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ORCIDBibTeX records: Tatsuya Akutsu
@article{DBLP:journals/access/GhafoorA24,
author = {Mamoona Ghafoor and
Tatsuya Akutsu},
title = {On the Generative Power of ReLU Network for Generating Similar Strings},
journal = {{IEEE} Access},
volume = {12},
pages = {52603--52622},
year = {2024},
url = {https://doi.org/10.1109/ACCESS.2024.3387306},
doi = {10.1109/ACCESS.2024.3387306},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/access/GhafoorA24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MuSAM24,
author = {Lixuan Mu and
Jiangning Song and
Tatsuya Akutsu and
Tomoya Mori},
title = {DiCleave: a deep learning model for predicting human Dicer cleavage
sites},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {13},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05638-4},
doi = {10.1186/S12859-024-05638-4},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MuSAM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/isci/ZhangQALCZ24,
author = {Yue Zhang and
Wuxiu Quan and
Tatsuya Akutsu and
Li Liu and
Hongmin Cai and
Bin Zhang},
title = {Accurate multi-view clustering to seek the cross-viewed yet uniform
sample assignment via tensor feature matching},
journal = {Inf. Sci.},
volume = {664},
pages = {120305},
year = {2024},
url = {https://doi.org/10.1016/j.ins.2024.120305},
doi = {10.1016/J.INS.2024.120305},
timestamp = {Fri, 31 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/isci/ZhangQALCZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2407-18560,
author = {Liangjie Sun and
Wai{-}Ki Ching and
Tatsuya Akutsu},
title = {On the Number of Observation Nodes in Boolean Networks},
journal = {CoRR},
volume = {abs/2407.18560},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2407.18560},
doi = {10.48550/ARXIV.2407.18560},
eprinttype = {arXiv},
eprint = {2407.18560},
timestamp = {Sat, 24 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2407-18560.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2408-05136,
author = {Bowen Song and
Jianshen Zhu and
Naveed Ahmed Azam and
Kazuya Haraguchi and
Liang Zhao and
Tatsuya Akutsu},
title = {Cycle-Configuration: {A} Novel Graph-theoretic Descriptor Set for
Molecular Inference},
journal = {CoRR},
volume = {abs/2408.05136},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2408.05136},
doi = {10.48550/ARXIV.2408.05136},
eprinttype = {arXiv},
eprint = {2408.05136},
timestamp = {Tue, 17 Sep 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2408-05136.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiaZLQRLMZADCS23,
author = {Xiaoti Jia and
Pei Zhao and
Fuyi Li and
Zhaohui Qin and
Haoran Ren and
Junzhou Li and
Chunbo Miao and
Quanzhi Zhao and
Tatsuya Akutsu and
Gensheng Dou and
Zhen Chen and
Jiangning Song},
title = {ResNetKhib: a novel cell type-specific tool for predicting lysine
2-hydroxyisobutylation sites via transfer learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad063},
doi = {10.1093/BIB/BBAD063},
timestamp = {Fri, 19 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiaZLQRLMZADCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XuLLGLSPLIYAS23,
author = {Jing Xu and
Fuyi Li and
Chen Li and
Xudong Guo and
Cornelia B. Landersdorfer and
Hsin{-}Hui Shen and
Anton Y. Peleg and
Jian Li and
Seiya Imoto and
Jianhua Yao and
Tatsuya Akutsu and
Jiangning Song},
title = {iAMPCN: a deep-learning approach for identifying antimicrobial peptides
and their functional activities},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad240},
doi = {10.1093/BIB/BBAD240},
timestamp = {Fri, 19 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/XuLLGLSPLIYAS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PanLBWGPAWIS23,
author = {Tong Pan and
Chen Li and
Yue Bi and
Zhikang Wang and
Robin B. Gasser and
Anthony W. Purcell and
Tatsuya Akutsu and
Geoffrey I. Webb and
Seiya Imoto and
Jiangning Song},
title = {PFresGO: an attention mechanism-based deep-learning approach for protein
annotation by integrating gene ontology inter-relationships},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad094},
