Tatsuya Akutsu

ORCID

Publication Activity (10 Years)

Years Active: 1988-2024
Publications (10 Years): 114

Top Venues

Publications

Yue Zhang, Wuxiu Quan, Tatsuya Akutsu, Li Liu, Hongmin Cai, Bin Zhang
Accurate multi-view clustering to seek the cross-viewed yet uniform sample assignment via tensor feature matching. Inf. Sci. 664 (2024)
Mamoona Ghafoor, Tatsuya Akutsu
On the Generative Power of ReLU Network for Generating Similar Strings. IEEE Access 12 (2024)
Liangjie Sun, Wai-Ki Ching, Tatsuya Akutsu
On the Number of Observation Nodes in Boolean Networks. CoRR (2024)
Lixuan Mu, Jiangning Song, Tatsuya Akutsu, Tomoya Mori
DiCleave: a deep learning model for predicting human Dicer cleavage sites. BMC Bioinform. 25 (1) (2024)
Tatsuya Akutsu, Avraham A. Melkman, Atsuhiro Takasu
On the Trade-off between the Number of Nodes and the Number of Trees in a Random Forest. CoRR (2023)
Avraham A. Melkman, Sini Guo, Wai-Ki Ching, Pengyu Liu, Tatsuya Akutsu
On the Compressive Power of Boolean Threshold Autoencoders. IEEE Trans. Neural Networks Learn. Syst. 34 (2) (2023)
Tong Pan, Chen Li, Yue Bi, Zhikang Wang, Robin B. Gasser, Anthony W. Purcell, Tatsuya Akutsu, Geoffrey I. Webb, Seiya Imoto, Jiangning Song
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships. Bioinform. 39 (3) (2023)
Yu Cao, Wenya Pi, Chun-Yu Lin, Ulrike Münzner, Masahiro Ohtomo, Tatsuya Akutsu
Common Attractors in Multiple Boolean Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (5) (2023)
Xiaoti Jia, Pei Zhao, Fuyi Li, Zhaohui Qin, Haoran Ren, Junzhou Li, Chunbo Miao, Quanzhi Zhao, Tatsuya Akutsu, Gensheng Dou, Zhen Chen, Jiangning Song
ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning. Briefings Bioinform. 24 (2) (2023)
Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
Molecular Design Based on Integer Programming and Splitting Data Sets by Hyperplanes. CoRR (2023)
Tomoya Mori, Toshiro Takase, Kuan-Chun Lan, Junko Yamane, Cantas Alev, Azuma Kimura, Kenji Osafune, Jun K. Yamashita, Tatsuya Akutsu, Hiroaki Kitano, Wataru Fujibuchi
eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio-temporal architectures of cells. BMC Bioinform. 24 (1) (2023)
Jiazhou Chen, Guoqiang Han, Aodan Xu, Tatsuya Akutsu, Hongmin Cai
Identifying miRNA-Gene Common and Specific Regulatory Modules for Cancer Subtyping by a High-Order Graph Matching Model. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (1) (2023)
Jing Xu, Fuyi Li, Chen Li, Xudong Guo, Cornelia Landersdorfer, Hsin-Hui Shen, Anton Y. Peleg, Jian Li, Seiya Imoto, Jianhua Yao, Tatsuya Akutsu, Jiangning Song
iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities. Briefings Bioinform. 24 (4) (2023)
Sini Guo, Pengyu Liu, Wai-Ki Ching, Tatsuya Akutsu
On the Distribution of Successor States in Boolean Threshold Networks. IEEE Trans. Neural Networks Learn. Syst. 33 (9) (2022)
Ruiming Li, Jung-Yu Lee, Jinn-Moon Yang, Tatsuya Akutsu
Densest subgraph-based methods for protein-protein interaction hot spot prediction. BMC Bioinform. 23 (1) (2022)
Meng Zhang, Cangzhi Jia, Fuyi Li, Chen Li, Yan Zhu, Tatsuya Akutsu, Geoffrey I. Webb, Quan Zou, Lachlan J. M. Coin, Jiangning Song
Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. Briefings Bioinform. 23 (2) (2022)
So Kumano, Tatsuya Akutsu
Comparison of the Representational Power of Random Forests, Binary Decision Diagrams, and Neural Networks. Neural Comput. 34 (4) (2022)
Ulrike Münzner, Tomoya Mori, Marcus Krantz, Edda Klipp, Tatsuya Akutsu
Identification of periodic attractors in Boolean networks using a priori information. PLoS Comput. Biol. 18 (1) (2022)
Jianshen Zhu, Naveed Ahmed Azam, Shengjuan Cao, Ryota Ido, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
Molecular Design Based on Integer Programming and Quadratic Descriptors in a Two-layered Model. CoRR (2022)
De-Shuang Huang, Kyungsook Han, Tatsuya Akutsu
Guest Editorial for Special Section on the 16th International Conference on Intelligent Computing (ICIC). IEEE ACM Trans. Comput. Biol. Bioinform. 19 (6) (2022)
