Works

Preprints

  1. Soh Ishiguro, Kana Ishida, Rina C Sakata, Hideto Mori, Mamoru Takana, Samuel King, Omar Bashth, Minori Ichiraku, Nanami Masuyama, Ren Takimoto, Yusuke Kijima, Arman Adel, Hiromi Toyoshima, Motoaki Seki, Ju Hee Oh, Anne-Sophie Archambault, Keiji Nishida, Akihiko Kondo, Satoru Kuhara, Hiroyuki Aburatani, Ramon I Klein Geltink, Yasuhiro Takashima, Nika Shakiba, and Nozomu Yachie.
    A multi-kingdom genetic barcoding system for precise target clone isolation. (2023)
    bioRxiv, doi Equally contributed.

Peer-Reviewed Papers

  1. Asako Tsubouchi, Yuri An, Yoko Kawamura, Yuichi Yanagihashi, Yuri Murata, Kazuki Teranishi, Soh Ishiguro, Hiroyuki Aburatani, Nozomu Yachie, and Sadao Ota. Pooled CRISPR screening of high-content cellular phenotypes by ghost cytometry.
    Accepted. doi †Equally contributed.
  2. Tomohiro Hino, Satoshi N. Omura, Ryoya Nakagawa, Tomoki Togashi, Satoru N. Takeda, Takafumi Hiramoto, Satoshi Tasaka, Hisato Hirano, Takeshi Tokuyama, Hideki Uosaki, Soh Ishiguro, Madina Kagieva, Hiroyuki Yamano, Yuki Ozaki, Daisuke Motooka, Hideto Mori, Yuhei Kirita, Yoshiaki Kise, Yuzuru Itoh, Satoaki Matoba, Hiroyuki Aburatani, Nozomu Yachie, Tautydas Karvelis, Virginijus Siksnys, Tsukasa Ohmori, Atsushi Hoshino, and Osamu Nureki. An AsCas12f-based compact genome editing tool derived by deep mutational scanning and structural analysis.
    Cell, 2023. †Equally contributed. doi
  3. Laura Greenstreet, Anton Afanassiev, Yusuke Kijima, Matthieu Heitz, Soh Ishiguro, Samuel King, Nozomu Yachie, and Geoffrey Schiebinger. The DNA-based global positioning system—a theoretical framework for large-scale spatial genomics.
    Cell Systems, 2023. †Equally contributed. doi
  4. Ryoya Nakagawa, Soh Ishiguro, Sae Okazaki, Hideto Mori, Mamoru Tanaka, Hiroyuki Aburatani, Nozomu Yachie, Hiroshi Nishimasu & Osamu Nureki. Engineered Campylobacter jejuni Cas9 variant with enhanced activity and broader targeting range. (2022)
    Communication Biology, doi

    CjCas9 plasmids are available at Addgene

  5. Naoki Konno, Yusuke Kijima, Keito Watano, Soh Ishiguro, Keiichiro Ono, Mamoru Tanaka, Hideto Mori, Nanami Masuyama, Dexter Pratt, Trey Ideker, Wataru Iwasaki & Nozomu Yachie. Deep distributed computing to reconstruct extremely large lineage trees. (2022)
    Nature Biotechnology, doi Equally contributed.

    FRACTAL (Github)

  6. Tsuyoshi Fukushima, Yosuke Tanaka, Keito Adachi, Nanami Masuyama, Shuhei Asada, Soh Ishiguro, Hideto Mori, Motoaki Seki, Nozomu Yachie, Susumu Goyama, & Toshio Kitamura. CRISPR/Cas9-mediated base-editing enables a chain reaction through sequential repair of sgRNA scaffold mutations. (2021) Scientific Reports, doi

    Plasmid is available at Addgene

  7. Soh Ishiguro and Nozomu Yachie. Highly multiplexed analysis of CRISPR genome editing outcomes in mammalian cells. (2021)
    Methods in Molecular Biology, Mammalian Cell Engineering p193–223. PDF

  8. Rina C. Sakata, Soh Ishiguro, Hideto Mori, Mamoru Tanaka, Kenji Tatsuno, Hiroki Ueda, Shogo Yamamoto, Motoaki Seki, Nanami Masuyama, Keiji Nishida, Hiroshi Nishimasu, Kazuharu Arakawa, Akihiko Kondo, Osamu Nureki, Masaru Tomita, Hiroyuki Aburatani & Nozomu Yachie. Base editors for simultaneous introduction of C-to-T and A-to-G mutations. (2020)
    Nature Biotechnology, doi, Equally contributed.

