Publications

Recent Journal Papers

For almost all the publications of Kiyoshi Asai, visit publicationslist.org

Goro Terai, Kiyoshi Asai, QRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity, Nucleic Acids Research, 2022;, gkac220, https://doi.org/10.1093/nar/gkac220

「RNA機能に直結する2次構造を予測する汎用的な手法を開発」との表題でプレス発表を行いました。

Masaki Tagashira, Kiyoshi Asai, ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures, Bioinformatics, Volume 38, Issue 3, 1 February 2022, Pages 710–719, https://doi.org/10.1093/bioinformatics/btab738

Kensuke Ninomiya Junichi Iwakiri Mahmoud Khamis Aly Yuriko Sakaguchi Shungo Adachi Tohru Natsume Goro Terai Kiyoshi Asai Tsutomu Suzuki Tetsuro Hirose, m6A modification of HSATIII lncRNAs regulates temperature-dependent splicing, The EMBO Journal (2021)40:e107976, https://doi.org/10.15252/embj.2021107976

Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada, PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores, Bioinformatics, Volume 37, Issue 5, 1 March 2021, Pages 589–595, https://doi.org/10.1093/bioinformatics/btaa835

Yoichiro Ito, Goro Terai, Misa Ishigami, Noriko Hashiba, Yasuyuki Nakamura, Takahiro Bamba, Ryota Kumokita, Tomohisa Hasunuma, Kiyoshi Asai, Jun Ishii, Akihiko Kondo, Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression, Nucleic Acids Research, Volume 48, Issue 22, 16 December 2020, Pages 13000–13012, https://doi.org/10.1093/nar/gkaa1066

Shun Sakuraba, Junichi Iwakiri, Michiaki Hamada, Tomoshi Kameda, Genichiro Tsuji, Yasuaki Kimura, Hiroshi Abe, and Kiyoshi Asai, Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters, J. Chem. Theory Comput. 2020, 16, 9, 5923–5935

Hiroki Takizawa, Junichi Iwakiri, Goro Terai, Kiyoshi Asai, Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model, Bioinformatics, Volume 36, Issue Supplement_1, July 2020, Pages i227–i235, https://doi.org/10.1093/bioinformatics/btaa469

Akito Taneda, Kiyoshi Asai, COSMO: A dynamic programming algorithm for multicriteria codon optimization,Computational and Structural Biotechnology Journal, Volume 18, 2020, Pages 1811-1818, ISSN 2001-0370, https://doi.org/10.1016/j.csbj.2020.06.035.

Goro Terai, Kiyoshi Asai, Improving the prediction accuracy of protein abundance in Escherichia coli using mRNA accessibility, Nucleic Acids Research, Volume 48, Issue 14, 20 August 2020, Page e81, https://doi.org/10.1093/nar/gkaa481