Katsuyuki Yugi
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View article: Dissociation of LAG-3 inhibitory cluster from TCR microcluster by immune checkpoint blockade
Dissociation of LAG-3 inhibitory cluster from TCR microcluster by immune checkpoint blockade Open
Lymphocyte activation gene (Lag)-3 is an inhibitory co-receptor and target of immune checkpoint inhibitor (ICI) therapy for cancer. The dynamic behavior of Lag-3 was analyzed at the immune synapse upon T-cell activation to elucidate the La…
View article: Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity
Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity Open
SUMMARY Dysregulation of liver metabolism associated with obesity during feeding and fasting leads to the breakdown of metabolic homeostasis. However, the underlying mechanism remains unknown. Here, we measured multi-omics data in the live…
View article: transomics2cytoscape: An automated software for interpretable 2.5-dimensional visualization of trans-omic networks
transomics2cytoscape: An automated software for interpretable 2.5-dimensional visualization of trans-omic networks Open
Biochemical network visualization is one of the essential technologies for mechanistic interpretation of omics data. In particular, recent advances in multi-omics measurement and analysis require the development of visualization methods th…
View article: A trans-omic analysis of metformin action in the liver
A trans-omic analysis of metformin action in the liver Open
Metformin is a drug for type 2 diabetes used as the first-line mainly in North America and Europe. Its mechanism of action is believed to lower blood glucose levels by inhibiting gluconeogenesis in the liver and increasing glucose consumpt…
View article: In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states
In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states Open
Metabolic regulation in skeletal muscle is essential for blood glucose homeostasis. Obesity causes insulin resistance in skeletal muscle, leading to hyperglycemia and type 2 diabetes. In this study, we performed multiomic analysis of the s…
View article: Meta-analysis of transcriptional regulatory networks for lipid metabolism in neural cells from schizophrenia patients based on an open-source intelligence approach
Meta-analysis of transcriptional regulatory networks for lipid metabolism in neural cells from schizophrenia patients based on an open-source intelligence approach Open
There have been a number of reports about the transcriptional regulatory networks in schizophrenia. However, most of these studies were based on a specific transcription factor or a single dataset, an approach that is inadequate to underst…
View article: Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin
Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin Open
[This corrects the article DOI: 10.1016/j.isci.2020.100855.].
View article: Trans-omic Analysis Reveals ROS-Dependent Pentose Phosphate Pathway Activation after High-Frequency Electrical Stimulation in C2C12 Myotubes
Trans-omic Analysis Reveals ROS-Dependent Pentose Phosphate Pathway Activation after High-Frequency Electrical Stimulation in C2C12 Myotubes Open
Skeletal muscle adaptation is mediated by cooperative regulation of metabolism, signal transduction, and gene expression. However, the global regulatory mechanism remains unclear. To address this issue, we performed electrical pulse stimul…
View article: Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes
Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes Open
Insulin regulates glucose metabolism through thousands of regulatory mechanisms; however, which regulatory mechanisms are keys to control glucose metabolism remains unknown. Here, we performed kinetic trans-omic analysis by integrating iso…
View article: Trans-omic analysis reveals allosteric and gene regulation-axes for altered glucose-responsive liver metabolism associated with obesity
Trans-omic analysis reveals allosteric and gene regulation-axes for altered glucose-responsive liver metabolism associated with obesity Open
Impaired glucose tolerance associated with obesity causes postprandial hyperglycemia and can lead to type 2 diabetes. To study the differences in liver metabolism in the healthy and obese states, we constructed and analyzed trans-omic gluc…
View article: Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics
Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics Open
We have presented 'trans-omics', a discipline that mechanistically connects multiple omic layers. The relationships between molecules of distinct omic layers are governed by reaction rate equations such as v = k [S] (v: reaction rate; k: r…
View article: Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data
Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data Open
Cellular signaling regulates various cellular functions via protein phosphorylation. Phosphoproteomic data potentially include information for a global regulatory network from signaling to cellular functions, but a procedure to reconstruct…
View article: Trans-omic analysis reveals fed and fasting insulin signal across phosphoproteome, transcriptome, and metabolome
Trans-omic analysis reveals fed and fasting insulin signal across phosphoproteome, transcriptome, and metabolome Open
SUMMARY The concentration and temporal pattern of insulin selectively regulate multiple cellular functions. To understand how insulin dynamics are interpreted by cells, we constructed a trans-omic network of insulin action in FAO hepatoma …