    Research highlight: Multitasking for base editors (Nature Review Genetics)
    Plasmids are available at Addgene
    狙ったDNA配列にC→TとA→Gの同時塩基置換を誘導する新ゲノム編集技術 (Press release in Japanese)
    2-in-1 base editors make two DNA edits at once (Chemical & Engineering News, June 3, 2020)
    塩基2種類を同時に置換 先端研など、ゲノム編集技術開発 (山形新聞)

  9. Yumi Murai, Takahiro Masuda, Yasuhide Onuma, Daniel Evans-Yamamoto, Nao Takeuchi, Hideto Mori, Nanami Masuyama, Soh Ishiguro, Nozomu Yachie, Kazuharu Arakawa. Complete Genome Sequence of Bacillus sp. Strain KH172YL63, Isolated from Deep-Sea Sediment. (2020) Microbiology Resource Announcements, Accepted.
  10. Soh Ishiguro, Hideto Mori, and Nozomu Yachie. DNA event recorders send past information of cells to the time of observation. (2019) Current Opinion in Chemical Biology, Vol. 52, pp54-62. PDF

  11. Daniel Evans-Yamamoto, Nao Takeuchi, Takahiro Masuda, Yumi Murai, Yasuhide Onuma, Hideto Mori, Nanami Masuyama, Soh Ishiguro, Nozomu Yachie, and Kazuharu Arakawa. Complete genome sequence of Psychrobacter sp. strain KH172YL61 isolated from deep-sea sediments in the Nankai Trough, Japan. (2019) Microbiology Resource Announcements, link
  12. Hideto Mori, Daniel Evans-Yamamoto, Soh Ishiguro, Masaru Tomita, and Nozomu Yachie. Fast and global detection of periodic sequence repeats in large genomic resources. (2018) Nucleic Acids Research, gky890, SPADE (software and example data)

  13. Hiroshi Nishimasu, Xi Shi, Soh Ishiguro, Linyi Gao, Seiichi Hirano, Sanae Okazaki, Taichi Noda, Omar O. Abudayyeh, Jonathan S. Gootenberg, Hideto Mori, Seiya Oura, Benjamin Holmes, Mamoru Tanaka, Motoaki Seki, Hisato Hirano, Hiroyuki Aburatani, Ryuichiro Ishitani, Masahito Ikawa, Nozomu Yachie, Feng Zhang, and Osamu Nureki. Engineered CRISPR-Cas9 nuclease with expanded targeting space. (2018)
    Science aas9129, Supplementary Materials, and Press release (In Japanese).

  14. Soh Ishiguro, Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, and Kumiko Ui-Tei. Base-pairing probability in the microRNA stem region affects the binding and editing specificity of human A-to-I editing enzymes ADAR1-p110 and ADAR2. (2018) RNA Biology. Equally contributed. PDF, and Supplementary Materials.

  15. Josephine Galipon, Rintaro Ishi, Soh Ishiguro, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, and Kumiko Ui-Tei. High-quality overlapping paired-end reads for the detection of A-to-I editing on small RNA. (2018) Methods in Molecular Biology. Equally contributed. Pubmed

  16. Yachie N, Robotic Biology Consortium & Natsume T. Robotic crowd biology with Maholo LabDroids. (2017) Nature Biotechnology. Pubmed ¶ Members of the Robotic Biology Consortium: Steering Group: Yachie N, Takahashi K, Katayama T, Sakurada T, Kanda GN, Takagi E, Hirose T, Katsura T, Moriya T, Kitano H, Tsujii J & Natsume T Robotics Group: Shiraki T, Kariyazaki H, Kamei M, Abe N, Fukuda T, Sawada Y, Hashiguchi Y, Matsukuma K, Murai S, Sasaki N, Ipposhi T, Urabe H, Kudo T, Umeno M, Ono S, Miyauchi K, Nakamura M, Kizaki T, Suyama T, Hatta T & Natsume T Information Technology Group: Ohta T, Takahashi K, Ozawa Y, Yachie N, Sakurada T, Matsukuma K, Murai S, Ihara S, Tamaki S, Antezana E, Garcia-Castro A, Perret J-L, Ishiguro S, Mori H, Evans-Yamamoto D, Masuyama N, Tomita M, Tsujii J, Katayama T & Kitano H Proteomics Group: Hatta T, Matsumoto M, Nakayama H, Shirasawa A, Shimbo K, Yamada N, Nakayama KI & Natsume T High-Content Cell Screening Group: Shimizu T & Saya H Epigenetics Group: Yamashita S, Matsushima T & Asahara H Clinical Group: Eguchi H, Mikamori M & Mori M.

Review Papers and Book Chapters

Posters

Talks

Fellowships

Funds

Awards

Teaching contribution