Yasubumi Sakakibara

According to our database, Yasubumi Sakakibara authored at least 85 papers between 1986 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Deep learning of multimodal networks with topological regularization for drug repositioning.

Yuto Ohnuki, Manato Akiyama, Yasubumi Sakakibara

J. Cheminformatics, December, 2024

2022

Graph Kernels Encoding Features of All Subgraphs by Quantum Superposition.

Kaito Kishi, Takahiko Satoh, Rudy Raymond, Naoki Yamamoto, Yasubumi Sakakibara

IEEE J. Emerg. Sel. Topics Circuits Syst., 2022

2021

Deep learning integration of molecular and interactome data for protein-compound interaction prediction.

Narumi Watanabe, Yuuto Ohnuki, Yasubumi Sakakibara

J. Cheminformatics, 2021

MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly.

Kuo-Ching Liang, Yasubumi Sakakibara

BMC Bioinform., 2021

2019

Guest Editorial for the 16th Asia Pacific Bioinformatics Conference.

Yoshihiro Yamanishi, Yasubumi Sakakibara, Yi-Ping Phoebe Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data.

Vasanthan Jayakumar, Yasubumi Sakakibara

Briefings Bioinform., 2019

2018

A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model.

Manato Akiyama, Kengo Sato, Yasubumi Sakakibara

J. Bioinform. Comput. Biol., 2018

Convolutional neural network based on SMILES representation of compounds for detecting chemical motif.

Maya Hirohara, Yutaka Saito, Yuki Koda, Kengo Sato, Yasubumi Sakakibara

BMC Bioinform., 2018

Convolutional neural networks for classification of alignments of non-coding RNA sequences.

Genta Aoki, Yasubumi Sakakibara

Bioinform., 2018

2017

Probabilistic Context-Free Grammars.

Yasubumi Sakakibara

Proceedings of the Encyclopedia of Machine Learning and Data Mining, 2017

2016

SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.

Mariko Tsuchiya, Kojiro Amano, Masaya Abe, Misato Seki, Sumitaka Hase, Kengo Sato, Yasubumi Sakakibara

Bioinform., 2016

2015

A Machine Learning Based Approach to de novo Sequencing of Glycans from Tandem Mass Spectrometry Spectrum.

Shotaro Kumozaki, Kengo Sato, Yasubumi Sakakibara

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

2012

Bacterial Computing and Molecular Communication.

Yasubumi Sakakibara, Satoshi Hiyama

Proceedings of the Handbook of Natural Computing, 2012

Foreword.

Yasubumi Sakakibara, Yongli Mi

Nat. Comput., 2012

An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds.

Masaomi Nakamura, Tsuyoshi Hachiya, Yutaka Saito, Kengo Sato, Yasubumi Sakakibara

BMC Bioinform., 2012

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.

Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara

Bioinform., 2012

COPICAT: a software system for predicting interactions between proteins and chemical compounds.

Yasubumi Sakakibara, Tsuyoshi Hachiya, Miho Uchida, Nobuyoshi Nagamine, Yohei Sugawara, Masahiro Yokota, Masaomi Nakamura, Kris Popendorf, Takashi Komori, Kengo Sato

Bioinform., 2012

SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer.

Kris Popendorf, Yasubumi Sakakibara

Bioinform., 2012

Poster: In silico microarray algorithm: Accurate and fast taxonomic profiling from short read sequences.

Tomoya Tagami, Tsuyoshi Hachiya, Yasubumi Sakakibara

Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

2011

Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures.

Yutaka Saito, Kengo Sato, Yasubumi Sakakibara

BMC Bioinform., 2011

MetaVelvet: an extension of Velvet assembler to <i>de novo</i> metagenome assembly from short sequence reads.

Toshiaki Namiki, Tsuyoshi Hachiya, Hideaki Tanaka, Yasubumi Sakakibara

Proceedings of the ACM International Conference on Bioinformatics, 2011

2010

Probabilistic Context-Free Grammars.

Yasubumi Sakakibara

Proceedings of the Encyclopedia of Machine Learning, 2010

Operon structure optimization by random self-assembly.

Yusuke Nakagawa, Katsuyuki Yugi, Kenji Tsuge, Mitsuhiro Itaya, Hiroshi Yanagawa, Yasubumi Sakakibara

Nat. Comput., 2010

A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures.

Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara

J. Bioinform. Comput. Biol., 2010

Robust and accurate prediction of noncoding RNAs from aligned sequences.

Yutaka Saito, Kengo Sato, Yasubumi Sakakibara

BMC Bioinform., 2010

Improvement of Structure Conservation Index with Centroid Estimators.

Yohei Okada, Kengo Sato, Yasubumi Sakakibara

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Development of a Bacteria Computer: From <i>in silico</i> Finite Automata to <i>in vitro</i> and <i>in vivo</i>.

Yasubumi Sakakibara

Proceedings of the Programs, Proofs, Processes, 6th Conference on Computability in Europe, 2010

2009

Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening.

