Yasubumi Sakakibara

Publication Activity (10 Years)

Years Active: 1986-2022
Publications (10 Years): 9

Top Topics

Tandem Mass Spectrometry

Comprehensive Evaluation

Redescription Mining

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

IEEE J. Emerg. Sel. Topics Circuits Syst.

Publications

Kaito Kishi, Takahiko Satoh, Rudy Raymond, Naoki Yamamoto, Yasubumi Sakakibara
Graph Kernels Encoding Features of All Subgraphs by Quantum Superposition. IEEE J. Emerg. Sel. Topics Circuits Syst. 12 (3) (2022)
Kuo-ching Liang, Yasubumi Sakakibara
MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly. BMC Bioinform. (6) (2021)
Narumi Watanabe, Yuuto Ohnuki, Yasubumi Sakakibara
Deep learning integration of molecular and interactome data for protein-compound interaction prediction. J. Cheminformatics 13 (1) (2021)
Vasanthan Jayakumar, Yasubumi Sakakibara
Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data. Briefings Bioinform. 20 (3) (2019)
Yoshihiro Yamanishi, Yasubumi Sakakibara, Yi-Ping Phoebe Chen
Guest Editorial for the 16th Asia Pacific Bioinformatics Conference. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (1) (2019)
Maya Hirohara, Yutaka Saito, Yuki Koda, Kengo Sato, Yasubumi Sakakibara
Convolutional neural network based on SMILES representation of compounds for detecting chemical motif. BMC Bioinform. (19) (2018)
Manato Akiyama, Kengo Sato, Yasubumi Sakakibara
A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model. J. Bioinform. Comput. Biol. 16 (6) (2018)
Genta Aoki, Yasubumi Sakakibara
Convolutional neural networks for classification of alignments of non-coding RNA sequences. Bioinform. 34 (13) (2018)
Mariko Tsuchiya, Kojiro Amano, Masaya Abe, Misato Seki, Sumitaka Hase, Kengo Sato, Yasubumi Sakakibara
SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing. Bioinform. 32 (12) (2016)
Shotaro Kumozaki, Kengo Sato, Yasubumi Sakakibara
A Machine Learning Based Approach to de novo Sequencing of Glycans from Tandem Mass Spectrometry Spectrum. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (6) (2015)
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. Bioinform. 28 (5) (2012)
Kris Popendorf, Yasubumi Sakakibara
SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer. Bioinform. 28 (9) (2012)
Tomoya Tagami, Tsuyoshi Hachiya, Yasubumi Sakakibara
Poster: In silico microarray algorithm: Accurate and fast taxonomic profiling from short read sequences. ICCABS (2012)
Yasubumi Sakakibara, Yongli Mi
Foreword. Nat. Comput. 11 (2) (2012)
Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. Bioinform. 28 (24) (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 Bioinform. 13 (S-17) (2012)
Yutaka Saito, Kengo Sato, Yasubumi Sakakibara
Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures. BMC Bioinform. 12 (S-1) (2011)
Toshiaki Namiki, Tsuyoshi Hachiya, Hideaki Tanaka, Yasubumi Sakakibara
metagenome assembly from short sequence reads. BCB (2011)
Yutaka Saito, Kengo Sato, Yasubumi Sakakibara
Robust and accurate prediction of noncoding RNAs from aligned sequences. BMC Bioinform. 11 (S-7) (2010)
Yusuke Nakagawa, Katsuyuki Yugi, Kenji Tsuge, Mitsuhiro Itaya, Hiroshi Yanagawa, Yasubumi Sakakibara
Operon structure optimization by random self-assembly. Nat. Comput. 9 (1) (2010)
Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures. J. Bioinform. Comput. Biol. 8 (4) (2010)
Yohei Okada, Kengo Sato, Yasubumi Sakakibara
Improvement of Structure Conservation Index with Centroid Estimators. Pacific Symposium on Biocomputing (2010)
Yasubumi Sakakibara
. CiE (2010)
Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures. WABI (2009)
Tsuyoshi Hachiya, Yasunori Osana, Kris Popendorf, Yasubumi Sakakibara
Accurate identification of orthologous segments among multiple genomes. Bioinform. 25 (11) (2009)
