Yukiko Matsuoka

发表

Establishment of Organoids From Human Epithelioid Sarcoma With the Air-Liquid Interface Organoid Cultures

Yoshinori Imura, Satoshi Takenaka, S. Sasagawa, 2022, Frontiers in Oncology.

Software Platform for Metabolic Network Reconstruction of Mycobacterium tuberculosis

Anup D. Shah, H. Kitano, Y. Asai, 2013 .

Disease-related cellular protein networks differentially affected under different EGFR mutations in lung adenocarcinoma

H. Kato, H. Saji, H. Koizumi, 2020, Scientific Reports.

Interleukin 34 (IL-34) cell-surface localization regulated by the molecular chaperone 78-kDa glucose-regulated protein facilitates the differentiation of monocytic cells

H. Tokumitsu, F. Yamane, N. Hatano, 2018, The Journal of Biological Chemistry.

An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation

Yukiko Matsuoka, Hiroaki Kitano, Jason E. Shoemaker, 2015, PLoS pathogens.

Weaving Knowledge into Biological Pathways in a Collaborative Manner

Yukiko Matsuoka, Hiroaki Kitano, Kazuhiro Fujita, 2015 .

Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map

Samik Ghosh, Yukiko Matsuoka, Hiroaki Kitano, 2013, Molecular Neurobiology.

Network-Guided Discovery of Influenza Virus Replication Host Factors

Tiago J. S. Lopes, Emily E. Ackerman, H. Kitano, 2018, mBio.

The Process Diagram: Rationale and Definition

H. Kitano, A. Funahashi, Yukiko Matsuoka, 2004 .

Influenza virus-host interactome screen as a platform for antiviral drug development.

Tiago J. S. Lopes, H. Kitano, M. Oyama, 2014, Cell host & microbe.

AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease

Samik Ghosh, Yukiko Matsuoka, Hiroshi Tanaka, 2012, BMC Systems Biology.

Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways

Samik Ghosh, Yukiko Matsuoka, Hiroaki Kitano, 2016, npj Systems Biology and Applications.

CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data

Tiago J. S. Lopes, H. Kitano, Samik Ghosh, 2012, BMC Genomics.

Lenvatinib plus anti-PD-1 antibody combination treatment activates CD8+ T cells through reduction of tumor-associated macrophage and activation of the interferon pathway

H. Kitano, Samik Ghosh, Ayako Yachie-Kinoshita, 2019, PloS one.

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases

Yukiko Matsuoka, Hiroaki Kitano, Martin H. Schaefer, 2011, Bioinform..

Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map

H. Kitano, Serge Eifes, A. del Sol, 2013, Molecular Neurobiology.

CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data

Tiago J. S. Lopes, H. Kitano, Samik Ghosh, 2012, BMC Genomics.

Network-Guided Discovery of Influenza Virus Replication Host Factors

Tiago J. S. Lopes, Emily E. Ackerman, H. Kitano, 2018, mBio.

A comprehensive pathway map of epidermal growth factor receptor signaling

H. Kitano, Y. Matsuoka, A. Funahashi, 2005, Molecular systems biology.

A comprehensive map of the mTOR signaling network

H. Kitano, E. Caron, Samik Ghosh, 2010, Molecular systems biology.

A comprehensive map of the influenza A virus replication cycle

Samik Ghosh, Yukiko Matsuoka, Hiroaki Kitano, 2013, BMC Systems Biology.

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

N. Kikuchi, H. Kitano, A. Funahashi, 2008, Proceedings of the IEEE.

Molecular Interaction Map of a Macrophage

Yukiko Matsuoka, Kanae Oda, Akira Funahashi, 2004 .

The Systems Biology Graphical Notation

Sarala M. Wimalaratne, Stuart L. Moodie, Frank T Bergman, 2009, Nature Biotechnology.

Metabolic syndrome and robustness tradeoffs.

J. Doyle, H. Kitano, M. Csete, 2004, Diabetes.

Using process diagrams for the graphical representation of biological networks

Yukiko Matsuoka, Hiroaki Kitano, Kanae Oda, 2005, Nature Biotechnology.

Software support for SBGN maps: SBGN-ML and LibSBGN

Yukiko Matsuoka, Hiroaki Kitano, Nicolas Le Novère, 2012, Bioinform..

CellDesigner: A Graphical Biological Network Editor and Workbench Interfacing Simulator

Yukiko Matsuoka, Hiroaki Kitano, Akira Funahashi, 2007 .

PathText: a text mining integrator for biological pathway visualizations

Yukiko Matsuoka, Hiroaki Kitano, Sophia Ananiadou, 2010, Bioinform..

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions

Yukiko Matsuoka, Hiroaki Kitano, Martin H. Schaefer, 2013, PLoS Comput. Biol..

Toward an integrated software platform for systems pharmacology

H. Kitano, Y. Asai, Samik Ghosh, 2013, Biopharmaceutics & drug disposition.

Software for systems biology: from tools to integrated platforms

H. Kitano, Y. Asai, Samik Ghosh, 2011, Nature Reviews Genetics.

Disease Severity Is Associated with Differential Gene Expression at the Early and Late Phases of Infection in Nonhuman Primates Infected with Different H5N1 Highly Pathogenic Avian Influenza Viruses

H. Kitano, C. Sasakawa, Eiryo Kawakami, 2014, Journal of Virology.

A comprehensive molecular interaction map of the budding yeast cell cycle

Samik Ghosh, Yukiko Matsuoka, Hiroaki Kitano, 2010, Molecular systems biology.

