Shinya Kuroda

发表

Inositol 1,4,5-Trisphosphate-Dependent Ca2+ Threshold Dynamics Detect Spike Timing in Cerebellar Purkinje Cells

M. Kawato, Tomokazu Doi, Shinya Kuroda, 2005, The Journal of Neuroscience.

Cerebellar aminergic neuromodulation: towards a functional understanding

K. Doya, N. Schweighofer, Shinya Kuroda, 2004, Brain Research Reviews.

Cerebellar supervised learning revisited: biophysical modeling and degrees-of-freedom control

Mitsuo Kawato, Nicolas Schweighofer, Shinya Kuroda, 2011, Current Opinion in Neurobiology.

Behavioral / Systems / Cognitive Inositol 1 , 4 , 5-Trisphosphate-Dependent Ca 2 Threshold Dynamics Detect Spike Timing in Cerebellar Purkinje Cells

M. Kawato, Tomokazu Doi, Shinya Kuroda, 2005 .

Ca2+‐independent phospholipase A2‐dependent sustained Rho‐kinase activation exhibits all‐or‐none response

H. Urakubo, Sudhir Sivakumaran, Shinya Kuroda, 2006, Genes to cells : devoted to molecular & cellular mechanisms.

Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks

Yutaka Suzuki, K. Nakayama, Shinya Kuroda, 2018, iScience.

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

Yutaka Suzuki, K. Nakayama, Shinya Kuroda, 2017, bioRxiv.

ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm

Haruka Ozaki, Wataru Iwasaki, Shinya Kuroda, 2016, Nature Genetics.

Requirement of an Allosteric Kinetics of NMDA Receptors for Spike Timing-Dependent Plasticity

H. Urakubo, R. Froemke, Shinya Kuroda, 2008, The Journal of Neuroscience.

Metabolism as a signal generator across trans-omic networks at distinct time scales

Shinya Kuroda, K. Yugi, 2018 .

Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity

Yutaka Suzuki, K. Nakayama, Shinya Kuroda, 2020, Science Signaling.

Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics

D. James, Shinya Kuroda, K. Yugi, 2019, Current Opinion in Systems Biology.

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

Yutaka Suzuki, K. Nakayama, Shinya Kuroda, 2019, bioRxiv.

Temporal coding of insulin action through multiplexing of the AKT pathway.

Shinya Kuroda, Yu-ichi Ozaki, Hiroyuki Kubota, 2012, Molecular cell.

The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns

Shinya Kuroda, T. Soga, K. Yugi, 2013 .

Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin

R. Scalzo, L. Quek, D. James, 2020, iScience.

Prediction and validation of the distinct dynamics of transient and sustained ERK activation

Shinya Kuroda, Yu-ichi Ozaki, S. Sasagawa, 2005, Nature Cell Biology.

Robustness and Compensation of Information Transmission of Signaling Pathways

Shinya Kuroda, Yu-ichi Ozaki, Hiroyuki Kubota, 2013, Science.

Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection.

Tina Toni, Michael P H Stumpf, Shinya Kuroda, 2012, Molecular bioSystems.

Analysis of cellular signal transduction from an information theoretic approach.

Shinsuke Uda, Shinya Kuroda, Shinya Kuroda, 2016, Seminars in cell & developmental biology.

Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics

Hiroyuki Kubota, Shinsuke Uda, Yu Toyoshima, 2010, Science Signaling.

Model-based control of the temporal patterns of intracellular signaling in silico

Masanori Koyama, S. Ishii, Shinya Kuroda, 2017, Biophysics and physicobiology.

Analysis of Development of Direction Selectivity in Retinotectum by a Neural Circuit Model with Spike Timing-Dependent Plasticity

Keiko Tanaka, Hidetoshi Urakubo, Shinya Kuroda, 2011, The Journal of Neuroscience.

Foundations of Systems Biology Foundations of Systems Biology Library of Congress Cataloging-in-publication Data

M. A. Keane, Jehoshua Bruck, M. Kawato, 2000 .

Robustness against additional noise in cellular information transmission.

Shinya Kuroda, Masashi Fujii, Takehiro Tottori, 2019, Physical review. E.

Origins of cell-to-cell variability, kinetic proof-reading and the robustness of MAPK signal transduction

Chris P. Barnes, S. Filippi, M. Stumpf, 2015, bioRxiv.

Small-Volume Effect Enables Robust, Sensitive, and Efficient Information Transfer in the Spine.

Shinya Kuroda, Masashi Fujii, Kaoru Ohashi, 2016, Biophysical journal.

Stochasticity in Ca2+ Increase in Spines Enables Robust and Sensitive Information Coding

H. Urakubo, Shinya Kuroda, Masashi Fujii, 2013, PloS one.

Single-Cell Information Analysis Reveals That Skeletal Muscles Incorporate Cell-to-Cell Variability as Information Not Noise.

