浅井 潔

論文

• PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures

  Takumi Otagaki, Goro Terai, Kiyoshi Asai, Junichi Iwakiri

  PLOS Computational Biology 21(11) e1013693-e1013693 2025年11月20日
• Consistent features observed in structural probing data of eukaryotic RNAs.

  Kazuteru Yamamura, Kiyoshi Asai, Junichi Iwakiri

  NAR genomics and bioinformatics 7(1) lqaf001 2025年3月
• Development of PCR Primer Enabling the Design of Flexible Sticky Ends for Efficient Concatenation of Long DNA Fragments

  Kohei Nomura, Kaoru Onda, Hirotaka Murase, Fumitaka Hashiya, Yukiteru Ono, Goro Terai, Natsuhisa Oka, Kiyoshi Asai, Daisuke Suzuki, Naho Takahashi …

  RSC Chemical Biology 2024年 査読有り
• The Effect of γ Phosphate Modified Deoxynucleotide Substrates on PCR Activity and Fidelity.

  Fumitaka Hashiya, Hirotaka Murase, Akash Chandela, Haruka Hiraoka, Masahito Inagaki, Yuko Nakashima, Naoko Abe, Mayu Nakamura, Goro Terai, Yasuaki Kimura …

  Chembiochem : a European journal of chemical biology 24(14) e202200572 2023年7月17日 査読有り
• Rtools: A Web Server for Various Secondary Structural Analyses on Single RNA Sequences.

  Yukiteru Ono, Kiyoshi Asai

  Methods in molecular biology (Clifton, N.J.) 2586 1-14 2023年
• Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7)

  Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A. Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata …

  Nature Communications 13(1) 2022年12月1日
• PBSIM3: a simulator for all types of PacBio and ONT long reads.

  Yukiteru Ono, Michiaki Hamada, Kiyoshi Asai

  NAR genomics and bioinformatics 4(4) lqac092 2022年12月 査読有り責任著者
• A streamlined strain engineering workflow with genome-wide screening detects enhanced protein secretion in Komagataella phaffii

  Yoichiro Ito, Misa Ishigami, Goro Terai, Yasuyuki Nakamura, Noriko Hashiba, Teruyuki Nishi, Hikaru Nakazawa, Tomohisa Hasunuma, Kiyoshi Asai, Mitsuo Umetsu …

  Communications Biology 5(1) 2022年12月 査読有り
• Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing

  Junichi Iwakiri, Kumiko Tanaka, Takeshi Chujo, Hiro Takakuwa, Tomohiro Yamazaki, Goro Terai, Kiyoshi Asai, Tetsuro Hirose

  RNA 29(2) 170-177 2022年11月16日 査読有り
• DDX41 coordinates RNA splicing and transcriptional elongation to prevent DNA replication stress in hematopoietic cells.

  Satoru Shinriki, Mayumi Hirayama, Akiko Nagamachi, Akihiko Yokoyama, Takeshi Kawamura, Akinori Kanai, Hidehiko Kawai, Junichi Iwakiri, Rin Liu, Manabu Maeshiro …

  Leukemia 36(11) 2605-2620 2022年11月 査読有り
• QRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity.

  Goro Terai, Kiyoshi Asai

  Nucleic acids research 2022年4月7日 査読有り責任著者
• ConsAlifold: Considering RNA Structural Alignments Improves Prediction Accuracy of RNA Consensus Secondary Structures.

  Masaki Tagashira, Kiyoshi Asai

  Bioinformatics (Oxford, England) 2021年10月25日 査読有り
• m ⁶ A modification of HSATIII lncRNAs regulates temperature‐dependent splicing

  Kensuke Ninomiya, Junichi Iwakiri, Mahmoud Khamis Aly, Yuriko Sakaguchi, Shungo Adachi, Tohru Natsume, Goro Terai, Kiyoshi Asai, Tsutomu Suzuki, Tetsuro Hirose

  The EMBO Journal 40(15) 2021年6月29日 査読有り
• Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression.

  Yoichiro Ito, Goro Terai, Misa Ishigami, Noriko Hashiba, Yasuyuki Nakamura, Takahiro Bamba, Ryota Kumokita, Tomohisa Hasunuma, Kiyoshi Asai, Jun Ishii …

  Nucleic acids research 48(22) 13000-13012 2020年12月 査読有り
• PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores

  Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada

  Bioinformatics 37(5) 589-595 2020年9月25日 査読有り
• Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters

  Shun Sakuraba, Junichi Iwakiri, Michiaki Hamada, Tomoshi Kameda, Genichiro Tsuji, Yasuaki Kimura, Hiroshi Abe, Kiyoshi Asai

  Journal of Chemical Theory and Computation 16(9) 5923-5935 2020年9月8日 査読有り最終著者
• Improving the prediction accuracy of protein abundance in Escherichia coli using mRNA accessibility

  Goro Terai, Kiyoshi Asai

  Nucleic Acids Research 48(14) e81-e81 2020年8月20日 査読有り
• Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model.

  Hiroki Takizawa, Junichi Iwakiri, Goro Terai, Kiyoshi Asai

  Bioinformatics (Oxford, England) 36(Supplement_1) i227-i235 2020年7月1日 査読有り
• RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp.

  Hiroki Takizawa, Junichi Iwakiri, Kiyoshi Asai

  BMC bioinformatics 21(1) 210-210 2020年5月24日 査読有り
• LncRNA‐dependent nuclear stress bodies promote intron retention through SR protein phosphorylation

  Kensuke Ninomiya, Shungo Adachi, Tohru Natsume, Junichi Iwakiri, Goro Terai, Kiyoshi Asai, Tetsuro Hirose

  The EMBO Journal 39(3) 2020年2月3日 査読有り