Publications

RNA Secondary Structure Prediction Based on Energy Models
This chapter introduces the RNA secondary structure prediction based on the nearest neighbor energy model, which is one of the most …
Manato Akiyama, Kengo Sato
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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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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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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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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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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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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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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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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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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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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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MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
The assembly of multiple genomes from mixed sequence reads is a bottleneck in metagenomic analysis. A single-genome assembly program …
Afiahayati, Kengo Sato, Yasubumi Sakakibara
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Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads
De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial …
Mayumi Kamada, Sumitaka Hase, Kengo Sato, Atsushi Toyoda, Asao Fujiyama, Yasubumi Sakakibara
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An extended genovo metagenomic assembler by incorporating paired-end information
Metagenomes present assembly challenges, when assembling multiple genomes from mixed reads of multiple species. An assembler for single …
Afiahayati, Kengo Sato, Yasubumi Sakakibara
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DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition
MOTIVATION: It is well known that the accuracy of RNA secondary structure prediction from a single sequence is limited, and thus a …
Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara
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An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds
BACKGROUND: Prediction of biochemical (metabolic) pathways has a wide range of applications, including the optimization of drug …
Masaomi Nakamura, Tsuyoshi Hachiya, Yutaka Saito, Kengo Sato, Yasubumi Sakakibara
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Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming
We present a web-based tool set Rtips for fast and accurate prediction of RNA 2D complex structures. Rtips comprises two computational …
Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu
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COPICAT: a software system for predicting interactions between proteins and chemical compounds
UNLABELLED: Since tens of millions of chemical compounds have been accumulated in public chemical databases, fast comprehensive …
Yasubumi Sakakibara, Tsuyoshi Hachiya, Miho Uchida, Nobuyoshi Nagamine, Yohei Sugawara, Masahiro Yokota, Masaomi Nakamura, Kris Popendorf, Takashi Komori, Kengo Sato
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Using binding profiles to predict binding sites of target RNAs
Prediction of RNA-RNA interaction is a key to elucidating possible functions of small non-coding RNAs, and a number of computational …
Unyanee Poolsap, Yuki Kato, Kengo Sato, Tatsuya Akutsu
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Improved measurements of RNA structure conservation with generalized centroid estimators
Identification of non-protein-coding RNAs (ncRNAs) in genomes is a crucial task for not only molecular cell biology but also …
Yohei Okada, Yutaka Saito, Kengo Sato, Yasubumi Sakakibara
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IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
MOTIVATION: Pseudoknots found in secondary structures of a number of functional RNAs play various roles in biological processes. Recent …
Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai
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CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences
Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, …
Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C Frith, Kiyoshi Asai
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Adaptive seeds tame genomic sequence comparison
The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to …
Szymon M Kiełbasa, Raymond Wan, Kengo Sato, Paul Horton, Martin C Frith
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Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures
BACKGROUND: Clustering of unannotated transcripts is an important task to identify novel families of noncoding RNAs (ncRNAs). Several …
Yutaka Saito, Kengo Sato, Yasubumi Sakakibara
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Improving the accuracy of predicting secondary structure for aligned RNA sequences
Considerable attention has been focused on predicting the secondary structure for aligned RNA sequences since it is useful not only for …
Michiaki Hamada, Kengo Sato, Kiyoshi Asai
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Prediction of RNA secondary structure by maximizing pseudo-expected accuracy
BACKGROUND: Recent studies have revealed the importance of considering the entire distribution of possible secondary structures in RNA …
Michiaki Hamada, Kengo Sato, Kiyoshi Asai
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Robust and accurate prediction of noncoding RNAs from aligned sequences
BACKGROUND: Computational prediction of noncoding RNAs (ncRNAs) is an important task in the post-genomic era. One common approach is to …
Yutaka Saito, Kengo Sato, Yasubumi Sakakibara
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RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
