Publication
最新の論文リストはこちらを参照してください。
2012
- K. Sato, Y. Kato, T. Akutsu, K. Asai, Y. Sakakibara
- DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition
- Bioinformatics, 28(24), 3218-3224, 2012.
- M. Nakamura, T. Hachiya, Y. Saito, K. Sato, Y. Sakakibara
- An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds
- BMC Bioinformatics (Proc. of InCoB 2012), 13(Suppl 17):S8, 2012.
- T. Namiki, T. Hachiya, H. Tanaka, Y. Sakakibara
- MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
- Nucleic Acids Research, 40(20), e155, 2012.
- K. Popendorf, Y. Sakakibara
- SAMSCOPE: an OpenGL-based real-time interatctive scale-free SAM viewer
- Bioinformatics, 28(9), 1276-1277, 2012.
- Y. Sakakibara, T. Hachiya, M. Uchida, N. Nagamine, Y. Sugawara, M. Yokota, M. Nakamura, K. Popendorf, T. Komori, K. Sato
- COPICAT: A software system for predicting interations between proteins and chemical compounds
- Bioinformatics, 28(5), 745-746, 2012.
2011
- M. Abe, S. Hase, M. Ogawa, Y. Okada, K. Sato, Y. Saito, Y. Sakakibara
- Comprehensive analysis of small non-coding RNAs in medaka transcriptome by deep RNA-seq approach
- 16th Annual Meeting of the RNA Society (RNA 2011), June 2011.
- Y. Okada, Y. Saito, K. Sato, and Y. Sakakibara
- Improved measurements of RNA structure conservation with generalized centroid estimators
- Frontiers in Genetics 2(54), 2011.
- Y. Saito, K. Sato, and Y. Sakakibara
- Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures
- BMC Bioinformatics, 12(Suppl 1), S48, 2011.
2010
- Y. Saito, K. Sato, and Y. Sakakibara
- Robust and accurate prediction of noncoding RNAs from aligned sequences
- BMC Bioinformatics, 11(Suppl 7), S3, 2010.
- K. Popendorf, T. Hachiya, Y. Osana, and Y. Sakakibara
- Murasaki: A fast, parallelizable algorithm to find anchors from multiple genomes
- PLoS ONE, 5(9), e12651, 2010.
- Y. Nishito, Y. Osana, T. Hachiya, K. Popendorf, A. Toyoda, A. Fujiyama, M. Itaya, and Y. Sakakibara
- Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data
- BMC Genomics, 11:243, 2010. (Highly accessed paper)
- K. Sato, M. Hamada, T. Mituyama, K. Asai, and Y. Sakakibara
- A non-parametric Bayesian approach for predicting RNA secondary structures
- Journal of Bioinformatics and Computational Biology, 8(4) 727-742, 2010.
- Y. Okada, K. Sato, Y. Sakakibara
- Improvement of Structure Conservation Index with Centroid Estimators
- Proceedings of 15th Pacific Symposium on Biocomputing (PSB 2010), 88-97, January, 2010.
2009
- T. Hachiya and Y. Sakakibara
- Sensitive Detection of Conserved Gene Clusters Unravels the Evolutionary Forces behind the Correlation between Protein Sequence Homology and Gene Order Conservation
- Genes, Genomes and Genomics, 3(1), in press, 2009.
- N. Nagamine, T. Shirakawa, Y. Minato, K. Torii, H. Kobayashi, M. Imoto, Y. Sakakibara
- Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening
- PLoS Computational Biology, 5(6), e1000397, (2009)
- T. Akama, K. Suzuki, K. Tanigawa, A. Kawashima, H. Wu, N. Nakata, Y. Osana, Y. Sakakibara, and N. Ishii
- Whole genome tiling array analysis of Mycobacterium leprae RNA reveals high expression of pseudogenes and non-coding regions
- Journal of Bacteriology, 191(10), 3321-3327, 2009.
