Yasubumi Sakakibara

Overview

Best Publications

• Stochastic context-free grammars for tRNA modeling.

  Sakakibara Y;Brown M;Hughey R;Mian Is

  574
  Citations

• RNA secondary structure prediction using deep learning with thermodynamic integration

  Kengo Sato;Manato Akiyama;Yasubumi Sakakibara

  469
  Citations

• Efficient learning of context-free grammars from positive structural examples

  Yasubumi Sakakibara

  288
  Citations

• Learning context-free grammars from structural data in polynomial time

  Yasubumi Sakakibara

  261
  Citations

• Recent advances of grammatical inference

  Yasubumi Sakakibara

  245
  Citations

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

  Maya Hirohara;Yutaka Saito;Yuki Koda;Kengo Sato

  206
  Citations

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

  Nobuyoshi Nagamine;Yasubumi Sakakibara

  135
  Citations

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

  Vasanthan Jayakumar;Yasubumi Sakakibara

  122
  Citations

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

  Yoshiyuki Suzuki;Seiichiro Ogawa;Yasubumi Sakakibara

  117
  Citations

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

  Afiahayati;Kengo Sato;Yasubumi Sakakibara

  115
  Citations

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

  Hiroshi Matsui;Kengo Sato;Yasubumi Sakakibara

  111
  Citations

• Building of a document classification tree by recursive optimization of keyword selection function

  Yasubumi Sakakibara;Kazuo Misue

  111
  Citations

• Grammatical inference in bioinformatics

  Y. Sakakibara

  110
  Citations

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

  Genta Aoki;Yasubumi Sakakibara

  105
  Citations

• DNA Computing and Molecular Programming

  Yasubumi Sakakibara;Yongli Mi

  85
  Citations

• Pair hidden Markov models on tree structures.

  Yasubumi Sakakibara

  82
  Citations

• Learning context-free grammars using tabular representations

  Yasubumi Sakakibara

  80
  Citations

• Learning Context-Free Grammars from Partially Structured Examples

  Yasubumi Sakakibara;Hidenori Muramatsu

  74
  Citations

• Identifying cooperative transcriptional regulations using protein-protein interactions.

  Nobuyoshi Nagamine;Yuji Kawada;Yasubumi Sakakibara

  64
  Citations

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

  Yasubumi Sakakibara;Mitsuhiro Kondo

  60
  Citations

• On learning from queries and counterexamples in the presence of noise

  Yasubumi Sakakibara

  50
  Citations

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

  Kengo Sato;Yuki Kato;Tatsuya Akutsu;Kiyoshi Asai

  40
  Citations

• Performance of a deep learning-based identification system for esophageal cancer from CT images.

  Masashi Takeuchi;Takumi Seto;Masahiro Hashimoto;Nao Ichihara

  34
  Citations

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

  Yasubumi Sakakibara;Michael Brown;Richard Hughey;I. Saira Mian

  33
  Citations

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

  Kris Popendorf;Hachiya Tsuyoshi;Yasunori Osana;Yasubumi Sakakibara

  33
  Citations

• Erratum: Accurate identification of orthologous segments among multiple genomes (Bioinformatics (2009) vol. 25 (7) (853-860))

  Tsuyoshi Hachiya;Yasunori Osana;Kris Popendorf;Yasubumi Sakakibara

  0
  Citations