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2020 – today
- 2025
[j206]Bin Zhang, Yue Zhang, Junyu Li, Jiazhou Chen, Tatsuya Akutsu, Yiu-Ming Cheung, Hongmin Cai:
Unsupervised Dual Deep Hashing With Semantic-Index and Content-Code for Cross-Modal Retrieval. IEEE Trans. Pattern Anal. Mach. Intell. 47(1): 387-399 (2025)- 2024
- [j205]Mamoona Ghafoor
, Tatsuya Akutsu:
On the Generative Power of ReLU Network for Generating Similar Strings. IEEE Access 12: 52603-52622 (2024) - [j204]Lixuan Mu, Jiangning Song, Tatsuya Akutsu, Tomoya Mori:
DiCleave: a deep learning model for predicting human Dicer cleavage sites. BMC Bioinform. 25(1): 13 (2024) - [j203]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: 120305 (2024) - [j202]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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(5): 1529-1541 (2024) - [j201]Qinyao Pan, Jie Zhong, Tatsuya Akutsu, Yang Liu, Rongjian Liu:
Distributed Pinning Control: Stabilizing Large Boolean Networks Subjected to Perturbations. IEEE Trans. Cybern. 54(11): 7094-7102 (2024) - [i19]Liangjie Sun, Wai-Ki Ching, Tatsuya Akutsu:
On the Number of Observation Nodes in Boolean Networks. CoRR abs/2407.18560 (2024) - [i18]Bowen Song, Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Tatsuya Akutsu:
Cycle-Configuration: A Novel Graph-theoretic Descriptor Set for Molecular Inference. CoRR abs/2408.05136 (2024) - [i17]Muniba Batool, Naveed Ahmed Azam, Jianshen Zhu, Kazuya Haraguchi, Liang Zhao, Tatsuya Akutsu:
A Unified Approach to Inferring Chemical Compounds with the Desired Aqueous Solubility. CoRR abs/2409.04301 (2024) - 2023
- [j200]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) - [j199]Jing Xu, Fuyi Li, Chen Li, Xudong Guo, Cornelia B. 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) - [j198]Yan Cui, Zhikang Wang, Xiaoyu Wang, Yiwen Zhang, Ying Zhang, Tong Pan, Zhe Zhang, Shanshan Li, Yuming Guo, Tatsuya Akutsu, Jiangning Song:
SMG: self-supervised masked graph learning for cancer gene identification. Briefings Bioinform. 24(6) (2023) - [j197]Fuyi Li, Cong Wang, Xudong Guo, Tatsuya Akutsu, Geoffrey I. Webb, Lachlan J. M. Coin, Lukasz A. Kurgan, Jiangning Song:
ProsperousPlus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction. Briefings Bioinform. 24(6) (2023) - [j196]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) - [j195]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): 252 (2023) - [j194]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): 421-431 (2023) - [j193]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): 2862-2873 (2023) - [j192]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): 921-931 (2023) - [i16]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 abs/2305.00801 (2023) - [i15]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 abs/2312.11540 (2023) - 2022
- [j191]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): 17058-17072 (2022) - [j190]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) - [j189]Chunting Liu, Jiangning Song, Hiroyuki Ogata, Tatsuya Akutsu:
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites. Bioinform. 38(23): 5160-5167 (2022) - [j188]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): 451 (2022) - [j187]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): 4270-4282 (2022) - [j186]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:
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. Nucleic Acids Res. 50(W1): 434-447 (2022) - [j185]So Kumano, Tatsuya Akutsu:
Comparison of the Representational Power of Random Forests, Binary Decision Diagrams, and Neural Networks. Neural Comput. 34(4): 1019-1044 (2022) - [j184]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) - [j183]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): 806-818 (2022) - [j182]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): 3124-3125 (2022) - [j181]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): 3233-3245 (2022) - [j180]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): 4147-4159 (2022) - [c95]Jianshen Zhu, Kazuya Haraguchi, Hiroshi Nagamochi, Tatsuya Akutsu:
Adjustive Linear Regression and Its Application to the Inverse QSAR. BIOINFORMATICS 2022: 144-151 - [c94]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: 21-28 - [c93]Tatsuya Akutsu, Tomoya Mori, Naotoshi Nakamura, Satoshi Kozawa, Yuhei Ueno, Thomas N. Sato:
On the Complexity of Tree Edit Distance with Variables. ISAAC 2022: 44:1-44:14 - [i14]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 abs/2209.13527 (2022) - 2021
- [j179]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): 18 (2021) - [j178]Xiaoqing Cheng, Wai-Ki Ching, Sini Guo, Tatsuya Akutsu:
Discrimination of attractors with noisy nodes in Boolean networks. Autom. 130: 109630 (2021) - [j177]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) - [j176]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) - [j175]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) - [j174]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) - [j173]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): 63 (2021) - [j172]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): 143 (2021) - [j171]Tatsuya Akutsu, Hongmin Cai:
Editorial: Inference of Biological Networks. Frontiers Bioinform. 1 (2021) - [j170]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) - [j169]Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura:
New and improved algorithms for unordered tree inclusion. Theor. Comput. Sci. 883: 83-98 (2021) - [c92]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: 360-363 - [c91]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: 628-644 - [c90]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: 197-209 - [i13]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 abs/2105.04802 (2021) - [i12]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 abs/2107.02381 (2021) - [i11]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 abs/2108.10266 (2021) - [i10]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 abs/2109.02628 (2021) - [i9]Tatsuya Akutsu, Avraham A. Melkman:
On the Size and Width of the Decoder of a Boolean Threshold Autoencoder. CoRR abs/2112.10933 (2021) - 2020
