KAZUKI NAKAMAE

Last Updated :2025/05/09

Affiliations, Positions
Hiroshima University Genome Editing Innovation Center, Assistant Professor, Collaborative Research Laboratory
Web Site
https://www.pt-bio.com/
https://bonohu.hiroshima-u.ac.jp/
https://github.com/KazukiNakamae
E-mail
kazuki-nakamaehiroshima-u.ac.jp
Other Contact Details
1C-01, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan, Japan
TEL : (+81)82-424-3989 FAX : (+81)
Self-introduction
I am developing software involved with the genome editing with my great collaborators.

Basic Information

Major Professional Backgrounds

  • 2024/04/01, PtBio Inc., Research and Development Department, Chief bioinformatician
  • 2022/04/01, Hiroshima University, Genome Editing Innovation Center, Assistant Professor, Collaborative Research Laboratory
  • 2020/04/01, 2024/03/31, PtBio Inc., Senior Researcher
  • 2020/04/01, 2022/03/31, Hiroshima University, Genome Editing Innovation Center, Postdoctoral Researcher

Educational Backgrounds

  • Hiroshima University, Graduate School of Science, Department of Mathematical and Life Sciences, Japan, 2017/04/01, 2020/03/23

Academic Degrees

  • Doctor of Science, Hiroshima University
  • Master of Science, Hiroshima University

Research Fields

  • Informatics;Frontiers of informatics;Life / Health / Medical informatics
  • Biological Sciences;Genome science;System genome science
  • Biological Sciences;Genome science;Medical genome science
  • Biological Sciences;Genome science;Genome biology

Research Keywords

  • Prime Editing
  • bioinformatics
  • BioDX
  • Gene knockout
  • Gene knockin
  • CRISPR-Cas9
  • Sequence Analysis
  • knock-in design
  • Genome Editing

Affiliated Academic Societies

Research Activities

Academic Papers

  1. ★, PtWAVE: a high-sensitive deconvolution software of sequencing trace for the detection of large indels in genome editing, BMC Bioinformatics, 26(1), 114-114, 20250429
    Link to Paper Search Results by DOI
  2. ★, Risk Prediction of RNA Off-Targets of CRISPR Base Editors in Tissue-Specific Transcriptomes Using Language Models, International Journal of Molecular Sciences, 26(4), 1723-1723, 20250218
    Link to Paper Search Results by DOI
  3. PtWAVE: A High-Sensitive deconvolution software of sequencing trace for the Detection of Large Indels in Genome Editing, bioRxiv, 20240417
    Link to Paper Search Results by DOI
  4. ★, DANGER analysis: risk-averse on/off-target assessment for CRISPR editing without a reference genome, Bioinformatics Advances, vbad114, 20230823
    Link to Paper Search Results by DOI
  5. Danger Analysis: Risk-Averse on/off-Target Assessment for CRISPR Editing Without a Reference Genome, bioRxiv, 20230313
    Link to Paper Search Results by DOI
  6. Frame Editors for Precise, Template-Free Frameshifting, bioRxiv, 20221206
    Link to Paper Search Results by DOI
  7. ★, Genome editing and bioinformatics, Gene and Genome Editing, 3–4(100018), 20221108
    Link to Paper Search Results by DOI
  8. 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, 20220630
  9. Biased genome editing using the local accumulation of DSB repair molecules system, NATURE COMMUNICATIONS, 9(1), 3270, 20180816
    Link to Paper Search Results by DOI
  10. ★, Establishment of expanded and streamlined pipeline of PITCh knock-in - a web-based design tool for MMEJ-mediated gene knock-in, PITCh designer, and the variations of PITCh, PITCh-TG and PITCh-KIKO, BIOENGINEERED, 8(3), 302-308, 20170428
    Link to Paper Search Results by DOI

