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

• 石黒宗, 加藤郁佳, 宮脇健行. "はじめよう！ 研究者ポッドキャスト―多様な研究者を"聴ける化"する新たなメディア", 実験医学 2021年11月号, 羊土社. ISSN 978-4-7581-2549-9 (2021). link
• 石黒宗. "Opinion-研究の現場から ポッドキャストで語るサイエンスとその魅力", 実験医学 2020年8月号, 羊土社. ISSN 978-4-7581-2535-2 (2020). link
• 石黒宗. "連載 ブレークスルーを狙うバイオテクノロジー: 空間トランスクリプトミクス①", 実験医学 2020年7月号, 羊土社. ISSN 978-4-7581-2534-5 (2020). link
• 森秀人, 石黒宗. "ウェットなデータストレージメディアとしてのDNA", 実験医学 2019年1月号, 羊土社. ISSN 02885514 (2019). link
• 谷内江望, 石黒宗. "全ゲノム合成時代における長鎖DNA合成の考え方", スマートセルインダストリー -微生物細胞を用いた物質生産の展望-, シーエムシー出版. ISSN 978-4-7813-1334-4. (2018). link
• 石黒宗, 増山七海, 谷内江望. "オミクス科学における実験数の組合せ爆発に挑むDNAバーコード技術", 生化学, 日本生化学会. ISSN 0037-1017 (2017). PDF
• 石黒宗, 森秀人, 谷内江望. "DNAバーコードおよびゲノム編集を用いた細胞系譜の一斉追跡技術", 生体の科学 68巻3号 解説, pp.273-281, 医学書院 (2017). link
• 石黒宗, 森秀人, 谷内江望. "DNAバーコードによる生命科学実験の限界突破", 実験医学増刷 はじめての数理モデルとシミュレーション, ISBN 978-4-7581-0361-9, 羊土社 (2017). link
• ガリポン・ジョゼフィーヌ, 石黒宗, 冨田勝, 程久美子. "RNA-SeqによるA-to-I RNA編集の検出", 実験医学 RNA-Seq実験ハンドブック, 113-118, ISBN 978-4-7581-0194-3, 羊土社 (2016). link

Posters

• Soh Ishiguro, Kana Ishida, Hideto Mori, Mamoru Takana, Nanami Masuyama, Motoaki Seki, Keiji Nishida, Akihiko Kondo, Satoru Kuhara, Masaru Tomita, Hiroyuki Aburatani, and Nozomu Yachie. A CRISPR–barcode technology to isolate a target clone from different cell population samples. Keystone Symposia, Genome Engineering: From Mechanisms to Therapies, Victoria, BC, Canada, 02/20/2019.
• Soh Ishiguro, Kana Ishida, Hideto Mori, Mamoru Takana, Nanami Masuyama, Motoaki Seki, Keiji Nishida, Akihiko Kondo, Satoru Kuhara, Masaru Tomita, Hiroyuki Aburatani, and Nozomu Yachie. A CRISPR–barcode technology to isolate a target clone from different cell population samples. Asia Synthetic Biology Association Meeting 2018, Jeju, Korea, 11/23/2018.
• Soh Ishiguro, Kana Ishida, Hideto Mori, Motoaki Seki, Nanami Masuyama, Rina Sakata, Mamoru Tanaka, Keiji Nishida, Akihiko Kondo, Masaru Tomita, Nozomu Yachie. Retrospective isolation of evolved clones from an initial cell population. Keio Life Science Symposium, 09/13/2018.
• Soh Ishiguro, Ayaka Matsuo, Masaru Tomita, Hiroyuki Aburatani, Nozomu Yachie. (2017) CRISPR/Cas9-based DNA barcode genetics to dissect clonal dynamics of heterogeneous cell populations, From Genetic Networks to a Cellular Wiring Diagram, 04/26/2017.
• Soh Ishiguro, Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, Kumiko Ui-Tei. (2015) "Genome-wide identification of A-to-I editing in human miRNA by ADAR isoform-specific RIP-sequencing", MBSJ2015, Kobe, Japan.
• 飯笹 久, 坂田 健一郎, Josephine Galipon, 石黒 宗, 前田 浩次郎, 柳原 五吉, 久保 貴紀, 吉山 裕規, 程 久美子, 浜田 淳一. (2015) RNA編集酵素ADAR2は、oncomiRのプロセッシングを制御する, 第17回日本RNA学会, 北海道.
• Josephine Galipon, Soh Ishiguro, Rintaro Ishii, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, Kumiko Ui-Tei. (2015) "A-to-I RNA editing fine-tunes miRNA function in human cells", 2nd Symposium on Complex Biodynamics and Networks, Tsuruoka Japan.
• Hisashi Iizasa, Kenichiro Sakata, Josephine Galipon, Kojiro Maeda, Soh Ishiguro, Nozomi Sakurai, Hironori, Yoshiyama, Kazuyoshi Yanagihara, Takanori Kubo, Yoshimasa Kitagawa, Hideyuki Kawauchi, Kumiko Ui-Tei, Junichi Hamada. (2015) "A-to-I RNA editing enzyme ADAR2 regulates malignancy in human pleural mesothelioma", Gordon Research Conference on RNA editing, Lucca, Italy.
• Soh Ishiguro, Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, Kumiko Ui-Tei. (2014) "Validation of A-to-I RNA editing sites identified by RIP-seq in human miRNAs", MBSJ2014, Yokohama, Japan.
• Josephine Galipon, Rintaro Ishii, Soh Ishiguro, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, Kumiko Ui-Tei. (2014) "Specificity of miRNA A-to-I editing by different human ADAR isoforms", RNAJ2014, Nagoya.
• 石黒 宗, 荒川和晴, 冨田勝. (2014) "超並列シーケンサーデータを用いたRNA編集サイトの検出ソフトウェアの開発", 第５回情報生命科学若手の会, 千葉.
• Soh Ishiguro, Kazuharu Arakawa, Masaru Tomita. (2013) "Benchmarking test for the detection methods of RNA editing sites based on RNA-seq data", MBSJ2013, Kobe.
• Soh Ishiguro, Kazuharu Arakawa, Masaru Tomita. (2013) "RNA-seqデータを用いたRNA編集サイト検出手法ベンチマーク", 第3回NGS現場の会, 神戸.
• Soh Ishiguro, Kazuharu Arakawa, Takekazu Kunieda, Hirokazu Kuwahara, Daiki D. Horikawa, Atsushi Toyoda, Toshiaki Katayama, Asao Fujiyama, Masaru Tomita. (2012) "Identification of RNA editing sites in tardigrade transcriptome from RNA-Seq data", MBSJ2012, Fukuoka.
• Soh Ishiguro, Kazuharu Arakawa, Takekazu Kunieda, Hirokazu Kuwahara, Daiki D. Horikawa, Atsushi Toyoda, Toshiaki Katayama, Asao Fujiyama, Masaru Tomita. (2012) "Identification of RNA editing sites in tardigrade transcriptome from RNA-Seq data", JSBi, Tokyo.
• Nobuaki Kono, Kazuharu Arakawa, Kazuki Oshita, Gembu Maryu, Soh Ishiguro, Taiyo Miyashita, Hidetoshi Itaya, Yuki Yoshida, Masaru Tomita. (2012) "Web Application for Pathway Visualization with Instinctive Interface for Metagenome data", 生命医薬情報学連合大会, 東京.
• 石黒 宗, 荒川 和晴, 冨田 勝. (2012) "次世代シーケンサーを用いたヨコヅナクマムシにおけるRNA editingの解析", 第2回NGS現場の会, 大阪.

