Yasubumi Sakakibara

Yasubumi Sakakibara, Tsuyoshi Hachiya, Tomoya Tagami, 2012, 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS).

Discriminative discovery of transcription factor binding sites from location data

Yasubumi Sakakibara, Yuji Kawada, 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).

Proceedings of the 8th international conference on Grammatical Inference: algorithms and applications

Satoshi Kobayashi, Tetsuro Nishino, Etsuji Tomita, 2006 .

On case-based learnability of languages

Christoph Globig, Steffen Lange, Klaus P. Jantke, 1997, New Generation Computing.

On Learning Smullyan's Elementary Formal Systems: Towards an Efficient Learning Method for Context-Sensitive Languages*

Yasubumi Sakakibara, 1991 .

Discriminative Detection of Cis-Acting Regulatory Variation From Location Data

Yasubumi Sakakibara, Yuji Kawada, 2006, APBC.

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

Yutaka Saito, Yasubumi Sakakibara, Kengo Sato, 2012, BMC Bioinformatics.

On Learning from Queries and Counterexamples in the Presence of Noise

Yasubumi Sakakibara, Y. Sakakibara, 1991, Inf. Process. Lett..

Construction of a question-answering program that automatically answers the medical licensing examination

Yoshinobu Kano, Yasubumi Sakakibara, Shino Ito, 2016 .

Grammatical inference in bioinformatics

Yasubumi Sakakibara, Y. Sakakibara, 2005, IEEE Transactions on Pattern Analysis and Machine Intelligence.

Sticker systems with complex structures

Satoshi Kobayashi, Yasubumi Sakakibara, 2001, Soft Comput..

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

Hiroki Kobayashi, Yasubumi Sakakibara, Kentaro Torii, 2009, PLoS Comput. Biol..

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

Yasubumi Sakakibara, 2005, Bull. EATCS.

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

Yasubumi Sakakibara, Manato Akiyama, Kengo Sato, 2017 .

Robust and accurate prediction of noncoding RNAs from aligned sequences

Yutaka Saito, Yasubumi Sakakibara, Kengo Sato, 2010, BMC Bioinformatics.

Simple recurrent networks as generalized hidden Markov models with distributed representations

Yasubumi Sakakibara, M. Golea, 1995, Proceedings of ICNN'95 - International Conference on Neural Networks.

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

Hiroshi Imai, Yasubumi Sakakibara, 2002, DNA.

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

Yasubumi Sakakibara, Y. Sakakibara, 1993, Machine Learning.

Exact Learning of Semilinear Sets

Kunihiko Hiraishi, Yuji Takada, Yasubumi Sakakibara, 1990, ALT.

Intensive In Vitro Experiments of Implementing and Executing Finite Automata in Test Tube

Yasubumi Sakakibara, Junna Kuramochi, 2005, DNA.

Bio-Molecular Computing of Finite-State Machine

Yasubumi Sakakibara, 2008, BIONETICS.

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

Satoshi Kobayashi, Takashi Yokomori, Akira Suyama, 2007, Formal Models, Languages and Applications.

Occam Algorithms for Learning From Noisy Examples

Yasubumi Sakakibara, 1990, ALT.

Operon Structure Optimization by Random Self-assembly

Kenji Tsuge, Yasubumi Sakakibara, Hiroshi Yanagawa, 2008, DNA.

Implementing in vivo cellular automata using toggle switch and inter-bacteria communication mechanism

Yasubumi Sakakibara, Katsuyuki Yugi, Yusaku Nakashima, 2007, 2007 2nd Bio-Inspired Models of Network, Information and Computing Systems.

In Vitro Translation-Based Computations

Yasubumi Sakakibara, Takahiro Hohsaka, 2003, DNA.

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

Yasubumi Sakakibara, Genta Aoki, Y. Sakakibara, 2018, Bioinform..

Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures

Hiroshi Matsui, Yasubumi Sakakibara, Kengo Sato, 2004, CSB.

Efficient Learning of Context-Free Grammars from Positive Structural Examples

Yasubumi Sakakibara, Y. Sakakibara, 1992, Inf. Comput..

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

Hiroshi Imai, Yasubumi Sakakibara, 2004, J. Autom. Lang. Comb..

Population Computation and Majority Inference in Test Tube

Yasubumi Sakakibara, 2001, DNA.

Directed acyclic graph kernels for structural RNA analysis

Kiyoshi Asai, Yasubumi Sakakibara, Kengo Sato, 2008, BMC Bioinformatics.

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

Yutaka Saito, Yasubumi Sakakibara, Kengo Sato, 2011, BMC Bioinformatics.

RNA secondary structure prediction using deep learning with thermodynamic integration

Yasubumi Sakakibara, Manato Akiyama, Kengo Sato, 2020, Nature Communications.

Development of an In Vivo Computer Based on Escherichia coli

Yasubumi Sakakibara, Kensaku Sakamoto, Hirotaka Nakagawa, 2005, DNA.

Learning Context-Free Grammars from Partially Structured Examples

Yasubumi Sakakibara, Hidenori Muramatsu, Y. Sakakibara, 2000, ICGI.