Invited Lecture, Oral Presentation, Poster Presentation

  1. Novel bioinformatics tools for enhanced safety and activity estimation of genome editing in plant science, Kazuki Nakamae, Saya Ide, Nagaki Ohnuki, Yoshiko Nakagawa, Keisuke Okuhara, Hidemasa Bono, IPSR International Forum on Plant Stress Sciences by/for Junior Researchers 2024, 2024/12/06, Without Invitation, English, Toshio Yamamoto, Okayama
    Related URL
  2. [2P-028]Development of Sanger Sequencing Analysis Software for Highly Sensitive Detection of Large Deletions Induced by Genome Editing, Kazuki Nakamae, Saya Ide, Nagaki Ohnuki, Yoshiko Nakagawa, Keisuke Okuhara, Hidemasa Bono, MBSJ2024, 2024/11/28, Without Invitation, Japanese, Hiroshi Kimura, Fukuoka
    Related URL
  3. Computational Resources for Industrial Application of Genome Editing, Kazuki Nakamae, JAACT2023, 2023/11/30, With Invitation, English, Nagoya, Japan
  4. [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, Kazuki Nakamae, MBSJ2023, 2312/06, Without Invitation, Japanese, Hidemasa Bono, Kazuki Nakamae, Kobe, Japan
  5. DANGER Analysis: A Novel Off-target Analysis Software to Assess Phenotypic Impact, Kazuki Nakamae, Hidemasa Bono, 8th Annual Meeting of The Japanese Society for Genome Editing, 2023/06/06, Without Invitation, English
  6. Pitch Designer 2.0: Fully Automated Sequence Design Tool for CRISPR-Cas9-Mediated Knock-in Using Template for Short Homology-Based DSB Repair, Kazuki Nakamae, Shota Nakade, Naoaki Sakamoto, Tetsushi Sakuma, Takashi Yamamoto, PAG30, 2023/01/13, Without Invitation, English, San Diego, CA, USA
  7. Pitch Designer 2.0: Fully Automated Sequence Design Tool for CRISPR-Cas9-Mediated Knock-in Using Template for Short Homology-Based DSB Repair, Kazuki Nakamae, Shota Nakade, Naoaki Sakamoto, Tetsushi Sakuma, Takashi Yamamoto, PAG 30, 2023/01/13, Without Invitation, English, San Diego, CA, USA
  8. Sequence-based parameters contributing to the efficiency and accuracy of MMEJ-assisted knock-in and Prime Editing, Kazuki Nakamae, Kunihisa Yamamoto, Mitsumasa Takenaga, Shota Nakade, Naomi Tagashira, Ichiro Nazuka, Akinori Awazu, Naoaki Sakamoto, Tetsushi Sakuma, Takashi Yamamoto, FASEB: The Genome Engineering Conference: Cutting-edge Research and Applications, 2022/06/26, Without Invitation, English, Lisbon, Portugal
  9. Computational resources for designing appropriate guide RNAs, Kazuki Nakamae, The 7th Annual Meeting of the Japanese Society for Genome Editing, 2022/06/06, With Invitation, Japanese
  10. Sequence-based parameters contributing to the efficiency of MMEJ-assisted knock-in and Prime Editing, Kazuki Nakamae, CSHL meetings: GENOME ENGINEERING: CRISPR FRONTIERS, 2021/08/18, Without Invitation, English, Online
  11. MaChIAto: detailed profiling tool for various genomic features affecting the efficacy of CRISPR-based genome editing, Kazuki Nakamae, The 43rd Annual Meeting of the Molecular Biology Society of Japan, 2020/12/02, Without Invitation, Japanese, The Molecular Biology Society of Japan
  12. Extended analysis of amplicon sequencing data with MaChIAto for prime editing, Kazuki Nakamae, Mitsumasa Takenaga, Shota Nakade, Ichiro Nazuka, Akinori Awazu, Naoaki Sakamoto, Tetsushi Sakuma, Takashi Yamamoto., CSHL meeting: GENOME ENGINEERING: CRISPR FRONTIERS, 2020/08/19, Without Invitation, English, Online
  13. Analysis of genomic and epigenomic features affecting the efficacy of MMEJ-assisted knock-in using machiato, Kazuki Nakamae, Frontiers in Genome Engineering 2019, 2019/11/26, Without Invitation, English, Kobe Convention Center, Kobe
  14. Detailed profiling with MaChIAto reveals various genomic and epigenomic features affecting the efficacy of MMEJ-assisted knock-in, Kazuki Nakamae, Genome Engineering: Frontiers of CRISPR/Cas, 2019/10/12, Without Invitation, English, Cold Spring Horbor Laboratory, Cold Spring Horbor, New York
  15. Analysis of genomic and epigenomic elements contributing to the efficiency of MMEJ-assisted knock-in, Kazuki Nakamae, The 4th annual meeting of for Japanese society for genome editing, 2019/06/05, Without Invitation, Japanese
  16. PITCh designer 2.0: Automated web-based design tool for MMEJ-mediated knock-in, Kazuki Nakamae, The 3rd annual meeting of for Japanese society for genome editing, 2018/06/19, Without Invitation, Japanese
  17. PITCh designer 2.0: fully automated sequence design tool for the generation and validation of MMEJ mediated knock in, Kazuki Nakamae, Keystone Symposia, Precision Genome Editing with Programmable Nucleases(B1), 2018/01/30, Without Invitation, English, Keystone Resort, Keystone, Colorado
  18. Automated web-based design tool for MMEJ-mediated gene knock-in, Kazuki Nakamae, Cold Spring Harbor meeting, Genome Engineering: The CRISPR-Cas Revolution, 2017/07/23, Without Invitation, English, Cold Spring Horbor Laboratory, Cold Spring Horbor, New York
  19. Automated web-based design tool for MMEJ-mediated gene knock-in, Kazuki Nakamae, The 2nd annual meeting of for Japanese society for genome editing, 2017/06/29, Without Invitation, Japanese

Works, etc.

  1. SNLmodel, Kazuki Nakamae, 2025/01/22, Software
    Related URL
  2. STL model, Kazuki Nakamae, 2025/01/22, Software
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  3. PROTECTiO, Kazuki Nakamae, 2025/01/22, Software
    Related URL
  4. PiCTURE, Kazuki Nakamae, 2025/01/22, Software
    Related URL
  5. PtWAVE, Kazuki Nakamae, 2024, Software
    Related URL
  6. DANGER Analysis, Kazuki Nakamae, 2023, Software
    Related URL
  7. Genome Editing Software Guide, Kazuki Nakamae, 2022, Web Service
    Related URL
  8. MaChIAto, Kazuki Nakamae, 2022, Software
    Related URL
  9. PITCh designer, Kazuki Nakamae, Software
    Related URL
  10. PITCh designer2.0, Kazuki Nakamae, Software
    Related URL

External Funds

Acceptance Results of Competitive Funds

  1. KAKENHI(Grant-in-Aid for Early-Career Scientists), Establishment and verification of phenotype risk assessment software for personal genome editing, 2024, 2025
  2. ROIS-DS-JOINT 2023, Developing prediction tool for off-target RNAs via CRISPR-Cas9 based on published transcriptome data, 2023, 2023
  3. ROIS-DS-JOINT 2022, Developing prediction tool for off-target RNAs via CRISPR-Cas9 based on published transcriptome data, 2022, 2022
  4. KAKENHI(Grant-in-Aid for Early-Career Scientists), The establishment of the Prime Editing database for personalized genetic medicine, 2021, 2022