Shahid Iqbal, Fang Ge, Fuyi Li, Tatsuya Akutsu, Yuanting Zheng, Robin B. Gasser, Dong-Jun Yu, Geoffrey I. Webb, Jiangning Song
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations. J. Chem. Inf. Model. 62 (17) (2022)
Trinh Van Giang, Tatsuya Akutsu, Kunihiko Hiraishi
An FVS-Based Approach to Attractor Detection in Asynchronous Random Boolean Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (2) (2022)
Zhen Chen, Xuhan Liu, Pei Zhao, Chen Li, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Chris Bain, Robin B. Gasser, Junzhou Li, Zuoren Yang, Xin Gao, Lukasz A. Kurgan, Jiangning Song
an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. Nucleic Acids Res. 50 (W1) (2022)
Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
A Method for Molecular Design Based on Linear Regression and Integer Programming. ICBBB (2022)
Tatsuya Akutsu, Tomoya Mori, Naotoshi Nakamura, Satoshi Kozawa, Yuhei Ueno, Thomas N. Sato
On the Complexity of Tree Edit Distance with Variables. ISAAC (2022)
Jianshen Zhu, Kazuya Haraguchi, Hiroshi Nagamochi, Tatsuya Akutsu
Adjustive Linear Regression and Its Application to the Inverse QSAR. BIOINFORMATICS (2022)
Fan Zhang, Jianshen Zhu, Rachaya Chiewvanichakorn, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
A new approach to the design of acyclic chemical compounds using skeleton trees and integer linear programming. Appl. Intell. 52 (15) (2022)
Chunting Liu, Jiangning Song, Hiroyuki Ogata, Tatsuya Akutsu
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites. Bioinform. 38 (23) (2022)
Jianshen Zhu, Naveed Ahmed Azam, Fan Zhang, Aleksandar Shurbevski, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
A Novel Method for Inferring Chemical Compounds With Prescribed Topological Substructures Based on Integer Programming. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (6) (2022)
Tatsuya Akutsu, Avraham A. Melkman
On the Size and Width of the Decoder of a Boolean Threshold Autoencoder. CoRR (2021)
Naveed Ahmed Azam, Jianshen Zhu, Yanming Sun, Yu Shi, Aleksandar Shurbevski, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming. Algorithms Mol. Biol. 16 (1) (2021)
Kouki Tanaka, Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
An Inverse QSAR Method Based on Decision Tree and Integer Programming. ICIC (2) (2021)
Naveed Ahmed Azam, Jianshen Zhu, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
Molecular Design Based on Artificial Neural Networks, Integer Programming and Grid Neighbor Search. BIBM (2021)
Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
An Improved Integer Programming Formulation for Inferring Chemical Compounds with Prescribed Topological Structures. IEA/AIE (1) (2021)
Ruiming Li, Chun-Yu Lin, Weifeng Guo, Tatsuya Akutsu
Weighted minimum feedback vertex sets and implementation in human cancer genes detection. BMC Bioinform. 22 (1) (2021)
Tatsuya Akutsu, Tomoya Mori, Naotoshi Nakamura, Satoshi Kozawa, Yuhei Ueno, Thomas N. Sato
Tree Edit Distance with Variables. Measuring the Similarity between Mathematical Formulas. CoRR (2021)
Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura
New and improved algorithms for unordered tree inclusion. Theor. Comput. Sci. 883 (2021)
Shahid Iqbal, Fuyi Li, Tatsuya Akutsu, David B. Ascher, Geoffrey I Webb, Jiangning Song
Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations. Briefings Bioinform. 22 (6) (2021)
Pengyu Liu, Jiangning Song, Chun-Yu Lin, Tatsuya Akutsu
ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites. BMC Bioinform. 22 (1) (2021)
Yan Zhu, Fuyi Li, Dongxu Xiang, Tatsuya Akutsu, Jiangning Song, Cangzhi Jia
Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks. Briefings Bioinform. 22 (4) (2021)
Shutao Mei, Fuyi Li, Dongxu Xiang, Rochelle Ayala, Pouya Faridi, Geoffrey I. Webb, Patricia T. Illing, Jamie Rossjohn, Tatsuya Akutsu, Nathan P. Croft, Anthony W. Purcell, Jiangning Song
Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules. Briefings Bioinform. 22 (5) (2021)
Motoki Kajiwara, Ritsuki Nomura, Felix Goetze, Masanori Kawabata, Yoshikazu Isomura, Tatsuya Akutsu, Masanori Shimono