doi = {10.1093/BIOINFORMATICS/BTAD094},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PanLBWGPAWIS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MoriTLYAKOYAKF23,
author = {Tomoya Mori and
Toshiro Takase and
Kuan{-}Chun Lan and
Junko Yamane and
Cantas Alev and
Azuma Kimura and
Kenji Osafune and
Jun K. Yamashita and
Tatsuya Akutsu and
Hiroaki Kitano and
Wataru Fujibuchi},
title = {eSPRESSO: topological clustering of single-cell transcriptomics data
to reveal informative genes for spatio-temporal architectures of cells},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {252},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05355-4},
doi = {10.1186/S12859-023-05355-4},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MoriTLYAKOYAKF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ChenHXAC23,
author = {Jiazhou Chen and
Guoqiang Han and
Aodan Xu and
Tatsuya Akutsu and
Hongmin Cai},
title = {Identifying miRNA-Gene Common and Specific Regulatory Modules for
Cancer Subtyping by a High-Order Graph Matching Model},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {20},
number = {1},
pages = {421--431},
year = {2023},
url = {https://doi.org/10.1109/TCBB.2022.3161635},
doi = {10.1109/TCBB.2022.3161635},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/ChenHXAC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/CaoPLMOA23,
author = {Yu Cao and
Wenya Pi and
Chun{-}Yu Lin and
Ulrike M{\"{u}}nzner and
Masahiro Ohtomo and
Tatsuya Akutsu},
title = {Common Attractors in Multiple Boolean Networks},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {20},
number = {5},
pages = {2862--2873},
year = {2023},
url = {https://doi.org/10.1109/TCBB.2023.3268795},
doi = {10.1109/TCBB.2023.3268795},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/CaoPLMOA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tnn/MelkmanGCLA23,
author = {Avraham A. Melkman and
Sini Guo and
Wai{-}Ki Ching and
Pengyu Liu and
Tatsuya Akutsu},
title = {On the Compressive Power of Boolean Threshold Autoencoders},
journal = {{IEEE} Trans. Neural Networks Learn. Syst.},
volume = {34},
number = {2},
pages = {921--931},
year = {2023},
url = {https://doi.org/10.1109/TNNLS.2021.3104646},
doi = {10.1109/TNNLS.2021.3104646},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tnn/MelkmanGCLA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2305-00801,
author = {Jianshen Zhu and
Naveed Ahmed Azam and
Kazuya Haraguchi and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Molecular Design Based on Integer Programming and Splitting Data Sets
by Hyperplanes},
journal = {CoRR},
volume = {abs/2305.00801},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2305.00801},
doi = {10.48550/ARXIV.2305.00801},
eprinttype = {arXiv},
eprint = {2305.00801},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2305-00801.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2312-11540,
author = {Tatsuya Akutsu and
Avraham A. Melkman and
Atsuhiro Takasu},
title = {On the Trade-off between the Number of Nodes and the Number of Trees
in a Random Forest},
journal = {CoRR},
volume = {abs/2312.11540},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2312.11540},
doi = {10.48550/ARXIV.2312.11540},
eprinttype = {arXiv},
eprint = {2312.11540},
timestamp = {Tue, 16 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2312-11540.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/apin/ZhangZCSNA22,
author = {Fan Zhang and
Jianshen Zhu and
Rachaya Chiewvanichakorn and
Aleksandar Shurbevski and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {A new approach to the design of acyclic chemical compounds using skeleton
trees and integer linear programming},
journal = {Appl. Intell.},
volume = {52},
number = {15},
pages = {17058--17072},
year = {2022},
url = {https://doi.org/10.1007/s10489-021-03088-6},
doi = {10.1007/S10489-021-03088-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/apin/ZhangZCSNA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangJLLZAWZCS22,
author = {Meng Zhang and
Cangzhi Jia and
Fuyi Li and
Chen Li and
Yan Zhu and
Tatsuya Akutsu and
Geoffrey I. Webb and
Quan Zou and
Lachlan J. M. Coin and
Jiangning Song},