- [j168]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): 124 (2020) - [j167]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): 1047-1057 (2020) - [j166]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): 1119-1135 (2020) - [j165]Weifeng Guo, Shaowu Zhang, Tao Zeng, Tatsuya Akutsu, Luonan Chen:
Network control principles for identifying personalized driver genes in cancer. Briefings Bioinform. 21(5): 1641-1662 (2020) - [j164]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): 1676-1696 (2020) - [j163]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): 704-712 (2020) - [j162]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): 1057-1065 (2020) - [j161]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): 52-64 (2020) - [j160]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): 253-273 (2020) - [j159]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): 1443-1451 (2020) - [j158]Pengyu Liu, Avraham A. Melkman, Tatsuya Akutsu:
Extracting boolean and probabilistic rules from trained neural networks. Neural Networks 126: 300-311 (2020) - [c89]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: 101-108 - [c88]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: 40-46 - [c87]Jingwen Zeng, Hongmin Cai, Tatsuya Akutsu:
Breast Cancer Subtype by Imbalanced Omics Data through A Deep Learning Fusion Model. ICBBB 2020: 78-83 - [c86]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: 433-444 - [i8]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 abs/2004.06367 (2020) - [i7]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 abs/2004.08381 (2020) - [i6]Avraham A. Melkman, Sini Guo, Wai-Ki Ching, Pengyu Liu, Tatsuya Akutsu:
On the Compressive Power of Boolean Threshold Autoencoders. CoRR abs/2004.09735 (2020) - [i5]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 abs/2009.09646 (2020) - [i4]Xiaoqing Cheng, Wai-Ki Ching, Sini Guo, Tatsuya Akutsu:
Discrimination of attractors with noisy nodes in Boolean networks. CoRR abs/2009.13198 (2020) - [i3]Tatsuya Akutsu, Hiroshi Nagamochi:
A novel method for inference of chemical compounds with prescribed topological substructures based on integer programming. CoRR abs/2010.09203 (2020)
2010 – 2019
- 2019
- [j157]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): 638-658 (2019) - [j156]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): 931-951 (2019) - [j155]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): 1669-1684 (2019) - [j154]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): 2150-2166 (2019) - [j153]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): 2185-2199 (2019) - [j152]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): 2267-2290 (2019) - [j151]Simone Marini, Francesca Vitali, Sara Rampazzi, Andrea Demartini, Tatsuya Akutsu:
Protease target prediction via matrix factorization. Bioinform. 35(6): 923-929 (2019) - [j150]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): 2017-2028 (2019) - [j149]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): 1940005:1-1940005:15 (2019) - [j148]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): 1940007:1-1940007:11 (2019) - [j147]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: 94-128 (2019) - [j146]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): 77-90 (2019) - [j145]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): 2383-2396 (2019) - 2018
- [b1]Tatsuya Akutsu:
Algorithms for Analysis, Inference, and Control of Boolean Networks. WorldScientific 2018, ISBN 9789813233423, pp. 1-228 - [j144]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): 684-687 (2018) - [j143]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): 2546-2555 (2018) - [j142]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): 4223-4231 (2018) - [j141]Peiying Ruan, Morihiro Hayashida, Tatsuya Akutsu, Jean-Philippe Vert:
Improving prediction of heterodimeric protein complexes using combination with pairwise kernel. BMC Bioinform. 19-S(1): 73-84 (2018) - [j140]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): 41-51 (2018) - [j139]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): 1071-1090 (2018) - [j138]Jinghui Li, Hiroshi Nagamochi, Tatsuya Akutsu:
Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs. IEEE ACM Trans. Comput. Biol. Bioinform. 15(2): 633-646 (2018) - [j137]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): 1853-1862 (2018) - [j136]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): 869-881 (2018) - [c85]Tatsuya Akutsu:
Algorithms for Analysis and Control of Boolean Networks. AlCoB 2018: 3-7 - [c84]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: 147-150 - [c83]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: 151-154 - [c82]Morihiro Hayashida, Hitoshi Koyano, Tatsuya Akutsu:
Grammar-based Compression for Directed and Undirected Generalized Series-parallel Graphs using Integer Linear Programming. BIOINFORMATICS 2018: 105-111 - [c81]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: 10:1-10:12 - [c80]Yuui Tamura, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu:
Enumerating Chemical Mono-Block 3-Augmented Trees with Two Junctions. ICBBB 2018: 48-55 - [c79]Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura:
New and Improved Algorithms for Unordered Tree Inclusion. ISAAC 2018: 27:1-27:12 - 2017
- [j135]Xiaoqing Cheng, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu:
Discrimination of singleton and periodic attractors in Boolean networks. Autom. 84: 205-213 (2017) - [j134]Yuki Kato, Tomoya Mori, Kengo Sato, Shingo Maegawa, Hiroshi Hosokawa, Tatsuya Akutsu:
An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data. Bioinform. 33(2): 202-209 (2017) - [j133]Tatsuya Akutsu:
Selected Papers from the 16th International Conference on Bioinformatics (InCoB 2017). J. Bioinform. Comput. Biol. 15(5): 1702003:1-1702003:2 (2017) - [j132]Tatsuya Akutsu, Jesper Jansson, Atsuhiro Takasu, Takeyuki Tamura:
On the parameterized complexity of associative and commutative unification. Theor. Comput. Sci. 660: 57-74 (2017) - [i2]Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura:
New Algorithms for Unordered Tree Inclusion. CoRR abs/1712.05517 (2017) - 2016
