John R. Yates

dnoise reduces Bruker timsTOF data size with minimal impact on analysis results.

The paper reports cryo-EM structures of cardiac AL amyloid fibrils from IGLV6 light chains, revealing conserved structural motifs and sequence-dependent folding mechanisms.

The paper quantifies spatial proteoforms in Alzheimer's disease by analyzing subcellular protein localization and identifies key pathways disrupted in disease progression.

This study shows that Hrs, an ESCRT-0 protein, modulates AMPA receptor currents and Ca2+-dependent signaling by sensing and responding to neuronal activity at synapses.

This paper introduces RIPUP, a rapid protease-based workflow for histone PTM analysis, showing improved PTM coverage and quantitative accuracy using TMT labeling and complementary proteases.

This paper describes the development and cGMP manufacturing of an HIV vaccine candidate for clinical trials, demonstrating scalable production and quality control.

This paper designs synthetic transmembrane subunits to stabilize and expand membrane proteins, demonstrating their utility in structural biology and disease treatment.

The paper characterizes extracellular vesicles from Alzheimer's disease and wild-type cerebrocortical organoids, finding differences in size, membrane structure, and proteomic content.

The paper identifies new ciliary proteins in the developing brain using proteomics and validates their roles in cortical development.

This study shows that Group A Streptococcus perforates macrophage phagolysosomes, releasing both host and bacterial proteins into the cytosol, which triggers inflammatory responses and contributes to disease pathology.

The paper identifies S-nitrosylation of STING as a redox modification driving aberrant cGAS-STING signaling in Alzheimer's disease, contributing to neuroinflammation and synaptic loss.

This study introduces a shotgun single-cell top-down proteomics method to profile proteoform diversity in cardiomyocytes, revealing significant molecular heterogeneity across individual cells.

This paper shows that Spt5's KOW domains and the Pol II stalk work together in yeast to regulate transcription termination and chromatin structure.

The paper maps protein-protein interactions of schizophrenia risk factors in rodent brains, revealing an interconnected disease network and showing how PCP perturbations alter these interactions.

This study uses proteomics to compare CSF from alcohol-dependent and non-dependent mice, identifying molecular changes linked to BBB dysfunction and neuroinflammation.

The paper shows that spaceflight triggers neural senescence via reactivation of dormant viral-like retroelements, and that reverse transcriptase inhibitors can reverse these effects.

This paper introduces a framework for interpreting single-cell proteomics data from patch-clamped neurons in acute brain slices, showing how retrieval quality affects proteomic outcomes.

Membrane-bound BG505 MD39.3 Env trimer delivered as mRNA-LNP reduced base-directed antibody responses in rabbits and macaques and elicited neutralizing antibodies, with memory B cell responses documented in macaques.

The paper examines how mutations and a deletion in the KP.3.1.1 SARS-CoV-2 spike protein affect ACE2 binding and antibody escape, revealing structural and functional insights into its evolution.

The paper presents a nanodisc platform for assembling transmembrane glycoproteins into vaccine candidates, demonstrating its utility in HIV vaccine development through structural and functional analyses.

The paper identifies Emerin as an activity-induced protein that gates neuronal plasticity by inhibiting protein synthesis and altering dendritic spine morphology.

The paper shows that PrPC ligands in human neurons trigger PLCγ1 signaling and an Arc/Arg3.1 response, indicating neuronal hyperactivity in prion disease.

The paper uses proximity proteomics to identify Git1 as a regulator of Smo signaling in the Hedgehog pathway, showing its role in Grk2 transport and Smo phosphorylation.

This study compares cleavable and uncleavable biotin-alkyne labels in BONCAT analysis, finding that cleavable labels improve protein identification and quantification.

CandyCollect is a microfluidic device for rapid, non-invasive salivary EV collection and analysis, showing consistent EV capture and concordant protein profiles.

The paper investigates whether perineuronal nets (PNNs) stabilize synaptic circuits and engram formation through high-resolution imaging and experimental approaches.

This study identifies key structural and glycosylation features of EtpA, an ETEC adhesin, and shows how antibodies target different epitopes to influence immune responses and pathogen-host interactions.

This study identifies acetylation of lysine 82 in TDP-43 as a mechanism causing nuclear loss of function and cytoplasmic accumulation, linked to neurodegenerative diseases like ALS.

The paper identifies a relationship between protein structure and glycan structure, introducing a glycoimpact matrix to predict glycosylation patterns and validate it through disease variants and engineered antibodies.

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.