MOTIVATION: Considerable attention has been focused on predicting RNA-RNA interaction since it is a key to identifying possible targets …
Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu
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A non-parametric Bayesian approach for predicting RNA secondary structures
Since many functional RNAs form stable secondary structures which are related to their functions, RNA secondary structure prediction is …
Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
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Improvement of structure conservation index with centroid estimators
RNAz, a support vector machine (SVM) approach for identifying functional non-coding RNAs (ncRNAs), has been proven to be one of the …
Yohei Okada, Kengo Sato, Yasubumi Sakakibara
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Improved prediction of transcription binding sites from chromatin modification data
In this paper we apply machine learning to the task of predicting transcription factor binding sites by combining information on …
Kengo Sato, Tom Whitington, Timothy L. Bailey, Paul Horton
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Gradient-based optimization of hyperparameters for base-pairing profile local alignment kernels
We have recently proposed novel kernel functions, called base-pairing profile local alignment (BPLA) kernels for discrimination and …
Kengo Sato, Yutaka Saito, Yasubumi Sakakibara
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CENTROIDFOLD: a web server for RNA secondary structure prediction
The CENTROIDFOLD web server (http://www.ncrna.org/centroidfold/) is a web application for RNA secondary structure prediction powered by …
Kengo Sato, Michiaki Hamada, Kiyoshi Asai, Toutai Mituyama
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Predictions of RNA secondary structure by combining homologous sequence information
MOTIVATION: Secondary structure prediction of RNA sequences is an important problem. There have been progresses in this area, but the …
Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
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Prediction of RNA secondary structure using generalized centroid estimators
MOTIVATION: Recent studies have shown that the methods for predicting secondary structures of RNAs on the basis of posterior decoding …
Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai
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Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans
Despite the accumulating research on noncoding RNAs (ncRNAs), it is likely that we are seeing only the tip of the iceberg regarding our …
Kensuke Morita, Yutaka Saito, Kengo Sato, Kotaro Oka, Kohji Hotta, Yasubumi Sakakibara
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CentoroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score
MOTIVATION: The importance of accurate and fast predictions of multiple alignments for RNA sequences has increased due to recent …
Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
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Software.ncrna.org: web servers for analyses of RNA sequences
We present web servers for analysis of non-coding RNA sequences on the basis of their secondary structures. Software tools for …
Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, Toutai Mituyama
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Directed acyclic graph kernels for structural RNA analysis
BACKGROUND: Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous …
Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
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PSSMTS: position specific scoring matrices on tree structures
Identifying non-coding RNA regions on the genome using computational methods is currently receiving a lot of attention. In general, it …
Kengo Sato, Kensuke Morita, Yasubumi Sakakibara
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Stem kernels for RNA sequence analyses
Several computational methods based on stochastic context-free grammars have been developed for modeling and analyzing functional RNA …
Yasubumi Sakakibara, Kris Popendorf, Nana Ogawa, Kiyoshi Asai, Kengo Sato
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Stem Kernels for RNA Sequence Analyses
Several computational methods based on stochastic context-free grammars have been developed for modeling and analyzing functional RNA …
Yasubumi Sakakibara, Kiyoshi Asai, Kengo Sato
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RNA secondary structural alignment with conditional random fields
MOTIVATION: The computational identification of non-coding RNA regions on the genome is currently receiving much attention. However, it …
Kengo Sato, Yasubumi Sakakibara
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Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures
MOTIVATION: Since the whole genome sequences of many species have been determined, computational prediction of RNA secondary structures …
Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara
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Preferential Presentation of Japanese Near-synonyms using Definition Statements
This paper proposes a new method of ranking near-synonyms ordered by their suitability of nuances in a particular context. Our method …
Hiroyuki Okamoto, Kengo Sato, Hiroaki Saito
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Extracting Word Sequence Correspondences with Support Vector Machines
This paper proposes a learning and extracting method of word sequence correspondences from non-aligned parallel corpora with Support …
Kengo Sato, Hiroaki Saito
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Maximum Entropy Model Learning of the Translation Rules
Kengo Sato, Masakazu Nakanishi
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Segmenting Sentences into Linky Strings Using D-bigram Statistics
It is obvious that segmentation takes an important role in natural language processing(NLP), especially for the languages whose …
Shiho Nobesawa, Junya Tsutsumi, Sun Da Jiang, Tomohisa Sano, Kengo Sato, Masakazu Nakanishi
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