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

Yasubumi Sakakibara, 1986, LP.

Probabilistic logical inference using quantities of DNA strands

Yasubumi Sakakibara, 2001, Proceedings of the 2001 Congress on Evolutionary Computation (IEEE Cat. No.01TH8546).

Predictive software models

Stan Matwin, Eyke Hüllermeier, Johannes Fürnkranz, 2004, Conference on Semantics in Text Processing.

Accurate identification of orthologous segments among multiple genomes

Kris Popendorf, Yasunori Osana, Yasubumi Sakakibara, 2009, Bioinform..

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

Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara, 2012, Bioinform..

Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars

David Haussler, Michael Brown, Kimmen Sjölander, 1994, CPM.

A Magic Pot : Self-assembly Computation Revisited

Satoshi Kobayashi, Takashi Yokomori, Yasubumi Sakakibara, 2002, Formal and Natural Computing.

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

Yasuo Tabei, Hiroshi Matsui, Kiyoshi Asai, 2008, Nucleic Acids Res..

Grammatical inference : algorithms and applications : 7th International Colloquium, ICGI 2004, Athens, Greece, October 11-13, 2004 : proceedings

Yasubumi Sakakibara, Georgios Paliouras, 2004 .

A noise model on learning sets of strings

Rani Siromoney, Yasubumi Sakakibara, 1992, COLT '92.

Multiple splicing systems and the universal computability

Satoshi Kobayashi, Yasubumi Sakakibara, 2001, Theor. Comput. Sci..

RNA secondary structural alignment with conditional random fields

Yasubumi Sakakibara, Kengo Sato, Y. Sakakibara, 2005, ECCB/JBI.

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

Yasubumi Sakakibara, Kengo Sato, Masaya Abe, 2016, Bioinform..

Proceedings of the 16th international conference on DNA computing and molecular programming

Yasubumi Sakakibara, Yongli Mi, Y. Sakakibara, 2010 .

Probabilistic Context-Free Grammars

Yasubumi Sakakibara, Y. Sakakibara, 2010, Encyclopedia of Machine Learning.

A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures

Kiyoshi Asai, Michiaki Hamada, Yasubumi Sakakibara, 2009, J. Bioinform. Comput. Biol..

Theory of Molecular Computation

Satoshi Kobayashi, Yasubumi Sakakibara, Y. Sakakibara, 2001 .

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

Yasubumi Sakakibara, Kengo Sato, Hiroshi Matsui, 2004 .

Learning context-free grammars from structural data in polynomial time

Yasubumi Sakakibara, Y. Sakakibara, 1988, COLT '88.

BIOINFORMATICS EDUCATION AT KEIO UNIVERSITY

Yasubumi Sakakibara, 2007 .

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

Kris Popendorf, Takashi Komori, Yasubumi Sakakibara, 2012, Bioinform..

Inductive inference of logic programs based on algebraic semantics

Yasubumi Sakakibara, Y. Sakakibara, 1990, New Generation Computing.

Stem Kernels for RNA Sequence Analyses

Kiyoshi Asai, Yasubumi Sakakibara, Kengo Sato, 2007, BIRD.

Recent Advances of DNA Based Computers

Yasubumi Sakakibara, 2007 .

Stem Kernels for RNA Sequence Analyses

Kiyoshi Asai, Kris Popendorf, Yasubumi Sakakibara, 2007, BIRD.

On the Semantics of Infinite Computations in Logic Programs(Mathematical Foundations of Computer Science and Their Applications)

Yasubumi Sakakibara, 1985 .

Stochastic Context-Free Grammars for Modeling RN

David Haussler, Michael Brown, Yasubumi Sakakibara, 1994, HICSS.

On semantics of logic programs with uncertainties

Yasubumi Sakakibara, 1988 .

Recent Advances of Grammatical Inference

Yasubumi Sakakibara, Y. Sakakibara, 1997, Theor. Comput. Sci..

Text classification and keyword extraction by learning decision trees

Takeshi Koshiba, Kazuo Misue, Yasubumi Sakakibara, 1993, Proceedings of 9th IEEE Conference on Artificial Intelligence for Applications.

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

Yasubumi Sakakibara, Mitsuhiro Kondo, Y. Sakakibara, 1999, International Conference on Machine Learning.

Grammatical Inference: An Old and New Paradigm

Yasubumi Sakakibara, Y. Sakakibara, 1995, ALT.

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

Hiroshi Matsui, Yasubumi Sakakibara, Kengo Sato, 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

Guest editorial to the special issue on grammatical inference

Georgios Paliouras, Yasubumi Sakakibara, 2006, Machine Learning.

Learning context-free grammars using tabular representations

Yasubumi Sakakibara, Y. Sakakibara, 2005, Pattern Recognit..

DNA-based algorithms for learning Boolean formulae

Yasubumi Sakakibara, Y. Sakakibara, 2003, Natural Computing.

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

Yasubumi Sakakibara, Nobuyoshi Nagamine, Y. Sakakibara, 2007, Bioinform..

