• 2508 Citations
  • 25 h-Index
1987 …2020

Research output per year

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Research Output

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
2 Citations (Scopus)

Guest Editorial for the 16th Asia Pacific Bioinformatics Conference

Yamanishi, Y., Sakakibara, Y. & Chen, Y. P. P., 2019 Jan 1, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 1, 8635414.

Research output: Contribution to journalEditorial

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

11 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

12 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

3 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
22 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, In : PloS one. 12, 11, e0188285.

Research output: Contribution to journalArticle

4 Citations (Scopus)
2016
Open Access

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

52 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, 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, 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

22 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

15 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

26 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

51 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

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, 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

Open Access
17 Citations (Scopus)

Bacterial computing and molecular communication

Sakakibara, Y. & Hiyama, S., 2012 Jan 1, Handbook of Natural Computing. Springer Berlin Heidelberg, Vol. 3-4. p. 1204-1232 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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, 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

12 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)

Foreword

Sakakibara, Y. & Mi, Y., 2012 Jun 1, In : Natural Computing. 11, 2, p. 185-186 2 p.

Research output: Contribution to journalEditorial

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, In : Nucleic acids research. 40, 20, p. e155

Research output: Contribution to journalArticle

346 Citations (Scopus)

Poster: In silico microarray algorithm: Accurate and fast taxonomic profiling from short read sequences

Tagami, T., Hachiya, T. & Sakakibara, Y., 2012 May 8, 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012. 6182660. (2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012).

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

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

43 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, In : Human mutation. 32, 7, p. 843-852 10 p.

Research output: Contribution to journalArticle

38 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

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

Namiki, T., Hachiya, T., Tanaka, H. & Sakakibara, Y., 2011 Dec 1, 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. p. 116-124 9 p. (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011).

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

13 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)

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, In : Genome Research. 20, 9, p. 1219-1228 10 p.

Research output: Contribution to journalArticle

95 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)

Development of a bacteria computer: From in silico finite automata to in vitro and in vivo

Sakakibara, Y., 2010 Jul 29, Programs, Proofs, Processes - 6th Conference on Computability in Europe, CiE 2010, Proceedings. p. 362-371 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6158 LNCS).

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)

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, In : Journal of Proteomics and Bioinformatics. 3, 4, p. 104-112 9 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)

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

Popendorf, K., Tsuyoshi, H., Osana, Y. & Sakakibara, Y., 2010, 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)