• 2459 Citations
  • 25 h-Index
1987 …2020

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Article
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)

Poly-γ-glutamic acid production of Bacillus subtilis (natto) in the absence of DegQ: A gain-of-function mutation in yabJ gene

Hong, L. T. T., Hachiya, T., Hase, S., Shiwa, Y., Yoshikawa, H., Sakakibara, Y., Nguyen, S. L. T. & Kimura, K., 2019 Jan 1, In : Journal of Bioscience and Bioengineering.

Research output: Contribution to journalArticle

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

9 Citations (Scopus)

Convolutional neural networks for classification of alignments of non-coding RNA sequences

Aoki, G. & Sakakibara, Y., 2018 Jul 1, In : Bioinformatics. 34, 13, p. i237-i244

Research output: Contribution to journalArticle

9 Citations (Scopus)

Time-Series Analysis of Tumorigenesis in a Murine Skin Carcinogenesis Model

Aoto, Y., Okumura, K., Hachiya, T., Hase, S., Wakabayashi, Y., Ishikawa, F. & Sakakibara, Y., 2018 Dec 1, In : Scientific Reports. 8, 1, 12994.

Research output: Contribution to journalArticle

2 Citations (Scopus)
2017

Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data

Jayakumar, V. & Sakakibara, Y., 2017 Nov 2, In : Briefings in Bioinformatics. 20, 3, p. 866-876 11 p., bbx147.

Research output: Contribution to journalArticle

Open Access
16 Citations (Scopus)
Open Access

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

4 Citations (Scopus)
2016

Genome sequence and analysis of the Japanese morning glory Ipomoea nil

Hoshino, A., Jayakumar, V., Nitasaka, E., Toyoda, A., Noguchi, H., Itoh, T., Shin, T., Minakuchi, Y., Koda, Y., Nagano, A. J., Yasugi, M., Honjo, M. N., Kudoh, H., Seki, M., Kamiya, A., Shiraki, T., Carninci, P., Asamizu, E., Nishide, H., Tanaka, S. & 14 others, Park, K. I., Morita, Y., Yokoyama, K., Uchiyama, I., Tanaka, Y., Tabata, S., Shinozaki, K., Hayashizaki, Y., Kohara, Y., Suzuki, Y., Sugano, S., Fujiyama, A., Iida, S. & Sakakibara, Y., 2016 Nov 8, In : Nature communications. 7, 13295.

Research output: Contribution to journalArticle

47 Citations (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

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

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)

Nordihydroguaiaretic acid disrupts the antioxidant ability of Helicobacter pylori through the repression of SodB activity in vitro

Tsugawa, H., Mori, H., Matsuzaki, J., Masaoka, T., Hirayama, T., Nagasawa, H., Sakakibara, Y., Suematsu, M. & Suzuki, H., 2015 Jan 1, In : BioMed Research International. 2015, 734548.

Research output: Contribution to journalArticle

6 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

19 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

Meis1 regulates epidermal stem cells and is required for skin tumorigenesis

Okumura, K., Saito, M., Isogai, E., Aoto, Y., Hachiya, T., Sakakibara, Y., Katsuragi, Y., Hirose, S., Kominami, R., Goitsuka, R., Nakamura, T. & Wakabayashi, Y., 2014 Jul 11, In : PloS one. 9, 7, e102111.

Research output: Contribution to journalArticle

14 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

25 Citations (Scopus)
2013

A bicyclic 1-deoxygalactonojirimycin derivative as a novel pharmacological chaperone for GM1 gangliosidosis

Takai, T., Higaki, K., Aguilar-Moncayo, M., Mena-Barragán, T., Hirano, Y., Yura, K., Yu, L., Ninomiya, H., García-Moreno, M. I., Sakakibara, Y., Ohno, K., Nanba, E., Ortiz Mellet, C., García Fernández, J. M. & Suzuki, Y., 2013 Mar, In : Molecular Therapy. 21, 3, p. 526-532 7 p.

Research output: Contribution to journalArticle

48 Citations (Scopus)

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)

Development of a rifampicin-resistant Bacillus subtilis strain for natto-fermentation showing enhanced exoenzyme production

Kubo, Y., Inaoka, T., Hachiya, T., Miyake, M., Hase, S., Nakagawa, R., Hasegawa, H., Funane, K., Sakakibara, Y. & Kimura, K., 2013 Jun 1, In : Journal of Bioscience and Bioengineering. 115, 6, p. 654-657 4 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)
7 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)

Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications

Kobayashi, H., Harada, H., Nakamura, M., Futamura, Y., Ito, A., Yoshida, M., Iemura, S. I., Shin-Ya, K., Doi, T., Takahashi, T., Natsume, T., Imoto, M. & Sakakibara, Y., 2012 Jun 19, In : BMC Chemical Biology. 12, 2.

