Kiyoshi Asai - Publications, H-index & Citations

Kiyoshi Asai

University of Tokyo

48H指数

230论文数

1.3W被引数

收录论文 42

发表时间

A method for estimating energy parameters of RNAs by differentiating base-pairing probabilities 一种通过区分碱基配对概率来估计RNA能量参数的方法

NAR GENOMICS AND BIOINFORMATICS

IF2.8

2025-12-01

PREAI

Yamamura, Kazuteru; Terai, Goro; Asai, Kiyoshi

PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures PseudoknotVisualizer：三维RNA结构中伪结的可视化

PLOS COMPUTATIONAL BIOLOGY

IF3.6

2025-11-21

PREAI

Otagaki, Takumi; Terai, Goro; Asai, Kiyoshi; Iwakiri, Junichi

Deep generative model of RNAs based on variational autoencoder with context-free grammar

BIOINFORMATICS

IF5.4

2025-08-01

PREAI

Terai, Goro; Asai, Kiyoshi

Consistent features observed in structural probing data of eukaryotic RNAs

genomics proteomics bioinformatics

IF2.8

2025-01-30

OAAI

Yamamura, Kazuteru; Asai, Kiyoshi; Iwakiri, Junichi

Development of PCR primers enabling the design of flexible sticky ends for efficient concatenation of long DNA fragments

RSC CHEMICAL BIOLOGY

IF3.1

2024-01-01

OAAI

Nomura, Kohei; Onda, Kaoru; Murase, Hirotaka; Hashiya, Fumitaka; Ono, Yukiteru; Terai, Goro; Oka, Natsuhisa; Asai, Kiyoshi; Suzuki, Daisuke; Takahashi, Naho; Hiraoka, Haruka; Inagaki, Masahito; Kimura, Yasuaki; Shimizu, Yoshihiro; Abe, Naoko; Abe, Hiroshi

PBSIM3: a simulator for all types of PacBio and ONT long reads

genomics proteomics bioinformatics

IF2.8

2022-12-01

OAAI

Ono, Yukiteru; Hamada, Michiaki; Asai, Kiyoshi

Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing

RNA

IF5

2022-11-16

OAAI

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

DDX41 coordinates RNA splicing and transcriptional elongation to prevent DNA replication stress in hematopoietic cells

LEUKEMIA

IF13.4

2022-10-14

OAAI

Shinriki, Satoru; Hirayama, Mayumi; Nagamachi, Akiko; Yokoyama, Akihiko; Kawamura, Takeshi; Kanai, Akinori; Kawai, Hidehiko; Iwakiri, Junichi; Liu, Rin; Maeshiro, Manabu; Tungalag, Saruul; Tasaki, Masayoshi; Ueda, Mitsuharu; Tomizawa, Kazuhito; Kataoka, Naoyuki; Ideue, Takashi; Suzuki, Yutaka; Asai, Kiyoshi; Tani, Tokio; Inaba, Toshiya; Matsui, Hirotaka

A streamlined strain engineering workflow with genome-wide screening detects enhanced protein secretion in Komagataella phaffii

COMMUNICATIONS BIOLOGY

IF5.1

2022-06-08

OAAI

Ito, Yoichiro; Ishigami, Misa; Terai, Goro; Nakamura, Yasuyuki; Hashiba, Noriko; Nishi, Teruyuki; Nakazawa, Hikaru; Hasunuma, Tomohisa; Asai, Kiyoshi; Umetsu, Mitsuo; Ishii, Jun; Kondo, Akihiko

QRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity

NUCLEIC ACIDS RESEARCH

IF13.1

2022-04-07

OAAI

Terai, Goro; Asai, Kiyoshi

m6A modification of HSATIII lncRNAs regulates temperature-dependent splicing HSATIII lncRNAs的m6A修饰调节温度依赖性剪接

EMBO JOURNAL

IF8.3

2021-06-29

OAAI

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

Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression

NUCLEIC ACIDS RESEARCH

IF13.1

2020-12-01

OAAI

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

Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters

JOURNAL OF CHEMICAL THEORY AND COMPUTATION

IF5.5

2020-07-29

OAAI

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

Improving the prediction accuracy of protein abundance in Escherichia coli using mRNA accessibility

NUCLEIC ACIDS RESEARCH

IF13.1

2020-06-06

OAAI

Terai, Goro; Asai, Kiyoshi

LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation LncRNA依赖性核应激体通过SR蛋白磷酸化促进内含子保留

EMBO JOURNAL

IF8.3

2019-11-29

100

OAAI

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

A robust model for quantitative prediction of the silencing efficacy of wild-type and A-to-I edited miRNAs

RNA BIOLOGY

IF3.4

2019-11-01

OAAI

Tian, Shen; Terai, Goro; Kobayashi, Yoshiaki; Kimura, Yasuaki; Abe, Hiroshi; Asai, Kiyoshi; Ui-Tei, Kumiko

Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

IF3.4

2019-09-01

PREAI

Nishida, Shimpei; Sakuraba, Shun; Asai, Kiyoshi; Hamada, Michiaki

Jointly aligning a group of DNA reads improves accuracy of identifying large deletions

NUCLEIC ACIDS RESEARCH

IF13.1

2017-11-22

OAAI

Shrestha, Anish M. S.; Frith, Martin C.; Asai, Kiyoshi; Richard, Hugues

Genome sequence of Aspergillus luchuensis NBRC 4314

DNA RESEARCH

IF2.9

2016-09-20

OAAI

Yamada, Osamu; Machida, Masayuki; Hosoyama, Akira; Goto, Masatoshi; Takahashi, Toru; Futagami, Taiki; Yamagata, Youhei; Takeuchi, Michio; Kobayashi, Tetsuo; Koike, Hideaki; Abe, Keietsu; Asai, Kiyoshi; Arita, Masanori; Fujita, Nobuyuki; Fukuda, Kazuro; Higa, Ken-ichi; Horikawa, Hiroshi; Ishikawa, Takeaki; Jinno, Koji; Kato, Yumiko; Kirimura, Kohtaro; Mizutani, Osamu; Nakasone, Kaoru; Sano, Motoaki; Shiraishi, Yohei; Tsukahara, Masatoshi; Gomi, Katsuya

Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function

JOURNAL OF CHEMICAL THEORY AND COMPUTATION

IF5.5

2016-08-17

PREAI

Iwakiri, Junichi; Hamada, Michiaki; Asai, Kiyoshi; Kameda, Tomoshi

研究方向