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Research Output 2004 2019

  • 1244 Citations
  • 15 h-Index
  • 44 Article
  • 5 Conference contribution
  • 1 Editorial
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Article
2019

Efficient generation of Knock-in/Knock-out marmoset embryo via CRISPR/Cas9 gene editing

Kumita, W., Sato, K., Suzuki, Y., Kurotaki, Y., Harada, T., Zhou, Y., Kishi, N., Sato, K., Aiba, A., Sakakibara, Y., Feng, G., Okano, H. & Sasaki, E., 2019 Dec 1, In : Scientific reports. 9, 1, 12719.

Research output: Contribution to journalArticle

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Callithrix
Embryonic Structures
Gene Knockout Techniques
Primates
2018
1 Citation (Scopus)
RNA
Thermodynamics
Learning systems
Benchmarking
Computational Biology

Convolutional neural network based on SMILES representation of compounds for detecting chemical motif

Hirohara, M., Saito, Y., Koda, Y., Sato, K. & Sakakibara, Y., 2018 Dec 31, In : BMC Bioinformatics. 19, 526.

Research output: Contribution to journalArticle

Learning
Neural Networks
Neural networks
Dermatoglyphics
Fingerprint
2017
2 Citations (Scopus)

An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data

Kato, Y., Mori, T., Sato, K., Maegawa, S., Hosokawa, H. & Akutsu, T., 2017 Jan 15, In : Bioinformatics. 33, 2, p. 202-209 8 p.

Research output: Contribution to journalArticle

RNA
Accessibility
Prediction
Interaction
Prediction Model
3 Citations (Scopus)

DEclust: A statistical approach for obtaining differential expression profiles of multiple conditions

Aoto, Y., Hachiya, T., Okumura, K., Hase, S., Sato, K., Wakabayashi, Y. & Sakakibara, Y., 2017 Nov 1, In : PLoS One. 12, 11, e0188285.

Research output: Contribution to journalArticle

Genes
transcriptome
Transcriptome
Gene expression
High-Throughput Nucleotide Sequencing
2016
1 Citation (Scopus)

Prediction of gene structures from RNA-seq data using dual decomposition

Inatsuki, T., Sato, K. & Sakakibara, Y., 2016 Mar 1, In : IPSJ Transactions on Bioinformatics. 9, p. 1-6 6 p.

Research output: Contribution to journalArticle

RNA Sequence Analysis
RNA
Genes
Decomposition
Eukaryota
7 Citations (Scopus)

Rtools: a web server for various secondary structural analyses on single RNA sequences

Hamada, M., Ono, Y., Kiryu, H., Sato, K., Kato, Y., Fukunaga, T., Mori, R. & Asai, K., 2016 Jul 8, In : Nucleic Acids Research. 44, W1, p. W302-W307

Research output: Contribution to journalArticle

RNA
Thermodynamics
Software
Mutation
1 Citation (Scopus)

SHARAKU: An algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing

Tsuchiya, M., Amano, K., Abe, M., Seki, M., Hase, S., Sato, K. & Sakakibara, Y., 2016 Jun 15, In : Bioinformatics. 32, 12, p. i369-i377

Research output: Contribution to journalArticle

High-Throughput Nucleotide Sequencing
Untranslated RNA
RNA
Sequencing
Cluster Analysis
2015
7 Citations (Scopus)
Mass Spectrometry
Tandem Mass Spectrometry
Sequencing
Mass spectrometry
Polysaccharides
31 Citations (Scopus)

MetaVelvet-SL: An extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning

Afiahayati, Sato, K. & Sakakibara, Y., 2015, In : DNA Research. 22, 1, p. 69-77 9 p.

Research output: Contribution to journalArticle

Metagenomics
Learning
Genome
Metagenome
Research
14 Citations (Scopus)

Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis

Sato, K., Kuroki, Y., Kumita, W., Fujiyama, A., Toyoda, A., Kawai, J., Iriki, A., Sasaki, E., Okano, H. & Sakakibara, Y., 2015 Nov 20, In : Scientific Reports. 5, 16894.

Research output: Contribution to journalArticle

Callithrix
Sequence Analysis
Genome
Genes
Chromosomes
13 Citations (Scopus)

Whole-genome sequencing and comparative genome analysis of bacillus subtilis strains isolated from non-salted fermented soybean foods

Kamada, M., Hase, S., Fujii, K., Miyake, M., Sato, K., Kimura, K. & Sakakibara, Y., 2015 Oct 27, In : PLoS One. 10, 10, e0141369.

Research output: Contribution to journalArticle

Bacilli
Bacillus subtilis
Soybeans
Genes
Genome
2014
23 Citations (Scopus)

Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads

Kamada, M., Hase, S., Sato, K., Toyoda, A., Fujiyama, A. & Sakakibara, Y., 2014 Oct 16, In : PLoS One. 9, 10, e109999.

Research output: Contribution to journalArticle

natto
Bacilli
Bacillus subtilis
Genes
Genome
2013
6 Citations (Scopus)

An extended genovo metagenomic assembler by incorporating paired-end information

Afiahayati, Sato, K. & Sakakibara, Y., 2013, In : PeerJ. 2013, 1, e196.