Identifying problematic drugs based on the characteristics of their targets

Yukiko Matsuoka, Hiroaki Kitano, Jason E. Shoemaker, 2015, Front. Pharmacol..

systemsDock: a web server for network pharmacology-based prediction and analysis

Yukiko Matsuoka, Yoshiyuki Asai, Kun-Yi Hsin, 2016, Nucleic Acids Res..

Modeling and simulation using CellDesigner.

Samik Ghosh, Yukiko Matsuoka, Hiroaki Kitano, 2014, Methods in molecular biology.

Integration of CellDesigner and SABIO-RK

Yukiko Matsuoka, Hiroaki Kitano, Akira Funahashi, 2007, Silico Biol..

Deconstructing the traditional Japanese medicine “Kampo”: compounds, metabolites and pharmacological profile of maoto, a remedy for flu-like symptoms

H. Kitano, A. Nishi, Masahiro Yamamoto, 2017, npj Systems Biology and Applications.

Consistent design schematics for biological systems: standardization of representation in biological engineering

Samik Ghosh, Yukiko Matsuoka, Hiroaki Kitano, 2009, Journal of The Royal Society Interface.

Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs

Yukiko Matsuoka, Hiroaki Kitano, Shinji Watanabe, 2012, BMC Systems Biology.

Deconstructing the traditional Japanese medicine “Kampo”: compounds, metabolites and pharmacological profile of maoto, a remedy for flu-like symptoms

H. Kitano, A. Nishi, Masahiro Yamamoto, 2017, npj Systems Biology and Applications.

Multi-dimensional computational pipeline for large-scale deep screening of compound effect assessment: an in silico case study on ageing-related compounds

Samik Ghosh, Yukiko Matsuoka, Hiroaki Kitano, 2019, npj Systems Biology and Applications.

A versatile platform for multilevel modeling of physiological systems: Template/instance framework for large-scale modeling and simulation

Samik Ghosh, Yukiko Matsuoka, Yoshiyuki Asai, 2013, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).

Social engineering for virtual 'big science' in systems biology.

Samik Ghosh, Yukiko Matsuoka, Hiroaki Kitano, 2011, Nature chemical biology.

BioPAX support in CellDesigner

Yukiko Matsuoka, Hiroaki Kitano, Anushya Muruganujan, 2011, Bioinform..

Payao: a community platform for SBML pathway model curation

Samik Ghosh, Yukiko Matsuoka, Hiroaki Kitano, 2010, Bioinform..

Systems Biology Graphical Notation: Process Diagram Level 1 Notes on Typographical Conventions

Yukiko Matsuoka, Hiroaki Kitano, Nicolas Le Novère, 2008 .

Connecting Text Mining and Pathways using the PathText Resource

Yukiko Matsuoka, Hiroaki Kitano, Naoaki Okazaki, 2008, LREC.

Celldesigner: A Modeling Tool for Biochemical Networks

Yukiko Matsuoka, Hiroaki Kitano, Norihiro Kikuchi, 2006, Proceedings of the 2006 Winter Simulation Conference.

Network Editor and Workbench Interfacing Simulator

Yukiko Matsuoka, Hiroaki Kitano, Akira Funahashi, 2007 .

Effects of maoto (ma-huang-tang) on host lipid mediator and transcriptome signature in influenza virus infection

H. Kitano, A. Nishi, A. Sugiyama, 2021, Scientific Reports.

Application of machine leaning approaches in drug target identification and network pharmacology

Samik Ghosh, Yukiko Matsuoka, Kun-Yi Hsin, 2015, 2015 International Conference on Intelligent Informatics and Biomedical Sciences (ICIIBMS).

LimeMap: a comprehensive map of lipid mediator metabolic pathways

H. Kitano, A. Nishi, Y. Kita, 2021, NPJ systems biology and applications.

Genetic characterization of a novel organoid from human malignant giant-cell tumor

Yoshinori Imura, Satoshi Takenaka, S. Sasagawa, 2023, Journal of bone oncology.

Bioinformatics Applications Note Systems Biology Biopax Support in Celldesigner

E. Demir, H. Mi, Yukiko Matsuoka, 2022 .

Systems Biology Graphical Notation: Process Diagram Level 1

H. Kitano, N. Novère, E. Demir, 2008 .

A comprehensive pathway map of epidermal growth factor receptor signaling

H. Kitano, Kanae Oda, Yukiko Matsuoka, 2005, Molecular systems biology.

Disease Severity Is Associated with Differential Gene Expression at the Early and Late Phases of Infection in Nonhuman Primates Infected with Different H5N1 Highly Pathogenic Avian Influenza Viruses

H. Kitano, C. Sasakawa, Eiryo Kawakami, 2014, Journal of Virology.

Erratum: The Systems Biology Graphical Notation

Samik Ghosh, Yukiko Matsuoka, Hiroaki Kitano, 2009, Nature Biotechnology.

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases

Martin H. Schaefer, Tiago J. S. Lopes, H. Kitano, 2011, Bioinform..