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Genetic Engineering, Gene Expression, Transcription, Chromatin Dynamics, Molecular Biology, Genetics
Japan

Activities

Employment (8)

Kyushu University: Fukuoka, JP

2023-03-01 to present | Professor (Medical Institute of Bioregulation)
Employment
Source: Self-asserted source
Hiroshi Ochiai

Hiroshima University: Higashi-Hiroshima, Hiroshima, JP

2021-04-01 to present | Associate professor (Graduate School of Integrated Sciences for Life)
Employment
Source: Self-asserted source
Hiroshi Ochiai

Hiroshima University: Higashi-Hiroshima, Hiroshima, JP

2019-04-01 to 2021-03-31 | Lecturer (Graduate School of Integrated Sciences for Life)
Employment
Source: Self-asserted source
Hiroshi Ochiai

Japan Science and Technology Agency: Higashi-Hiroshima, Hiroshima, JP

2015-10-01 to 2019-03-31 | PRESTO researcher (Graduate school of Science, Hiroshima University)
Employment
Source: Self-asserted source
Hiroshi Ochiai

Hiroshima University: Higashi-Hiroshima, JP

2013-04-01 to 2015-09-30 | Lecturer (Special Appointment) (Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD))
Employment
Source: Self-asserted source
Hiroshi Ochiai

Hiroshima University: Hiroshima, JP

2012-06-01 to 2013-03-30 | Assistant Professor (Research Institute for Radiation Biology and Medicine)
Employment
Source: Self-asserted source
Hiroshi Ochiai

Hiroshima University: Hiroshima, JP

2011-04-01 to 2012-05-30 | JSPS Research Fellow (PD) (Reseach Institute for Radiation Biology and Medicine)
Employment
Source: Self-asserted source
Hiroshi Ochiai

Hiroshima University: Higashi-Hiroshima, JP

2009-04-01 to 2011-03-30 | JSPS Research Fellow (DC2) (Department of Mathematical and Life Sciences)
Employment
Source: Self-asserted source
Hiroshi Ochiai

Education and qualifications (1)

Hiroshima University: Higashi-Hiroshima, JP

2008-04-01 to 2011-03-30 | Ph.D. (Department of Mathematical and Life Sciences)
Education
Source: Self-asserted source
Hiroshi Ochiai

Works (50 of 53)

Items per page:
Page 1 of 2

Image Analysis Protocol for DNA/RNA/Immunofluorescence (IF)-seqFISH Data

Computational Methods for 3D Genome Analysis
2025 | Book chapter
Part of ISBN: 978-1-0716-4136-1
Contributors: Ohishi, Hiroaki and Ochiai, Hiroshi; Nakato, Ryuichiro
Source: Self-asserted source
Hiroshi Ochiai
grade
Preferred source (of 2)‎

Intercellular mRNA transfer alters the human pluripotent stem cell state.

Proceedings of the National Academy of Sciences of the United States of America
2025-01-22 | Journal article
Contributors: Yoneyama Y; Ranran ZHANG; Maezawa M; Hideki Masaki; Kimura M; Yuqi Cai; Mike Adam; Parameswaran S; Naoaki MIZUNO; Joydeep Bhadury et al.
Source: Self-asserted source
Hiroshi Ochiai

MEGA-FISH: multi-omics extensible GPU-accelerated FISH processing framework for huge-scale spatial omics

2024-12-09 | Preprint
Contributors: Yuma Ito; Kosuke Tomimatsu; Masao Nagasaki; Hiroshi Ochiai; Yasuyuki Ohkawa
Source: check_circle
Crossref

Transcription-coupled changes in genomic region proximities during transcriptional bursting

Science Advances
2024-12-06 | Journal article
Contributors: Hiroaki Ohishi; Soya Shinkai; Hitoshi Owada; Takeru Fujii; Kazufumi Hosoda; Shuichi Onami; Takashi Yamamoto; Yasuyuki Ohkawa; Hiroshi Ochiai
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

In siliconanoscope to study the interplay of genome organization and transcription regulation

2024-10-25 | Preprint
Contributors: Soundhararajan Gopi; Giovanni B Brandani; Cheng Tan; Jaewoon Jung; Chenyang Gu; Azuki Mizutani; Hiroshi Ochiai; Yuji Sugita; Shoji Takada
Source: check_circle
Crossref

