Kengo Sato
Keio University
Machine learningComputer scienceBioinformaticsRNABiology
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Publications 71
#1Vasanthan Jayakumar (Keio: Keio University)H-Index: 4
#2Hiromi Ishii (Keio: Keio University)
Last. Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
view all 10 authors...
BACKGROUND: The common marmoset (Callithrix jacchus) is one of the most studied primate model organisms. However, the marmoset genomes available in the public databases are highly fragmented and filled with sequence gaps, hindering research advances related to marmoset genomics and transcriptomics. RESULTS: Here we utilize single-molecule, long-read sequence data to improve and update the existing genome assembly and report a near-complete genome of the common marmoset. The assembly is of 2.79 G...
#1Wakako Kumita (Central Institute for Experimental Animals)H-Index: 2
#2Kenya Sato (Central Institute for Experimental Animals)H-Index: 3
Last. Erika Sasaki (Central Institute for Experimental Animals)H-Index: 21
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Genetically modified nonhuman primates (NHP) are useful models for biomedical research. Gene editing technologies have enabled production of target-gene knock-out (KO) NHP models. Target-gene-KO/knock-in (KI) efficiency of CRISPR/Cas9 has not been extensively investigated in marmosets. In this study, optimum conditions for target gene modification efficacies of CRISPR/mRNA and CRISPR/nuclease in marmoset embryos were examined. CRISPR/nuclease was more effective than CRISPR/mRNA in avoiding mosai...
1 CitationsSource
#1Maya Hirohara (Keio: Keio University)H-Index: 1
#2Yutaka Saito (AIST: National Institute of Advanced Industrial Science and Technology)H-Index: 7
Last. Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
view all 5 authors...
Previous studies have suggested deep learning to be a highly effective approach for screening lead compounds for new drugs. Several deep learning models have been developed by addressing the use of various kinds of fingerprints and graph convolution architectures. However, these methods are either advantageous or disadvantageous depending on whether they (1) can distinguish structural differences including chirality of compounds, and (2) can automatically discover effective features. We develope...
3 CitationsSource
#1Manato Akiyama (Keio: Keio University)H-Index: 1
#2Kengo Sato (Keio: Keio University)H-Index: 18
Last. Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
view all 3 authors...
A popular approach for predicting RNA secondary structure is the thermodynamic nearest-neighbor model that finds a thermodynamically most stable secondary structure with minimum free energy (MFE). ...
1 CitationsSource
#1Jinyan Li (UTS: University of Technology, Sydney)H-Index: 36
#2Kenta Nakai (UTokyo: University of Tokyo)H-Index: 43
Last. Limsoon Wong (NUS: National University of Singapore)H-Index: 48
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#1Tatsuya Mizuguchi (Keio: Keio University)
#2Shino Ito (Keio: Keio University)H-Index: 1
Last. Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
view all 4 authors...
#1Manato Akiyama (Keio: Keio University)H-Index: 1
#2Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
Last. Kengo Sato (Keio: Keio University)H-Index: 18
view all 3 authors...
Motivation: Existing approaches for predicting RNA secondary structures depend on how to decompose a secondary structure into substructures, so-called the architecture, to define their parameter space. However, the architecture has not been sufficiently investigated especially for pseudoknotted secondary structures. Results: In this paper, we propose a novel algorithm to directly infer base-pairing probabilities with neural networks that does not depend on the architecture of RNA secondary struc...
#1Yoshimasa Aoto (Keio: Keio University)H-Index: 2
#2Tsuyoshi Hachiya (Iwate Medical University)H-Index: 12
Last. Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
view all 7 authors...
High-throughput RNA sequencing technology is widely used to comprehensively detect and quantify cellular gene expression. Thus, numerous analytical methods have been proposed for identifying differentially expressed genes (DEGs) between paired samples such as tumor and control specimens, but few studies have reported methods for analyzing differential expression under multiple conditions. We propose a novel method, DEclust, for differential expression analysis among more than two matched samples...
3 CitationsSource
#1Yuki Kato (Osaka University)H-Index: 11
#2Tomoya Mori (Kyoto University)H-Index: 4
Last. Tatsuya Akutsu (Kyoto University)H-Index: 39
view all 6 authors...
MOTIVATION: RNA-RNA interactions via base pairing play a vital role in the post-transcriptional regulation of gene expression. Efficient identification of targets for such regulatory RNAs needs not only discriminative power for positive and negative RNA-RNA interacting sequence data but also accurate prediction of interaction sites from positive data. Recently, a few studies have incorporated interaction site accessibility into their prediction methods, indicating the enhancement of predictive p...
1 CitationsSource
#1Michiaki Hamada (AIST: National Institute of Advanced Industrial Science and Technology)H-Index: 17
#2Yukiteru OnoH-Index: 11
Last. Kiyoshi Asai (AIST: National Institute of Advanced Industrial Science and Technology)H-Index: 38
view all 8 authors...
The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequ...
9 CitationsSource