- [j131]Wenpin Hou, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu:
Finding and Analyzing the Minimum Set of Driver Nodes in control of Boolean Networks. Adv. Complex Syst. 19(3): 1650006:1-1650006:32 (2016) - [j130]Chen Li, Catherine Ching Han Chang, Jeremy Nagel, Benjamin T. Porebski, Morihiro Hayashida, Tatsuya Akutsu, Jiangning Song, Ashley M. Buckle:
Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. Briefings Bioinform. 17(2): 270-282 (2016) - [j129]Jira Jindalertudomdee, Morihiro Hayashida, Yang Zhao, Tatsuya Akutsu:
Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order. BMC Bioinform. 17: 113 (2016) - [j128]Yu Bao, Morihiro Hayashida, Tatsuya Akutsu:
LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length. BMC Bioinform. 17: 487:1-487:11 (2016) - [j127]Takanori Hasegawa, Atsushi Niida, Tomoya Mori, Teppei Shimamura, Rui Yamaguchi, Satoru Miyano, Tatsuya Akutsu, Seiya Imoto:
A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models. Comput. Stat. Data Anal. 94: 63-74 (2016) - [j126]Jira Jindalertudomdee, Morihiro Hayashida, Tatsuya Akutsu:
Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach. J. Comput. Biol. 23(8): 625-640 (2016) - [j125]Xiaoqing Cheng, Tomoya Mori, Yushan Qiu, Wai-Ki Ching, Tatsuya Akutsu:
Exact Identification of the Structure of a Probabilistic Boolean Network from Samples. IEEE ACM Trans. Comput. Biol. Bioinform. 13(6): 1107-1116 (2016) - [c78]Jira Jindalertudomdee, Morihiro Hayashida, Jiangning Song, Tatsuya Akutsu:
Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network. BIBE 2016: 7-12 - [c77]Takeyuki Tamura, Tatsuya Akutsu, Chun-Yu Lin, Jinn-Moon Yang:
Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks. BIBE 2016: 57-63 - [c76]Fei He, Akiyoshi Hanai, Hiroshi Nagamochi, Tatsuya Akutsu:
Enumerating Naphthalene Isomers of Tree-like Chemical Graphs. BIOINFORMATICS 2016: 258-265 - [c75]Tomoya Mori, Atsuhiro Takasu, Jesper Jansson, Jaewook Hwang, Takeyuki Tamura, Tatsuya Akutsu:
Similar subtree search using extended tree inclusion. ICDE 2016: 1558-1559 - 2015
- [j124]Yang Zhao, Morihiro Hayashida, Yue Cao, Jaewook Hwang, Tatsuya Akutsu:
Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs. BMC Bioinform. 16: 128:1-128:13 (2015) - [j123]Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Teppei Shimamura, Satoru Miyano, Seiya Imoto, Tatsuya Akutsu:
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. BMC Syst. Biol. 9: 14 (2015) - [j122]Tomoya Mori, Max Flöttmann, Marcus Krantz, Tatsuya Akutsu, Edda Klipp:
Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks. BMC Syst. Biol. 9: 45 (2015) - [j121]Chia-Jung Chang, Takeyuki Tamura, Kun-Mao Chao, Tatsuya Akutsu:
A Fixed-Parameter Algorithm for Detecting a Singleton Attractor in an AND/OR Boolean Network with Bounded Treewidth. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 98-A(1): 384-390 (2015) - [j120]Wei Lu, Takeyuki Tamura, Jiangning Song, Tatsuya Akutsu:
Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model. J. Comput. Biol. 22(2): 85-110 (2015) - [j119]Xiao Cong, Tatsuya Akutsu:
Matrix Network: A New Data Structure for Efficient Enumeration of Microstates of a Genetic Regulatory Network. J. Inf. Process. 23(6): 804-813 (2015) - [j118]Tatsuya Akutsu, Takeyuki Tamura, Avraham A. Melkman, Atsuhiro Takasu:
On the complexity of finding a largest common subtree of bounded degree. Theor. Comput. Sci. 590: 2-16 (2015) - [j117]Tomoya Mori, Atsuhiro Takasu, Jesper Jansson, Jaewook Hwang, Takeyuki Tamura, Tatsuya Akutsu:
Similar Subtree Search Using Extended Tree Inclusion. IEEE Trans. Knowl. Data Eng. 27(12): 3360-3373 (2015) - [c74]Yushan Qiu, Xiaoqing Cheng, Wai-Ki Ching, Hao Jiang, Tatsuya Akutsu:
On observability of attractors in Boolean Networks. BIBM 2015: 263-266 - 2014
- [j116]Natsu Nakajima, Tatsuya Akutsu:
Network Completion for Static Gene Expression Data. Adv. Bioinformatics 2014: 382452:1-382452:9 (2014) - [j115]Mingjun Wang, Xing-Ming Zhao, Hao Tan, Tatsuya Akutsu, James C. Whisstock, Jiangning Song:
Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. Bioinform. 30(1): 71-80 (2014) - [j114]Hongmin Cai, Peiying Ruan, Michael Kwok-Po Ng, Tatsuya Akutsu:
Feature weight estimation for gene selection: a local hyperlinear learning approach. BMC Bioinform. 15: 70 (2014) - [j113]Peiying Ruan, Morihiro Hayashida, Osamu Maruyama, Tatsuya Akutsu:
Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels. BMC Bioinform. 15(S-2): S6 (2014) - [j112]Yushan Qiu, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu:
On control of singleton attractors in multiple Boolean networks: integer programming-based method. BMC Syst. Biol. 8(S-1): S7 (2014) - [j111]Jose C. Nacher, Tatsuya Akutsu:
Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets. J. Complex Networks 2(4): 394-412 (2014) - [j110]Morihiro Hayashida, Tatsuya Akutsu:
Domain-Based Approaches to Prediction and Analysis of Protein-Protein Interactions. Int. J. Knowl. Discov. Bioinform. 4(1): 24-41 (2014) - [j109]Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tatsuya Akutsu:
An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data. J. Comput. Biol. 21(11): 785-798 (2014) - [j108]Masaki Suzuki, Hiroshi Nagamochi, Tatsuya Akutsu:
Efficient enumeration of monocyclic chemical graphs with given path frequencies. J. Cheminformatics 6(1): 31 (2014) - [j107]Tatsuya Akutsu, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu:
Efficient exponential-time algorithms for edit distance between unordered trees. J. Discrete Algorithms 25: 79-93 (2014) - [c73]Tatsuya Akutsu, Jesper Jansson, Atsuhiro Takasu, Takeyuki Tamura:
On the Parameterized Complexity of Associative and Commutative Unification. IPEC 2014: 15-27 - 2013
- [j106]Tatsuya Akutsu, Takeyuki Tamura:
A Polynomial-Time Algorithm for Computing the Maximum Common Connected Edge Subgraph of Outerplanar Graphs of Bounded Degree. Algorithms 6(1): 119-135 (2013) - [j105]Yang Zhao, Takeyuki Tamura, Tatsuya Akutsu, Jean-Philippe Vert:
Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. Bioinform. 29(17): 2178-2185 (2013) - [j104]Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu:
Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso. BMC Syst. Biol. 7(S-2): S15 (2013) - [j103]Hao Jiang, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu:
On the Complexity of Inference and Completion of Boolean Networks from Given Singleton Attractors. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 96-A(11): 2265-2274 (2013) - [j102]Xi Chen, Tatsuya Akutsu, Takeyuki Tamura, Wai-Ki Ching:
Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming. Int. J. Data Min. Bioinform. 7(3): 321-343 (2013) - [j101]Yang Zhao, Morihiro Hayashida, Jira Jindalertudomdee, Hiroshi Nagamochi, Tatsuya Akutsu:
Breadth-First Search Approach to Enumeration of Tree-like Chemical Compounds. J. Bioinform. Comput. Biol. 11(6) (2013) - [j100]Avraham A. Melkman, Tatsuya Akutsu:
An Improved Satisfiability Algorithm for Nested Canalyzing Functions and its Application to Determining a Singleton Attractor of a Boolean Network. J. Comput. Biol. 20(12): 958-969 (2013) - [j99]Tatsuya Akutsu, Daiji Fukagawa, Magnús M. Halldórsson, Atsuhiro Takasu, Keisuke Tanaka:
Approximation and parameterized algorithms for common subtrees and edit distance between unordered trees. Theor. Comput. Sci. 470: 10-22 (2013) - [c72]Natsu Nakajima, Tatsuya Akutsu:
Network Completion for Time Varying Genetic Networks. CISIS 2013: 553-558 - [c71]Tatsuya Akutsu, Takeyuki Tamura, Avraham A. Melkman, Atsuhiro Takasu:
On the Complexity of Finding a Largest Common Subtree of Bounded Degree. FCT 2013: 4-15 - [c70]Jose C. Nacher, Tatsuya Akutsu:
Analysis on critical nodes in controlling complex networks using dominating sets. SITIS 2013: 649-654 - [i1]Tatsuya Akutsu, Takeyuki Tamura, Atsuhiro Takasu:
On the Parameterized Complexity of Associative and Commutative Unification. CoRR abs/1310.0919 (2013) - 2012
- [j98]Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara:
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. Bioinform. 28(24): 3218-3224 (2012) - [j97]Tatsuya Akutsu, Daiji Fukagawa, Jesper Jansson, Kunihiko Sadakane:
Inferring a graph from path frequency. Discret. Appl. Math. 160(10-11): 1416-1428 (2012) - [j96]Morihiro Hayashida, Peiying Ruan, Tatsuya Akutsu:
A quadsection algorithm for grammar-based image compression. Integr. Comput. Aided Eng. 19(1): 23-38 (2012) - [j95]Tatsuya Akutsu, Yang Zhao, Morihiro Hayashida, Takeyuki Tamura:
Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks. IEICE Trans. Inf. Syst. 95-D(12): 2960-2970 (2012) - [j94]Yang Zhao, Morihiro Hayashida, Jose C. Nacher, Hiroshi Nagamochi, Tatsuya Akutsu:
Protein complex prediction via improved verification methods using constrained domain-domain matching. Int. J. Bioinform. Res. Appl. 8(3/4): 210-227 (2012) - [j93]Tatsuya Akutsu, Avraham A. Melkman, Takeyuki Tamura:
Singleton and 2-periodic attractors of sign-definite Boolean networks. Inf. Process. Lett. 112(1-2): 35-38 (2012) - [j92]Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu:
A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees. J. Comput. Biol. 19(10): 1089-1104 (2012) - [j91]Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu:
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming. Nucleic Acids Res. 40(Web-Server-Issue): 29-34 (2012) - [j90]Tatsuya Akutsu, Sven Kosub, Avraham A. Melkman, Takeyuki Tamura:
Finding a Periodic Attractor of a Boolean Network. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1410-1421 (2012) - [c69]Tatsuya Akutsu, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu:
Efficient Exponential Time Algorithms for Edit Distance between Unordered Trees. CPM 2012: 360-372 - [c68]Tatsuya Akutsu, Takeyuki Tamura:
On the Complexity of the Maximum Common Subgraph Problem for Partial k-Trees of Bounded Degree. ISAAC 2012: 146-155 - [c67]Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu:
Predicting protein-RNA residue-base contacts using two-dimensional conditional random field. ISB 2012: 152-157 - [c66]Tatsuya Akutsu, Takeyuki Tamura:
A Polynomial-Time Algorithm for Computing the Maximum Common Subgraph of Outerplanar Graphs of Bounded Degree. MFCS 2012: 76-87 - [c65]Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura:
Finding Conserved Regions in Protein Structures Using Support Vector Machines and Structure Alignment. PRIB 2012: 233-242 - 2011
- [j89]Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai:
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinform. 27(13): 85-93 (2011) - [j88]Ozgur Demir-Kavuk, Mayumi Kamada, Tatsuya Akutsu, Ernst-Walter Knapp:
Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features. BMC Bioinform. 12: 412 (2011) - [j87]Daiji Fukagawa, Takeyuki Tamura, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu:
A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures. BMC Bioinform. 12(S-1): S13 (2011) - [j86]Masaaki Shimizu, Hiroshi Nagamochi, Tatsuya Akutsu:
Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies. BMC Bioinform. 12(S-14): S3 (2011) - [j85]Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu:
Conditional random field approach to prediction of protein-protein interactions using domain information. BMC Syst. Biol. 5(S-1): S8 (2011) - [j84]Tatsuya Akutsu, Hiroshi Nagamochi:
Kernel Methods for Chemical Compounds: From Classification to Design. IEICE Trans. Inf. Syst. 94-D(10): 1846-1853 (2011) - [j83]Takeyuki Tamura, Yang Cong, Tatsuya Akutsu, Wai-Ki Ching:
An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles. IEICE Trans. Inf. Syst. 94-D(12): 2393-2399 (2011) - [j82]Morihiro Hayashida, Tatsuya Akutsu:
Measuring the Similarity of Protein Structures Using Image Compression Algorithms. IEICE Trans. Inf. Syst. 94-D(12): 2468-2478 (2011) - [j81]Jiangning Song, Hao Tan, Sarah E. Boyd, Hong-Bin Shen, Khalid Mahmood, Geoffrey I. Webb, Tatsuya Akutsu, James C. Whisstock, Robert N. Pike:
Bioinformatic Approaches for Predicting substrates of Proteases. J. Bioinform. Comput. Biol. 9(1): 149-178 (2011) - [j80]Unyanee Poolsap, Yuki Kato, Kengo Sato, Tatsuya Akutsu:
Using binding Profiles to Predict binding sites of Target RNAs. J. Bioinform. Comput. Biol. 9(6): 697-713 (2011) - [j79]Tatsuya Akutsu, Avraham A. Melkman, Takeyuki Tamura, Masaki Yamamoto:
Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions. J. Comput. Biol. 18(10): 1275-1290 (2011) - [j78]Tomoki Imada, Shunsuke Ota, Hiroshi Nagamochi, Tatsuya Akutsu:
Efficient Enumeration of Stereoisomers of Outerplanar Chemical Graphs Using Dynamic Programming. J. Chem. Inf. Model. 51(11): 2788-2807 (2011) - [j77]Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu, Takeyuki Tamura:
Exact algorithms for computing the tree edit distance between unordered trees. Theor. Comput. Sci. 412(4-5): 352-364 (2011) - [c64]Tatsuya Akutsu, Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita:
An Improved Clique-Based Method for Computing Edit Distance between Unordered Trees and Its Application to Comparison of Glycan Structures. CISIS 2011: 536-540 - 2010
- [j76]Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu:
Approximating Tree Edit Distance through String Edit Distance. Algorithmica 57(2): 325-348 (2010) - [j75]Jiangning Song, Hao Tan, Hong-Bin Shen, Khalid Mahmood, Sarah E. Boyd, Geoffrey I. Webb, Tatsuya Akutsu, James C. Whisstock:
Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinform. 26(6): 752-760 (2010) - [j74]Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu:
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinform. 26(18) (2010) - [j73]Jose C. Nacher, Morihiro Hayashida, Tatsuya Akutsu:
The role of internal duplication in the evolution of multi-domain proteins. Biosyst. 101(2): 127-135 (2010) - [j72]Yang Zhao, Morihiro Hayashida, Tatsuya Akutsu:
Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures. BMC Bioinform. 11(S-11): S4 (2010) - [j71]Morihiro Hayashida, Tatsuya Akutsu:
Comparing biological networks via graph compression. BMC Syst. Biol. 4(S-2): S13 (2010) - [j70]Tatsuya Akutsu:
Tree Edit Distance Problems: Algorithms and Applications to Bioinformatics. IEICE Trans. Inf. Syst. 93-D(2): 208-218 (2010) - [j69]Takeyuki Tamura, Tatsuya Akutsu:
Exact Algorithms for Finding a Minimum Reaction Cut under a Boolean Model of Metabolic Networks. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 93-A(8): 1497-1507 (2010) - [j68]Takeyuki Tamura, Kazuhiro Takemoto, Tatsuya Akutsu:
Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets. Int. J. Knowl. Discov. Bioinform. 1(1): 14-31 (2010) - [j67]Jiangning Song, Kazuhiro Takemoto, Hongbin Shen, Hao Tan, M. Michael Gromiha, Tatsuya Akutsu:
Prediction of Protein Folding Rates from Structural Topology and Complex Network Properties. Inf. Media Technol. 5(3): 980-993 (2010) - [j66]Avraham A. Melkman, Takeyuki Tamura, Tatsuya Akutsu:
Determining a singleton attractor of an AND/OR Boolean network in O(1.587n) time. Inf. Process. Lett. 110(14-15): 565-569 (2010) - [j65]Tatsuya Akutsu:
A bisection algorithm for grammar-based compression of ordered trees. Inf. Process. Lett. 110(18-19): 815-820 (2010) - [j64]Yusuke Ishida, Yuki Kato, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu:
Branch-and-Bound Algorithms for Enumerating Treelike Chemical Graphs with Given Path Frequency Using Detachment-Cut. J. Chem. Inf. Model. 50(5): 934-946 (2010) - [c63]Xi Chen, Tatsuya Akutsu, Takeyuki Tamura, Wai-Ki Ching:
Finding optimal control policy in Probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming. BIBM 2010: 240-246 - [c62]Morihiro Hayashida, Peiying Ruan, Tatsuya Akutsu:
A Quadsection Algorithm for Grammar-Based Image Compression. FGIT 2010: 234-248 - [c61]Atsuhiro Takasu, Daiji Fukagawa, Tatsuya Akutsu:
A Variational Bayesian EM Algorithm for Tree Similarity. ICPR 2010: 1056-1059 - [c60]Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu:
Dynamic Programming Algorithms for RNA Structure Prediction with Binding Sites. Pacific Symposium on Biocomputing 2010: 98-107
2000 – 2009
- 2009
- [j63]Jose C. Nacher, Morihiro Hayashida, Tatsuya Akutsu:
Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs. Biosyst. 95(2): 155-159 (2009) - [j62]J. B. Brown, Tatsuya Akutsu:
Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology. BMC Bioinform. 10 (2009) - [j61]Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu:
Prediction of RNA secondary structure with pseudoknots using integer programming. BMC Bioinform. 10(S-1) (2009) - [j60]Takeyuki Tamura, Tatsuya Akutsu:
Detecting a Singleton Attractor in a Boolean Network Utilizing SAT Algorithms. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 92-A(2): 493-501 (2009) - [j59]Tatsuya Akutsu, Takeyuki Tamura:
On Finding a Fixed Point in a Boolean Network with Maximum Indegree 2. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 92-A(8): 1771-1778 (2009) - [j58]Tatsuya Akutsu, Morihiro Hayashida, Shuqin Zhang, Wai-Ki Ching, Michael K. Ng:
Analyses and Algorithms for Predecessor and Control Problems for Boolean Networks of Bounded Indegree. Inf. Media Technol. 4(2): 338-349 (2009) - [j57]Yuki Kato, Tatsuya Akutsu, Hiroyuki Seki:
Dynamic Programming Algorithms and Grammatical Modeling for Protein Beta-Sheet Prediction. J. Comput. Biol. 16(7): 945-957 (2009) - [j56]Takeyuki Tamura, Tatsuya Akutsu:
Algorithms for Singleton Attractor Detection in Planar and Nonplanar AND/OR Boolean Networks. Math. Comput. Sci. 2(3): 401-420 (2009) - [j55]Yuki Kato, Tatsuya Akutsu, Hiroyuki Seki:
A grammatical approach to RNA-RNA interaction prediction. Pattern Recognit. 42(4): 531-538 (2009) - [c59]Tatsuya Akutsu, Takeyuki Tamura, Katsuhisa Horimoto:
Completing Networks Using Observed Data. ALT 2009: 126-140 - [c58]Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura:
Integer programming-based methods for attractor detection and control of boolean networks. CDC 2009: 5610-5617 - [c57]Yang Cong, Takeyuki Tamura, Tatsuya Akutsu, Wai-Ki Ching:
Efficient computation of impact degrees for multiple reactions in metabolic networks with cycles. DTMBIO 2009: 67-70 - [c56]Takeyuki Tamura, Kazuhiro Takemoto, Tatsuya Akutsu:
Measuring Structural Robustness of Metabolic Networks under a Boolean Model Using Integer Programming and Feedback Vertex Sets. CISIS 2009: 819-824 - [c55]Jose C. Nacher, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu:
A Bipartite Graph Based Model of Protein Domain Networks. Complex (1) 2009: 525-535 - [c54]Atsuhiro Takasu, Daiji Fukagawa, Tatsuya Akutsu:
Latent Topic Extraction from Relational Table for Record Matching. Discovery Science 2009: 449-456 - [c53]Tomoki Imada, Shunsuke Ota, Hiroshi Nagamochi, Tatsuya Akutsu:
Enumerating Stereoisomers of Tree Structured Molecules Using Dynamic Programming. ISAAC 2009: 14-23 - [c52]Daiji Fukagawa, Tatsuya Akutsu, Atsuhiro Takasu:
Constant Factor Approximation of Edit Distance of Bounded Height Unordered Trees. SPIRE 2009: 7-17 - 2008
- [j54]Jiangning Song, Hao Tan, Kazuhiro Takemoto, Tatsuya Akutsu:
HSEpred: predict half-sphere exposure from protein sequences. Bioinform. 24(13): 1489-1497 (2008) - [j53]Kazuhiro Takemoto, Tatsuya Akutsu:
Origin of structural difference in metabolic networks with respect to temperature. BMC Syst. Biol. 2: 82 (2008) - [j52]Morihiro Hayashida, Takeyuki Tamura, Tatsuya Akutsu, Shuqin Zhang, Wai-Ki Ching:
Algorithms and Complexity Analyses for Control of Singleton Attractors in Boolean Networks. EURASIP J. Bioinform. Syst. Biol. 2008 (2008) - [j51]Morihiro Hayashida, Fuyan Sun, Sachiyo Aburatani, Katsuhisa Horimoto, Tatsuya Akutsu:
Integer programming-based approach to allocation of reporter genes for cell array analysis. Int. J. Bioinform. Res. Appl. 4(4): 385-399 (2008) - [j50]Morihiro Hayashida, Tatsuya Akutsu, Hiroshi Nagamochi:
A Clustering Method for Analysis of Sequence Similarity Networks of Proteins Using Maximal Components of Graphs. Inf. Media Technol. 3(2): 341-350 (2008) - [j49]Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu:
Improved approximation of the largest common subtree of two unordered trees of bounded height. Inf. Process. Lett. 109(2): 165-170 (2008) - [j48]Hiroki Fujiwara, Jiexun Wang, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu:
Enumerating Treelike Chemical Graphs with Given Path Frequency. J. Chem. Inf. Model. 48(7): 1345-1357 (2008) - [c51]Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura:
Algorithms for Inference, Analysis and Control of Boolean Networks. AB 2008: 1-15 - [c50]Takeyuki Tamura, Tatsuya Akutsu:
An Improved Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes. AB 2008: 216-229 - [c49]Alvis Brazma, Satoru Miyano, Tatsuya Akutsu:
Preface. APBC 2008 - [c48]Morihiro Hayashida, Tatsuya Akutsu:
Image Compression-based Approach to Measuring the Similarity of Protein Structures. APBC 2008: 221-230 - [c47]Yuki Kato, Tatsuya Akutsu, Hiroyuki Seki:
Prediction of Protein Beta-Sheets: Dynamic Programming versus Grammatical Approach. PRIB 2008: 66-77 - [p2]Tatsuya Akutsu:
Bioinformatics. Wiley Encyclopedia of Computer Science and Engineering 2008 - [e1]Alvis Brazma, Satoru Miyano, Tatsuya Akutsu:
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, APBC 2008, 14-17 January 2008, Kyoto, Japan. Advances in Bioinformatics and Computational Biology 6, Imperial College Press 2008, ISBN 978-1-84816-108-5 [contents] - 2007
- [j47]Wai-Ki Ching, Shuqin Zhang, Michael K. Ng, Tatsuya Akutsu:
An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks. Bioinform. 23(12): 1511-1518 (2007) - [j46]Kazuhiro Takemoto, Jose C. Nacher, Tatsuya Akutsu:
Correlation between structure and temperature in prokaryotic metabolic networks. BMC Bioinform. 8 (2007) - [j45]Takeyuki Tamura, Tatsuya Akutsu:
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition. BMC Bioinform. 8 (2007) - [j44]Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott:
On the complexity of deriving position specific score matrices from positive and negative sequences. Discret. Appl. Math. 155(6-7): 676-685 (2007) - [j43]Edward R. Dougherty, Tatsuya Akutsu, Paul Dan Cristea, Ahmed H. Tewfik:
Genetic Regulatory Networks. EURASIP J. Bioinform. Syst. Biol. 2007 (2007) - [j42]Shuqin Zhang, Morihiro Hayashida, Tatsuya Akutsu, Wai-Ki Ching, Michael Kwok-Po Ng:
Algorithms for Finding Small Attractors in Boolean Networks. EURASIP J. Bioinform. Syst. Biol. 2007 (2007) - [j41]Takeyuki Tamura, Tatsuya Akutsu:
Approximation Algorithms for Optimal RNA Secondary Structures Common to Multiple Sequences. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 90-A(5): 917-923 (2007) - [j40]Shuqin Zhang, Wai-Ki Ching, Michael K. Ng, Tatsuya Akutsu:
Simulation study in Probabilistic Boolean Network models for genetic regulatory networks. Int. J. Data Min. Bioinform. 1(3): 217-240 (2007) - [j39]Tatsuya Akutsu, Hiroki Arimura, Shinichi Shimozono:
Hardness Results on Local Multiple Alignment of Biological Sequences. Inf. Media Technol. 2(2): 514-522 (2007) - [c46]Tatsuya Akutsu, Daiji Fukagawa:
Inferring a Chemical Structure from a Feature Vector Based on Frequency of Labeled Paths and Small Fragments. APBC 2007: 165-174 - [c45]Morihiro Hayashida, Tatsuya Akutsu, Hiroshi Nagamochi:
A Novel Clustering Method for Analysis of Biological Networks using Maximal Components of Graphs. APBC 2007: 257-266 - [c44]Takeyuki Tamura, Tatsuya Akutsu:
An O(1.787n)-Time Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes. FCT 2007: 494-505 - [c43]Atsuhiro Takasu, Daiji Fukagawa, Tatsuya Akutsu:
Statistical Learning Algorithm for Tree Similarity. ICDM 2007: 667-672 - [c42]Jiexun Wang, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu:
An Efficient Algorithm for Generating Colored Outerplanar Graphs. TAMC 2007: 573-583 - [p1]Jose C. Nacher, Morihiro Hayashida, Tatsuya Akutsu:
Topological aspects of protein networks. Emergent Intelligence of Networked Agents 2007: 147-158 - 2006
- [j38]Hiroto Saigo, Jean-Philippe Vert, Tatsuya Akutsu:
Optimizing amino acid substitution matrices with a local alignment kernel. BMC Bioinform. 7: 246 (2006) - [j37]Tatsuya Akutsu, Morihiro Hayashida, Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto:
Dynamic Programming and Clique Based Approaches for Protein Threading with Profiles and Constraints. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 89-A(5): 1215-1222 (2006) - [j36]Daiji Fukagawa, Tatsuya Akutsu:
Fast Algorithms for Comparison of Similar Unordered Trees. Int. J. Found. Comput. Sci. 17(3): 703-729 (2006) - [j35]Tatsuya Akutsu:
Algorithms for Point Set Matching with K-differences. Int. J. Found. Comput. Sci. 17(4): 903-918 (2006) - [j34]Tatsuya Akutsu:
A relation between edit distance for ordered trees and edit distance for Euler strings. Inf. Process. Lett. 100(3): 105-109 (2006) - [j33]K. C. Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, Tatsuya Akutsu:
Protein Threading with Profiles and Distance Constraints Using Clique Based Algorithms. J. Bioinform. Comput. Biol. 4(1): 19-42 (2006) - [j32]Michael K. Ng, Shuqin Zhang, Wai-Ki Ching, Tatsuya Akutsu:
A Control Model for Markovian Genetic Regulatory Networks. Trans. Comp. Sys. Biology 5: 36-48 (2006) - [c41]Tatsuya Akutsu, Morihiro Hayashida, Wai-Ki Ching, Michael K. Ng:
On the Complexity of Finding Control Strategies for Boolean Networks. APBC 2006: 99-108 - [c40]Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu:
Approximating Tree Edit Distance Through String Edit Distance. ISAAC 2006: 90-99 - [c39]Jose C. Nacher, Jean-Marc Schwartz, Minoru Kanehisa, Tatsuya Akutsu:
Identification of metabolic units induced by environmental signals. ISMB (Supplement of Bioinformatics) 2006: 375-383 - 2005
- [j31]Masumi Itoh, Susumu Goto, Tatsuya Akutsu, Minoru Kanehisa:
Fast and accurate database homology search using upper bounds of local alignment scores. Bioinform. 21(7): 912-921 (2005) - [j30]Kiyoko F. Aoki, Hiroshi Mamitsuka, Tatsuya Akutsu, Minoru Kanehisa:
A score matrix to reveal the hidden links in glycans. Bioinform. 21(8): 1457-1463 (2005) - [j29]Wai-Ki Ching, Michael K. Ng, Eric S. Fung, Tatsuya Akutsu:
On construction of stochastic genetic networks based on gene expression sequences. Int. J. Neural Syst. 15(4): 297-310 (2005) - [j28]Daiji Fukagawa, Tatsuya Akutsu:
Performance analysis of a greedy algorithm for inferring Boolean functions. Inf. Process. Lett. 93(1): 7-12 (2005) - [j27]K. C. Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Tatsuya Akutsu:
Protein Side-chain Packing Problem: a Maximum Edge-weight Clique Algorithmic Approach. J. Bioinform. Comput. Biol. 3(1): 103-126 (2005) - [j26]Pierre Mahé, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert:
Graph Kernels for Molecular Structure-Activity Relationship Analysis with Support Vector Machines. J. Chem. Inf. Model. 45(4): 939-951 (2005) - [j25]Nobuhisa Ueda, Kiyoko F. Aoki-Kinoshita, Atsuko Yamaguchi, Tatsuya Akutsu, Hiroshi Mamitsuka:
A Probabilistic Model for Mining Labeled Ordered Trees: Capturing Patterns in Carbohydrate Sugar Chains. IEEE Trans. Knowl. Data Eng. 17(8): 1051-1064 (2005) - [c38]Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, Tatsuya Akutsu:
Clique-based algorithms for protein threading with profiles and constraints. APBC 2005: 51-64 - [c37]Tatsuya Akutsu, Daiji Fukagawa:
Inferring a Graph from Path Frequency. CPM 2005: 371-382 - [c36]Shuqin Zhang, Michael K. Ng, Wai-Ki Ching, Tatsuya Akutsu:
A linear control model for gene intervention in a genetic regulatory network. GrC 2005: 354-358 - 2004
- [j24]Yuichiro Hourai, Tatsuya Akutsu, Yutaka Akiyama:
Optimizing substitution matrices by separating score distributions. Bioinform. 20(6): 863-873 (2004) - [j23]Hiroto Saigo, Jean-Philippe Vert, Nobuhisa Ueda, Tatsuya Akutsu:
Protein homology detection using string alignment kernels. Bioinform. 20(11): 1682-1689 (2004) - [j22]Jose C. Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa, Tatsuya Akutsu:
Clustering under the line graph transformation: application to reaction network. BMC Bioinform. 5: 207 (2004) - [j21]Tatsuya Akutsu:
Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data. J. Comput. Biol. 11(2/3): 449-462 (2004) - [j20]Kiyoko F. Aoki, Atsuko Yamaguchi, Nobuhisa Ueda, Tatsuya Akutsu, Hiroshi Mamitsuka, Susumu Goto, Minoru Kanehisa:
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res. 32(Web-Server-Issue): 267-272 (2004) - [j19]Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Tatsuya Akutsu, Minoru Kanehisa, Hiroshi Mamitsuka:
Managing and Analyzing Carbohydrate Data. SIGMOD Rec. 33(2): 33-38 (2004) - [c35]Dukka Bahadur, Tatsuya Akutsu, Etsuji Tomita, Tomokazu Seki:
Protein Side-chain Packing Problem: A Maximum Edge-weight Clique Algorithmic Approach. APBC 2004: 191-200 - [c34]Tatsuya Akutsu, Morihiro Hayashida, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto:
Protein Threading with Profiles and Constraints. BIBE 2004: 537-544 - [c33]Tatsuya Akutsu:
Algorithms for Point Set Matching with k-Differences. COCOON 2004: 249-258 - [c32]Pierre Mahé, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert:
Extensions of marginalized graph kernels. ICML 2004 - [c31]Daiji Fukagawa, Tatsuya Akutsu:
Fast Algorithms for Comparison of Similar Unordered Trees. ISAAC 2004: 452-463 - [c30]Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, Hiroshi Mamitsuka:
Application of a new probabilistic model for recognizing complex patterns in glycans. ISMB/ECCB (Supplement of Bioinformatics) 2004: 6-14 - 2003
- [j18]Tatsuya Akutsu, Kyotetsu Kanaya, Akira Ohyama, Asao Fujiyama:
Point matching under non-uniform distortions. Discret. Appl. Math. 127(1): 5-21 (2003) - [j17]Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
A simple greedy algorithm for finding functional relations: efficient implementation and average case analysis. Theor. Comput. Sci. 292(2): 481-495 (2003) - [j16]Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano:
Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model. Theor. Comput. Sci. 298(1): 235-251 (2003) - [c29]Tatsuya Akutsu:
Computational and Statistical Methods in Bioinformatics. Active Mining 2003: 11-33 - [c28]Daiji Fukagawa, Tatsuya Akutsu:
Performance Analysis of a Greedy Algorithm for Inferring Boolean Functions. Discovery Science 2003: 114-127 - [c27]Morihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu:
Inferring strengths of protein-protein interactions from experimental data using linear programming. ECCB 2003: 58-65 - [c26]Daisuke Shinozaki, Tatsuya Akutsu, Osamu Maruyama:
Finding optimal degenerate patterns in DNA sequences. ECCB 2003: 206-214 - [c25]Tatsuya Akutsu:
Efficient extraction of mapping rules of atoms from enzymatic reaction data. RECOMB 2003: 1-8 - 2002
- [c24]Tatsuya Akutsu, Sascha Ott:
Inferring a Union of Halfspaces from Examples. COCOON 2002: 117-126 - [c23]Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott:
On the Complexity of Deriving Position Specific Score Matrices from Examples. CPM 2002: 168-177 - 2000
