Improving the prediction accuracy of protein abundance in Escherichia coli using mRNA accessibility von Terai, Goro, Asai, Kiyoshi

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ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures von Tagashira, Masaki, Asai, Kiyoshi

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Motif-independent prediction of a secondary metabolism gene cluster using comparative genomics: application to sequenced genomes of Aspergillus and ten other filamentous fungal spe... von Takeda, Itaru, Umemura, Myco, Koike, Hideaki, Asai, Kiyoshi, Machida, Masayuki

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A fast structural multiple alignment method for long RNA sequences von Tabei, Yasuo, Kiryu, Hisanori, Kin, Taishin, Asai, Kiyoshi

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PBSIM: PacBio reads simulator--toward accurate genome assembly von Ono, Yukiteru, Asai, Kiyoshi, Hamada, Michiaki

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COSMO: A dynamic programming algorithm for multicriteria codon optimization von Taneda, Akito, Asai, Kiyoshi

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RNA Structural Alignments, Part II: Non-Sankoff Approaches for Structural Alignments von Asai, Kiyoshi, Hamada, Michiaki

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Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations von KIRYU, Hisanori, ASAI, Kiyoshi

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A semi-supervised learning approach for RNA secondary structure prediction von Yonemoto, Haruka, Asai, Kiyoshi, Hamada, Michiaki

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A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA) von Hamada, Michiaki, Asai, Kiyoshi

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Prediction of RNA secondary structure using generalized centroid estimators von Hamada, Michiaki, Kiryu, Hisanori, Sato, Kengo, Mituyama, Toutai, Asai, Kiyoshi

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A local multiple alignment method for detection of non-coding RNA sequences von Tabei, Yasuo, Asai, Kiyoshi

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m6A modification of HSATIII lncRNAs regulates temperature‐dependent splicing von Ninomiya, Kensuke, Iwakiri, Junichi, Aly, Mahmoud Khamis, Sakaguchi, Yuriko, Adachi, Shungo, Natsume, Tohru, Terai, Goro, Asai, Kiyoshi, Suzuki, Tsutomu, Hirose, Tetsuro

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Comprehensive prediction of lncRNA-RNA interactions in human transcriptome von Terai, Goro, Iwakiri, Junichi, Kameda, Tomoshi, Hamada, Michiaki, Asai, Kiyoshi

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PBSIM3: a simulator for all types of PacBio and ONT long reads von Ono, Yukiteru, Hamada, Michiaki, Asai, Kiyoshi

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RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp von Takizawa, Hiroki, Iwakiri, Junichi, Asai, Kiyoshi

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Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens von Tsukui, Takahiro, Nagano, Nozomi, Umemura, Myco, Kumagai, Toshitaka, Terai, Goro, Machida, Masayuki, Asai, Kiyoshi

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regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila von Saito, Kuniaki, Inagaki, Sachi, Mituyama, Toutai, Kawamura, Yoshinori, Ono, Yukiteru, Sakota, Eri, Kotani, Hazuki, Asai, Kiyoshi, Siomi, Haruhiko, Siomi, Mikiko C

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Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing von Iwakiri, Junichi, Tanaka, Kumiko, Chujo, Takeshi, Takakuwa, Hiro, Yamazaki, Tomohiro, Terai, Goro, Asai, Kiyoshi, Hirose, Tetsuro

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

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