• 1398 Citations
  • 16 h-Index
20042020

Research output per year

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Research Output

  • 1398 Citations
  • 16 h-Index
  • 45 Article
  • 5 Conference contribution
  • 2 Editorial
2020

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data

Jayakumar, V., Ishii, H., Seki, M., Kumita, W., Inoue, T., Hase, S., Sato, K., Okano, H., Sasaki, E. & Sakakibara, Y., 2020 Apr 2, In : BMC Genomics. 21, 243.

Research output: Contribution to journalArticle

Open Access
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
1 Citation (Scopus)
2018
2 Citations (Scopus)

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

10 Citations (Scopus)

Introduction to Selected Papers from GIW2018

Li, J., Nakai, K., Zheng, Y., Sato, K. & Wong, L., 2018 Dec 1, In : Journal of Bioinformatics and Computational Biology. 16, 6, 18020055.

Research output: Contribution to journalEditorial

2017

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

2 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, In : PloS one. 12, 11, e0188285.

Research output: Contribution to journalArticle

4 Citations (Scopus)
2016

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

1 Citation (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

10 Citations (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

1 Citation (Scopus)
2015
7 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 Jan 1, In : DNA Research. 22, 1, p. 69-77 9 p.

Research output: Contribution to journalArticle

42 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

20 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

15 Citations (Scopus)
2014

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

25 Citations (Scopus)
2013

An extended genovo metagenomic assembler by incorporating paired-end information

Afiahayati, Sato, K. & Sakakibara, Y., 2013 Dec 2, In : PeerJ. 2013, 1, e196.

Research output: Contribution to journalArticle

8 Citations (Scopus)
2012

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 : Unknown Journal. 13 Suppl 17, p. S8

Research output: Contribution to journalArticle

17 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 1, In : Bioinformatics. 28, 5, p. 745-746 2 p., bts031.

Research output: Contribution to journalArticle

11 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 1, In : Bioinformatics. 28, 24, p. 3218-3224 7 p.

Research output: Contribution to journalArticle

18 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 1, In : Nucleic acids research. 40, W1, p. W29-W34

Research output: Contribution to journalArticle

7 Citations (Scopus)
2011

Adaptive seeds tame genomic sequence comparison

Kiełbasa, S. M., Wan, R., Sato, K., Horton, P. & Frith, M. C., 2011 Mar 1, In : Genome Research. 21, 3, p. 487-493 7 p.

Research output: Contribution to journalArticle

451 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, p. W100-W106

Research output: Contribution to journalArticle

15 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

9 Citations (Scopus)

Improved measurements of RNA structure conservation with generalized centroid estimators

Okada, Y., Saito, Y., Sato, K. & Sakakibara, Y., 2011 Dec 1, In : Frontiers in Genetics. 2, AUG, Article 54.

Research output: Contribution to journalArticle

Improving the accuracy of predicting secondary structure for aligned RNA sequences

Hamada, M., Sato, K. & Asai, K., 2011 Jan 1, In : Nucleic acids research. 39, 2, p. 393-402 10 p.

Research output: Contribution to journalArticle

33 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 1, In : Bioinformatics. 27, 13, p. i85-i93 btr215.

Research output: Contribution to journalArticle

100 Citations (Scopus)

Using binding profiles to predict binding sites of target RNAs

Poolsap, U., Kato, Y., Sato, K. & Akutsu, T., 2011 Dec 1, In : Journal of Bioinformatics and Computational Biology. 9, 6, p. 697-713 17 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)
2010

A non-parametric bayesian approach for predicting rna secondary structures

Sato, K., Hamada, M., Mituyama, T., Asai, K. & Sakakibara, Y., 2010 Aug 1, In : Journal of Bioinformatics and Computational Biology. 8, 4, p. 727-742 16 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Improved prediction of transcription binding sites from chromatin modification data

Sato, K., Whitington, T., Bailey, T. L. & Horton, P., 2010 Aug 20, 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010. p. 220-226 7 p. 5510323. (2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Improvement of structure conservation index with centroid estimators

Okada, Y., Sato, K. & Sakakibara, Y., 2010 Dec 1, Pacific Symposium on Biocomputing 2010, PSB 2010. p. 88-97 10 p. (Pacific Symposium on Biocomputing 2010, PSB 2010).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 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

17 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., 2010 Sep 4, In : Bioinformatics. 26, 18, p. i460-i466 btq372.

Research output: Contribution to journalArticle

47 Citations (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

1 Citation (Scopus)
2009

A non-parametric bayesian approach for predicting RNA secondary structures

Sato, K., Hamada, M., Mituyama, T., Asai, K. & Sakakibara, Y., 2009 Nov 2, Algorithms in Bioinformatics - 9th International Workshop, WABI 2009, Proceedings. p. 286-297 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5724 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (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

35 Citations (Scopus)

CentroidFold: A web server for RNA secondary structure prediction

Sato, K., Hamada, M., Asai, K. & Mituyama, T., 2009 Aug 4, In : Nucleic acids research. 37, SUPPL. 2, p. W277-W280

Research output: Contribution to journalArticle

165 Citations (Scopus)
6 Citations (Scopus)
1 Citation (Scopus)

Prediction of RNA secondary structure using generalized centroid estimators

Hamada, M., Kiryu, H., Sato, K., Mituyama, T. & Asai, K., 2009 Feb 1, In : Bioinformatics. 25, 4, p. 465-473 9 p.

Research output: Contribution to journalArticle

139 Citations (Scopus)

Predictions of RNA secondary structure by combining homologous sequence information

Hamada, M., Sato, K., Kiryu, H., Mituyama, T. & Asai, K., 2009 Jun 9, In : Bioinformatics. 25, 12, p. i330-i338

Research output: Contribution to journalArticle

30 Citations (Scopus)

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

2008

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

5 Citations (Scopus)

PSSMTS: Position specific scoring matrices on tree structures

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

Research output: Contribution to journalArticle

4 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, p. W75-78

Research output: Contribution to journalArticle

5 Citations (Scopus)
2007

Stem kernels for RNA sequence analyses

Sakakibara, Y., Asai, K. & Sato, K., 2007 Aug 27, Bioinformatics Research and Development - First International Conference, BIRD 2007 Proceedings. p. 278-291 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4414 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Stem kernels for RNA sequence analyses

Sakakibara, Y., Popendorf, K., Ogawa, N., Asai, K. & Sato, K., 2007 Oct 1, In : Journal of Bioinformatics and Computational Biology. 5, 5, p. 1103-1122 20 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)
2005

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

47 Citations (Scopus)

RNA secondary structural alignment with conditional random fields

Sato, K. & Sakakibara, Y., 2005 Sep 1, In : Bioinformatics. 21, SUPPL. 2, p. ii237-ii242

Research output: Contribution to journalArticle

53 Citations (Scopus)