- [j15]Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
Inferring qualitative relations in genetic networks and metabolic pathways. Bioinform. 16(8): 727-734 (2000) - [j14]Tatsuya Akutsu:
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discret. Appl. Math. 104(1-3): 45-62 (2000) - [j13]Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function. J. Comput. Biol. 7(3-4): 331-343 (2000) - [j12]Tatsuya Akutsu, Magnús M. Halldórsson:
On the approximation of largest common subtrees and largest common point sets. Theor. Comput. Sci. 233(1-2): 33-50 (2000) - [c22]Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
A Simple Greedy Algorithm for Finding Functional Relations: Efficient Implementation and Average Case Anaylsis. Discovery Science 2000: 86-98 - [c21]Tatsuya Akutsu, Hiroki Arimura, Shinichi Shimozono:
On approximation algorithms for local multiple alignment. RECOMB 2000: 1-7 - [c20]Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. RECOMB 2000: 8-14
1990 – 1999
- 1999
- [j11]Tatsuya Akutsu:
Approximation and Exact Algorithms for RNA Secondary Structure Prediction and Recognition of Stochastic Context-free Languages. J. Comb. Optim. 3(2-3): 321-336 (1999) - [j10]Tatsuya Akutsu, Satoru Miyano:
On the Approximation of Protein Threading. Theor. Comput. Sci. 210(2): 261-275 (1999) - [c19]Tatsuya Akutsu, Kyotetsu Kanaya, Akira Ohyama, Asao Fujiyama:
Matching of Spots in 2D Electrophoresis Images. Point Matching Under Non-uniform Distortions. CPM 1999: 212-222 - [c18]Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model. Pacific Symposium on Biocomputing 1999: 17-28 - 1998
- [j9]Tatsuya Akutsu:
On determining the congruence of point sets in d dimensions. Comput. Geom. 9(4): 247-256 (1998) - [j8]Tatsuya Akutsu, Hisao Tamaki, Takeshi Tokuyama:
Distribution of Distances and Triangles in a Point Set and Algorithms for Computing the Largest Common Point Sets. Discret. Comput. Geom. 20(3): 307-331 (1998) - [c17]Tatsuya Akutsu, Mutsunori Yagiura:
On the Complexity of Deriving Score Functions from Examples for Problems in Molecular Biology. ICALP 1998: 832-843 - [c16]Tatsuya Akutsu:
Approximation and Exact Algorithms for RNA Secondary Structure Prediction and Recognition of Stochastic Context-Free Languages. ISAAC 1998: 337-346 - [c15]Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano:
Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions. SODA 1998: 695-702 - 1997
- [j7]Tatsuya Akutsu, Kentaro Onizuka, Masato Ishikawa:
Rapid protein fragment search using hash functions based on the Fourier transform. Comput. Appl. Biosci. 13(4): 357-364 (1997) - [c14]Tatsuya Akutsu, Hisao Tamaki, Takeshi Tokuyama:
Distribution of Distances and Triangles in a Point Set and Algorithms for Computing the Largest Common Point Sets. SCG 1997: 314-323 - [c13]Tatsuya Akutsu, Satoru Miyano:
On the approximation of protein threading. RECOMB 1997: 3-8 - 1996
- [c12]Tatsuya Akutsu, Feng Bao:
Approximating Minimum Keys and Optimal Substructure Screens. COCOON 1996: 290-299 - [c11]Atsuhiro Takasu, Tatsuya Akutsu, Moonis Ali:
Sampling Effectiveness in Discovering Functional Relationships in Databases. IEA/AIE 1996: 455-460 - 1995
- [j6]Tatsuya Akutsu:
A Parallel Algorithm for Determining the Congruence of Point Sets in Three-Dimensions. IEICE Trans. Inf. Syst. 78-D(4): 321-325 (1995) - [j5]Tatsuya Akutsu:
Approximate String Matching with don't Care Characters. Inf. Process. Lett. 55(5): 235-239 (1995) - [c10]Tatsuya Akutsu, Kentaro Onizuka, Masato Ishikawa:
New hashing techniques and their application to a protein structure database system. HICSS (5) 1995: 197-206 - 1994
- [j4]Tatsuya Akutsu, Atsuhiro Takasu:
On PAC Learnability of Functional Depencies. New Gener. Comput. 12(4): 359-374 (1994) - [c9]Tatsuya Akutsu:
Approximate String Matching with Don't Care Characters. CPM 1994: 240-249 - [c8]Tatsuya Akutsu:
Efficient and Robust Three-Dimensional Pattern Matching Algorithms Using Hashing and Dynamic Programming Techniques. HICSS (5) 1994: 225-234 - [c7]Tatsuya Akutsu:
On Determining the Congruity of Point Sets in Higher Dimensions. ISAAC 1994: 38-46 - [c6]Tatsuya Akutsu, Magnús M. Halldórsson:
On the Approximation of Largest Common Subtrees and Largest Common Point Sets. ISAAC 1994: 405-413 - 1993
- [j3]Einoshin Suzuki, Tatsuya Akutsu, Setsuo Ohsuga:
Knowledge-based system for computer-aided drug design. Knowl. Based Syst. 6(2): 114-126 (1993) - [c5]Tatsuya Akutsu:
A Linear Time Pattern Matching Algorithm Between a String and a Tree. CPM 1993: 1-10 - 1992
- [c4]Tatsuya Akutsu, Atsuhiro Takasu:
On PAC Learnability of Functional Dependencies. ALT 1992: 229-239 - [c3]Tatsuya Akutsu:
Algorithms for Determining the Geometrical Congruity in Two and Three Dimensions. ISAAC 1992: 279-288 - 1991
- [j2]Tatsuya Akutsu:
A new method of computer representation of stereochemistry. Transforming a stereochemical structure into a graph. J. Chem. Inf. Comput. Sci. 31(3): 414-417 (1991) - [j1]Tatsuya Akutsu, Einoshin Suzuki, Setsuo Ohsuga:
Logic-based approach to expert systems in chemistry. Knowl. Based Syst. 4(2): 103-116 (1991) - [c2]Tatsuya Akutsu, Satoshi Yaoi, Kazunari Sato, Susumu Enomoto:
Development and comparison of search algorithms for robot motion planning in the configuration space. IROS 1991: 429-434
1980 – 1989
- 1988
- [c1]Tatsuya Akutsu, Setsuo Ohsuga:
CHEMILOG - A Logic Programming Language/System for Chemical Information Processing. FGCS 1988: 1176-1183
Coauthor Index
[j204] [j200] [j199] [j198] [j197] [j196] [j190] [j189] [j187] [j186] [j177] [j176] [j175] [j174] [j173] [j167] [j166] [j164] [j163] [j162] [j161] [j157] [j156] [j155] [j154] [j153] [j152] [j150] [j149] [j144] [j143] [j142] [j137] [j130] [c78] [j120] [j115] [j104] [c67] [j85] [j81] [j75] [j67] [j54]
[j169] [j160] [j155] [j137] [c81] [c79] [j135] [j132] [i2] [j131] [c77] [c75] [j121] [j120] [j118] [j117] [j112] [j107] [c73] [j106] [j105] [j103] [j102] [c71] [i1] [j95] [j93] [j92] [j90] [c69] [c68] [c66] [c65] [j87] [j83] [j79] [j77] [c64] [j69] [j68] [j66] [c63] [j60] [j59] [j56] [c59] [c58] [c57] [c56] [j52] [c51] [c50] [j45] [j41] [c44]
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