Nobuyoshi Nagamine, Takayuki Shirakawa, Yusuke Minato, Kentaro Torii, Hiroki Kobayashi, Masaya Imoto, Yasubumi Sakakibara

PLoS Comput. Biol., 2009

Support Vector Machine Prediction of N- and O-glycosylation Sites Using Whole Sequence Information and Subcellular Localization.

Kenta Sasaki, Nobuyoshi Nagamine, Yasubumi Sakakibara

Inf. Media Technol., 2009

Accurate identification of orthologous segments among multiple genomes.

Tsuyoshi Hachiya, Yasunori Osana, Kris Popendorf, Yasubumi Sakakibara

Bioinform., 2009

Sequence and Structural Analyses for Functional Non-coding RNAs.

Yasubumi Sakakibara, Kengo Sato

Proceedings of the Algorithmic Bioprocesses, 2009

2008

Software.ncrna.org: web servers for analyses of RNA sequences.

Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, Toutai Mituyama

Nucleic Acids Res., 2008

Directed acyclic graph kernels for structural RNA analysis.

Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara

BMC Bioinform., 2008

Bio-Molecular Computing of Finite-State Machine.

Yasubumi Sakakibara

Proceedings of the 3rd International ICST Conference on Bio-Inspired Models of Network, 2008

2007

Guest editorial to the special issue on grammatical inference.

Georgios Paliouras, Yasubumi Sakakibara

Mach. Learn., 2007

Stem Kernels for RNA Sequence Analyses.

Yasubumi Sakakibara, Kris Popendorf, Nana Ogawa, Kiyoshi Asai, Kengo Sato

J. Bioinform. Comput. Biol., 2007

Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data.

Nobuyoshi Nagamine, Yasubumi Sakakibara

Bioinform., 2007

Probabilistic Inference in Test Tube and its Application to Gene Expression Profiles.

Yasubumi Sakakibara, Takashi Yokomori, Satoshi Kobayashi, Akira Suyama

Proceedings of the Formal Models, 2007

Stem Kernels for RNA Sequence Analyses.

Yasubumi Sakakibara, Kiyoshi Asai, Kengo Sato

Proceedings of the Bioinformatics Research and Development, First International Conference, 2007

Implementing in vivo Cellular Automata using Toggle Switch and Inter-Bacteria Communication Mechanism.

Yasubumi Sakakibara, Hirotaka Nakagawa, Yusaku Nakashima, Katsuyuki Yugi

Proceedings of the 2nd International ICST Conference on Bio-Inspired Models of Network, 2007

2006

Discriminative Detection of Cis-Acting Regulatory Variation From Location Data.

Yuji Kawada, Yasubumi Sakakibara

Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, 2006

2005

Learning context-free grammars using tabular representations.

Yasubumi Sakakibara

Pattern Recognit., 2005

Grammatical Inference in Bioinformatics.

Yasubumi Sakakibara

IEEE Trans. Pattern Anal. Mach. Intell., 2005

Development of a Bacteria Computer: From in silico Finite Automata to in virto AND in vivo.

Yasubumi Sakakibara

Bull. EATCS, 2005

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.

Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara

Bioinform., 2005

RNA secondary structural alignment with conditional random fields.

Kengo Sato, Yasubumi Sakakibara

Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

Development of an <i>In Vivo</i> Computer Based on <i>Escherichia coli</i>.

Hirotaka Nakagawa, Kensaku Sakamoto, Yasubumi Sakakibara

Proceedings of the DNA Computing, 11th International Workshop on DNA Computing, 2005

Intensive <i>In Vitro</i> Experiments of Implementing and Executing Finite Automata in Test Tube.

Junna Kuramochi, Yasubumi Sakakibara

Proceedings of the DNA Computing, 11th International Workshop on DNA Computing, 2005

Discriminative Discovery of Transcription Factor Binding Sites from Location Data.

Yuji Kawada, Yasubumi Sakakibara

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005

2004

A DNA-Based Computational Model Using a Specific Type of Restriction Enzymes.

Yasubumi Sakakibara, Hiroshi Imai

J. Autom. Lang. Comb., 2004

An Algorithm for Testing Structure Freeness of Biomolecular Sequences.

Satoshi Kobayashi, Takashi Yokomori, Yasubumi Sakakibara

Proceedings of the Aspects of Molecular Computing, 2004

2003

DNA-based algorithms for learning Boolean formulae.

Yasubumi Sakakibara

Nat. Comput., 2003

Pair hidden Markov models on tree structures.

Yasubumi Sakakibara

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

In Vitro Translation-Based Computations.

Yasubumi Sakakibara, Takahiro Hohsaka

Proceedings of the DNA Computing, 9th International Workshop on DNA Based Computers, 2003

2002

A DNA-based Computational Model Using a Specific Type of Restriction Enzyme.

Yasubumi Sakakibara, Hiroshi Imai

Proceedings of the DNA Computing, 8th International Workshop on DNA Based Computers, 2002

A Magic Pot : Self-assembly Computation Revisited.

Takashi Yokomori, Yasubumi Sakakibara, Satoshi Kobayashi

Proceedings of the Formal and Natural Computing, 2002

2001

Multiple splicing systems and the universal computability.