title = {Critical assessment of computational tools for prokaryotic and eukaryotic
promoter prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab551},
doi = {10.1093/BIB/BBAB551},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhangJLLZAWZCS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuSOA22,
author = {Chunting Liu and
Jiangning Song and
Hiroyuki Ogata and
Tatsuya Akutsu},
title = {MSNet-4mC: learning effective multi-scale representations for identifying
{DNA} N4-methylcytosine sites},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5160--5167},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac671},
doi = {10.1093/BIOINFORMATICS/BTAC671},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuSOA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiLYA22,
author = {Ruiming Li and
Jung{-}Yu Lee and
Jinn{-}Moon Yang and
Tatsuya Akutsu},
title = {Densest subgraph-based methods for protein-protein interaction hot
spot prediction},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {451},
year = {2022},
url = {https://doi.org/10.1186/s12859-022-04996-1},
doi = {10.1186/S12859-022-04996-1},
timestamp = {Thu, 17 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiLYA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/IqbalGLAZGYWS22,
author = {Shahid Iqbal and
Fang Ge and
Fuyi Li and
Tatsuya Akutsu and
Yuanting Zheng and
Robin B. Gasser and
Dong{-}Jun Yu and
Geoffrey I. Webb and
Jiangning Song},
title = {{PROST:} AlphaFold2-aware Sequence-Based Predictor to Estimate Protein
Stability Changes upon Missense Mutations},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {17},
pages = {4270--4282},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.2c00799},
doi = {10.1021/ACS.JCIM.2C00799},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/IqbalGLAZGYWS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ChenLZLWLABGLYG22,
author = {Zhen Chen and
Xuhan Liu and
Pei Zhao and
Chen Li and
Yanan Wang and
Fuyi Li and
Tatsuya Akutsu and
Chris Bain and
Robin B. Gasser and
Junzhou Li and
Zuoren Yang and
Xin Gao and
Lukasz A. Kurgan and
Jiangning Song},
title = {\emph{iFeatureOmega: } an integrative platform for engineering, visualization
and analysis of features from molecular sequences, structural and
ligand data sets},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{W1}},
pages = {434--447},
year = {2022},
url = {https://doi.org/10.1093/nar/gkac351},
doi = {10.1093/NAR/GKAC351},
timestamp = {Mon, 17 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ChenLZLWLABGLYG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/neco/KumanoA22,
author = {So Kumano and
Tatsuya Akutsu},
title = {Comparison of the Representational Power of Random Forests, Binary
Decision Diagrams, and Neural Networks},
journal = {Neural Comput.},
volume = {34},
number = {4},
pages = {1019--1044},
year = {2022},
url = {https://doi.org/10.1162/neco\_a\_01486},
doi = {10.1162/NECO\_A\_01486},
timestamp = {Thu, 21 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/neco/KumanoA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/MunznerMKKA22,
author = {Ulrike M{\"{u}}nzner and
Tomoya Mori and
Marcus Krantz and
Edda Klipp and
Tatsuya Akutsu},
title = {Identification of periodic attractors in Boolean networks using a
priori information},
journal = {PLoS Comput. Biol.},
volume = {18},
number = {1},
year = {2022},
url = {https://doi.org/10.1371/journal.pcbi.1009702},
doi = {10.1371/JOURNAL.PCBI.1009702},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/MunznerMKKA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/GiangAH22,
author = {Trinh Van Giang and
Tatsuya Akutsu and
Kunihiko Hiraishi},
title = {An FVS-Based Approach to Attractor Detection in Asynchronous Random
Boolean Networks},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {19},
number = {2},
pages = {806--818},
year = {2022},
url = {https://doi.org/10.1109/TCBB.2020.3028862},
doi = {10.1109/TCBB.2020.3028862},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/GiangAH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/HuangHA22,
author = {De{-}Shuang Huang and
Kyungsook Han and
Tatsuya Akutsu},
