Research Summary

Selected Publications

• 1.Kazuhiro Ikkyu, Itoshi Nikaido
  "The Effect of Multi-task Learning on the Prediction of Neoantigen–MHC Class II Binding"
  IEEE Transactions on Computational Biology and Bioinformatics, 1-12. (2025)
• 2. Koki Tsuyuzaki, Manabu Ishii, Itoshi Nikaido
  "Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data."
  BMC bioinformatics 24(1) 420-420 (2023)
• 3. Hitomi Takada^*, Yohei Sasagawa^*, Mika Yoshimura, Kaori Tanaka, Yoshimi Iwayama, Tetsutaro Hayashi, Ayako Isomura-Matoba, Itoshi Nikaido^†, Akira Kurisaki^†
  "Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis."
  Nature communications 14(1) 3750-3750 (2023)
• 4. Maik Herbig, Akihiro Isozaki, Dino Di Carlo, Jochen Guck, Nao Nitta, Robert Damoiseaux, Shogo Kamikawaji, Eigo Suyama, Hirofumi Shintaku, Angela Ruohao Wu, Itoshi Nikaido, Keisuke Goda
  "Best practices for reporting throughput in biomedical research."
  Nature methods 19(6) 633-634 (2022)
• 5. Ritsuko Morita, Noriko Sanzen, Hiroko Sasaki, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Takaki Yamamoto, Tatsuo Shibata, Takaya Abe, Hiroshi Kiyonari, Yasuhide Furuta, Itoshi Nikaido, Hironobu Fujiwara.
  "Tracing the origin of hair follicle stem cells."
  Nature, 594, (7864), (2021)
• 6. Hiroshi Ochiai^†, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Akihito Harada, Yukiko Shimizu, Kenta Nakano, Noriko Saitoh, Zhe Liu, Takashi Yamamoto, Tadashi Okamura, Yasuyuki Ohkawa, Hiroshi Kimura, Itoshi Nikaido^†.
  "Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells."
  Science advances, 6, (25), eaaz6699, (2020)
• 7. Elisabetta Mereu, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J McCarthy, Adrián Álvarez-Varela, Eduard Batlle, Sagar, Dominic Grün, Julia K Lau, Stéphane C Boutet, Chad Sanada, Aik Ooi, Robert C Jones, Kelly Kaihara, Chris Brampton, Yasha Talaga, Yohei Sasagawa, Kaori Tanaka, Tetsutaro Hayashi, Caroline Braeuning, Cornelius Fischer, Sascha Sauer, Timo Trefzer, Christian Conrad, Xian Adiconis, Lan T Nguyen, Aviv Regev, Joshua Z Levin, Swati Parekh, Aleksandar Janjic, Lucas E Wange, Johannes W Bagnoli, Wolfgang Enard, Marta Gut, Rickard Sandberg, Itoshi Nikaido, Ivo Gut, Oliver Stegle, Holger Heyn.
  "Benchmarking single-cell RNA-sequencing protocols for cell atlas projects."
  Nature biotechnology, 38, (6), 747-755, (2020)
• 8. Kenta Sato, Koki Tsuyuzaki, Kentaro Shimizu, Itoshi Nikaido.
  "CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing."
  Genome biology, 20, (1), (2019)
• 9. Tetsutaro Hayashi, Haruka Ozaki, Yohei Sasagawa, Mana Umeda, Hiroki Danno, Itoshi Nikaido.
  "Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs."
  Nature Communications, 9, (1), 619, (2018)
• 10. Yohei Sasagawa, Hiroki Danno, Hitomi Takada, Masashi Ebisawa, Kaori Tanaka, Tetsutaro Hayashi, Akira Kurisaki, Itoshi Nikaido.
  "Quartz-Seq2: A high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads."
  Genome Biology, 19, (1), (2018)

Recent Research Results

• 

  Sep. 25, 2020
  Scientists identify the molecules responsible for transcriptional bursting

• 

  Apr. 7, 2020
  RIKEN group leads world in single-cell transcriptome profiling

• 

  May 11, 2018
  New single-cell RNA sequencing methods could lead to better regenerative therapies

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