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A Machine Learning Based Approach to de novo Sequencing of Glycans from Tandem Mass Spectrometry Spectrum
Recently, glycomics has been actively studied and various technologies for glycomics have been rapidly developed. Currently, tandem …
Shotaro Kumozaki, Kengo Sato, Yasubumi Sakakibara
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Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis
The first draft of the common marmoset (Callithrix jacchus) genome was published by the Marmoset Genome Sequencing and Analysis …
Kengo Sato, Yoko Kuroki, Wakako Kumita, Asao Fujiyama, Atsushi Toyoda, Jun Kawai, Atsushi Iriki, Erika Sasaki, Hideyuki Okano, Yasubumi Sakakibara
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Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods
Bacillus subtilis is the main component in the fermentation of soybeans. To investigate the genetics of the soybean-fermenting B. …
Mayumi Kamada, Sumitaka Hase, Kazushi Fujii, Masato Miyake, Kengo Sato, Keitarou Kimura, Yasubumi Sakakibara
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MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
The assembly of multiple genomes from mixed sequence reads is a bottleneck in metagenomic analysis. A single-genome assembly program …
Afiahayati, Kengo Sato, Yasubumi Sakakibara
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Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads
De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial …
Mayumi Kamada, Sumitaka Hase, Kengo Sato, Atsushi Toyoda, Asao Fujiyama, Yasubumi Sakakibara
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An extended genovo metagenomic assembler by incorporating paired-end information
Metagenomes present assembly challenges, when assembling multiple genomes from mixed reads of multiple species. An assembler for single …
Afiahayati, Kengo Sato, Yasubumi Sakakibara
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An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds
BACKGROUND: Prediction of biochemical (metabolic) pathways has a wide range of applications, including the optimization of drug …
Masaomi Nakamura, Tsuyoshi Hachiya, Yutaka Saito, Kengo Sato, Yasubumi Sakakibara
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DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition
MOTIVATION: It is well known that the accuracy of RNA secondary structure prediction from a single sequence is limited, and thus a …
Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara
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Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming
We present a web-based tool set Rtips for fast and accurate prediction of RNA 2D complex structures. Rtips comprises two computational …
Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu
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COPICAT: a software system for predicting interactions between proteins and chemical compounds
UNLABELLED: Since tens of millions of chemical compounds have been accumulated in public chemical databases, fast comprehensive …
Yasubumi Sakakibara, Tsuyoshi Hachiya, Miho Uchida, Nobuyoshi Nagamine, Yohei Sugawara, Masahiro Yokota, Masaomi Nakamura, Kris Popendorf, Takashi Komori, Kengo Sato
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