Inhibitory neurons exhibit high controlling ability in the cortical microconnectome. PLoS Comput. Biol. 17 (4) (2021)
Naveed Ahmed Azam, Jianshen Zhu, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
Molecular Design Based on Artificial Neural Networks, Integer Programming and Grid Neighbor Search. CoRR (2021)
Xiaoqing Cheng, Wai-Ki Ching, Sini Guo, Tatsuya Akutsu
Discrimination of attractors with noisy nodes in Boolean networks. Autom. 130 (2021)
Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
An Inverse QSAR Method Based on Linear Regression and Integer Programming. CoRR (2021)
Ryota Ido, Shengjuan Cao, Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
A Method for Inferring Polymers Based on Linear Regression and Integer Programming. CoRR (2021)
Tatsuya Akutsu, Hongmin Cai
Editorial: Inference of Biological Networks. Frontiers Bioinform. 1 (2021)
Ruopeng Xie, Jiahui Li, Jiawei Wang, Wei Dai, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Trevor Lithgow, Jiangning Song, Yanju Zhang
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy. Briefings Bioinform. 22 (3) (2021)
Naveed Ahmed Azam, Rachaya Chiewvanichakorn, Fan Zhang, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
A Novel Method for the Inverse QSAR/QSPR based on Artificial Neural Networks and Mixed Integer Linear Programming with Guaranteed Admissibility. BIOINFORMATICS (2020)
Weifeng Guo, Shaowu Zhang, Tao Zeng, Tatsuya Akutsu, Luonan Chen
Network control principles for identifying personalized driver genes in cancer. Briefings Bioinform. 21 (5) (2020)
Xiaoqing Cheng, Wai-Ki Ching, Sini Guo, Tatsuya Akutsu
Discrimination of attractors with noisy nodes in Boolean networks. CoRR (2020)
Jingwen Zeng, Hongmin Cai, Tatsuya Akutsu
Breast Cancer Subtype by Imbalanced Omics Data through A Deep Learning Fusion Model. ICBBB (2020)
Naveed Ahmed Azam, Jianshen Zhu, Yanming Sun, Yu Shi, Aleksandar Shurbevski, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
A Novel Method for Inference of Acyclic Chemical Compounds with Bounded Branch-height Based on Artificial Neural Networks and Integer Programming. CoRR (2020)
Fuyi Li, André Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, Alexander Ian Smith, Tatiana T. Marquez-Lago, Jian Li, Jiangning Song
Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information. Genom. Proteom. Bioinform. 18 (1) (2020)
Yuui Tamura, Yuhei Nishiyama, Chenxi Wang, Yanming Sun, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
Enumerating Chemical Graphs with Mono-block 2-Augmented Tree Structure from Given Upper and Lower Bounds on Path Frequencies. CoRR (2020)
Avraham A. Melkman, Sini Guo, Wai-Ki Ching, Pengyu Liu, Tatsuya Akutsu
On the Compressive Power of Boolean Threshold Autoencoders. CoRR (2020)
Rachaya Chiewvanichakorn, Chenxi Wang, Zhe Zhang, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
A Method for the Inverse QSAR/QSPR Based on Artificial Neural Networks and Mixed Integer Linear Programming. ICBBB (2020)
Zhen Chen, Pei Zhao, Fuyi Li, Yanan Wang, Alexander Ian Smith, Geoffrey I. Webb, Tatsuya Akutsu, Abdelkader Baggag, Halima Bensmail, Jiangning Song
Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences. Briefings Bioinform. 21 (5) (2020)
Tatsuya Akutsu, Hiroshi Nagamochi
A novel method for inference of chemical compounds with prescribed topological substructures based on integer programming. CoRR (2020)
Fan Zhang, Jianshen Zhu, Rachaya Chiewvanichakorn, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
A New Integer Linear Programming Formulation to the Inverse QSAR/QSPR for Acyclic Chemical Compounds Using Skeleton Trees. IEA/AIE (2020)
Feiqi Wang, Tatsuya Akutsu, Tomoya Mori
Comparison of Pseudoknotted RNA Secondary Structures by Topological Centroid Identification and Tree Edit Distance. J. Comput. Biol. 27 (9) (2020)
Pengyu Liu, Avraham A. Melkman, Tatsuya Akutsu
Extracting boolean and probabilistic rules from trained neural networks. Neural Networks 126 (2020)
Tatsuya Akutsu, Avraham A. Melkman, Takeyuki Tamura