Research output: Contribution to journalArticle

6 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

17 Citations (Scopus)

MetaVelvet: An extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Namiki, T., Hachiya, T., Tanaka, H. & Sakakibara, Y., 2012 Nov 1, In : Nucleic acids research. 40, 20, p. e155

Research output: Contribution to journalArticle

341 Citations (Scopus)

SAMSCOPE: An opengl-based real-time interactive scale-free SAM viewer

Popendorf, K. & Sakakibara, Y., 2012 May 1, In : Bioinformatics. 28, 9, p. 1276-1277 2 p., bts122.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Tuning glycosidase inhibition through aglycone interactions: Pharmacological chaperones for Fabry disease and GM1 gangliosidosis

Aguilar-Moncayo, M., Takai, T., Higaki, K., Mena-Barragán, T., Hirano, Y., Yura, K., Li, L., Yu, Y., Ninomiya, H., García-Moreno, M. I., Ishii, S., Sakakibara, Y., Ohno, K., Nanba, E., Ortiz Mellet, C., García Fernández, J. M. & Suzuki, Y., 2012 Jun 6, In : Chemical Communications. 48, 52, p. 6514-6516 3 p.

Research output: Contribution to journalArticle

42 Citations (Scopus)
2011

Chemical chaperone therapy: Chaperone effect on mutant enzyme and cellular pathophysiology in β-galactosidase deficiency

Higaki, K., Li, L., Bahrudin, U., Okuzawa, S., Takamuram, A., Yamamoto, K., Adachi, K., Paraguison, R. C., Takai, T., Ikehata, H., Tominaga, L., Hisatome, I., Iida, M., Ogawa, S., Matsuda, J., Ninomiya, H., Sakakibara, Y., Ohno, K., Suzuki, Y. & Nanba, E., 2011 Jul 1, In : Human mutation. 32, 7, p. 843-852 10 p.

Research output: Contribution to journalArticle

37 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

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)

Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences

Shang, W. H., Hori, T., Toyoda, A., Kato, J., Popendorf, K., Sakakibara, Y., Fujiyama, A. & Fukagawa, T., 2010 Sep 1, In : Genome Research. 20, 9, p. 1219-1228 10 p.

Research output: Contribution to journalArticle

94 Citations (Scopus)

Construction of a genetic AND gate under a new standard for assembly of genetic parts

Ayukawa, S., Kobayashi, A., Nakashima, Y., Takagi, H., Hamada, S., Uchiyama, M., Yugi, K., Murata, S., Sakakibara, Y., Hagiya, M., Yamamura, M. & Kiga, D., 2010 Dec 2, In : BMC Genomics. 11, SUPPL. 4, S16.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Molecular basis of chemical chaperone effects of N-octyl-β-valienamine on human β-glucosidase in low/neutral pH conditions

Jo, H., Yugi, K., Ogawa, S., Suzuki, Y. & Sakakibara, Y., 2010 Apr 1, In : Journal of Proteomics and Bioinformatics. 3, 4, p. 104-112 9 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Murasaki: A fast, parallelizable algorithm to find anchors from multiple genomes

Popendorf, K., Tsuyoshi, H., Osana, Y. & Sakakibara, Y., 2010 Nov 1, In : PloS one. 5, 9, e12651.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Operon structure optimization by random self-assembly

Nakagawa, Y., Yugi, K., Tsuge, K., Itaya, M., Yanagawa, H. & Sakakibara, Y., 2010 Jan 1, In : Natural Computing. 9, 1, p. 173-181 9 p.

Research output: Contribution to journalArticle

2 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)

Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data

Nishito, Y., Osana, Y., Hachiya, T., Popendorf, K., Toyoda, A., Fujiyama, A., Itaya, M. & Sakakibara, Y., 2010 Apr 16, In : BMC Genomics. 11, 1, 243.

Research output: Contribution to journalArticle

64 Citations (Scopus)
2009

Accurate identification of orthologous segments among multiple genomes

Hachiya, T., Osana, Y., Popendorf, K. & Sakakibara, Y., 2009 Apr 7, In : Bioinformatics. 25, 7, p. 853-860 8 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)
6 Citations (Scopus)
1 Citation (Scopus)

Integrating statistical predictions and experimental verifications for enhancing protein-chemical interaction predictions in virtual screening

Nagamine, N., Shirakawa, T., Minato, Y., Torii, K., Kobayashi, H., Imoto, M. & Sakakibara, Y., 2009 Jun 1, In : PLoS Computational Biology. 5, 6, e1000397.

Research output: Contribution to journalArticle

40 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

17 Citations (Scopus)