A5058814000- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Genetics, Bioinformatics, and Biomedical Research
- Cell Image Analysis Techniques
- Genetics, Aging, and Longevity in Model Organisms
- Microbial Metabolic Engineering and Bioproduction
- Gene expression and cancer classification
- Scientific Computing and Data Management
- Reproductive Biology and Fertility
- Genomics and Chromatin Dynamics
- Developmental Biology and Gene Regulation
- CRISPR and Genetic Engineering
- Molecular Biology Techniques and Applications
- Genetic Mapping and Diversity in Plants and Animals
- Animal Genetics and Reproduction
- Pluripotent Stem Cells Research
- Plant nutrient uptake and metabolism
- Morphological variations and asymmetry
- Plant Reproductive Biology
- Spaceflight effects on biology
- Single-cell and spatial transcriptomics
- Chromosomal and Genetic Variations
- Evolutionary Algorithms and Applications
- Biomedical Text Mining and Ontologies
- Genomics and Phylogenetic Studies
RIKEN Center for Biosystems Dynamics Research
2014-2024
RIKEN Advanced Science Institute
2011-2020
RIKEN
2018
Japan Science and Technology Agency
2004-2012
Keio University
1997-2012
RIKEN Center for Integrative Medical Sciences
2008
Systems Biology Institute
1998
Sony Computer Science Laboratories
1998
A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals institutes across diverse modalities facing these have designed specification process (OME-NGFF) address needs. This paper brings together wide range those members describe cloud-optimized itself-OME-Zarr-along with tools data resources available today increase FAIR access remove barriers...
Motivation: Rapid advances in live-cell imaging analysis and mathematical modeling have produced a large amount of quantitative data on spatiotemporal dynamics biological objects ranging from molecules to organisms. There is now crucial need bring these amounts together centrally coherent systematic manner. This will facilitate the reuse this for further analysis. Results: We developed Systems Science Biological Dynamics database (SSBD) store share data. SSBD currently provides 311 sets...
A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals institutes across diverse modalities facing these have designed specification process (OME-NGFF) address needs. This paper brings together wide range those members describe cloud-optimized itself -- OME-Zarr along with tools data resources available today increase FAIR access remove...
Abstract SSBD (https://ssbd.riken.jp) is a platform for the sharing and reuse of bioimaging data. As part efforts to build data ecosystem, has recently been updated two-tiered resource comprising SSBD:repository, public repository all types reported in journals, SSBD:database, an added-value database curated, highly reusable, metadata-rich This update addresses conflicting demands rapid publication richly annotated data, thereby promoting reuse. With this update, now positioned as core...
During animal development, cells undergo dynamic changes in position and gene expression. A collection of quantitative information about morphological dynamics under a wide variety perturbations would provide rich resource for understanding the molecular mechanisms development. Here, we created database, Worm Developmental Dynamics Database (http://so.qbic.riken.jp/wddd/), which stores cell division early Caenorhabditis elegans embryos with single genes silenced by RNA-mediated interference....
Abstract Summary High-throughput chromosome conformation capture (Hi-C) is a widely used assay for studying the three-dimensional (3D) genome organization across whole genome. Here, we present PHi-C2, Python package supported by mathematical and biophysical polymer modeling that converts input Hi-C matrix data into model’s dynamics, structural conformations rheological features. The updated optimization algorithm regenerating highly similar provides fast accurate optimal solution compared to...
Abstract Motivation: Large-scale gene expression profiles measured in deletion mutants are invaluable sources for identifying regulatory networks. Signed directed graph (SDG) is the most common representation of networks genetics and cell biology. However, no practical procedure that deduces SDGs consistent with such has been developed. Results: We developed DBRF–MEGN (difference-based regulation finding–minimum equivalent network) method which an algorithm parsimonious mutants. Positive (or...
Abstract Motivation: Recent progress in live-cell imaging and modeling techniques has resulted generation of a large amount quantitative data (from experimental measurements computer simulations) on spatiotemporal dynamics biological objects such as molecules, cells organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing analyzing these data, are often not compatible with each other because different formats. Results:...
BD5 is a new binary data format based on HDF5 (hierarchical version 5). It can be used for representing quantitative biological dynamics obtained from bioimage informatics techniques and mechanobiological simulations. Biological Dynamics Markup Language (BDML) an XML (Extensible Language)-based open that also to represent such data; however, it becomes difficult access in BDML files when the file size large because parsing XML-based requires computational resources first read whole...
In gene function analysis, it is arduous to identify individually, and the way screen out all involved genes according a particular phenotype or disease usually shows us little information for specific problem. We present data-driven analysis system based on wild type (WT) embryos study concrete of each associated with certain category abnormal phenotypes. It can be applied very few RNAi embryos. Instead presupposing gene, its confirmed by statistical testing built models. The scheme...
Wet and dry biological data are potentially complementary. By visually integrating the initiation developmental processes of organisms, we might reveal new causalities in data. Here present an integrated visualization system for a causality network constructed from phenotypic characters their related scientific literature. To obtain characters, applied bio-imaging informatics techniques to wet experiments. The character was rendered CausalNet system, which provides both explanatory...
Abstract Nuclear detection in embryos is an indispensable process for quantitative analysis of the development multicellular organisms. Due to overlap distribution pixel intensity nuclear and cytoplasmic regions large variation even within same type cellular components different embryos, it difficult separate from surrounding region differential interference contrast (DIC) microscope image. This study explores a discriminative representation local patch around fixed pixel, called top-ranked...
SUMMARY Recent advances in bioimage informatics techniques have yielded quantitative data on multicellular dynamics from microscopy images of animal development. Several such collections been created for Caenorhabditis elegans embryos under various gene silencing conditions. However, because the limited depth datasets, it is impractical to apply standard statistical methods these collections. Here, we a deep collection nuclear division during first three rounds cell C. embryos, which 263...
Nuclear detection in embryos is an indispensable process for quantitative analysis of the development multicellular organisms. Due to overlap distribution nuclear and cytoplasmic intensities large variation even within same type tissues different embryos, it difficult separate regions from surrounding region differential interference contrast (DIC) microscope image. This study explores a discriminative representation texton around fixed pixel, called Top-ranked Intensity-ordered Descriptor...