Ernesto Satoshi Nakayasu

This study profiles multi-omics data in Picochlorum celeri under CO2 limitation, revealing a CO2-dependent switch in Rubisco subunits and extensive post-translational modifications.

This study identifies a novel E3 ligase secreted by Pseudomonas aeruginosa that regulates virulence through ubiquitin modification.

The paper introduces RomicsProcessor, a reproducible-by-design tool for multi-omics and spatial-omics analysis that enforces FAIR principles and ensures computational reproducibility.

This study shows that NHR-68 in C. elegans links intestinal lipid metabolism to immune and behavioral responses through gut-brain signaling.

The paper identifies carbamylation as a regulatory modification in β-cell metabolism and insulin processing in T1D by analyzing proteomic changes in NOD and MIN6 cells.

This study evaluates plasma extracellular vesicle proteomics for identifying predictive biomarkers of type 1 diabetes development, finding 448 differentially abundant proteins and a 0.81 AUC in predicting islet autoimmunity.

This study identifies a novel lipid signaling pathway involving iPLA2β that links ER stress to β-cell apoptosis in T1D, revealing transcriptional regulation by iDLs and potential therapeutic targets.

This paper benchmarks feature screening methods for omics data classification, finding BcorSIS to be the most effective and efficient across various datasets.

This study shows calorie restriction delays type 1 diabetes onset in NOD mice by enhancing glucose homeostasis and promoting a pro-tolerogenic islet microenvironment through increased PD-L1 expression.

PTMOverlay visualizes post-translational modifications across species by aligning PTM sites to protein sequences, revealing conserved modifications in bacterial central carbon metabolism.

The paper uses single-islet proteomics to analyze pseudo-temporal immune responses and beta-cell dysfunction in stage 1 T1D, identifying key pathways involved in islet dysfunction.

This study identifies sex-specific islet responses to inflammation and shows that estrogen reduces inflammatory signaling and promotes immune tolerance in beta cells, contributing to sex differences in type 1 diabetes susceptibility.

This study shows that proinflammatory stress in beta cells increases ceramide-enriched extracellular vesicles via nSMase2, which may affect paracrine signaling in diabetes.

This paper develops a genetic code expansion platform for in vivo study of lysine acetylation in non-model bacteria, demonstrating its use in a non-E. coli strain.

This study investigates changes in human milk composition after SARS-CoV-2 infection or vaccination using multi-omics approaches, finding greater compositional changes post-infection than post-vaccination.

This study benchmarks label-free and TMT-MS2 methods for spatial proteome mapping, showing label-free provides deeper coverage and higher dynamic range, while TMT-MS2 offers faster throughput.

The paper validates 12 biomarkers from a small T1D cohort using data augmentation, identifying 7 significantly altered markers linked to T1D risk.

The paper identifies conserved bacterial protein methylation, showing ribosomal protein L11 methylation regulates stringent response signaling and ribosomal homeostasis.

This paper introduces a de novo metaproteomics pipeline using a deep learning model to identify soil microbiome composition and functions without relying on metagenomic data.

The paper analyzes C. auris gene expression and extracellular vesicle RNA changes under caspofungin treatment to understand resistance mechanisms.

The paper investigates lipid composition changes in insulitis models and identifies ARH3 as a regulator of beta-cell apoptosis through PLA2G6 signaling.

This study shows that pro-inflammatory cytokines reveal plasticity in β-cell regulatory landscapes and identify T1D-associated variants disrupting cytokine-responsive enhancers.

Q4SRM is a software tool that rapidly assesses the quality of targeted proteomics experiments by monitoring stable-isotope labeled standards.