Talks

• Soh Ishiguro, (2019). A CRISPR–barcode technology to isolate a target clone from different cell population samples, 4th Annual Meeting of The Japanese Society for Genome Editing, Tokyo, Japan, 06/04/2019.
• Soh Ishiguro, (2019). A CRISPR–barcode technology to isolate a target clone from different cell population samples, LSBM retreat 2019, Hakone, Japan, 04/02/2019.
• 石黒 宗, (2018). 不均質ながん細胞の振る舞いを計測するDNAメモリーデバイス技術, 生命科学講演会「計測・情報科学をもちいた新しい生命科学の潮流」, 東大駒場キャンパス公開2018.
• Soh Ishiguro, Nozomu Yachie. (2015). Impact of defects in 'protein ladders' supporting intracellular pathways, Joint Workshop on Synthetic and Systems Biology, Yamagata.
• 石黒 宗, Galipon Josephine, 石井 倫太郎, 鈴木 穣, 近藤 伸二, 岡田 眞里子, 冨田 勝, 程 久美子. (2014). ヒトのADARアイソフォームによるA-to-I miRNA編集の検出とその発現解析, 第6会生命情報科学若手の会, 神戸.
• SFC Open Research Forum 2013, 2013/11/22 at Tokyo Midtown.

Fellowships

• JSPS Overseas Research Fellowships, Japan Society for the Promotion of Science (April 2021 – )
• Young Leaders Scholarship from The Ryoichi Sasakawa Young Leaders Fellowship Fund (April 2016 – March 2017).
• JSPS Research Fellowship for Young Scientist (DC1) from Japan Society for the Promotion of Science (April 2016 – March 2019).

Funds

• Taikichiro Mori Memorial Research Grants from Taikichiro Mori Memorial Research Fund (April 2018).
• Taikichiro Mori Memorial Research Grants from Taikichiro Mori Memorial Research Fund (April 2013 – March 2014).
• Taikichiro Mori Memorial Research Grants from Taikichiro Mori Memorial Research Fund (April 2014 – March 2015).
• Yamagishi Student Project Support Program (B4) from Mr. Kotaro Yamagishi, Co-Founder of GREE (June 2013 – February 2014).

Awards

• Inoue Research Award for Young Scientists. Feb 2023
• SFC STUDENT AWARD 2020, Keio University, 2010/03/13.
• Best Poster Award, The 13th International Workshop on Advanced Genomics. 2019/06/27.

Teaching contribution

• 2017, Lecturer, Keio University, 14_B6167: Introduction to Bioinformatics.