Anti-phase clustering of regulatory factors shapes gene transcription burst

2024-09-11 | Preprint
Contributors: Bitong Li; Yew Yan Wong; Neftali Flores-Rodriguez; Tara Davidson; Matthew S Graus; Valeriia Smialkovska; Hiroaki Ohishi; Angelika Feldmann; Hiroshi Ochiai; Mathias Francois
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition

Nucleic Acids Research
2024-08-12 | Journal article
Contributors: Ximena Garate; Pablo Aurelio Gómez-García; Manuel Fernández Merino; Marta Cadevall Angles; Chenggan Zhu; Alvaro Castells-García; Ilyas Ed-daoui; Laura Martin; Hiroshi Ochiai; Maria Victoria Neguembor et al.
Source: check_circle
Crossref

Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states

Nature Communications
2024-05-08 | Journal article
Contributors: Kosuke Tomimatsu; Takeru Fujii; Ryoma Bise; Kazufumi Hosoda; Yosuke Taniguchi; Hiroshi Ochiai; Hiroaki Ohishi; Kanta Ando; Ryoma Minami; Kaori Tanaka et al.
Source: check_circle
Crossref

STREAMING-Tag System: Technology to Enable Visualization of Transcriptional Activity and Subnuclear Localization of Specific Endogenous Genes

Methods in Molecular Biology
2023 | Book chapter
Part of ISBN: 9781071627235
Part of ISBN: 9781071627242
Part of ISSN: 1064-3745
Part of ISSN: 1940-6029
Contributors: Hiroshi Ochiai; Hiroaki Ohishi
Source: Self-asserted source
Hiroshi Ochiai

Transcription-coupled changes in higher-order genomic structure and transcription hub viscosity prolong enhancer-promoter connectivity

2023-11-27 | Preprint
Contributors: Hiroaki Ohishi; Soya Shinkai; Hitoshi Owada; Takeru Fujii; Kazufumi Hosoda; Shuichi Onami; Takashi Yamamoto; Yasuyuki Ohkawa; Hiroshi Ochiai
Source: check_circle
Crossref

Precise immunofluorescence canceling for highly multiplexed imaging capturing specific cell state

2023-10-18 | Preprint
Contributors: Kosuke Tomimatsu; Takeru Fujii; Ryoma Bise; Kazufumi Hosoda; Yosuke Taniguchi; Hiroshi Ochiai; Hiroaki Ohishi; Kanta Ando; Ryoma Minami; Kaori Tanaka et al.
Source: check_circle
Crossref

Organization of transcription and 3D genome as revealed by live-cell imaging

Current Opinion in Structural Biology
2023-08 | Journal article
Part of ISSN: 0959-440X
Contributors: Hiroshi Ochiai; Hiroaki Ohishi; Yuko Sato; Hiroshi Kimura
Source: Self-asserted source
Hiroshi Ochiai

Facilitating genome function understanding using genome editing dependent bioimaging techniques

Gene and Genome Editing
2023-06 | Journal article
Contributors: Hiroshi Ochiai
Source: check_circle
Crossref

STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity

Nature Communications
2022-12-20 | Journal article | Author
Part of ISSN: 2041-1723
Contributors: Hiroaki Ohishi; Seiru Shimada; Satoshi Uchino; Jieru Li; Yuko Sato; Manabu Shintani; owada hitoshi; Yasuyuki Ohkawa; Alexandros Pertsinidis; Takashi Yamamoto et al.
Source: Self-asserted source
Hiroshi Ochiai

Ribosomal protein L5 facilitates rDNA-bundled condensate and nucleolar assembly

Life Science Alliance
2022-07 | Journal article
Part of ISSN: 2575-1077
Source: Self-asserted source
Hiroshi Ochiai

iPSC reprogramming-mediated aneuploidy correction in autosomal trisomy syndromes

PLOS ONE
2022-03-10 | Journal article
Part of ISSN: 1932-6203
Source: Self-asserted source
Hiroshi Ochiai

STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity

bioRxiv
2022-01-06 | Preprint
Source: Self-asserted source
Hiroshi Ochiai

Distinctive nuclear zone for RAD51-mediated homologous recombinational DNA repair

2021-11-30 | Other
Contributors: Yasunori Horikoshi; Hiroki Shima; Jiying Sun; Wataru Kobayashi; Volker J. Schmid; Hiroshi Ochiai; Lin Shi; Atsuhiko Fukuto; Yasuha Kinugasa; Hitoshi Kurumizaka et al.
Source: check_circle
Crossref

