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Convolutional neural network based on SMILES representation of compounds for detecting chemical motif
BACKGROUND: Previous studies have suggested deep learning to be a highly effective approach for screening lead compounds for new drugs. …
Maya Hirohara, Yutaka Saito, Yuki Koda, Kengo Sato, Yasubumi Sakakibara
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DEclust: A statistical approach for obtaining differential expression profiles of multiple conditions
High-throughput RNA sequencing technology is widely used to comprehensively detect and quantify cellular gene expression. Thus, …
Yoshimasa Aoto, Tsuyoshi Hachiya, Kazuhiro Okumura, Sumitaka Hase, Kengo Sato, Yuichi Wakabayashi, Yasubumi Sakakibara
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An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data
MOTIVATION: RNA-RNA interactions via base pairing play a vital role in the post-transcriptional regulation of gene expression. …
Yuki Kato, Tomoya Mori, Kengo Sato, Shingo Maegawa, Hiroshi Hosokawa, Tatsuya Akutsu
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Generation of a Nonhuman Primate Model of Severe Combined Immunodeficiency Using Highly Efficient Genome Editing
Recent advances in genome editing have facilitated the generation of nonhuman primate (NHP) models, with potential to unmask the …
Kenya Sato, Ryo Oiwa, Wakako Kumita, Rachel Henry, Tetsushi Sakuma, Ryoji Ito, Ryoko Nozu, Takashi Inoue, Ikumi Katano, Kengo Sato, Norio Okahara, Junko Okahara, Yoshihisa Shimizu, Masafumi Yamamoto, Kisaburo Hanazawa, Takao Kawakami, Yoshie Kametani, Ryuji Suzuki, Takeshi Takahashi, Edward J Weinstein, Takashi Yamamoto, Yasubumi Sakakibara, Sonoko Habu, Jun-Ichi Hata, Hideyuki Okano, Erika Sasaki
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Rtools: a web server for various secondary structural analyses on single RNA sequences
The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their …
Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai
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SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing
MOTIVATION: Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. …
Mariko Tsuchiya, Kojiro Amano, Masaya Abe, Misato Seki, Sumitaka Hase, Kengo Sato, Yasubumi Sakakibara
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Prediction of Gene Structures from RNA-seq Data Using Dual Decomposition
Numerous computational algorithms for predicting protein-coding genes from genomic sequences have been developed, and hidden Markov …
Tatsumu Inatsuki, Kengo Sato, Yasubumi Sakakibara
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A Machine Learning Based Approach to de novo Sequencing of Glycans from Tandem Mass Spectrometry Spectrum
Recently, glycomics has been actively studied and various technologies for glycomics have been rapidly developed. Currently, tandem …
Shotaro Kumozaki, Kengo Sato, Yasubumi Sakakibara
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Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis
The first draft of the common marmoset (Callithrix jacchus) genome was published by the Marmoset Genome Sequencing and Analysis …
Kengo Sato, Yoko Kuroki, Wakako Kumita, Asao Fujiyama, Atsushi Toyoda, Jun Kawai, Atsushi Iriki, Erika Sasaki, Hideyuki Okano, Yasubumi Sakakibara
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Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods
Bacillus subtilis is the main component in the fermentation of soybeans. To investigate the genetics of the soybean-fermenting B. …
Mayumi Kamada, Sumitaka Hase, Kazushi Fujii, Masato Miyake, Kengo Sato, Keitarou Kimura, Yasubumi Sakakibara
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