Masaki Matsumoto

Physiological mapping and prediction reveal stress-responsive translation initiation landscapes

This study introduces TISCA2 and IncepTIS to map and predict stress-responsive translation initiation sites, revealing tissue-specific patterns and enabling engineered mRNA 5' leaders.

Characterizing lipoprotein profiles in coronary atherosclerosis development through quantitative lipidomics and proteomics approaches

This study uses lipidomics and proteomics to analyze lipoprotein changes in coronary atherosclerosis, finding ceramide molecules are significantly associated with early stage progression.

Unveiling novel signaling roles for human KDELR3 and KDELR1KDELRs Control AGR2 Biogenesis

The paper shows KDELR1 and KDELR3 regulate AGR2 production oppositely, revealing a novel regulatory circuit involving ERp44-KDELR3 interactions.

Global loss of responsiveness in key regulator metabolites and elevated enzyme proteins as metabolic dysregulation in skeletal muscle and liver of obese mice during starvation

The paper examines metabolic adaptations during starvation in obese mice, finding impaired responsiveness and elevated enzyme expression in skeletal muscle and liver.

Data-Independent Acquisition (DIA)-Based Label-Free Redox Proteomics (DIALRP) Reveals Novel Oxidative Stress Responsive Translation Factors

This study introduces DIALRP, a DIA-MS-based redox proteomics method, to identify oxidative stress-responsive translation factors in prostate cancer cells.

Structural robustness and temporal vulnerability of the starvation-responsive metabolic network in liver of healthy and obese mice

The paper examines how obesity disrupts the temporally ordered metabolic network in the liver during starvation, revealing structural robustness but temporal vulnerability.

Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity

The paper compares metabolic dysregulation in obese mice during feeding and fasting using multi-omics data, revealing opposite metabolic shifts linked to obesity.

Extracellular disposal of nuclear waste by APP: a protective mechanism impaired in Alzheimer's disease

This study identifies APP's role in extracellular disposal of nuclear waste, showing its impairment in Alzheimer's disease and suggesting it as a therapeutic target.

LIGHTHOUSE illuminates therapeutics for a variety of diseases including COVID-19

LIGHTHOUSE identifies novel therapeutics for diseases including cancer, bacterial infections, and COVID-19 using a graph-based deep learning approach without requiring 3D structural data.

Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism

This paper introduces OMELET, a method to infer metabolic flux from multi-omic data, and applies it to identify obesity-associated dysregulation in liver glucose metabolism.

Trans-omic analysis reveals allosteric and gene regulation-axes for altered glucose-responsive liver metabolism associated with obesity

The paper analyzes trans-omic data from healthy and obese mice to reveal that glucose-responsive liver metabolism is regulated by rapid changes in metabolites and gene expression in the healthy state, and by slow transcriptional regulation in the obese state.

mitoNEET Regulates Mitochondrial Iron Homeostasis Interacting with Transferrin Receptor

This study identifies mitoNEET as a protein that interacts with transferrin receptor to regulate mitochondrial iron homeostasis, leading to increased iron content and ROS production in the heart when mitoNEET is disrupted.

Trans-omic analysis reveals fed and fasting insulin signal across phosphoproteome, transcriptome, and metabolome

The paper constructs a trans-omic network of insulin action using phosphoproteomic, transcriptomic, and metabolomic data to identify fed and fasting insulin signals.