Rchr
J-GLOBAL ID：202001005862920480
Update date: Sep. 22, 2025
Nakamae Kazuki
ナカマエ カズキ | Nakamae Kazuki
Affiliation and department：
Job title：
Assistant Professor
Other affiliations (1)：
-
PtBio Inc.
Research and Development Division
Chief bioinformatician
Research field (2)：
Genomics
, Systems genomics
Research keywords (7)：
Off-target
, RNA-seq
, Prime Editing
, Amplicon sequencing analysis
, gene knock-in design
, CRISPR
, genome editing
Research theme for competitive and other funds (4)：
- 2024 - 2026 Establishment and verification of phenotype risk assessment software for personal genome editing
- 2021 - 2023 The establishment of the Prime Editing database for personalized genetic medicine
- 2023 - 2023 ROIS-DS-JOINT 2023:Joint Research Program/一般共同研究
- 2022 - 2022 ROIS-DS-JOINT 2022:Joint Research Program/一般共同研究
Papers (6)：
-
Kazuki Nakamae, Saya Ide, Nagaki Ohnuki, Yoshiko Nakagawa, Keisuke Okuhara, Hidemasa Bono. PtWAVE: a high-sensitive deconvolution software of sequencing trace for the detection of large indels in genome editing. BMC Bioinformatics. 2025. 26. 1. 114-114
-
Kazuki Nakamae, Takayuki Suzuki, Sora Yonezawa, Kentaro Yamamoto, Taro Kakuzaki, Hiromasa Ono, Yuki Naito, Hidemasa Bono. Risk Prediction of RNA Off-Targets of CRISPR Base Editors in Tissue-Specific Transcriptomes Using Language Models. International Journal of Molecular Sciences. 2025. 26. 4. 1723-1723
-
Kazuki Nakamae, Hidemasa Bono. DANGER analysis: risk-averse on/off-target assessment for CRISPR editing without a reference genome. Bioinformatics Advances. 2023. 3. 1. vbad114
-
Kazuki Nakamae, Hidemasa Bono. Genome editing and bioinformatics. Gene and Genome Editing. 2022. 3-4. 100018-100018
-
Shota Nakade, Keiji Mochida, Atsushi Kunii, Kazuki Nakamae, Tomomi Aida, Kohichi Tanaka, Naoaki Sakamoto, Tetsushi Sakuma, Takashi Yamamoto. Biased genome editing using the local accumulation of DSB repair molecules system. Nature communications. 2018. 9. 1. 3270-3270
ｍore...
MISC (5)：
-
Kazuki Nakamae, Takayuki Suzuki, Sora Yonezawa, Kentaro Yamamoto, Taro Kakuzaki, Hiromasa Ono, Yuki Naito, Hidemasa Bono. Risk Prediction of RNA Off-Targets of CRISPR Base Editors in Tissue-Specific Transcriptomes Using Language Models. bioRxiv. 2025
-
Kazuki Nakamae, Saya Ide, Nagaki Ohnuki, Yoshiko Nakagawa, Keisuke Okuhara, Hidemasa Bono. PtWAVE: A High-Sensitive deconvolution software of sequencing trace for the Detection of Large Indels in Genome Editing. bioRxiv. 2024
-
Kazuki Nakamae, Taro Kakuzaki, Kentaro Yamamoto. Machine learning of transcriptome data treated with DNA base editor. BioHackrXiv. 2023
-
Shota Nakade, Kazuki Nakamae, Tzu-Chieh Tang, Dou Yu, Tetsushi Sakuma, Takashi Yamamoto, Timothy K. Lu. Frame Editors for Precise, Template-Free Frameshifting. bioRxiv. 2022
-
Kazuki Nakamae, Mitsumasa Takenaga, Shota Nakade, Akinori Awazu, Naoaki Sakamoto, Takashi Yamamoto, Tetsushi Sakuma. Detailed profiling with MaChIAto reveals various genomic and epigenomic features affecting the efficacy of knock-out, short homology-based knock-in and Prime Editing. bioRxiv. 2022
Books (3)：
-
バイオDBとウェブツール : ラボで使える最新70選 : 知る・学ぶ・使う、バイオDX時代の羅針盤
羊土社 2022 ISBN:9784758104067
-
みんなのバイオDX〜公共データの海で宝探しをはじめよう
羊土社 2021
-
ゲノム編集実験スタンダード : 完全版 : CRISPR-Cas9の設計・作製と各生物種でのプロトコールを徹底解説
羊土社 2019 ISBN:9784758122443
Lectures and oral presentations (20)：
-
Novel bioinformatics tools for enhanced safety and activity estimation of genome editing in plant science
(IPSR International Forum on Plant Stress Sciences by/for Junior Researchers 2024 2024)
-
[2P-028]Development of Sanger Sequencing Analysis Software for Highly Sensitive Detection of Large Deletions Induced by Genome Editing
(MBSJ2024 2024)
-
[1AS-17-03]Developing Computational Resources of Safety Assessment for Genome Editing - Aiming for a Society Where Genome Breeding Can Be Undertaken with Low-Risk Genome Editing
(MBSJ2023 2023)
-
Computational Resources for Industrial Application of Genome Editing
(JAACT2023 2023)
-
Pitch Designer 2.0: Fully Automated Sequence Design Tool for CRISPR-Cas9-Mediated Knock-in Using Template for Short Homology-Based DSB Repair
(PAG30 2023)
ｍore...
Works (9)：
-
SNLmodel
Kazuki Nakamae 2025 - 現在
-
STL model
Kazuki Nakamae 2025 - 現在
-
PROTECTiO
Kazuki Nakamae 2025 - 現在
-
PiCTURE
Kazuki Nakamae 2025 - 現在
-
PtWAVE
Kazuki Nakamae 2024 - 現在
ｍore...
Education (1)：
- 2017 - 2020 Hiroshima University Graduate School of Science Department of Mathematical and Life Sciences
Work history (4)：
- 2024/07 - 現在 PtBio Inc. Research and Development Division Chief bioinformatician
- 2022/04 - 現在 Hiroshima University Genome Editing Innovation Center Assistant Professor
- 2020/04 - 2024/03 PtBio Inc. Senior Researcher
- 2020/04 - 2022/03 Hiroshima University Genome Editing Innovation Center Postdoctoral Researcher
Committee career (1)：
- 2022/07 - 現在 Japanese Society for Genome Editing 教育実習委員会委員
Awards (1)：
- 2023/06 - 日本ゲノム編集学会 第8回大会 ポスター賞 研究員・ポスドクの部 DANGER Analysis:表現型への影響を評価する新規オフターゲット解析ツール
Association Membership(s) (2)：
The Molecular Biology Society of Japan
, The Japanese Society for Genome Editing
