Tatsuya Akutsu

Research interests

Publications

• iLearnPlus:a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization

  Nucleic Acids Research · 2021 · 10.1093/nar/gkab122

• Procleave: Predicting Protease-Specific Substrate Cleavage Sites by Combining Sequence and Structural Information

  Genomics Proteomics & Bioinformatics · 2020 · 10.1016/j.gpb.2019.08.002

• iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data

  Briefings in Bioinformatics · 2019 · https://doi.org/10.1093/bib/bbz041

• Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences

  Briefings in Bioinformatics · 2019 · 10.1093/bib/bbz112

• A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction

  Briefings in Bioinformatics · 2019 · 10.1093/bib/bbz051

• Large-scale comparative assessment of computational predictors for lysine post-translational modification sites

  Briefings in Bioinformatics · 2018 · 10.1093/bib/bby089

• Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors

  Bioinformatics · 2018 · 10.1093/bioinformatics/bty155

• PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework

  Journal of Theoretical Biology · 2018 · 10.1016/j.jtbi.2018.01.023

• Quokka : a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome

  Bioinformatics · 2018 · 10.1093/bioinformatics/bty522

• iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites

  Briefings in Bioinformatics · 2018 · 10.1093/bib/bby028

• PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy

  Bioinformatics · 2017 · 10.1093/bioinformatics/btx670

• PROSPER: An Integrated Feature-Based Tool for Predicting Protease Substrate Cleavage Sites

  PLoS ONE · 2012 · 10.1371/journal.pone.0050300

• Dominating scale-free networks with variable scaling exponent: heterogeneous networks are not difficult to control

  New Journal of Physics · 2012 · 10.1088/1367-2630/14/7/073005

• Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features

  BMC Bioinformatics · 2011 · 10.1186/1471-2105-12-412

• IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

  Bioinformatics · 2011 · 10.1093/bioinformatics/btr215

• Cascleave: towards more accurate prediction of caspase substrate cleavage sites

  Bioinformatics · 2010 · 10.1093/bioinformatics/btq043

• Control of Boolean networks: Hardness results and algorithms for tree structured networks

  Journal of Theoretical Biology · 2006 · https://doi.org/10.1016/j.jtbi.2006.09.023

• Graph Kernels for Molecular Structure−Activity Relationship Analysis with Support Vector Machines

  Journal of Chemical Information and Modeling · 2005 · 10.1021/ci050039t

• A novel representation of protein sequences for prediction of subcellular location using support vector machines

  Protein Science · 2005 · 10.1110/ps.051597405

• Protein homology detection using string alignment kernels

  Bioinformatics · 2004 · https://doi.org/10.1093/bioinformatics/bth141

• Extensions of marginalized graph kernels

  · 2004 · 10.1145/1015330.1015446

• Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function

  Journal of Computational Biology · 2000 · 10.1089/106652700750050817

• Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots

  Discrete Applied Mathematics · 2000 · 10.1016/s0166-218x(00)00186-4

• Inferring qualitative relations in genetic networks and metabolic pathways

  Bioinformatics · 2000 · https://doi.org/10.1093/bioinformatics/16.8.727

• IDENTIFICATION OF GENETIC NETWORKS FROM A SMALL NUMBER OF GENE EXPRESSION PATTERNS UNDER THE BOOLEAN NETWORK MODEL

  Journal · 1998 · https://doi.org/10.1142/9789814447300_0003

Current projects

No projects listed.