Publications

* Co-first author. †Corresponding author. See also my Google Scholar profile.

Preprints

2.　Ryuichi Ono†, Naoki Konno†, Yuki Nishimura, Chikara Furusawa. Host range and ARG dissemination are shaped by distinct survival strategies of conjugative plasmids. bioRxiv (2025).

1.　Chunhui Hao*†, Naoki Konno*†, Makoto Ito, Laurence J Belcher, Wataru Iwasaki, Stuart West. Cooperation shapes bacterial niche breadth evolution and patterns of diversification. bioRxiv (2024).

Journal Articles

7.　Morito Sakuma, Naoki Konno, Sevan Gholipour, John Z Chen, Nobuhiko Tokuriki†. Widespread promiscuous alkaline phosphatases underscore early microbial phosphite utilization. PNAS (2025).

6.　Naoki Konno†, Keita Miyake, Satoshi Nishino, Kimiho Omae, Haruaki Yanagisawa, Saburo Tsuru, Yuki Nishimura, Masahide Kikkawa, Chikara Furusawa, and Wataru Iwasaki. Repeatability of Protein Structural Evolution Following Convergent Gene Fusions. Nature Communications (2025).  Press Release (Japanese) / Press Release (English) / Blog post (by others)

5.　Yui Uchida†, Tasuku Ishida, Satomi Ono, Shunya Kuroda, Aimi Kobayashi, Naoki Konno, Yoshitaka Tanaka, et al. Meeting Report: The First Evo-Devo Young Researchers Meeting. Development, Growth & Differentiation,  67 (6): 331–35. (2025)

4.　Naoki Konno†, Shintaro Maeno, Yasuhiro Tanizawa, Masanori Arita, Akihito Endo & Wataru Iwasaki†. Evolutionary paths toward multi-level convergence of lactic acid bacteria in fructose-rich environments. Communications Biology, 7, 902 (2024).

3.　Naoki Konno†, Wataru Iwasaki†. Machine learning enables prediction of metabolic system evolution in bacteria. Science Advances, Vol. 9, Issue 2. eadc9130 (2023). Press Release / Talk movie (English) / Talk movie (Japanese)

2.　Nanami Masuyama*, Naoki Konno*, Nozomu Yachie†. Molecular Recorders to track cellular events. Science, Vol. 377, Issue 6605, 469-470 (2022). 

1.　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. Nature Biotechnology, Vol. 40, 566-575 (2022). Press Release / Cover Art / Movie

Japanese Reviews

5.　今野直輝, 「ゲノム設計時代に向けた進化予測モデル」、月刊細胞、Vol. 57 No. 8、20-23 (2025)

4.　今野直輝, 岩崎渉, 「機械学習による細菌の代謝システムの進化予測」、Bioscience and Industry、Vol. 81 No.6、2163-2166 (2023) 

3.　今野直輝, 谷内江望, 「巨大細胞系譜推定を可能にする深層分散コンピューティング」、実験医学、Vol. 40 No.13、2163-2166 (2022) Number of access Top-3 in 2022

2.　今野直輝 (谷内江研究室編) 「ブレークスルーを狙うバイオテクノロジー　進化生物学に触発されたバイオテクノロジー②」 実験医学、Vol.37 No.18、3159-3167 (2019)

1.　今野直輝 (谷内江研究室編) 「ブレークスルーを狙うバイオテクノロジー　進化生物学に触発されたバイオテクノロジー①」 実験医学、Vol.37 No.14、2362-2368 (2019)

Books

1.　Yachie N, Masuyama N, Seki M, Yamamoto-Evans D, Ishiguro S, Mori H, Sakata R, Konno N, Matsuo H & Kijima Y. “Augmented Biology—the next X” (written in Japanese) Edited by Nozomu Yachie (2021) Yodosha, ISBN 978-4-7581-2252-8

Essays

5.　今野直輝,「進化予測モデル Evodictor による薬剤耐性の伝播予測」日本ゲノム微生物学会ニュースレター, No. 31, (2025)

4.　今野直輝,「古細菌のゲノム進化を細菌のゲノム進化から予測する」日本ゲノム微生物学会ニュースレター, No. 25, (2022)

3.　今野直輝,「生命の進化・発生の過程を計算機で解く」理学部ニュース, 東京大学 (2022)

2.　今野直輝,「機械学習による微生物生命システム進化の法則解明と未来予測」日本ゲノム微生物学会ニュースレター, No. 23, (2021)

1.　今野直輝,「進化予測モデルで見つけ出すバクテリア代謝系進化の法則性」日本進化学会ニュース, Vol. 21. No. 3. (2020)