Protein design via deep learning von Ding, Wenze, Nakai, Kenta, Gong, Haipeng

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Predicting protein–peptide binding residues via interpretable deep learning von Wang, Ruheng, Jin, Junru, Zou, Quan, Nakai, Kenta, Wei, Leyi

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PrognoScan: a new database for meta-analysis of the prognostic value of genes von Mizuno, Hideaki, Kitada, Kunio, Nakai, Kenta, Sarai, Akinori

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Editorial: Emerging talents in computational genomics von Iwata, Junichi, Nakai, Kenta

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DNA Methylation Pattern as Important Epigenetic Criterion in Cancer von Ghavifekr Fakhr, Mehrdad, Farshdousti Hagh, Majid, Shanehbandi, Dariush, Baradaran, Behzad

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Information Science Should Take a Lead in Future Biomedical Research von Nakai, Kenta

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A hypothetical trivalent epigenetic code that affects the nature of human ESCs von Ishikawa, Yasuhisa, Nakai, Kenta

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Tools for the Recognition of Sorting Signals and the Prediction of Subcellular Localization of Proteins From Their Amino Acid Sequences von Imai, Kenichiro, Nakai, Kenta

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DeepBIO: an automated and interpretable deep-learning platform for high-throughput biological sequence prediction, functional annotation and visualization analysis von Wang, Ruheng, Jiang, Yi, Jin, Junru, Yin, Chenglin, Yu, Haoqing, Wang, Fengsheng, Feng, Jiuxin, Su, Ran, Nakai, Kenta, Zou, Quan, Wei, Leyi

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iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations von Jin, Junru, Yu, Yingying, Wang, Ruheng, Zeng, Xin, Pang, Chao, Jiang, Yi, Li, Zhongshen, Dai, Yutong, Su, Ran, Zou, Quan, Nakai, Kenta, Wei, Leyi

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Prediction of subcellular locations of proteins: Where to proceed von Imai, Kenichiro, Nakai, Kenta

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DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information von Sierro, Nicolas, Makita, Yuko, de Hoon, Michiel, Nakai, Kenta

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Extreme value theory as a framework for understanding mutation frequency distribution in cancer genomes von Tokutomi, Natsuki, Nakai, Kenta, Sugano, Sumio

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Biomarker discovery by integrated joint non-negative matrix factorization and pathway signature analyses von Fujita, Naoya, Mizuarai, Shinji, Murakami, Katsuhiko, Nakai, Kenta

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A bacterial small RNA regulates the adaptation of Helicobacter pylori to the host environment von Kinoshita-Daitoku, Ryo, Kiga, Kotaro, Miyakoshi, Masatoshi, Otsubo, Ryota, Ogura, Yoshitoshi, Sanada, Takahito, Bo, Zhu, Phuoc, Tuan Vo, Okano, Tokuju, Iida, Tamako, Yokomori, Rui, Kuroda, Eisuke, Hirukawa, Sayaka, Tanaka, Mototsugu, Sood, Arpana, Subsomwong, Phawinee, Ashida, Hiroshi, Binh, Tran Thanh, Nguyen, Lam Tung, Van, Khien Vu, Ho, Dang Quy Dung, Nakai, Kenta, Suzuki, Toshihiko, Yamaoka, Yoshio, Hayashi, Tetsuya, Mimuro, Hitomi

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The Jmjd3- Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection von Akira, Shizuo, Satoh, Takashi, Takeuchi, Osamu, Vandenbon, Alexis, Yasuda, Koubun, Tanaka, Yoshiaki, Kumagai, Yutaro, Miyake, Tohru, Matsushita, Kazufumi, Okazaki, Toshihiko, Saitoh, Tatsuya, Honma, Kiri, Matsuyama, Toshifumi, Yui, Katsuyuki, Tsujimura, Tohru, Standley, Daron M, Nakanishi, Kenji, Nakai, Kenta

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Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s von Lee, Jong-Hun, Park, Sung-Joon, Nakai, Kenta

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A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations von Jia, Hao, Park, Sung-Joon, Nakai, Kenta

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scIMC: a platform for benchmarking comparison and visualization analysis of scRNA-seq data imputation methods von Dai, Chichi, Jiang, Yi, Yin, Chenglin, Su, Ran, Zeng, Xiangxiang, Zou, Quan, Nakai, Kenta, Wei, Leyi

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HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species von López, Yosvany, Nakai, Kenta, Patil, Ashwini

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