生命データサイエンス研究室
生命データサイエンス研究室
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IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
MOTIVATION: Pseudoknots found in secondary structures of a number of functional RNAs play various roles in biological processes. Recent …
Kengo Sato
,
Yuki Kato
,
Michiaki Hamada
,
Tatsuya Akutsu
,
Kiyoshi Asai
引用
DOI
Adaptive seeds tame genomic sequence comparison
The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to …
Szymon M Kiełbasa
,
Raymond Wan
,
Kengo Sato
,
Paul Horton
,
Martin C Frith
引用
DOI
Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures
BACKGROUND: Clustering of unannotated transcripts is an important task to identify novel families of noncoding RNAs (ncRNAs). Several …
Yutaka Saito
,
Kengo Sato
,
Yasubumi Sakakibara
引用
DOI
Improving the accuracy of predicting secondary structure for aligned RNA sequences
Considerable attention has been focused on predicting the secondary structure for aligned RNA sequences since it is useful not only for …
Michiaki Hamada
,
Kengo Sato
,
Kiyoshi Asai
引用
DOI
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy
BACKGROUND: Recent studies have revealed the importance of considering the entire distribution of possible secondary structures in RNA …
Michiaki Hamada
,
Kengo Sato
,
Kiyoshi Asai
引用
DOI
Robust and accurate prediction of noncoding RNAs from aligned sequences
BACKGROUND: Computational prediction of noncoding RNAs (ncRNAs) is an important task in the post-genomic era. One common approach is to …
Yutaka Saito
,
Kengo Sato
,
Yasubumi Sakakibara
引用
DOI
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
MOTIVATION: Considerable attention has been focused on predicting RNA-RNA interaction since it is a key to identifying possible targets …
Yuki Kato
,
Kengo Sato
,
Michiaki Hamada
,
Yoshihide Watanabe
,
Kiyoshi Asai
,
Tatsuya Akutsu
引用
DOI
A non-parametric Bayesian approach for predicting RNA secondary structures
Since many functional RNAs form stable secondary structures which are related to their functions, RNA secondary structure prediction is …
Kengo Sato
,
Michiaki Hamada
,
Toutai Mituyama
,
Kiyoshi Asai
,
Yasubumi Sakakibara
引用
DOI
Improvement of structure conservation index with centroid estimators
RNAz, a support vector machine (SVM) approach for identifying functional non-coding RNAs (ncRNAs), has been proven to be one of the …
Yohei Okada
,
Kengo Sato
,
Yasubumi Sakakibara
引用
DOI
Gradient-based optimization of hyperparameters for base-pairing profile local alignment kernels
We have recently proposed novel kernel functions, called base-pairing profile local alignment (BPLA) kernels for discrimination and …
Kengo Sato
,
Yutaka Saito
,
Yasubumi Sakakibara
引用
DOI
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