Research output: Contribution to journalArticle

Metagenomics
Metagenome
Genes
Genome
Restaurants
2012
16 Citations (Scopus)

An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds.

Nakamura, M., Hachiya, T., Saito, Y., Sato, K. & Sakakibara, Y., 2012, In : BMC Bioinformatics. 13 Suppl 17

Research output: Contribution to journalArticle

Chemical compounds
Pathway
Efficient Algorithms
Prediction
Metabolic Networks and Pathways
11 Citations (Scopus)

COPICAT: A software system for predicting interactions between proteins and chemical compounds

Sakakibara, Y., Hachiya, T., Uchida, M., Nagamine, N., Sugawara, Y., Yokota, M., Nakamura, M., Popendorf, K., Komori, T. & Sato, K., 2012 Mar, In : Bioinformatics. 28, 5, p. 745-746 2 p., bts031.

Research output: Contribution to journalArticle

Chemical compounds
Software System
Software
Lead compounds
Proteins
17 Citations (Scopus)

DAFS: Simultaneous aligning and folding of RNA sequences via dual decomposition

Sato, K., Kato, Y., Akutsu, T., Asai, K. & Sakakibara, Y., 2012 Dec, In : Bioinformatics. 28, 24, p. 3218-3224 7 p.

Research output: Contribution to journalArticle

Folding
RNA
Alignment
Decomposition
Decompose
7 Citations (Scopus)

Rtips: Fast and accurate tools for RNA 2D structure prediction using integer programming

Kato, Y., Sato, K., Asai, K. & Akutsu, T., 2012 Jul, In : Nucleic Acids Research. 40, W1

Research output: Contribution to journalArticle

RNA
2011
392 Citations (Scopus)

Adaptive seeds tame genomic sequence comparison

Kiełbasa, S. M., Wan, R., Sato, K., Horton, P. & Frith, M. C., 2011 Mar, In : Genome Research. 21, 3, p. 487-493 7 p.

Research output: Contribution to journalArticle

Seeds
DNA
14 Citations (Scopus)

CentroidHomfold-LAST: Accurate prediction of RNA secondary structure using automatically collected homologous sequences

Hamada, M., Yamada, K., Sato, K., Frith, M. C. & Asai, K., 2011 Jul 1, In : Nucleic Acids Research. 39, SUPPL. 2

Research output: Contribution to journalArticle

Sequence Homology
RNA
RNA Sequence Analysis
8 Citations (Scopus)

Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures

Saito, Y., Sato, K. & Sakakibara, Y., 2011 Feb 15, In : BMC Bioinformatics. 12, SUPPL. 1, S48.

Research output: Contribution to journalArticle

Untranslated RNA
Sequence Alignment
Secondary Structure
RNA
Cluster Analysis

Improved measurements of RNA structure conservation with generalized centroid estimators

Okada, Y., Saito, Y., Sato, K. & Sakakibara, Y., 2011, In : Frontiers in Genetics. 2, AUG, Article 54.

Research output: Contribution to journalArticle

Untranslated RNA
RNA
Base Pairing
Genome
Computational Biology
32 Citations (Scopus)

Improving the accuracy of predicting secondary structure for aligned RNA sequences

Hamada, M., Sato, K. & Asai, K., 2011 Jan, In : Nucleic Acids Research. 39, 2, p. 393-402 10 p.

Research output: Contribution to journalArticle

Untranslated RNA
Computational Biology
89 Citations (Scopus)

IPknot: Fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

Sato, K., Kato, Y., Hamada, M., Akutsu, T. & Asai, K., 2011 Jul, In : Bioinformatics. 27, 13, btr215.

Research output: Contribution to journalArticle

RNA Secondary Structure
Integer programming
Integer Programming
RNA
Prediction
44 Citations (Scopus)

RactIP: Fast and accurate prediction of RNA-RNA interaction using integer programming

Kato, Y., Sato, K., Hamada, M., Watanabe, Y., Asai, K. & Akutsu, T., 2011, In : Bioinformatics. 27, 13, p. i460-i466

Research output: Contribution to journalArticle

Integer programming
Integer Programming
RNA
Prediction
Interaction
6 Citations (Scopus)

Using binding profiles to predict binding sites of target RNAs

Poolsap, U., Kato, Y., Sato, K. & Akutsu, T., 2011 Dec, In : Journal of Bioinformatics and Computational Biology. 9, 6, p. 697-713 17 p.

Research output: Contribution to journalArticle

Antisense RNA
Binding sites
RNA
Binding Sites
Small Untranslated RNA
2010
7 Citations (Scopus)

A non-parametric bayesian approach for predicting rna secondary structures

Sato, K., Hamada, M., Mituyama, T., Asai, K. & Sakakibara, Y., 2010 Aug, In : Journal of Bioinformatics and Computational Biology. 8, 4, p. 727-742 16 p.

