Directed acyclic graph kernels for structural RNA analysis (2008)
Sato, Kengo, Mituyama, Toutai, Asai, Kiyoshi, Sakakibara, Yasubumi
Abstract Background Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel methods...
Intelligent DNA Chips: Logical Operation of Gene Expression Profiles on DNA Computers (2001)
Yasubumi Sakakibara, Akira Suyama, Sciences Tob
Wepro oo a new type o DNA chips withlohPBq o eratioR executable. In DNAcoP"fiBqC researches, so, metho ds have been develo edto represent and evaluateBo oat functioR o DNA strands. Byemplo ying the...
Stochastic Context-Free Grammars for tRNA Modeling (2000)
Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjolander, Rebecca C. Underwood
Stochastic context-free grammars (SCFGs) are applied to the problems of folding, aligning and modeling families of tRNA sequences. SCFGs capture the sequences' common primary and secondary structure...
Learning Languages by Collecting Cases and Tuning Parameters (1998)
Yasubumi Sakakibara, Klaus P. Jantke
. We investigate the problem of case-based learning of formal languages. Case-based reasoning and learning is a currently booming area of artificial intelligence. The formal framework for case-based...
On Case-Based Learnability of Languages (1997)
Christoph Globig, Klaus P. Jantke, Steffen Lange, Yasubumi Sakakibara
Case-based reasoning is deemed an important technology to alleviate the bottleneck of knowledge acquisition in Artificial Intelligence (AI). In case-based reasoning, knowledge is represented in the...
Learning Languages by Collecting Cases and Tuning Parameters (1997)
Yasubumi Sakakibara, Klaus P. Jantke
. We investigate the problem of case-based learning of formal languages. Case-based reasoning and learning is a currently booming area of artificial intelligence. The formal framework for case-based...
Splicing on Tree-like Structures (1997)
Yasubumi Sakakibara, Claudio Ferretti
In this paper, we provide a method to accelerate the power of splicing systems. We introduce the splicing systems on trees to be built as partially annealed single strands, that is a quite similar...
Splicing on Tree-like Structures (1997)
Yasubumi Sakakibara, Claudio Ferretti
In this paper, we provide a method to accelerate the power of splicing systems. We introduce the splicing systems on trees to be built as partially annealed single strands, that is a quite similar...
On Case-Based Learnability of Languages (1997)
Christoph Globig, Klaus P. Jantke, Steffen Lange, Yasubumi Sakakibara
Case-based reasoning is deemed an important technology to alleviate the bottleneck of knowledge acquisition in Artificial Intelligence (AI). In case-based reasoning, knowledge is represented in the...
On Case-Based Learnability of Languages (1997)
Christoph Globig, Klaus P. Jantke, Steffen Lange, Yasubumi Sakakibara
Case-based reasoning is deemed an important technology to alleviate the bottleneck of knowledge acquisition in Artificial Intelligence (AI). In case-based reasoning, knowledge is represented in the...
Learning Languages by Collecting Cases and Tuning Parameters (1997)
Yasubumi Sakakibara, Klaus P. Jantke
. We investigate the problem of case-based learning of formal languages. Case-based reasoning and learning is a currently booming area of artificial intelligence. The formal framework for case-based...
On case-based learnability of languages (1997)
Globig, Christoph, Jantke, Klaus P., Lange, Steffen, Sakakibara, Yasubumi
Case-based reasoning is deemed an important technology to alleviate the bottleneck of knowledge acquisition in Artificial Intelligence (AI). In case-based reasoning, knowledge is represented in the...
On Case-Based Learnability of Languages (1996)
Christoph Globig, Klaus P. Jantke, Steffen Lange, Yasubumi Sakakibara
Case-based reasoning is deemed an important technology to alleviate the bottleneck of knowledge acquisition in Artificial Intelligence (AI). In case-based reasoning, knowledge is represented in the...
Stochastic Context-Free Grammars for tRNA Modeling (1994)
Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Rebecca C. Underwood
Stochastic context-free grammars (SCFGs) are applied to the problems of folding, aligning and modeling families of tRNA sequences. SCFGs capture the sequences' common primary and secondary structure...
Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars (1994)
Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjolander, Rebecca C. Underwood, ...
Stochastic context-free grammars (SCFGs) can be applied to the problems of folding, aligning and modeling families of homologous RNA sequences. SCFGs capture the sequences' common primary and...
Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjolander, Rebecca C. Underwood
Stochastic context-free grammars (SCFGs) are applied to the problems of folding, aligning and modeling families of homologous RNA sequences. SCFGs capture the sequences' common primary and secondary...
Stochastic Context-Free Grammars for tRNA Modeling (1994)
Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjolander, Rebecca C. Underwood
Stochastic context-free grammars (SCFGs) are applied to the problems of folding, aligning and modeling families of tRNA sequences. SCFGs capture the sequences' common primary and secondary structure...
Stochastic Context-Free Grammars for Modeling RNA (1993)
Yasubumi Sakakibara, Michael Brown, Rebecca C. Underwood, I. Saira Mian
Stochastic context-free grammars (SCFGs) are used to fold, align and model a family of homologous RNA sequences. SCFGs capture the sequences' common primary and secondary structure and generalize the...
Stochastic Context-Free Grammars for Modeling RNA (1993)
Yasubumi Sakakibara, Michael Brown, Rebecca C. Underwood, I. Saira Mian, David Haussler
this paper, we apply stochastic context-free grammars (SCFGs) to the problems of statistical modeling, database searching, multiple alignment, and prediction of the secondary structure of RNA...
Algorithmic learning of formal languages and decision trees / (1992)
"January, 1992."
Splicing on Tree-like Structures (1970)
Yasubumi Sakakibara, Claudio Ferretti
In this paper, we provide a method to accelerate the power of splicing systems. We introduce the splicing systems on trees to be built as partially annealed single strands, that is a quite similar...
Identifying cooperative transcriptional regulations using protein–protein interactions
Nagamine, Nobuyoshi, Kawada, Yuji, Sakakibara, Yasubumi
Cooperative transcriptional activations among multiple transcription factors (TFs) are important to understand the mechanisms of complex transcriptional regulations in eukaryotes. Previous studies...
Identifying cooperative transcriptional regulations using protein–protein interactions
Nagamine, Nobuyoshi, Kawada, Yuji, Sakakibara, Yasubumi
Cooperative transcriptional activations among multiple transcription factors (TFs) are important to understand the mechanisms of complex transcriptional regulations in eukaryotes. Previous studies...
Software.ncrna.org: web servers for analyses of RNA sequences
Asai, Kiyoshi, Kiryu, Hisanori, Hamada, Michiaki, Tabei, Yasuo, Sato, Kengo, Matsui, Hiroshi, ...
We present web servers for analysis of non-coding RNA sequences on the basis of their secondary structures. Software tools for structural multiple sequence alignments, structural pairwise sequence...