A5008451312- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Embedded Systems Design Techniques
- Cell Image Analysis Techniques
- Tardigrade Biology and Ecology
- Parallel Computing and Optimization Techniques
- Interconnection Networks and Systems
- Computational Drug Discovery Methods
- Image Processing Techniques and Applications
- 3D Printing in Biomedical Research
- Biocrusts and Microbial Ecology
- Cellular Mechanics and Interactions
- Advanced Fluorescence Microscopy Techniques
- Protein Structure and Dynamics
- Genetics, Aging, and Longevity in Model Organisms
- Biomedical Text Mining and Ontologies
- Microtubule and mitosis dynamics
- Spaceflight effects on biology
- Pluripotent Stem Cells Research
- Reproductive Biology and Fertility
- Genetics, Bioinformatics, and Biomedical Research
- Scientific Computing and Data Management
- Single-cell and spatial transcriptomics
- Genomics and Chromatin Dynamics
Keio University
2016-2025
Development Fund
2020
Sumitomo Dainippon Pharma (United States)
2019
Systems Biology Institute
2005-2012
European Bioinformatics Institute
2012
University of Manchester
2012
Leibniz Institute of Plant Genetics and Crop Plant Research
2012
University of Southern California
2011
Memorial Sloan Kettering Cancer Center
2011
Research Organization of Information and Systems
2010
Understanding of the logic and dynamics gene-regulatory biochemical networks is a major challenge systems biology. To facilitate this research topic, we have developed modeling/simulating tool called CellDesigner. CellDesigner primarily has capabilities to visualize, model, simulate networks. Two characteristics embedded in boost its usability create/import/export models: 1) solidly defined comprehensive graphical representation (systems biology notation) network models 2) markup language...
Researchers around the world join forces to reconstruct molecular processes of virus-host interactions aiming combat cause ongoing pandemic.
Abstract For a better understanding of the mechanisms behind cellular functions, quantification heterogeneity in an organism or cells is essential. Recently, importance quantifying temperature has been highlighted, as it correlates with biochemical reaction rates. Several methods for detecting intracellular have recently established. Here we develop novel method sensing living based on imaging technique fluorescence quantum dots. We apply to quantify difference human derived neuronal cell...
We need to effectively combine the knowledge from surging literature with complex datasets propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets intervention. Here, we describe a large-scale community effort build an open access, interoperable computable repository COVID-19 molecular mechanisms. The Disease Map (C19DMap) is graphical, interactive representation disease-relevant mechanisms linking many sources. Notably, it computational...
Abstract Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The (available in C++ Java) makes it easy developers to add SBGN support their tools, whereas format facilitates exchange of between compatible applications. also supports validation maps, which simplifies task ensuring compliance with detailed specifications. With this effort we hope increase adoption...
During embryogenesis, cells repeatedly divide and dynamically change their positions in three-dimensional (3D) space. A robust accurate algorithm to acquire the 3D of would help reveal mechanisms embryogenesis. To quantitative criteria embryogenesis from time-series microscopic images, image processing algorithms such as segmentation have been applied. Because embryos are considerably crowded, an segment individual detail accurately is needed. quantify nuclear region every cell a...
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging reproduce reuse simulations, in part, because the numerous formats methods for simulating various subsystems scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find use simulation tools, we developed BioSimulators (https://biosimulators.org), central registry of capabilities...
Hyperthermia can be induced to exploit the thermal intolerance of cancer cells, which is worse than that normal as a potential noninvasive treatment. To develop an effective hyperthermia treatment, cytotoxicity cells should comprehensively investigated. However, conduct such investigations, culture temperature must accurately regulated. We previously reported system in could regulated by employing metallic vessels. appropriate conditions for depend on cell species. Consequently, several...
The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification drug repurposing.
We provide an evaluation for electrically tunable lens (ETL), combined with a microscope system, from the viewpoint of tracking intracellular protein complexes. measured correlation between quantitative axial focus shift and control current ETL, determined stabilization time refocusing to evaluate electrical focusing behaviour our system. also confirmed that change relative magnification by associated resolution does not influence ability find targets. By applying ETL system observe...
Network-based parallel processing using commodity personal computers has been widely developed. Since such systems require high degree of flexibility and scalability wiring, a high-speed network with an irregular topology is often needed. In traditional routing algorithms for networks, available paths are considerably restricted in order to avoid deadlocks. this paper we propose novel algorithm called left-up-first turn (L-turn routing), which makes better traffic balancing networks by...
Recursive Diagonal Torus (RDT), a class of interconnection network is proposed for massively parallel computers with up to 2/sup 16/ nodes. By making the best use recursively structured diagonal mesh (torus) connection, RDT has smaller diameter (e.g., it 11 10/ nodes) number links per node (i.e., 8 node) than those hypercube. A simple routing algorithm, called vector routing, which near-optimal and easy implement also proposed. Although congestion on upper rank tori sometimes degrades...
ABSTRACT Microtubules execute diverse mitotic events that are spatially and temporally separated; the underlying regulation is poorly understood. By combining drug treatments, large-scale immunoprecipitation mass spectrometry, we report first comprehensive map of phase-specific protein interactions microtubule-end binding protein, EB1. EB1 interacts with some, but not all, its partners throughout mitosis. We show interaction Astrin-SKAP complex, a key regulator chromosome segregation,...
Tactile reproduction technology represents a promising advancement within the rapidly expanding field of virtual/augmented reality, necessitating development innovative methods specifically tailored to correspond with tactile sensory labels. Since human perception is known be influenced by visual information, this study has developed cross-modal display using Conditional Generative Adversarial Networks, CGANs, generate both mechanical and information. Initially, evaluation experiments were...
In assisted reproduction, many factors in the culture environment, including light, temperature, pH, and media, can reduce preimplantation embryo viability. Laboratory glassware is also a known risk factor for vitro embryos; however, underlying mechanisms that disrupt embryonic development remain unclear. We identified Zn eluted from as an embryotoxic substance. mouse embryos, induced delayed development, abnormalities chromosome segregation, cytokinesis, zygotic gene activation (e.g....