title = {Guest Editorial for Special Section on the 16th International Conference
on Intelligent Computing {(ICIC)}},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {19},
number = {6},
pages = {3124--3125},
year = {2022},
url = {https://doi.org/10.1109/TCBB.2022.3150232},
doi = {10.1109/TCBB.2022.3150232},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/HuangHA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ZhuAZSHZNA22,
author = {Jianshen Zhu and
Naveed Ahmed Azam and
Fan Zhang and
Aleksandar Shurbevski and
Kazuya Haraguchi and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {A Novel Method for Inferring Chemical Compounds With Prescribed Topological
Substructures Based on Integer Programming},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {19},
number = {6},
pages = {3233--3245},
year = {2022},
url = {https://doi.org/10.1109/TCBB.2021.3112598},
doi = {10.1109/TCBB.2021.3112598},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/ZhuAZSHZNA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tnn/GuoLCA22,
author = {Sini Guo and
Pengyu Liu and
Wai{-}Ki Ching and
Tatsuya Akutsu},
title = {On the Distribution of Successor States in Boolean Threshold Networks},
journal = {{IEEE} Trans. Neural Networks Learn. Syst.},
volume = {33},
number = {9},
pages = {4147--4159},
year = {2022},
url = {https://doi.org/10.1109/TNNLS.2021.3055841},
doi = {10.1109/TNNLS.2021.3055841},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tnn/GuoLCA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/ZhuHNA22,
author = {Jianshen Zhu and
Kazuya Haraguchi and
Hiroshi Nagamochi and
Tatsuya Akutsu},
editor = {Ronny Lorenz and
Ana Fred and
Hugo Gamboa},
title = {Adjustive Linear Regression and Its Application to the Inverse {QSAR}},
booktitle = {Proceedings of the 15th International Joint Conference on Biomedical
Engineering Systems and Technologies, {BIOSTEC} 2022, Volume 3: BIOINFORMATICS,
Online Streaming, February 9-11, 2022},
pages = {144--151},
publisher = {{SCITEPRESS}},
year = {2022},
url = {https://doi.org/10.5220/0010853700003123},
doi = {10.5220/0010853700003123},
timestamp = {Tue, 13 Aug 2024 14:18:08 +0200},
biburl = {https://dblp.org/rec/conf/biostec/ZhuHNA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbbb/ZhuAH0NA22,
author = {Jianshen Zhu and
Naveed Ahmed Azam and
Kazuya Haraguchi and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {A Method for Molecular Design Based on Linear Regression and Integer
Programming},
booktitle = {{ICBBB} 2022: 12th International Conference on Bioscience, Biochemistry
and Bioinformatics, Tokyo, Japan, January 7 - 10, 2022},
pages = {21--28},
publisher = {{ACM}},
year = {2022},
url = {https://doi.org/10.1145/3510427.3510431},
doi = {10.1145/3510427.3510431},
timestamp = {Sun, 17 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbbb/ZhuAH0NA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isaac/AkutsuMNKUS22,
author = {Tatsuya Akutsu and
Tomoya Mori and
Naotoshi Nakamura and
Satoshi Kozawa and
Yuhei Ueno and
Thomas N. Sato},
editor = {Sang Won Bae and
Heejin Park},
title = {On the Complexity of Tree Edit Distance with Variables},
booktitle = {33rd International Symposium on Algorithms and Computation, {ISAAC}
2022, December 19-21, 2022, Seoul, Korea},
series = {LIPIcs},
volume = {248},
pages = {44:1--44:14},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2022},
url = {https://doi.org/10.4230/LIPIcs.ISAAC.2022.44},
doi = {10.4230/LIPICS.ISAAC.2022.44},
timestamp = {Wed, 21 Aug 2024 22:46:00 +0200},
biburl = {https://dblp.org/rec/conf/isaac/AkutsuMNKUS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2209-13527,
author = {Jianshen Zhu and
Naveed Ahmed Azam and
Shengjuan Cao and
Ryota Ido and
Kazuya Haraguchi and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Molecular Design Based on Integer Programming and Quadratic Descriptors
in a Two-layered Model},
journal = {CoRR},
volume = {abs/2209.13527},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2209.13527},
doi = {10.48550/ARXIV.2209.13527},
eprinttype = {arXiv},
