生命データサイエンス研究室
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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
引用
DOI
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
引用
DOI
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
引用
DOI
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
引用
DOI
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
引用
DOI
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
引用
DOI
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
引用
DOI
Using binding profiles to predict binding sites of target RNAs
Prediction of RNA-RNA interaction is a key to elucidating possible functions of small non-coding RNAs, and a number of computational …
Unyanee Poolsap
,
Yuki Kato
,
Kengo Sato
,
Tatsuya Akutsu
引用
DOI
Improved measurements of RNA structure conservation with generalized centroid estimators
Identification of non-protein-coding RNAs (ncRNAs) in genomes is a crucial task for not only molecular cell biology but also …
Yohei Okada
,
Yutaka Saito
,
Kengo Sato
,
Yasubumi Sakakibara
引用
DOI
CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences
Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, …
Michiaki Hamada
,
Koichiro Yamada
,
Kengo Sato
,
Martin C Frith
,
Kiyoshi Asai
引用
DOI
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