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Research Output 1987 2019

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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

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

Bacilli
Bacillus subtilis
Glutamic Acid
Genes
Mutation
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
8 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

Untranslated RNA
RNA
Cluster Analysis
Alignment
Neural Networks

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

Carcinogenesis
Skin
Neoplasms
Genome
Papilloma
2017
9 Citations (Scopus)

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
Genes
Genome
Genome Size
Sequence Analysis
Technology
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
Electronic medical equipment
Health
Analog to digital conversion
39 Citations (Scopus)

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

Ipomoea nil
morning
genome
Sequence Analysis
Convolvulaceae
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
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
30 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
4 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

Masoprocol
Helicobacter pylori
Antioxidants
Stomach
Gerbillinae
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
13 Citations (Scopus)

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

Stem cells
skin (animal)
carcinogenesis
stem cells
Skin
22 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
47 Citations (Scopus)

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

GM1 Gangliosidosis
Pharmacology
Enzymes
Mucopolysaccharidosis IV
Galactosidases
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
6 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

levansucrase
Bacilli
DNA-Directed RNA Polymerases
Rifampin
Bacillus subtilis
7 Citations (Scopus)
Lateral Ventricles
Primates
Pressure
Population
Genes
2012
15 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
6 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, In : BMC Chemical Biology. 12, 2.

Research output: Contribution to journalArticle

Screening
Proteins
Computer Simulation
Affinity chromatography
Network protocols
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

Foreword

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

Research output: Contribution to journalArticle

314 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, In : Nucleic Acids Research. 40, 20

Research output: Contribution to journalArticle

Metagenome
Genome
Metagenomics
6 Citations (Scopus)

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

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

Research output: Contribution to journalArticle

OpenGL
Genome
Visualization
Genes
Real-time
41 Citations (Scopus)

Tuning glycosidase inhibition through aglycone interactions: Pharmacological chaperones for Fabry disease and GM 1 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 Jul 4, In : Chemical Communications. 48, 52, p. 6514-6516 3 p.

Research output: Contribution to journalArticle

Galactosidases
Glycoside Hydrolases
Tuning
2011
35 Citations (Scopus)

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

Galactosidases
Enzymes
Therapeutics
Mutant Proteins
Mutation
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
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
83 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

Centromere
Nucleic Acid Repetitive Sequences
Microsatellite Repeats
Chickens
Kinetochores
10 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

operator regions
Logic gates
Nucleic Acid Regulatory Sequences
Gene expression
Plasmids
11 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

Glucosidases
Enzymes
Free energy
Hydrolases
Hydrogen bonds
15 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

Anchors
Genes
Genome
genome
Program processors
2 Citations (Scopus)

Operon structure optimization by random self-assembly

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

Research output: Contribution to journalArticle

Self assembly
Genes
Biosynthesis
Genetic engineering
Bacilli
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
60 Citations (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

Soy Foods
Bacillus subtilis
Genome
Genes
Operon
2009
23 Citations (Scopus)

Accurate identification of orthologous segments among multiple genomes

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

Research output: Contribution to journalArticle

Anchors
Genome
Genes
Bacterial Genomes
Molecular Sequence Annotation
83 Citations (Scopus)
GM1 Gangliosidosis
Galactosidases
Enzymes
Gaucher Disease
Glucosidases

Erratum: Accurate identification of orthologous segments among multiple genomes (Bioinformatics (2009) vol. 25 (7) (853-860))

Hachiya, T., Osana, Y., Popendorf, K. & Sakakibara, Y., 2009 Jun, In : Bioinformatics. 25, 11, p. 1474 1 p.

Research output: Contribution to journalArticle

Bioinformatics
Genes
6 Citations (Scopus)
Small Nucleolar RNA
Untranslated RNA
Caenorhabditis elegans
Base Pairing
Genome
1 Citation (Scopus)
Base Pairing
36 Citations (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, In : PLoS Computational Biology. 5, 6, e1000397.

Research output: Contribution to journalArticle

Virtual Screening
chemical interactions
Screening
screening
Proteins

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