eprint = {2209.13527},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2209-13527.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AzamZSSSZNA21,
author = {Naveed Ahmed Azam and
Jianshen Zhu and
Yanming Sun and
Yu Shi and
Aleksandar Shurbevski and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {A novel method for inference of acyclic chemical compounds with bounded
branch-height based on artificial neural networks and integer programming},
journal = {Algorithms Mol. Biol.},
volume = {16},
number = {1},
pages = {18},
year = {2021},
url = {https://doi.org/10.1186/s13015-021-00197-2},
doi = {10.1186/S13015-021-00197-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/AzamZSSSZNA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/automatica/ChengCGA21,
author = {Xiaoqing Cheng and
Wai{-}Ki Ching and
Sini Guo and
Tatsuya Akutsu},
title = {Discrimination of attractors with noisy nodes in Boolean networks},
journal = {Autom.},
volume = {130},
pages = {109630},
year = {2021},
url = {https://doi.org/10.1016/j.automatica.2021.109630},
doi = {10.1016/J.AUTOMATICA.2021.109630},
timestamp = {Tue, 15 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/automatica/ChengCGA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XieLWDLMALSZ21,
author = {Ruopeng Xie and
Jiahui Li and
Jiawei Wang and
Wei Dai and
Andr{\'{e}} Leier and
Tatiana T. Marquez{-}Lago and
Tatsuya Akutsu and
Trevor Lithgow and
Jiangning Song and
Yanju Zhang},
title = {DeepVF: a deep learning-based hybrid framework for identifying virulence
factors using the stacking strategy},
journal = {Briefings Bioinform.},
volume = {22},
number = {3},
year = {2021},
url = {https://doi.org/10.1093/bib/bbaa125},
doi = {10.1093/BIB/BBAA125},
timestamp = {Fri, 23 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/XieLWDLMALSZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhuLXASJ21,
author = {Yan Zhu and
Fuyi Li and
Dongxu Xiang and
Tatsuya Akutsu and
Jiangning Song and
Cangzhi Jia},
title = {Computational identification of eukaryotic promoters based on cascaded
deep capsule neural networks},
journal = {Briefings Bioinform.},
volume = {22},
number = {4},
year = {2021},
url = {https://doi.org/10.1093/bib/bbaa299},
doi = {10.1093/BIB/BBAA299},
timestamp = {Sun, 31 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhuLXASJ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MeiLXAFWIRACPS21,
author = {Shutao Mei and
Fuyi Li and
Dongxu Xiang and
Rochelle Ayala and
Pouya Faridi and
Geoffrey I. Webb and
Patricia T. Illing and
Jamie Rossjohn and
Tatsuya Akutsu and
Nathan P. Croft and
Anthony W. Purcell and
Jiangning Song},
title = {Anthem: a user customised tool for fast and accurate prediction of
binding between peptides and {HLA} class {I} molecules},
journal = {Briefings Bioinform.},
volume = {22},
number = {5},
year = {2021},
url = {https://doi.org/10.1093/bib/bbaa415},
doi = {10.1093/BIB/BBAA415},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MeiLXAFWIRACPS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/IqbalLAAWS21,
author = {Shahid Iqbal and
Fuyi Li and
Tatsuya Akutsu and
David B. Ascher and
Geoffrey I. Webb and
Jiangning Song},
title = {Assessing the performance of computational predictors for estimating
protein stability changes upon missense mutations},
journal = {Briefings Bioinform.},
volume = {22},
number = {6},
year = {2021},
url = {https://doi.org/10.1093/bib/bbab184},
doi = {10.1093/BIB/BBAB184},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/IqbalLAAWS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuSLA21,
author = {Pengyu Liu and
Jiangning Song and
Chun{-}Yu Lin and
Tatsuya Akutsu},
title = {ReCGBM: a gradient boosting-based method for predicting human dicer
cleavage sites},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {63},
year = {2021},
url = {https://doi.org/10.1186/s12859-021-03993-0},
doi = {10.1186/S12859-021-03993-0},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuSLA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiLGA21,
author = {Ruiming Li and
Chun{-}Yu Lin and
Weifeng Guo and
Tatsuya Akutsu},
title = {Weighted minimum feedback vertex sets and implementation in human