Nobuyoshi Nagamine, Takayuki Shirakawa, Yusuke Minato, Kentaro Torii, Hiroki Kobayashi, Masaya Imoto, Yasubumi Sakakibara
Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening. PLoS Comput. Biol. 5 (6) (2009)
Yasubumi Sakakibara, Kengo Sato
Sequence and Structural Analyses for Functional Non-coding RNAs. Algorithmic Bioprocesses (2009)
Tsuyoshi Hachiya, Yasunori Osana, Kris Popendorf, Yasubumi Sakakibara
Accurate identification of orthologous segments among multiple genomes. Bioinform. 25 (7) (2009)
Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
Directed acyclic graph kernels for structural RNA analysis. BMC Bioinform. 9 (2008)
Yusuke Nakagawa, Katsuyuki Yugi, Kenji Tsuge, Mitsuhiro Itaya, Hiroshi Yanagawa, Yasubumi Sakakibara
Operon Structure Optimization by Random Self-assembly. DNA (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 Res. 36 (Web-Server-Issue) (2008)
Yasubumi Sakakibara
Bio-Molecular Computing of Finite-State Machine. BIONETICS (2008)
Nobuyoshi Nagamine, Yasubumi Sakakibara
Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data. Bioinform. 23 (15) (2007)
Yasubumi Sakakibara, Takashi Yokomori, Satoshi Kobayashi, Akira Suyama
Probabilistic Inference in Test Tube and its Application to Gene Expression Profiles. Formal Models, Languages and Applications (2007)
Yasubumi Sakakibara, Kris Popendorf, Nana Ogawa, Kiyoshi Asai, Kengo Sato
Stem Kernels for RNA Sequence Analyses. J. Bioinform. Comput. Biol. 5 (5) (2007)
Yasubumi Sakakibara, Kiyoshi Asai, Kengo Sato
Stem Kernels for RNA Sequence Analyses. BIRD (2007)
Georgios Paliouras, Yasubumi Sakakibara
Guest editorial to the special issue on grammatical inference. Mach. Learn. 66 (1) (2007)
Yasubumi Sakakibara, Hirotaka Nakagawa, Yusaku Nakashima, Katsuyuki Yugi
Implementing in vivo Cellular Automata using Toggle Switch and Inter-Bacteria Communication Mechanism. BIONETICS (2007)
Yuji Kawada, Yasubumi Sakakibara
Discriminative Detection of Cis-Acting Regulatory Variation From Location Data. APBC (2006)
Yasubumi Sakakibara
Learning context-free grammars using tabular representations. Pattern Recognit. 38 (9) (2005)
Yasubumi Sakakibara
Grammatical Inference in Bioinformatics. IEEE Trans. Pattern Anal. Mach. Intell. 27 (7) (2005)
Yuji Kawada, Yasubumi Sakakibara
Discriminative Discovery of Transcription Factor Binding Sites from Location Data. CSB (2005)
Kengo Sato, Yasubumi Sakakibara
RNA secondary structural alignment with conditional random fields. ECCB/JBI (2005)
Hirotaka Nakagawa, Kensaku Sakamoto, Yasubumi Sakakibara
. DNA (2005)
Junna Kuramochi, Yasubumi Sakakibara
Experiments of Implementing and Executing Finite Automata in Test Tube. DNA (2005)
Yasubumi Sakakibara
Development of a Bacteria Computer: From in silico Finite Automata to in virto AND in vivo. Bull. EATCS 87 (2005)
Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara
Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures. Bioinform. 21 (11) (2005)
Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara
Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures. CSB (2004)
Satoshi Kobayashi, Takashi Yokomori, Yasubumi Sakakibara
An Algorithm for Testing Structure Freeness of Biomolecular Sequences. Aspects of Molecular Computing (2004)
Yasubumi Sakakibara, Hiroshi Imai
A DNA-Based Computational Model Using a Specific Type of Restriction Enzymes. J. Autom. Lang. Comb. 9 (1) (2004)
Yasubumi Sakakibara
Pair hidden Markov models on tree structures. ISMB (Supplement of Bioinformatics) (2003)
Yasubumi Sakakibara, Takahiro Hohsaka
In Vitro Translation-Based Computations. DNA (2003)
Yasubumi Sakakibara
DNA-based algorithms for learning Boolean formulae. Nat. Comput. 2 (2) (2003)
Yasubumi Sakakibara, Hiroshi Imai
A DNA-based Computational Model Using a Specific Type of Restriction Enzyme. DNA (2002)
Takashi Yokomori, Yasubumi Sakakibara, Satoshi Kobayashi