Improved Hardness of Maximum Common Subgraph Problems on Labeled Graphs of Bounded Treewidth and Bounded Degree. Int. J. Found. Comput. Sci. 31 (2) (2020)
Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Alexander Ian Smith, Zongyuan Ge, Jiawei Wang, Trevor Lithgow, Jiangning Song
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. Bioinform. 36 (3) (2020)
Shutao Mei, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Kailin Giam, Nathan P. Croft, Tatsuya Akutsu, Alexander Ian Smith, Jian Li, Jamie Rossjohn, Anthony W. Purcell, Jiangning Song
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. Briefings Bioinform. 21 (4) (2020)
Jianshen Zhu, Chenxi Wang, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
A Novel Method for Inference of Chemical Compounds of Cycle Index Two with Desired Properties Based on Artificial Neural Networks and Integer Programming. Algorithms 13 (5) (2020)
Fuyi Li, Jinxiang Chen, André Leier, Tatiana T. Marquez-Lago, Quanzhong Liu, Yanze Wang, Jerico Nico De Leon Revote, Alexander Ian Smith, Tatsuya Akutsu, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song
DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites. Bioinform. 36 (4) (2020)
Kyousuke Yamashita, Ryuji Masui, Xiang Zhou, Chenxi Wang, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
Enumerating Chemical Graphs with Two Disjoint Cycles Satisfying Given Path Frequency Specifications. CoRR (2020)
Zhen Chen, Pei Zhao, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Yan Zhu, David R. Powell, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Alexander Ian Smith, Roger J. Daly, Jian Li, Jiangning Song
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. Briefings Bioinform. 21 (3) (2020)
Tatsuya Akutsu, Avraham A. Melkman
Identification of the Structure of a Probabilistic Boolean Network From Samples Including Frequencies of Outcomes. IEEE Trans. Neural Networks Learn. Syst. 30 (8) (2019)
Simone Marini, Francesca Vitali, Sara Rampazzi, Andrea Demartini, Tatsuya Akutsu
Protease target prediction via matrix factorization. Bioinform. 35 (6) (2019)
Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher
Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles. J. Bioinform. Comput. Biol. 17 (3) (2019)
Jiangning Song, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Neil D. Rawlings, Geoffrey I. Webb, Kuo-Chen Chou
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites. Briefings Bioinform. 20 (2) (2019)
Yuhei Nishiyama, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
Resource Cut, a New Bounding Procedure to Algorithms for Enumerating Tree-Like Chemical Graphs. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (1) (2019)
Fuyi Li, Yanan Wang, Chen Li, Tatiana T. Marquez-Lago, André Leier, Neil D. Rawlings, Gholamreza Haffari, Jerico Nico De Leon Revote, Tatsuya Akutsu, Kuo-Chen Chou, Anthony W. Purcell, Robert N. Pike, Geoffrey I. Webb, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, James C. Whisstock, Jiangning Song
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. Briefings Bioinform. 20 (6) (2019)
Yu Bao, Simone Marini, Takeyuki Tamura, Mayumi Kamada, Shingo Maegawa, Hiroshi Hosokawa, Jiangning Song, Tatsuya Akutsu
Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features. Briefings Bioinform. 20 (5) (2019)
Hitoshi Koyano, Morihiro Hayashida, Tatsuya Akutsu
Optimal string clustering based on a Laplace-like mixture and EM algorithm on a set of strings. J. Comput. Syst. Sci. 106 (2019)
Yanju Zhang, Ruopeng Xie, Jiawei Wang, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Jiangning Song
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework. Briefings Bioinform. 20 (6) (2019)
Jiawei Wang, Bingjiao Yang, Yi An, Tatiana T. Marquez-Lago, André Leier, Jonathan Wilksch, Qingyang Hong, Yang Zhang, Morihiro Hayashida, Tatsuya Akutsu, Geoffrey I. Webb, Richard A. Strugnell, Jiangning Song, Trevor Lithgow
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. Briefings Bioinform. 20 (3) (2019)