Single-gene imaging links genome topology, promoter–enhancer communication and transcription control

Nature Structural & Molecular Biology
2020-11 | Journal article
Contributors: Jieru Li; Angela Hsu; Yujing Hua; Guanshi Wang; Lingling Cheng; Hiroshi Ochiai; Takashi Yamamoto; Alexandros Pertsinidis
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells

Science Advances
2020-06-17 | Journal article
Contributors: Hiroshi Ochiai; Tetsutaro Hayashi; Mana Umeda; Mika Yoshimura; Akihito Harada; Yukiko Shimizu; Kenta Nakano; Noriko Saitoh; Zhe Liu; Takashi Yamamoto et al.
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

PHi-C: deciphering Hi-C data into polymer dynamics

NAR Genomics and Bioinformatics
2020-06-01 | Journal article
Contributors: Soya Shinkai; Masaki Nakagawa; Takeshi Sugawara; Yuichi Togashi; Hiroshi Ochiai; Ryuichiro Nakato; Yuichi Taniguchi; Shuichi Onami
Source: check_circle
Crossref

Insufficiency of ciliary cholesterol in hereditary Zellweger syndrome

The EMBO Journal
2020-05-05 | Journal article
Part of ISSN: 0261-4189
Part of ISSN: 1460-2075
Source: Self-asserted source
Hiroshi Ochiai
grade
Preferred source (of 3)‎

Real-Time Observation of Localization and Expression (ROLEX) System for Live Imaging of the Transcriptional Activity and Nuclear Position of a Specific Endogenous Gene

Methods in Molecular Biology
2019 | Book
EID:

2-s2.0-85071422234

Contributors: Ochiai, H.
Source: Self-asserted source
Hiroshi Ochiai via Scopus - Elsevier

Role of dynamic nuclear deformation on genomic architecture reorganization

PLOS Computational Biology
2019-09-11 | Journal article
Contributors: Sungrim Seirin-Lee; Alexandre V. Morozov; Fumitaka Osakada; Junichi Takeda; Satoshi Tashiro; Ryo Kobayashi; Takashi Yamamoto; Hiroshi Ochiai
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells

2019-08-15 | Other
Contributors: Hiroshi Ochiai; Tetsutaro Hayashi; Mana Umeda; Mika Yoshimura; Akihito Harada; Yukiko Shimizu; Kenta Nakano; Noriko Saitoh; Hiroshi Kimura; Zhe Liu et al.
Source: check_circle
Crossref

Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells

Cell
2019-05 | Journal article
Part of ISSN: 0092-8674
Source: Self-asserted source
Hiroshi Ochiai
grade
Preferred source (of 2)‎

PHi-C: deciphering Hi-C data into polymer dynamics

2019-03-12 | Other
Contributors: Soya Shinkai; Masaki Nakagawa; Takeshi Sugawara; Yuichi Togashi; Hiroshi Ochiai; Ryuichiro Nakato; Yuichi Taniguchi; Shuichi Onami
Source: check_circle
Crossref

Construction and Evaluation of Zinc Finger Nucleases

Methods in Molecular Biology
2017 | Book chapter
Part of ISBN: 9781493971275
Part of ISBN: 9781493971282
Part of ISSN: 1064-3745
Part of ISSN: 1940-6029
Source: Self-asserted source
Hiroshi Ochiai
grade
Preferred source (of 2)‎

Dynamic changes in the interchromosomal interaction of early histone gene loci during development of sea urchin

Journal of Cell Science
2017-12-15 | Journal article
Part of ISSN: 0021-9533
Part of ISSN: 1477-9137
Source: Self-asserted source
Hiroshi Ochiai
grade
Preferred source (of 2)‎

Ligation-mediated PCR with a back-to-back adapter reduces amplification bias resulting from variations in GC content

Analytical Biochemistry
2017-08 | Journal article
Part of ISSN: 0003-2697
Source: Self-asserted source
Hiroshi Ochiai
grade
Preferred source (of 2)‎

Analysis of individual differences in radiosensitivity using genome editing

Annals of the ICRP
2016-06 | Journal article
Part of ISSN: 0146-6453
Part of ISSN: 1872-969X
Source: Self-asserted source
Hiroshi Ochiai
grade
Preferred source (of 2)‎