cancer genes detection},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {143},
year = {2021},
url = {https://doi.org/10.1186/s12859-021-04062-2},
doi = {10.1186/S12859-021-04062-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiLGA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fbinf/AkutsuC21,
author = {Tatsuya Akutsu and
Hongmin Cai},
title = {Editorial: Inference of Biological Networks},
journal = {Frontiers Bioinform.},
volume = {1},
year = {2021},
url = {https://doi.org/10.3389/fbinf.2021.821978},
doi = {10.3389/FBINF.2021.821978},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/fbinf/AkutsuC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/KajiwaraNGKIAS21,
author = {Motoki Kajiwara and
Ritsuki Nomura and
Felix Goetze and
Masanori Kawabata and
Yoshikazu Isomura and
Tatsuya Akutsu and
Masanori Shimono},
title = {Inhibitory neurons exhibit high controlling ability in the cortical
microconnectome},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {4},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1008846},
doi = {10.1371/JOURNAL.PCBI.1008846},
timestamp = {Sun, 15 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/KajiwaraNGKIAS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AkutsuJLTT21,
author = {Tatsuya Akutsu and
Jesper Jansson and
Ruiming Li and
Atsuhiro Takasu and
Takeyuki Tamura},
title = {New and improved algorithms for unordered tree inclusion},
journal = {Theor. Comput. Sci.},
volume = {883},
pages = {83--98},
year = {2021},
url = {https://doi.org/10.1016/j.tcs.2021.06.013},
doi = {10.1016/J.TCS.2021.06.013},
timestamp = {Tue, 17 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/AkutsuJLTT21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/AzamZH0NA21,
author = {Naveed Ahmed Azam and
Jianshen Zhu and
Kazuya Haraguchi and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
editor = {Yufei Huang and
Lukasz A. Kurgan and
Feng Luo and
Xiaohua Hu and
Yidong Chen and
Edward R. Dougherty and
Andrzej Kloczkowski and
Yaohang Li},
title = {Molecular Design Based on Artificial Neural Networks, Integer Programming
and Grid Neighbor Search},
booktitle = {{IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2021, Houston, TX, USA, December 9-12, 2021},
pages = {360--363},
publisher = {{IEEE}},
year = {2021},
url = {https://doi.org/10.1109/BIBM52615.2021.9669710},
doi = {10.1109/BIBM52615.2021.9669710},
timestamp = {Tue, 20 Aug 2024 07:54:45 +0200},
biburl = {https://dblp.org/rec/conf/bibm/AzamZH0NA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icic/TanakaZAHZNA21,
author = {Kouki Tanaka and
Jianshen Zhu and
Naveed Ahmed Azam and
Kazuya Haraguchi and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
editor = {De{-}Shuang Huang and
Kang{-}Hyun Jo and
Jianqiang Li and
Valeriya V. Gribova and
Abir Hussain},
title = {An Inverse {QSAR} Method Based on Decision Tree and Integer Programming},
booktitle = {Intelligent Computing Theories and Application - 17th International
Conference, {ICIC} 2021, Shenzhen, China, August 12-15, 2021, Proceedings,
Part {II}},
series = {Lecture Notes in Computer Science},
volume = {12837},
pages = {628--644},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-84529-2\_53},
doi = {10.1007/978-3-030-84529-2\_53},
timestamp = {Tue, 20 Aug 2024 07:54:43 +0200},
biburl = {https://dblp.org/rec/conf/icic/TanakaZAHZNA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ieaaie/ZhuAHZNA21,
author = {Jianshen Zhu and
Naveed Ahmed Azam and
Kazuya Haraguchi and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
editor = {Hamido Fujita and
Ali Selamat and
Jerry Chun{-}Wei Lin and
Moonis Ali},
title = {An Improved Integer Programming Formulation for Inferring Chemical
Compounds with Prescribed Topological Structures},
booktitle = {Advances and Trends in Artificial Intelligence. Artificial Intelligence
Practices - 34th International Conference on Industrial, Engineering
and Other Applications of Applied Intelligent Systems, {IEA/AIE} 2021,
Kuala Lumpur, Malaysia, July 26-29, 2021, Proceedings, Part {I}},
series = {Lecture Notes in Computer Science},
volume = {12798},
pages = {197--209},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-79457-6\_17},