N. Fujii, Shinya Kuroda, Hiroyuki Kubota, 2020, Cell reports.

Trans-omic Analysis Reveals ROS-Dependent Pentose Phosphate Pathway Activation after High-Frequency Electrical Stimulation in C2C12 Myotubes

Yutaka Suzuki, N. Fujii, Shinya Kuroda, 2020, iScience.

In Vitro Reconstitution of a Memory Switch of CaMKII by NMDA Receptor-Derived Peptide Running title: Reconstitution of a CaMKII Memory Switch

H. Urakubo, Shin Ishii, Shinya Kuroda, 2019 .

Logical design of oral glucose ingestion pattern minimizing blood glucose in humans

Masanori Koyama, S. Ishii, Shinya Kuroda, 2018, npj Systems Biology and Applications.

Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects

Shinya Kuroda, Hiroyuki Kubota, Masashi Fujii, 2018, npj Systems Biology and Applications.

Trans-omics analysis of insulin action reveals a cell growth subnetwork which co-regulates anabolic processes

N. Perrimon, M. Bulyk, Yanhui Hu, 2022, iScience.

System Identification Using Compressed Sensing Reveals Signaling-Decoding System by Gene Expression

Shinya Kuroda, Hiroyuki Kubota, Masashi Fujii, 2017, bioRxiv.

Logical design of oral glucose ingestion pattern minimizing blood glucose in humans

Masanori Koyama, S. Ishii, Shinya Kuroda, 2019, npj Systems Biology and Applications.

Construction of an inter-organ transomic network for whole-body metabolism

Shinya Kuroda, Toshiya Kokaji, 2022, Current Opinion in Endocrine and Metabolic Research.

Development of a microfluidic cell culture and monitoring system for intracellular signaling studies

H. Kimura, T. Fujii, Shinya Kuroda, 2018, bioRxiv.

In Vivo Decoding Mechanisms of the Temporal Patterns of Blood Insulin by the Insulin-AKT Pathway in the Liver.

Shinya Kuroda, Hiroyuki Kubota, Shinsuke Uda, 2018, Cell systems.

Acquirement of direction selectivity through STDP in retinotectum

H. Urakubo, Shinya Kuroda, Minoru Honda, 2009, Neuroscience Research.

Effects of low-carbohydrate diet and resistance exercise training on physical characteristics and concentrations of plasma metabolites and hormones

Shinya Kuroda, Masashi Fujii, Daisuke Hoshino, 2019, Japanese Journal of Physical Fitness and Sports Medicine.

Specific features of transient Ras and sustained Rap1 activation

Shinya Kuroda, Yu-ichi Ozaki, Shinsuke Uda, 2009 .

Experimental and computational aspects of signaling mechanisms of spike‐timing‐dependent plasticity

Keiko Tanaka, Hidetoshi Urakubo, Shinya Kuroda, 2009, HFSP journal.

Exploration of Signal Transduction Pathways in Cerebellar Long-Term Depression by Kinetic Simulation

M. Kawato, S. Kuroda, N. Schweighofer, 2001, The Journal of Neuroscience.

NMDAR-Mediated Ca2+ Increase Shows Robust Information Transfer in Dendritic Spines.

Shinya Kuroda, Masashi Fujii, Takehiro Tottori, 2019, Biophysical journal.

“Small and many” is the strategy for robust and efficient information transfer in dendritic spines

Shinya Kuroda, Masashi Fujii, Takehiro Tottori, 2018, bioRxiv.

A common framework of signal processing in the induction of cerebellar LTD and cortical STDP

Hidetoshi Urakubo, Shinya Kuroda, Takuya Koumura, 2013, Neural Networks.

In vitro reconstitution of a CaMKII memory switch by an NMDA receptor-derived peptide.

Shin Ishii, Hidetoshi Urakubo, Shinya Kuroda, 2014, Biophysical journal.

Kinetic simulation study of cerebellar long-term depression

N. Schweighofer, Shinya Kuroda, 2001 .

System identification of signaling dependent gene expression with different time-scale data

Naoki Matsuda, Katsumi Konishi, Hiroyuki Kubota, 2017, PLoS Comput. Biol..

Laguerre Filter Analysis with Partial Least Square Regression Reveals a Priming Effect of ERK and CREB on c-FOS Induction

Shinsuke Uda, Takumi Wada, Takamasa Kudo, 2016, PloS one.

Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling

Sarah Filippi, Takumi Wada, Katsuyuki Kunida, 2016, Cell reports.

Temporal Coding of Insulin Signaling

Shinya Kuroda, Hiroyuki Kubota, 2015 .