Single-Base Pair Genome Editing in Human Cells by Using Site-Specific Endonucleases

International Journal of Molecular Sciences
2015-09-03 | Journal article
Source: Self-asserted source
Hiroshi Ochiai

Simultaneous live imaging of the transcription and nuclear position of specific genes

Nucleic Acids Research
2015-06-19 | Journal article
DOI:

10.1093/nar/gkv624

Source: Self-asserted source
Hiroshi Ochiai
grade
Preferred source (of 2)‎

The Microtubule-Depolymerizing Activity of a Mitotic Kinesin Protein KIF2A Drives Primary Cilia Disassembly Coupled with Cell Proliferation

Cell Reports
2015-02 | Journal article
DOI:

10.1016/j.celrep.2015.01.003

Contributors: Tatsuo Miyamoto; Kosuke Hosoba; Hiroshi Ochiai; Ekaterina Royba; Hideki Izumi; Tetsushi Sakuma; Takashi Yamamoto; Brian David Dynlacht; Shinya Matsuura
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search
grade
Preferred source (of 2)‎

Live dynamics on femtoinjection of GFP-tagged nucleosome chaperones into HeLa cell

JSAP-OSA Joint Symposia, JSAP 2014
2014 | Conference paper
EID:

2-s2.0-85088742696

Contributors: Takami, T.; Uewaki, J.-I.; Ochiai, H.; Koyama, M.; Ogawa, Y.; Saito, M.; Matsuoka, H.; Tate, S.-I.
Source: Self-asserted source
Hiroshi Ochiai via Scopus - Elsevier

Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells

Scientific Reports
2014-11-20 | Journal article
PMID:

25410303

Source: Self-asserted source
Hiroshi Ochiai

TALEN-mediated single-base-pair editing identification of an intergenic mutation upstream of BUB1B as causative of PCS (MVA) syndrome

Proceedings of the National Academy of Sciences
2014-01 | Journal article
DOI:

10.1073/pnas.1317008111

Part of ISSN:

0027-8424

Contributors: H. Ochiai; T. Miyamoto; A. Kanai; K. Hosoba; T. Sakuma; Y. Kudo; K. Asami; A. Ogawa; A. Watanabe; T. Kajii et al.
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search

Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity

Sci. Rep.
2013-11 | Journal article
DOI:

10.1038/srep03379

Part of ISSN:

2045-2322

Contributors: Tetsushi Sakuma; Hiroshi Ochiai; Takehito Kaneko; Tomoji Mashimo; Daisuke Tokumasu; Yuto Sakane; Ken-ichi Suzuki; Tatsuo Miyamoto; Naoaki Sakamoto; Shinya Matsuura et al.
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search

High efficiency TALENs enable F0 functional analysis by targeted gene disruption in Xenopus laevis embryos

Biology Open
2013-05 | Journal article
DOI:

10.1242/bio.20133855

Part of ISSN:

2046-6390

Contributors: K.-i. T. Suzuki; Y. Isoyama; K. Kashiwagi; T. Sakuma; H. Ochiai; N. Sakamoto; N. Furuno; A. Kashiwagi; T. Yamamoto
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search
grade
Preferred source (of 2)‎

Efficient TALEN construction and evaluation methods for human cell and animal applications

Genes Cells
2013-04 | Journal article
DOI:

10.1111/gtc.12037

Part of ISSN:

1356-9597

Contributors: Tetsushi Sakuma; Sayaka Hosoi; Knut Woltjen; Ken-ichi Suzuki; Keiko Kashiwagi; Housei Wada; Hiroshi Ochiai; Tatsuo Miyamoto; Narudo Kawai; Yasunori Sasakura et al.
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search

Equarin is involved as an FGF signaling modulator in chick lens differentiation

Developmental Biology
2012-08 | Journal article
DOI:

10.1016/j.ydbio.2012.05.029

Part of ISSN:

0012-1606

Contributors: Xiaohong Song; Yuya Sato; Athary Felemban; Ayako Ito; Mahmud Hossain; Hiroshi Ochiai; Takashi Yamamoto; Kiyotoshi Sekiguchi; Hideaki Tanaka; Kunimasa Ohta
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search

Non-transgenic genome modifications in a hemimetabolous insect using zinc-finger and TAL effector nucleases

