業績リスト

@article{Ohishi2025,
title = {Image Analysis Protocol for DNA/RNA/Immunofluorescence (IF)-seqFISH Data},
author = {Hiroaki Ohishi and Hiroshi Ochiai},
editor = {Ryuichiro Nakato},
url = {https://doi.org/10.1007/978-1-0716-4136-1_24},
doi = {10.1007/978-1-0716-4136-1_24},
isbn = {978-1-0716-4136-1},
year  = {2024},
date = {2024-09-17},
urldate = {2024-09-17},
booktitle = {Computational Methods for 3D Genome Analysis},
journal = {Methods Mol. Biol.},
volume = {Methods Mol. Biol. (Clifton, NJ)},
pages = {419\textendash432},
publisher = {Springer US},
address = {New York, NY},
abstract = {Imaging-based spatial multi-omics technologies facilitate the analysis of higher-order genomic structures, gene transcription, and the localization of proteins and posttranslational modifications (PTMs) at the single-allele level, thereby enabling detailed observations of biological phenomena, including transcription machinery within cells and tissues. This chapter details the principles of such technologies, with a focus on DNA/RNA/immunofluorescence (IF) sequential fluorescence in situ hybridization (seqFISH). A comprehensive step-by-step protocol for image analysis is provided, covering image preprocessing, spot detection, and data visualization. For practical application, complete Jupyter Notebook codes are made available on GitHub (https://github.com/Ochiai-Lab/seqFISH_analysis).},
keywords = {Review},
pubstate = {published},
tppubtype = {article}
}

@article{10.1016/j.ggedit.2022.100022,
title = {Facilitating genome function understanding using genome editing dependent bioimaging techniques},
author = {Hiroshi Ochiai},
doi = {10.1016/j.ggedit.2022.100022},
issn = {2666-3880},
year  = {2023},
date = {2023-06-01},
urldate = {2022-01-01},
journal = {Gene and Genome Editing},
volume = {5},
pages = {100022},
abstract = {Genomic DNA is highly folded and is stored in the nucleus. In multicellular organisms, genomic DNA exhibits cell type-specific higher-order structures, including specific enhancer\textendashpromoter interactions, which have recently been shown to be relevant for cell type-specific regulation of gene expression. However, when the distances between specific enhancers and promoters were measured, cell-to-cell heterogeneity was unexpectedly large and, in some cases, did not correlate with the transcriptional state. These phenomena can be revealed by simultaneously visualizing specific genomic regions and the biological phenomena of interest. In this mini-review, I introduce methodologies for visualizing specific genomic DNA regions and provide detailed examples of how these techniques are being used to elucidate the mechanisms of transcriptional regulation.},
keywords = {Review},
pubstate = {published},
tppubtype = {article}
}

@article{Matsuura:2016gt,
title = {Analysis of individual differences in radiosensitivity using genome editing.},
author = {Shinya Matsuura and Ekaterina Royba and Silvia N Akutsu and Hiromi Yanagihara and Hiroshi Ochiai and Yoshiki Kudo and Satoshi Tashiro and Tatsuo Miyamoto},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed\&id=27012844\&retmode=ref\&cmd=prlinks},
doi = {10.1177/0146645316633941},
year  = {2016},
date = {2016-06-01},
journal = {Ann ICRP},
volume = {45},
number = {1 Suppl},
pages = {290--296},
abstract = {Current standards for radiological protection of the public have been uniformly established. However, individual differences in radiosensitivity are suggested to exist in human populations, which could be caused by nucleotide variants of DNA repair genes. In order to verify if such genetic variants are responsible for individual differences in radiosensitivity, they could be introduced into cultured human cells for evaluation. This strategy would make it possible to analyse the effect of candidate nucleotide variants on individual radiosensitivity, independent of the diverse genetic background. However, efficient gene targeting in cultured human cells is difficult due to the low frequency of homologous recombination (HR) repair. The development of artificial nucleases has enabled efficient HR-mediated genome editing to be performed in cultured human cells. A novel genome editing strategy, 'transcription activator-like effector nuclease (TALEN)-mediated two-step single base pair editing', has been developed, and this was used to introduce a nucleotide variant associated with a chromosomal instability syndrome bi-allelically into cultured human cells to demonstrate that it is the causative mutation. It is proposed that this editing technique will be useful to investigate individual radiosensitivity.},
keywords = {Review},
pubstate = {published},
tppubtype = {article}
}

@article{Ochiai:2015bt,
title = {Single-Base Pair Genome Editing in Human Cells by Using Site-Specific Endonucleases},
author = {Hiroshi Ochiai},
url = {http://www.mdpi.com/1422-0067/16/9/21128/htm},
doi = {10.3390/ijms160921128},
year  = {2015},
date = {2015-09-01},
urldate = {2015-09-01},
journal = {Int J Mol Sci},
volume = {16},
number = {9},
pages = {21128--21137},
publisher = {Multidisciplinary Digital Publishing Institute},
abstract = {Genome-wide association studies have identified numerous single-nucleotide polymorphisms (SNPs) associated with human diseases or phenotypes. However, causal relationships between most SNPs and the associated disease have not been established, owing to technical challenges such as unavailability of suitable cell lines. Recently, efficient editing of a single base pair in the genome was achieved using programmable site-specific nucleases. This technique enables experimental confirmation of the causality between SNPs and disease, and is potentially valuable in clinical applications. In this review, I introduce the molecular basis and describe examples of single-base pair editing in human cells. I also discuss the challenges associated with the technique, as well as possible solutions.},
keywords = {Review},
pubstate = {published},
tppubtype = {article}
}