcomes.

This study shows Rvb1/Rvb2 proteins link transcription and translation during glucose starvation by sequestering mRNAs into granules and modulating their translatability.

The paper identifies conserved spliceosomal proteins in fungi and humans that regulate splicing efficiency and suppress weak splice sites, suggesting a role in enabling intron diversity through error limitation.

This study uses cortical organoids derived from patients with 16p11.2 CNV to show altered neurodevelopmental processes, including changes in organoid size, neuronal maturation, and migration.

The paper maps O-glycosylation sites on SARS-CoV-2 spike protein produced in insect and human cells, identifying 25 sites with distinct patterns between ectodomains and RBD.

This study shows that Cul3 haploinsufficiency in mice causes social and cognitive deficits, cortical volume reduction, and cytoskeletal defects, which are rescued by RhoA inhibition.

This study uses CPP to identify CFTR conformational changes during biogenesis and misfolding, revealing a novel opening mechanism and highlighting the role of the ICL2:NBD2 interface.

This study identifies host proteins interacting with SARS-CoV-2 spike protein, showing that D614G mutation affects spike processing and tropism, and introduces pCtSEA to analyze cell type-specific interactions.

The paper identifies SNPC-1.3 as a male-specific transcription factor that regulates piRNA expression in C. elegans and shows its sex-specific regulation by TRA-1.

This study shows that PIR-1 dephosphorylates ppp-RNAs and is essential for 26G-RNA maturation and regulation of gene expression in C. elegans.

This study uses proteomic techniques to profile newly synthesized proteins in AD transgenic mice, revealing age-dependent changes and dysregulated vesicle transport networks prior to Aβ accumulation.

The paper shows TyrRS mediates a late integrated stress response by inhibiting translation and protecting cells from prolonged stress through nuclear translocation.

The paper identifies trans regulators of ADAR1 and ADAR2 using BioID and mass-spectrometry, validating novel interactors as RNA editing regulators.

The paper investigates the mechanisms and organization of clathrin transport and presynaptic targeting in neurons, revealing stable transport-packets and their role in synaptic clathrin organization.

This study identifies tick saliva proteins injected during feeding using LC-MS/MS, finding 284 conserved proteins that may serve as vaccine targets.

The paper shows that DNA methylation persists in Cryptococcus neoformans despite the loss of a de novo methyltransferase, with methylation patterns maintained through replication and natural selection.

The paper identifies five novel genes required for RNAi-mediated transposon suppression in C. neoformans, revealing a non-Dicer RNase III and nucleolar factors involved in endo-siRNA biogenesis.

TargetSeeker-MS identifies drug targets on a proteome scale using EBPS-MS data, showing reproducibility in C. elegans and HEK293 samples treated with benomyl.

This study shows CCDC11 is essential for cytokinesis and cell-cell adhesion via RhoA regulation, linking it to heterotaxy disease pathogenesis.

The paper identifies CBD-1 as a scaffold protein in C. elegans that forms two distinct complexes for vitelline layer assembly and egg activation, revealing its multifaceted role in eggshell formation and fertilization.

The paper shows that MET-2/SETDB1 and its interactors LIN-65/ATF7IP and ARLE-14/ARL14EP regulate the timing of heterochromatin formation during C. elegans embryogenesis.

The paper develops a method to profile spliceosome-bound RNA at nucleotide resolution in yeast, revealing non-canonical splicing events and substrate features influencing catalytic efficiency.

The paper identifies novel proteins synthesized in response to visual experience in Xenopus tectal neurons and shows their role in structural and behavioral plasticity.

PATS identifies novel peptides from existing mass spectrometry data by filtering the peptidome and using interactome data to infer protein function.