Nat Comms
2012-08 | Journal article
DOI:

10.1038/ncomms2020

Part of ISSN:

2041-1723

Contributors: Takahito Watanabe; Hiroshi Ochiai; Tetsushi Sakuma; Hadley W. Horch; Naoya Hamaguchi; Taro Nakamura; Tetsuya Bando; Hideyo Ohuchi; Takashi Yamamoto; Sumihare Noji et al.
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search

Zinc-finger nuclease-mediated targeted insertion of reporter genes for quantitative imaging of gene expression in sea urchin embryos

Proceedings of the National Academy of Sciences
2012-07-03 | Journal article
DOI:

10.1073/pnas.1202768109

Part of ISSN:

0027-8424

Contributors: H. Ochiai; N. Sakamoto; K. Fujita; M. Nishikawa; K.-i. Suzuki; S. Matsuura; T. Miyamoto; T. Sakuma; T. Shibata; T. Yamamoto
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search

Efficient targeted mutagenesis of the chordate Ciona intestinalis genome with zinc-finger nucleases

Develop. Growth Differ.
2012-06 | Journal article
DOI:

10.1111/j.1440-169x.2012.01355.x

Part of ISSN:

0012-1592

Contributors: Narudo Kawai; Hiroshi Ochiai; Tetsushi Sakuma; Lixy Yamada; Hitoshi Sawada; Takashi Yamamoto; Yasunori Sasakura
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search

Targeted disruption of exogenous EGFP gene in medaka using zinc-finger nucleases

Develop. Growth Differ.
2012-06 | Journal article
DOI:

10.1111/j.1440-169x.2012.01357.x

Part of ISSN:

0012-1592

Contributors: Satoshi Ansai; Hiroshi Ochiai; Yuta Kanie; Yasuhiro Kamei; Yuki Gou; Takeshi Kitano; Takashi Yamamoto; Masato Kinoshita
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search

HpSumf1 is involved in the activation of sulfatases responsible for regulation of skeletogenesis during sea urchin development

Dev Genes Evol
2011-08 | Journal article
DOI:

10.1007/s00427-011-0368-2

Part of ISSN:

0949-944X

Contributors: Tetsushi Sakuma; Kazuya Ohnishi; Kazumasa Fujita; Hiroshi Ochiai; Naoaki Sakamoto; Takashi Yamamoto
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search

Targeted mutagenesis in the sea urchin embryo using zinc-finger nucleases

Developmental Biology
2010-08 | Journal article
DOI:

10.1016/j.ydbio.2010.05.416

Part of ISSN:

0012-1606

Contributors: Hiroshi Ochiai; Kazumasa Fujita; Ken-ichi T. Suzuki; Masatoshi Nishikawa; Tatsuo Shibata; Naoaki Sakamoto; Takashi Yamamoto
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search

Targeted mutagenesis in the sea urchin embryo using zinc-finger nucleases

Genes to Cells
2010-07-02 | Journal article
DOI:

10.1111/j.1365-2443.2010.01425.x

Part of ISSN:

1356-9597

Contributors: Hiroshi Ochiai; Kazumasa Fujita; Ken-ichi Suzuki; Masatoshi Nishikawa; Tatsuo Shibata; Naoaki Sakamoto; Takashi Yamamoto
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search

Dicer is Required for the Normal Development of Sea Urchin, Hemicentrotus pulcherrimus

Zoological Science
2010-06 | Journal article
DOI:

10.2108/zsj.27.477

Part of ISSN:

0289-0003

Contributors: Yuka Okamitsu; Takashi Yamamoto; Takayoshi Fujii; Hiroshi Ochiai; Naoaki Sakamoto
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search

Role of the nanos homolog during sea urchin development

Dev. Dyn.
2009-10 | Journal article
DOI:

10.1002/dvdy.22074

Part of ISSN:

1058-8388

Contributors: Takayoshi Fujii; Naoaki Sakamoto; Hiroshi Ochiai; Kazumasa Fujita; Yuka Okamitsu; Noriko Sumiyoshi; Takuya Minokawa; Takashi Yamamoto
Source: Self-asserted source
Hiroshi Ochiai via Crossref Metadata Search
Items per page:
Page 1 of 2

Peer review (3 reviews for 2 publications/grants)

Review activity for Nature communications (2)
Review activity for Neoplasia. (1)