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Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery
Computational analysis of RNA sequences constitutes a crucial step in the field of RNA biology. As in other domains of the life …
Kengo Sato, Michiaki Hamada
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Direct inference of base-pairing probabilities with neural networks improves prediction of RNA secondary structures with pseudoknots
Existing approaches to predicting RNA secondary structures depend on how the secondary structure is decomposed into substructures, that …
Manato Akiyama, Yasubumi Sakakibara, Kengo Sato
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Integer programming for selecting set of informative markers in paternity inference
BACKGROUND: Parentage information is fundamental to various life sciences. Recent advances in sequencing technologies have made it …
Soichiro Nishiyama, Kengo Sato, Ryutaro Tao
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Prediction of RNA secondary structure including pseudoknots for long sequences
RNA structural elements called pseudoknots are involved in various biological phenomena including ribosomal frameshifts. Because it is …
Kengo Sato, Yuki Kato
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A max-margin model for predicting residue-base contacts in protein-RNA interactions
Protein-RNA interactions (PRIs) are essential for many biological processes, so understanding aspects of the sequences and structures …
Shunya Kashiwagi, Kengo Sato, Yasubumi Sakakibara
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A web server for designing molecular switches composed of two interacting RNAs
The programmability of RNA-RNA interactions through intermolecular base-pairing has been successfully exploited to design a variety of …
Akito Taneda, Kengo Sato
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RNA secondary structure prediction using deep learning with thermodynamic integration
Accurate predictions of RNA secondary structures can help uncover the roles of functional non-coding RNAs. Although machine …
Kengo Sato, Manato Akiyama, Yasubumi Sakakibara
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An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data
BACKGROUND: The common marmoset (Callithrix jacchus) is one of the most studied primate model organisms. However, the marmoset genomes …
Vasanthan Jayakumar, Hiromi Ishii, Misato Seki, Wakako Kumita, Takashi Inoue, Sumitaka Hase, Kengo Sato, Hideyuki Okano, Erika Sasaki, Yasubumi Sakakibara
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Efficient generation of Knock-in/Knock-out marmoset embryo via CRISPR/Cas9 gene editing
Genetically modified nonhuman primates (NHP) are useful models for biomedical research. Gene editing technologies have enabled …
Wakako Kumita, Kenya Sato, Yasuhiro Suzuki, Yoko Kurotaki, Takeshi Harada, Yang Zhou, Noriyuki Kishi, Kengo Sato, Atsu Aiba, Yasubumi Sakakibara, Guoping Feng, Hideyuki Okano, Erika Sasaki
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A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model
A popular approach for predicting RNA secondary structure is the thermodynamic nearest-neighbor model that finds a thermodynamically …
Manato Akiyama, Kengo Sato, Yasubumi Sakakibara
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