A Magic Pot : Self-assembly Computation Revisited. Formal and Natural Computing (2002)
Yasubumi Sakakibara, Satoshi Kobayashi
Sticker systems with complex structures. Soft Comput. 5 (2) (2001)
Satoshi Kobayashi, Yasubumi Sakakibara, Takashi Yokomori
Approximate identification of finite elasticity. Where Mathematics, Computer Science, Linguistics and Biology Meet (2001)
Yasubumi Sakakibara
Probabilistic logical inference using quantities of DNA strands. CEC (2001)
Satoshi Kobayashi, Yasubumi Sakakibara
Multiple splicing systems and the universal computability. Theor. Comput. Sci. 264 (1) (2001)
Yasubumi Sakakibara
Population Computation and Majority Inference in Test Tube. DNA (2001)
Yasubumi Sakakibara
Solving Computational Learning Problems of Boolean Formulae on DNA Computers. DNA Computing (2000)
Yasubumi Sakakibara, Hidenori Muramatsu
Learning Context-Free Grammars from Partially Structured Examples. ICGI (2000)
Yasubumi Sakakibara, Claudio Ferretti
Splicing on Tree-Like Structures. Theor. Comput. Sci. 210 (2) (1999)
Yasubumi Sakakibara, Mitsuhiro Kondo
GA-based Learning of Context-Free Grammars using Tabular Representations. ICML (1999)
Yasubumi Sakakibara, Claudio Ferretti
Splicing on tree-like structures. DNA Based Computers (1997)
Yasubumi Sakakibara
Recent Advances of Grammatical Inference. Theor. Comput. Sci. 185 (1) (1997)
Christoph Globig, Klaus P. Jantke, Steffen Lange, Yasubumi Sakakibara
On Case Based Learnability of Language. New Gener. Comput. 15 (1) (1997)
Mostefa Golea, Masahiro Matsuoka, Yasubumi Sakakibara
Stochastic simple recurrent neural networks. ICGI (1996)
Yasubumi Sakakibara, Kazuo Misue, Takeshi Koshiba
A machine learning approach to knowledge acquisitions from text databases. Int. J. Hum. Comput. Interact. 8 (3) (1996)
Yasubumi Sakakibara, Mostefa Golea
Simple recurrent networks as generalized hidden Markov models with distributed representations. ICNN (1995)
Yasubumi Sakakibara
Grammatical Inference: An Old and New Paradigm. ALT (1995)
Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjölander, Rebecca C. Underwood, David Haussler
Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars. CPM (1994)
Yasubumi Sakakibara, Michael Brown, Rebecca C. Underwood, I. Saira Mian, David Haussler
Stochastic Context-Free Grammars for Modeling RN. HICSS (5) (1994)
Yasubumi Sakakibara, Klaus P. Jantke, Steffen Lange
Learning Languages by Collecting Cases and Tuning Parameters. AII/ALT (1994)
Yasubumi Sakakibara
Noise-Tolerant Occam Algorithms and Their Applications to Learning Decision Trees. Mach. Learn. 11 (1993)
Yasubumi Sakakibara
Efficient Learning of Context-Free Grammars from Positive Structural Examples Inf. Comput. 97 (1) (1992)
Yasubumi Sakakibara, Rani Siromoney
A Noise Model on Learning Sets of Strings. COLT (1992)
Yasubumi Sakakibara
On Learning from Queries and Counterexamples in the Presence of Noise. Inf. Process. Lett. 37 (5) (1991)
Yuji Takada, Yasubumi Sakakibara, Takeshi Ohtani
ACE: A syntax-directed editor customizable from examples and queries. ALT (1991)
Yasubumi Sakakibara
Learning Context-Free Grammars from Structural Data in Polynomial Time. Theor. Comput. Sci. 76 (2-3) (1990)
Yasubumi Sakakibara
Inductive inference of logic programs based on algebraic semantics. New Gener. Comput. 7 (4) (1990)
Yasubumi Sakakibara
Occam Algorithms for Learning From Noisy Examples. ALT (1990)
Yuji Takada, Kunihiko Hiraishi, Yasubumi Sakakibara
Exact Learning of Semilinear Sets. ALT (1990)
Yasubumi Sakakibara
An Efficient Learning of Context-Free Grammars for Bottom-Up Parsers. FGCS (1988)
Yasubumi Sakakibara
Learning Context-Free Grammars from Structural Data in Polynomial Time. COLT (1988)
Yasubumi Sakakibara
Programming in Modal Logic: An Extension of PROLOG based on Modal Logic. LP (1986)