Satoshi Kobayashi, Yasubumi Sakakibara

Theor. Comput. Sci., 2001

Sticker systems with complex structures.

Yasubumi Sakakibara, Satoshi Kobayashi

Soft Comput., 2001

Population Computation and Majority Inference in Test Tube.

Yasubumi Sakakibara

Proceedings of the DNA Computing, 7th International Workshop on DNA-Based Computers, 2001

Probabilistic logical inference using quantities of DNA strands.

Yasubumi Sakakibara

Proceedings of the 2001 Congress on Evolutionary Computation, 2001

Approximate identification of finite elasticity.

Satoshi Kobayashi, Yasubumi Sakakibara, Takashi Yokomori

Proceedings of the Where Mathematics, 2001

2000

Learning Context-Free Grammars from Partially Structured Examples.

Yasubumi Sakakibara, Hidenori Muramatsu

Proceedings of the Grammatical Inference: Algorithms and Applications, 2000

Solving Computational Learning Problems of Boolean Formulae on DNA Computers.

Yasubumi Sakakibara

Proceedings of the DNA Computing, 6th International Workshop on DNA-Based Computers, 2000

1999

Splicing on Tree-Like Structures.

Yasubumi Sakakibara, Claudio Ferretti

Theor. Comput. Sci., 1999

GA-based Learning of Context-Free Grammars using Tabular Representations.

Yasubumi Sakakibara, Mitsuhiro Kondo

Proceedings of the Sixteenth International Conference on Machine Learning (ICML 1999), Bled, Slovenia, June 27, 1999

1997

Recent Advances of Grammatical Inference.

Yasubumi Sakakibara

Theor. Comput. Sci., 1997

On Case Based Learnability of Language.

Christoph Globig, Klaus P. Jantke, Steffen Lange, Yasubumi Sakakibara

New Gener. Comput., 1997

1996

A machine learning approach to knowledge acquisitions from text databases.

Yasubumi Sakakibara, Kazuo Misue, Takeshi Koshiba

Int. J. Hum. Comput. Interact., 1996

Stochastic simple recurrent neural networks.

Mostefa Golea, Masahiro Matsuoka, Yasubumi Sakakibara

Proceedings of the Grammatical Inference: Learning Syntax from Sentences, 1996

1995

Simple recurrent networks as generalized hidden Markov models with distributed representations.

Yasubumi Sakakibara, Mostefa Golea

Proceedings of International Conference on Neural Networks (ICNN'95), Perth, WA, Australia, November 27, 1995

Grammatical Inference: An Old and New Paradigm.

Yasubumi Sakakibara

Proceedings of the Algorithmic Learning Theory, 6th International Conference, 1995

1994

Stochastic Context-Free Grammars for Modeling RN.

Yasubumi Sakakibara, Michael Brown, Rebecca C. Underwood, I. Saira Mian, David Haussler

Proceedings of the 27th Annual Hawaii International Conference on System Sciences (HICSS-27), 1994

Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars.

Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjölander, Rebecca C. Underwood, David Haussler

Proceedings of the Combinatorial Pattern Matching, 5th Annual Symposium, 1994

Learning Languages by Collecting Cases and Tuning Parameters.

Yasubumi Sakakibara, Klaus P. Jantke, Steffen Lange

Proceedings of the Algorithmic Learning Theory, 1994

1993

Noise-Tolerant Occam Algorithms and Their Applications to Learning Decision Trees.

Yasubumi Sakakibara

Mach. Learn., 1993

1992

Efficient Learning of Context-Free Grammars from Positive Structural Examples

Yasubumi Sakakibara

Inf. Comput., March, 1992

A Noise Model on Learning Sets of Strings.

Yasubumi Sakakibara, Rani Siromoney

Proceedings of the Fifth Annual ACM Conference on Computational Learning Theory, 1992

1991

On Learning from Queries and Counterexamples in the Presence of Noise.

Yasubumi Sakakibara

Inf. Process. Lett., 1991

ACE: A syntax-directed editor customizable from examples and queries.

Yuji Takada, Yasubumi Sakakibara, Takeshi Ohtani

Proceedings of the Algorithmic Learning Theory, 2nd International Workshop, 1991

1990

Learning Context-Free Grammars from Structural Data in Polynomial Time.

Yasubumi Sakakibara

Theor. Comput. Sci., 1990

Inductive inference of logic programs based on algebraic semantics.

Yasubumi Sakakibara

New Gener. Comput., 1990

Exact Learning of Semilinear Sets.

Yuji Takada, Kunihiko Hiraishi, Yasubumi Sakakibara

Proceedings of the Algorithmic Learning Theory, First International Workshop, 1990

Occam Algorithms for Learning From Noisy Examples.

Yasubumi Sakakibara

Proceedings of the Algorithmic Learning Theory, First International Workshop, 1990

1988

An Efficient Learning of Context-Free Grammars for Bottom-Up Parsers.

Yasubumi Sakakibara

Proceedings of the International Conference on Fifth Generation Computer Systems, 1988

1986

Programming in Modal Logic: An Extension of PROLOG based on Modal Logic.

Yasubumi Sakakibara

Proceedings of the Logic Programming '86, 1986