The Extraction of Simple Relationships in Growth Factor-Specific Multiple-Input and Multiple-Output Systems in Cell-Fate Decisions by Backward Elimination PLS Regression

Hiroyuki Kubota, Shinsuke Uda, Takamasa Kudo, 2013, PloS one.

Temporal Decoding of MAP Kinase and CREB Phosphorylation by Selective Immediate Early Gene Expression

Shinsuke Uda, Shinya Kuroda, Yu-ichi Ozaki, 2013, PloS one.

Latent process genes for cell differentiation are common decoders of neurite extension length

Shinsuke Uda, Katsuyuki Yugi, Shinya Kuroda, 2012, Journal of Cell Science.

A Quantitative Image Cytometry Technique for Time Series or Population Analyses of Signaling Networks

Hiroyuki Kubota, Shinsuke Uda, Shinya Kuroda, 2010, PloS one.

Timing-Dependent Actions of NGF Required for Cell Differentiation

Hiroyuki Kubota, Shinsuke Uda, Shinya Kuroda, 2010, PloS one.

Dynamic characteristics of transient responses.

Shinya Kuroda, Yu-ichi Ozaki, S. Sasagawa, 2005, Journal of biochemistry.

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

Yutaka Suzuki, K. Nakayama, Shinya Kuroda, 2021, bioRxiv.

Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes

L. Quek, D. James, Shinya Kuroda, 2020, iScience.

Whole‐body clearing of beetles by successive treatment with hydrogen peroxide and CUBIC reagents

Shinya Kuroda, Monto Kuroda, 2020, Entomological Science.

Mesenchymal-epithelial transition during somitic segmentation is regulated by differential roles of Cdc42 and Rac1.

Shinya Kuroda, K. Kaibuchi, Yoshiko Takahashi, 2004, Developmental cell.

In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states

Shinya Kuroda, T. Soga, Yunfan Bai, 2022, Scientific Reports.

An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver.

K. Nakayama, Shinya Kuroda, Y. Ohkawa, 2021, Cell reports.

Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers.

Hiroyuki Kubota, Katsuyuki Yugi, Shinya Kuroda, 2016, Trends in biotechnology.

Quantitative metabolic fluxes regulated by trans-omic networks

Shinya Kuroda, S. Ohno, Saori Uematsu, 2022, The Biochemical journal.

Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin

R. Scalzo, L. Quek, D. James, 2020, iScience.

Reconstruction of insulin signal flow from phosphoproteome and metabolome data.

K. Nakayama, Shinya Kuroda, K. Ikeda, 2014, Cell reports.

Metabolism-Centric Trans-Omics.

Shinya Kuroda, K. Yugi, 2017, Cell systems.

Raf Kinase Inhibitory Protein is Required for Cerebellar Long-Term Synaptic Depression by Mediating PKC-Dependent MAPK Activation

Dongwon Lee, Shinya Kuroda, Bokyoung Lee, 2012, The Journal of Neuroscience.

An optogenetic system for interrogating the temporal dynamics of Akt

Shinya Kuroda, Hiroyuki Kubota, T. Ozawa, 2015, Scientific Reports.

Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin

Yutaka Suzuki, Shinya Kuroda, Miharu Sato, 2016, Science Signaling.

Features extracted using tensor decomposition reflect the biological features of the temporal patterns of human blood multimodal metabolome

Shinya Kuroda, Y-h. Taguchi, Ken-ichi Hironaka, 2022, bioRxiv.

Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans

Shinya Kuroda, T. Soga, Hiroyuki Kubota, 2022, NPJ systems biology and applications.

Imaging and Single‐Cell Measurement Technologies

Shinya Kuroda, Yu-ichi Ozaki, 2011 .

Fat Induces Glucose Metabolism in Nontransformed Liver Cells and Promotes Liver Tumorigenesis

D. di Bernardo, D. Lambrechts, Robert Schmieder, 2021, Cancer Research.

Sensitivity control through attenuation of signal transfer efficiency by negative regulation of cellular signalling

Shinsuke Uda, Yu Toyoshima, Shinya Kuroda, 2012, Nature Communications.

Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data

K. Nakayama, Shinya Kuroda, Kentaro Kawata, 2018, Genes to cells : devoted to molecular & cellular mechanisms.

Optogenetic decoding of Akt2-regulated metabolic signaling pathways in skeletal muscle cells using transomics analysis

Shinya Kuroda, T. Soga, Kentaro Kawata, 2023, Science Signaling.

Faculty Opinions recommendation of Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data.

Katsuyuki Yugi, Shinya Kuroda, Shinya Kuroda, 2017 .

Faculty Opinions recommendation of Systems biology. Accurate information transmission through dynamic biochemical signaling networks.

Katsuyuki Kunida, Shinya Kuroda, Shinya Kuroda, 2017 .

Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle

Yutaka Suzuki, K. Nakayama, Shinya Kuroda, 2021, iScience.

Dynamic Metabolomics Reveals that Insulin Primes the Adipocyte for Glucose Metabolism.

Sean J. Humphrey, R. Scalzo, L. Quek, 2017, Cell reports.

A Mass Conserved Reaction–Diffusion System Captures Properties of Cell Polarity

Shuji Ishihara, Shinya Kuroda, Atsushi Mochizuki, 2006, PLoS Comput. Biol..

Omics-based label-free metabolic flux inference reveals dysregulation of glucose metabolism in liver associated with obesity

Yutaka Suzuki, K. Nakayama, Shinya Kuroda, 2021 .

Spatial Localization of Synapses Required for Supralinear Summation of Action Potentials and EPSPs

Takeshi Aihara, Masataka Watanabe, Shunsuke Kondo, 2004, Journal of Computational Neuroscience.

Monitoring and mathematical modeling of mitochondrial ATP in myotubes at single-cell level reveals two distinct population with different kinetics

Haruki Inoue, Hiroyuki Noji, Naoki Matsuda, 2020, Quantitative Biology.

Glucose Homeostatic Law: Insulin Clearance Predicts the Progression of Glucose Intolerance in Humans

Hiroyuki Kubota, Shinsuke Uda, Yu Toyoshima, 2015, PloS one.

Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans

Shinya Kuroda, T. Soga, Hiroyuki Kubota, 2022, npj Systems Biology and Applications.

Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects

Shinya Kuroda, Hiroyuki Kubota, Masashi Fujii, 2018, npj Systems Biology and Applications.

DI/cle, a Measure Consisting of Insulin Sensitivity, Secretion, and Clearance, Captures Diabetic States

Shinya Kuroda, Hikaru Sugimoto, Ken-ichi Hironaka, 2023, bioRxiv.

Insulin Effectiveness, a Measure Consisting of Insulin Sensitivity, 1 Secretion, and Clearance, Captures Differences Between Diabetic and 2 Nondiabetic States 3

Wataru, Shinya Kuroda, Hikaru Sugimoto, 2022 .

Cell-to-cell variability serves as information not noise

Shinya Kuroda, Ken-ichi Hironaka, Takumi Wada, 2021 .

A Conceptual Molecular Network for Chemotactic Behaviors Characterized by Feedback of Molecules Cycling Between the Membrane and the Cytosol

Shinya Kuroda, K. Matsushima, S. Ishihara, 2010, Science Signaling.

Automatic Quantitative Segmentation of Myotubes Reveals Single-cell Dynamics of S6 Kinase Activation.

Hiroyuki Noji, Takumi Wada, Katsuyuki Kunida, 2018, Cell structure and function.

Comparison of hepatic responses to glucose perturbation between healthy and obese mice based on the edge type of network structures

Shinya Kuroda, T. Soga, Hiroyuki Kubota, 2023, Scientific Reports.

Bidirectional changes of hepatic and peripheral insulin clearance characterize abnormal temporal patterns of serum insulin concentration in diabetic subjects

Shinya Kuroda, Hiroyuki Kubota, Masashi Fujii, 2017, bioRxiv.

A common framework of signal processing in the induction of cerebellar LTD and cortical STDP

H. Urakubo, Shinya Kuroda, Takuya Koumura, 2013, Neural Networks.

Robustness against additional noise in cellular information transmission.

Shinya Kuroda, Masashi Fujii, Takehiro Tottori, 2019, Physical review. E.

The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns

Shinya Kuroda, K. Yugi, Hiroyuki Kubota, 2013, Molecular systems biology.

Temporal coding of insulin action through multiplexing of the AKT pathway.

Shinya Kuroda, Yu-ichi Ozaki, Hiroyuki Kubota, 2012, Molecular cell.

DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle

Shinya Kuroda, Atsushi Hatano, Hiroyuki Kubota, 2023, Scientific reports.

[Simulation of IP3/Ca2+ signaling pathway in neurons: the system of coincidence detection of input timing in cerebellar Purkinje cells].

M. Kawato, Tomokazu Doi, Shinya Kuroda, 2003, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.

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

K. Nakayama, Shinya Kuroda, T. Soga, 2022, iScience.

System Identification Using Compressed Sensing Reveals Signaling-Decoding System by Gene Expression

Shinya Kuroda, Hiroyuki Kubota, Masashi Fujii, 2017, bioRxiv.

Single-cell information analysis reveals small intra- and large intercellular variations increase cellular information capacity

N. Fujii, Shinya Kuroda, Hiroyuki Kubota, 2019, bioRxiv.

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

Shinya Kuroda, Atsushi Hatano, K. Yugi, 2023, bioRxiv.