Research output: Contribution to journalArticle

Bayes Theorem
RNA
Stochastic Processes
Context free grammars
Bioinformatics
16 Citations (Scopus)

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy

Hamada, M., Sato, K. & Asai, K., 2010 Nov 30, In : BMC Bioinformatics. 11, 586.

Research output: Contribution to journalArticle

RNA Secondary Structure
RNA
Base Pairing
Prediction
Secondary Structure
1 Citation (Scopus)

Robust and accurate prediction of noncoding RNAs from aligned sequences

Saito, Y., Sato, K. & Sakakibara, Y., 2010 Oct 15, In : BMC Bioinformatics. 11, SUPPL. 7, S3.

Research output: Contribution to journalArticle

Untranslated RNA
RNA
Base Pairing
Alignment
prediction
2009
31 Citations (Scopus)

CentroidAlign: Fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score

Hamada, M., Sato, K., Kiryu, H., Mituyama, T. & Asai, K., 2009 Oct 6, In : Bioinformatics. 25, 24, p. 3236-3243 8 p., btp580.

Research output: Contribution to journalArticle

Computational Biology
RNA
Alignment
Benchmarking
Untranslated RNA
147 Citations (Scopus)

CentroidFold: A web server for RNA secondary structure prediction

Sato, K., Hamada, M., Asai, K. & Mituyama, T., 2009, In : Nucleic Acids Research. 37, SUPPL. 2

Research output: Contribution to journalArticle

RNA
Benchmarking
Sequence Alignment
Ointments
Base Pairing
6 Citations (Scopus)
Small Nucleolar RNA
Untranslated RNA
Caenorhabditis elegans
Base Pairing
Genome
1 Citation (Scopus)
Base Pairing
129 Citations (Scopus)

Prediction of RNA secondary structure using generalized centroid estimators

Hamada, M., Kiryu, H., Sato, K., Mituyama, T. & Asai, K., 2009 Feb, In : Bioinformatics. 25, 4, p. 465-473 9 p.

Research output: Contribution to journalArticle

RNA Secondary Structure
Centroid
RNA
Base Pairing
Estimator
29 Citations (Scopus)

Predictions of RNA secondary structure by combining homologous sequence information

Hamada, M., Sato, K., Kiryu, H., Mituyama, T. & Asai, K., 2009, In : Bioinformatics. 25, 12

Research output: Contribution to journalArticle

RNA Secondary Structure
Sequence Homology
RNA
Prediction
Secondary Structure

Sequence and structural analyses for functional non-coding RNAs

Sakakibara, Y. & Sato, K., 2009, In : Natural Computing Series. 9783540888680, p. 63-79 17 p.

Research output: Contribution to journalArticle

RNA
Kernel Function
Context-free Grammar
Secondary Structure
Discrimination
2008
4 Citations (Scopus)

Directed acyclic graph kernels for structural RNA analysis

Sato, K., Mituyama, T., Asai, K. & Sakakibara, Y., 2008 Jul 22, In : BMC Bioinformatics. 9, 318.

Research output: Contribution to journalArticle

Untranslated RNA
Directed Acyclic Graph
RNA
kernel
Base Pairing
4 Citations (Scopus)

PSSMTS: Position specific scoring matrices on tree structures

Sato, K., Morita, K. & Sakakibara, Y., 2008 Jan, In : Journal of Mathematical Biology. 56, 1-2, p. 201-214 14 p.

Research output: Contribution to journalArticle

Position-Specific Scoring Matrices
Tree Structure
RNA
Scoring
Untranslated RNA
5 Citations (Scopus)

Software.ncrna.org: web servers for analyses of RNA sequences.

Asai, K., Kiryu, H., Hamada, M., Tabei, Y., Sato, K., Matsui, H., Sakakibara, Y., Terai, G. & Mituyama, T., 2008 Jul 1, In : Nucleic Acids Research. 36, Web Server issue

Research output: Contribution to journalArticle

RNA Sequence Analysis
Sequence Alignment
Software
Untranslated RNA
2007
10 Citations (Scopus)

Stem kernels for RNA sequence analyses

Sakakibara, Y., Popendorf, K., Ogawa, N., Asai, K. & Sato, K., 2007 Oct, In : Journal of Bioinformatics and Computational Biology. 5, 5, p. 1103-1122 20 p.

Research output: Contribution to journalArticle

RNA Sequence Analysis
RNA
Genome
Amino Acid Sequence Homology
Untranslated RNA
2006
Artificial Intelligence
Bioinformatics
Computational Biology
Computer science
Artificial intelligence
2005
47 Citations (Scopus)

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures

Matsui, H., Sato, K. & Sakakibara, Y., 2005 Jun 1, In : Bioinformatics. 21, 11, p. 2611-2617 7 p.

Research output: Contribution to journalArticle

RNA
Grammar
Hidden Markov models
Alignment
Tree Structure
52 Citations (Scopus)

RNA secondary structural alignment with conditional random fields

Sato, K. & Sakakibara, Y., 2005 Sep, In : Bioinformatics. 21, SUPPL. 2

Research output: Contribution to journalArticle

Conditional Random Fields
RNA
Untranslated RNA
Alignment
Open Reading Frames