- Y. Nakagawa, K. Yugi, K. Tsuge, M. Itaya, H. Yanagawa and Y. Sakakibara
- Operon structure optimization by random self-assembly
- Natural Computing, DOI-10.1007/s11047-009-9141-0, 2009
- Y. Suzuki, S. Ogawa, Y. Sakakibara
- Chaperone Therapy for Neuronopathic Lysosomal Diseases: Competitive Inhibitors as Chemical Chaperones for Enhancement of Mutant Enzyme Activities
- Perspectives in Medicinal Chemistry, 3, 1-14, 2009.
- K. Sato, Y. Saito, Y. Sakakibara
- Gradient-based Optimization of Hyperparamers for Base-pairing Profile Local Alignment Kernels
- Genome Informatics, 23(1), 128-38, 2009.
- J. Kawarama, S. Hase, T. Hachiya, K. Hotta, Y. Sakakibara
- Genome-wide detections of non-coding RNAs on Ciona intestinalis genome: from in silico search of snoRNA to full-length sequencing and expression analysis
- 5th International Tunicate Meeting, Okinawa, June 2009.
- Hachiya, T., Osana, Y., Popendorf, K., and Sakakibara
- Accurate identification of orthologous segments among multiple genomes
- Bioinformatics, 25(7), 853-860 , 2009
- K. Sasaki, Nobuyoshi Nagamine, and Y. Sakakibara
- Support vector machine prediction of N- and O-glycosylation sites using whole sequence information and subcellular localization
- IPSJ Transactions on Bioinformatics, 2, 25-35, 2009
- K. Morita(*), Y. Saito(*), K. Sato(*), K. Oka, K. Hotta, and Y. Sakakibara (* Joint First Authors)
- Genome-wide searching with base-pairing kernel functions for non-coding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans
- Nucleic Acids Research, 37(3), 999-1009, 2009.
2008
- K. Sato, T. Mituyama, K Asai, and Y. Sakakibara
- Directed acyclic graph kernels for structural RNA analysis
- BMC Bioinformatics, 9:318 , 2008
- K. Asai, H. Kiryu, M. Hamada, Y. Tabei, K. Sato, H. Matsui, Y. Sakakibara, G. Terai, and T. Mituyama
- Software.ncrna.org: web servers for analyses of RNA sequences
- Nucleic Acids Research, doi:10.1093/nar/gkn222, 2008
- Y. Nakagawa, K. Yugi, K. Tsuge, M. Itaya, H. Yanagawa, Y. Sakakibara
- Operon structure optimization by random self-assembly
- 14th International Meeting on DNA Computing, Prague, 2008
- Y. Saito, K. Sato, and Y. Sakakibara
- Detection of secondary-structure conserved regions by genome comparison
- The 2008 Annual Conference of Japanese Society for Bioinformatics (JSBi 2008), T11（口頭発表）, 2008
- Y. Sugawara, N. Nagamine, Y. Sakakibara
- Mining chemical fragments via SMILES representation
- The 2008 Annual Conference of Japanese Society for Bioinformatics (JSBi 2008), T06（口頭発表）, 2008
2007
- K. Sasaki, Nobuyoshi Nagamine, and Y. Sakakibara
- Support vector machine prediction of glycosylation sites using the whole sequence information and subcellular localization
- The 2007 Annual Conference of Japanese Society for Bioinformatics (JSBi 2007), T16（口頭発表）, 2007
- Y. Sakakibara, N. Ogawa, K. Popendorf, K. Asai, and K. Sato
- Stem kernels for RNA sequence analyses
- Journal of Bioinformatics and Computational Biology, Vol.5, Issue 5, 1103-1122, 2007.
- K. Popendorf, Y. Osana, T. Hachiya, and Y. Sakakibara
- Murasaki - homology detection across multiple large-scale genomes
- Fifth Annual RECOMB Satellite Workshop on Comparative Genomics, San Diego, USA, 2007.
- Y. Osana, K. Popendorf, and Y. Sakakibara
- GMV - a multi-platform comparative genome browser for Murasaki
- Fifth Annual RECOMB Satellite Workshop on Comparative Genomics, San Diego, USA, 2007.
- N.Nagamine and Y.Sakakibara
- Statistical prediction of protein窶田hemical interactions based on chemical structure and mass spectrometry data
- Bioinformatics, Vol.23, No.15, 2004-2012, 2007.