Splicing on Tree-Like Structures

Yasubumi Sakakibara, Claudio Ferretti, Y. Sakakibara, 1999, Theor. Comput. Sci..

Solving Computational Learning Problems of Boolean Formulae on DNA Computers

Yasubumi Sakakibara, 2000, DNA Computing.

Accurate identification of orthologous segments among multiple genomes

Kris Popendorf, Yasunori Osana, Yasubumi Sakakibara, 2009, Bioinform..

Direct inference of base-pairing probabilities with neural networks improves RNA secondary structure prediction with pseudoknots

Yasubumi Sakakibara, Manato Akiyama, Kengo Sato, 2018, bioRxiv.

Approximate identification of finite elasticity

Satoshi Kobayashi, Takashi Yokomori, Yasubumi Sakakibara, 2001, Where Mathematics, Computer Science, Linguistics and Biology Meet.

An extended genovo metagenomic assembler by incorporating paired-end information

Afiahayati, Yasubumi Sakakibara, Kengo Sato, 2013, PeerJ.

An Algorithm for Testing Structure Freeness of Biomolecular Sequences

Satoshi Kobayashi, Takashi Yokomori, Yasubumi Sakakibara, 2004, Aspects of Molecular Computing.

Extension of question-answering program to automatically answering the medical licensing examination to drug related questions

Yasubumi Sakakibara, Kengo Sato, Shino Ito, 2018 .

Splicing on tree-like structures

Yasubumi Sakakibara, Claudio Ferretti, 1997, DNA Based Computers.

A hybrid convolutional neural network-extreme learning machine with augmented dataset for dna damage classification using comet assay from buccal mucosa sample

Afiahayati, Edgar Anarossi, Ryna Dwi Yanuaryska, 2021 .

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

Kuo-ching Liang, Yasubumi Sakakibara, Y. Sakakibara, 2021, BMC Bioinformatics.

Generation of a Nonhuman Primate Model of Severe Combined Immunodeficiency Using Highly Efficient Genome Editing.

Tetsushi Sakuma, Hideyuki Okano, Yasubumi Sakakibara, 2016, Cell stem cell.

Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences.

Tetsuya Hori, Kris Popendorf, Yasubumi Sakakibara, 2010, Genome research.

The Dugesia ryukyuensis Database as a Molecular Resource for Studying Switching of the Reproductive System

Kiyokazu Agata, Yasubumi Sakakibara, Kazuya Kobayashi, 2007, Zoological science.

DEclust: A statistical approach for obtaining differential expression profiles of multiple conditions

Yasubumi Sakakibara, Yuichi Wakabayashi, Kengo Sato, 2017, PloS one.

Support vector machine prediction of N-and O-glycosylation sites using whole sequence information and subcellular localization

Yasubumi Sakakibara, Nobuyoshi Nagamine, Y. Sakakibara, 2009 .

Identifying cooperative transcriptional regulations using protein–protein interactions

Yasubumi Sakakibara, Nobuyoshi Nagamine, Y. Sakakibara, 2005, Nucleic acids research.

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Yasubumi Sakakibara, Toshiaki Namiki, Tsuyoshi Hachiya, 2012, Nucleic acids research.

SYANAC: SYnthetic biological Automaton for Noughts And Crosses

Satoshi Murata, Masami Hagiya, Masayuki Yamamura, 2007 .

[Development of a large-scale comparative genome system and its application to the analysis of mycobacteria genomes].

Kris Popendorf, Yasunori Osana, Yasubumi Sakakibara, 2007, Nihon Hansenbyo Gakkai zasshi = Japanese journal of leprosy : official organ of the Japanese Leprosy Association.

Construction of a genetic AND gate under a new standard for assembly of genetic parts

Satoshi Murata, Masami Hagiya, Masayuki Yamamura, 2010, BMC Genomics.

Molecular basis of chemical chaperone effects of N-octyl-β-valienamine on human β-glucosidase in low/neutral pH conditions

Seiichiro Ogawa, Yasubumi Sakakibara, Katsuyuki Yugi, 2010 .

Murasaki: A Fast, Parallelizable Algorithm to Find Anchors from Multiple Genomes

Kris Popendorf, Yasunori Osana, Yasubumi Sakakibara, 2010, PloS one.

Chaperone Therapy for Neuronopathic Lysosomal Diseases: Competitive Inhibitors as Chemical Chaperones for Enhancement of Mutant Enzyme Activities

Seiichiro Ogawa, Yasubumi Sakakibara, Y. Sakakibara, 2009, Perspectives in medicinal chemistry.

A bicyclic 1-deoxygalactonojirimycin derivative as a novel pharmacological chaperone for GM1 gangliosidosis.

Kei Yura, Yasubumi Sakakibara, Katsumi Higaki, 2013, Molecular therapy : the journal of the American Society of Gene Therapy.

RNA Structural Alignment with Conditional Random Fields

Yasubumi Sakakibara, Kengo Sato, 2005 .

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning

Afiahayati, Yasubumi Sakakibara, Kengo Sato, 2014, DNA research : an international journal for rapid publication of reports on genes and genomes.