Jiawei Wang, Jiahui Li, Bingjiao Yang, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Morihiro Hayashida, Tatsuya Akutsu, Yanju Zhang, Kuo-Chen Chou, Joel Selkrig, Tieli Zhou, Jiangning Song, Trevor Lithgow
Bastion3: a two-layer ensemble predictor of type III secreted effectors. Bioinform. 35 (12) (2019)
Zhen Chen, Xuhan Liu, Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Geoffrey I. Webb, Dakang Xu, Alexander Ian Smith, Lei Li, Kuo-Chen Chou, Jiangning Song
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. Briefings Bioinform. 20 (6) (2019)
Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Jiangning Song, Tatsuya Akutsu
Deep learning with evolutionary and genomic profiles for identifying cancer subtypes. J. Bioinform. Comput. Biol. 17 (3) (2019)
Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura
New and Improved Algorithms for Unordered Tree Inclusion. ISAAC (2018)
Jinghui Li, Hiroshi Nagamochi, Tatsuya Akutsu
Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (2) (2018)
Yuui Tamura, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
Enumerating Chemical Mono-Block 3-Augmented Trees with Two Junctions. ICBBB (2018)
Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Tatsuya Akutsu
Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes. BIBE (2018)
Takeyuki Tamura, Wei Lu, Jiangning Song, Tatsuya Akutsu
Computing Minimum Reaction Modifications in a Boolean Metabolic Network. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (6) (2018)
Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher
Convolutional Neural Network Approach to Lung Cancer Classification Integrating Protein Interaction Network and Gene Expression Profiles. BIBE (2018)
Jiangning Song, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Gholamreza Haffari, Kuo-Chen Chou, Geoffrey I. Webb, Robert N. Pike
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy. Bioinform. 34 (4) (2018)
Tatsuya Akutsu
Algorithms for Analysis and Control of Boolean Networks. AlCoB (2018)
Yu Bao, Morihiro Hayashida, Pengyu Liu, Masayuki Ishitsuka, Jose C. Nacher, Tatsuya Akutsu
Analysis of Critical and Redundant Vertices in Controlling Directed Complex Networks Using Feedback Vertex Sets. J. Comput. Biol. 25 (10) (2018)
Tatsuya Akutsu, Colin de la Higuera, Takeyuki Tamura
A Simple Linear-Time Algorithm for Computing the Centroid and Canonical Form of a Plane Graph and Its Applications. CPM (2018)
Avraham A. Melkman, Xiaoqing Cheng, Wai-Ki Ching, Tatsuya Akutsu
Identifying a Probabilistic Boolean Threshold Network From Samples. IEEE Trans. Neural Networks Learn. Syst. 29 (4) (2018)
Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Anthony W. Purcell, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, Jiangning Song, Kuo-Chen Chou
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome. Bioinform. 34 (24) (2018)
Peiying Ruan, Morihiro Hayashida, Tatsuya Akutsu, Jean-Philippe Vert
Improving prediction of heterodimeric protein complexes using combination with pairwise kernel. BMC Bioinform. (1) (2018)
Morihiro Hayashida, Hitoshi Koyano, Tatsuya Akutsu
Grammar-based Compression for Directed and Undirected Generalized Series-parallel Graphs using Integer Linear Programming. BIOINFORMATICS (2018)
Jiawei Wang, Bingjiao Yang, André Leier, Tatiana T. Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Yanju Zhang, Tatsuya Akutsu, Kuo-Chen Chou, Richard A. Strugnell, Jiangning Song, Trevor Lithgow
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. Bioinform. 34 (15) (2018)
Takuya Mori, Hayliang Ngouv, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher
ncRNA-disease association prediction based on sequence information and tripartite network. BMC Syst. Biol. 12 (1) (2018)
Xiaoqing Cheng, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu
Discrimination of singleton and periodic attractors in Boolean networks. Autom. 84 (2017)
Tatsuya Akutsu
Selected Papers from the 16th International Conference on Bioinformatics (InCoB 2017). J. Bioinform. Comput. Biol. 15 (5) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Tatsuya Akutsu