- K. Sato, K. Morita, and Y. Sakakibara
- PSSMTS: position specific scoring matrices on tree structures
- Journal of Mathematical Biology, Online First (DOI 10.1007/s00285-007-0108-4), 2007.
- Y. Sakakibara, H. Nakagawa, Y. Nakashima, and K. Yugi
- Implementing in vivo cellular automata using toggle switch and inter-bacteria communication mechanism
- to be presented at Workshop on Computing and Communications from Biological Systems, Budapest, Hungary, 2007.
- S. Ayukawa, A. Kobayashi, Y. Nakashima, H. Takagi, S. Hamada, M. Uchiyama, K. Yugi, S. Murata, Y. Sakakibara, M. Hagiya, M. Yamamura, and D. Kiga
- SYANAC: SYnthetic biological automaton for noughts and crosses
- IET Synthetic Biology, Vol.1, Issue 1.2, 64-67, 2007.
- 榊原康文, 長名保範, K. Popendorf
- 比較ゲノム解析システムの開発とマイコバクテリアゲノムへの応用
- Japanese Journal of Leprosy, Vol.76, 251-256, 2007.
- N. Ishii, K. Nakahigashi, T. Baba, K. Yugi, M. Tomita
- Multiple high-throughput analyses monitor the response of E. coli to perturbations
- Science, Vol.316, No.5824, 593-7, 2007.
2006
- Y. Sakakibara, T. Yokomori, S. Kobayashi, and A. Suyama
- Probabilistic Inference in Test Tube and Its Application to Gene Expression Profiles, Formal Models, Languages And Applications (edited by Subramanian et al.)
- World Scientific Pub., 304-319, 2006.
2005
- K.Sato and Y.Sakakibara
- RNA Structural Alignment with Conditional Random Fields
- Bioinformatics, Vol.21, Suppl.2, ii237-ii242 (ECCB 2005, Madrid, Spain).
- N.Nagamine and Y.Sakakibara
- Identifying cooperative transcriptional regulations using protein-protein interactions
- Nucleic Acids Research, Vol.33, No.15, 4828-4837, 2005.
- J.Kuramochi and Y.Sakakibara
- Intensive in vitro experiments of implementing and executing finite automata in test tube
- Proceedings of 11th International Meeting on DNA Based Computers, London, Ontario, 59-67, 2005.
- H.Nakagawa, K.Sakamoto, and Y.Sakakibara
- Development of an in vivo computer based on Escherichia coli
- Proceedings of 11th International Meeting on DNA Based Computers, London, Ontario, 68-77, 2005.
- Y.Sakakibara
- Grammatical Inference in Bioinformatics
- IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol.27, No.7, 1051-1062, 2005.
- H.Matsui , K.Sato , and Y.Sakakibara
- Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures
- Bioinformatics, Vol.21, No.11, 2611-2617, 2005.
2004
- H.Matsui, K.Sato and Y.Sakakibara
- Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures
- Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (CSB 04), 290-299, 2004.
- Y.Sakakibara and H.Imai
- A DNA-based Computational Model using a Specific Type of Restriction Enzymes
- Journal of Automata, Languages and Combinatorics, Vol.9, No.1, 111-119, 2004.
2003
- Y.Sakakibara
- Pair Hidden Markov Models on Tree Structures
- Bioinformatics, Vol.19, i232-i240, 2003.
- Y.Sakakibara
- DNA-based Algorithms for Learning Boolean Formulae
- Natural Computing, Vol.2, No.2, 153-171, 2003.
- Y.Sakakibara and T.Hohsaka
- In Vitro Translation-based Computations
- Proceedings of 9th International Meeting on DNA Based Computers, Madison, Wisconsin, 175-179, 2003.
- Y.Sakakibara
- Pair Hidden Markov Models on Tree Structures
- Proceedings of 11th International Conference on Intelligent Systems for Molecular Biology (ISMB 2003), Brisbane, Australia, i232-i240, 2003.
2002
- Y.Sakakibara and H.Imai
- A DNA-based Computational Model using a Specific Type of Restriction Enzyme
- Proceedings of 8th International Meeting on DNA Based Computers, Hakkaido, Japan, 290-300, 2002.