Kengo Sato

Yasubumi Sakakibara, Tsuyoshi Hachiya, Miho Uchida, Nobuyoshi Nagamine, Yohei Sugawara, Masahiro Yokota, Masaomi Nakamura, Kris Popendorf, Takashi Komori, Kengo Sato: COPICAT: a software system for predicting interactions between proteins and chemical compounds. Bioinformatics 28(5): 745-746 (2012)

Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara: DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. Bioinformatics 28(24): 3218-3224 (2012)

Masaomi Nakamura, Tsuyoshi Hachiya, Yutaka Saito, Kengo Sato, Yasubumi Sakakibara: An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds. BMC Bioinformatics 13(S-17): S8 (2012)

Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu: Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming. Nucleic Acids Research 40(Web-Server-Issue): 29-34 (2012)

Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai: IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics [ISMB/ECCB] 27(13): 85-93 (2011)

Yutaka Saito, Kengo Sato, Yasubumi Sakakibara: Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures. BMC Bioinformatics 12(S-1): S48 (2011)

Unyanee Poolsap, Yuki Kato, Kengo Sato, Tatsuya Akutsu: Using binding Profiles to Predict binding sites of Target RNAs. J. Bioinformatics and Computational Biology 9(6): 697-713 (2011)

Michiaki Hamada, Kengo Sato, Kiyoshi Asai: Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Research 39(2): 393-402 (2011)

Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C. Frith, Kiyoshi Asai: CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. Nucleic Acids Research 39(Web-Server-Issue): 100-106 (2011)

Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu: RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics 26(18) (2010)

Michiaki Hamada, Kengo Sato, Kiyoshi Asai: Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinformatics 11: 586 (2010)

Yutaka Saito, Kengo Sato, Yasubumi Sakakibara: Robust and accurate prediction of noncoding RNAs from aligned sequences. BMC Bioinformatics 11(S-7): S3 (2010)

Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara: A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures. J. Bioinformatics and Computational Biology 8(4): 727-742 (2010)

Kengo Sato, Tom Whitington, Timothy L. Bailey, Paul Horton: Improved prediction of transcription binding sites from chromatin modification data. CIBCB 2010: 1-7

Yohei Okada, Kengo Sato, Yasubumi Sakakibara: Improvement of Structure Conservation Index with Centroid Estimators. Pacific Symposium on Biocomputing 2010: 88-97

Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai: Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics 25(4): 465-473 (2009)

Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai: Predictions of RNA secondary structure by combining homologous sequence information. Bioinformatics 25(12) (2009)

Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai: CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. Bioinformatics 25(24): 3236-3243 (2009)

Kengo Sato, Michiaki Hamada, Kiyoshi Asai, Toutai Mituyama: CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Research 37(Web-Server-Issue): 277-280 (2009)

Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara: A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures. WABI 2009: 286-297

Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara: Directed acyclic graph kernels for structural RNA analysis. BMC Bioinformatics 9 (2008)

Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, Toutai Mituyama: Software.ncrna.org: web servers for analyses of RNA sequences. Nucleic Acids Research 36(Web-Server-Issue): 75-78 (2008)

Yasubumi Sakakibara, Kris Popendorf, Nana Ogawa, Kiyoshi Asai, Kengo Sato: Stem Kernels for RNA Sequence Analyses. J. Bioinformatics and Computational Biology 5(5): 1103-1122 (2007)

Yasubumi Sakakibara, Kiyoshi Asai, Kengo Sato: Stem Kernels for RNA Sequence Analyses. BIRD 2007: 278-291

Yasubumi Sakakibara, Satoshi Kobayashi, Kengo Sato, Tetsuro Nishino, Etsuji Tomita (Eds.): Grammatical Inference: Algorithms and Applications, 8th International Colloquium, ICGI 2006, Tokyo, Japan, September 20-22, 2006, Proceedings. Lecture Notes in Computer Science 4201, Springer 2006, isbn 3-540-45264-8

Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara: Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures. Bioinformatics 21(11): 2611-2617 (2005)

Kengo Sato, Yasubumi Sakakibara: RNA secondary structural alignment with conditional random fields. ECCB/JBI 2005: 242

Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara: Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures. CSB 2004: 290-299

Kengo Sato, Hiroaki Saito: Extracting Word Sequence Correspondences with Support Vector Machines. COLING 2002

Kengo Sato, Masakazu Nakanishi: Maximum Entropy Model Learning of the Translation Rules. COLING-ACL 1998: 1171-1175

Shiho Nobesawa, Junya Tsutsumi, Sun Da Jiang, Tomohisa Sano, Kengo Sato, Masakazu Nakanishi: Segmenting Sentences into Linky Strings Using D-bigram Statistics. COLING 1996: 586-591