doi = {10.1007/978-3-030-79457-6\_17},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ieaaie/ZhuAHZNA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2105-04802,
author = {Tatsuya Akutsu and
Tomoya Mori and
Naotoshi Nakamura and
Satoshi Kozawa and
Yuhei Ueno and
Thomas N. Sato},
title = {Tree Edit Distance with Variables. Measuring the Similarity between
Mathematical Formulas},
journal = {CoRR},
volume = {abs/2105.04802},
year = {2021},
url = {https://arxiv.org/abs/2105.04802},
eprinttype = {arXiv},
eprint = {2105.04802},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2105-04802.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2107-02381,
author = {Jianshen Zhu and
Naveed Ahmed Azam and
Kazuya Haraguchi and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {An Inverse {QSAR} Method Based on Linear Regression and Integer Programming},
journal = {CoRR},
volume = {abs/2107.02381},
year = {2021},
url = {https://arxiv.org/abs/2107.02381},
eprinttype = {arXiv},
eprint = {2107.02381},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2107-02381.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2108-10266,
author = {Naveed Ahmed Azam and
Jianshen Zhu and
Kazuya Haraguchi and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Molecular Design Based on Artificial Neural Networks, Integer Programming
and Grid Neighbor Search},
journal = {CoRR},
volume = {abs/2108.10266},
year = {2021},
url = {https://arxiv.org/abs/2108.10266},
eprinttype = {arXiv},
eprint = {2108.10266},
timestamp = {Fri, 27 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2108-10266.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2109-02628,
author = {Ryota Ido and
Shengjuan Cao and
Jianshen Zhu and
Naveed Ahmed Azam and
Kazuya Haraguchi and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {A Method for Inferring Polymers Based on Linear Regression and Integer
Programming},
journal = {CoRR},
volume = {abs/2109.02628},
year = {2021},
url = {https://arxiv.org/abs/2109.02628},
eprinttype = {arXiv},
eprint = {2109.02628},
timestamp = {Mon, 20 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2109-02628.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2112-10933,
author = {Tatsuya Akutsu and
Avraham A. Melkman},
title = {On the Size and Width of the Decoder of a Boolean Threshold Autoencoder},
journal = {CoRR},
volume = {abs/2112.10933},
year = {2021},
url = {https://arxiv.org/abs/2112.10933},
eprinttype = {arXiv},
eprint = {2112.10933},
timestamp = {Tue, 04 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2112-10933.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithms/ZhuWSNA20,
author = {Jianshen Zhu and
Chenxi Wang and
Aleksandar Shurbevski and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {A Novel Method for Inference of Chemical Compounds of Cycle Index
Two with Desired Properties Based on Artificial Neural Networks and
Integer Programming},
journal = {Algorithms},
volume = {13},
number = {5},
pages = {124},
year = {2020},
url = {https://doi.org/10.3390/a13050124},
doi = {10.3390/A13050124},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithms/ZhuWSNA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenZLMLRZPAWCS20,
author = {Zhen Chen and
Pei Zhao and
Fuyi Li and
Tatiana T. Marquez{-}Lago and
Andr{\'{e}} Leier and
Jerico Nico De Leon Revote and
Yan Zhu and
David R. Powell and
Tatsuya Akutsu and
Geoffrey I. Webb and
Kuo{-}Chen Chou and
Alexander Ian Smith and
Roger J. Daly and
Jian Li and
Jiangning Song},
title = {iLearn : an integrated platform and meta-learner for feature engineering,
machine-learning analysis and modeling of DNA, {RNA} and protein sequence
data},
journal = {Briefings Bioinform.},
volume = {21},
number = {3},
pages = {1047--1057},
year = {2020},
url = {https://doi.org/10.1093/bib/bbz041},
doi = {10.1093/BIB/BBZ041},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenZLMLRZPAWCS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MeiLLMGCASLRPS20,
author = {Shutao Mei and
Fuyi Li and
Andr{\'{e}} Leier and
Tatiana T. Marquez{-}Lago and
Kailin Giam and
Nathan P. Croft and
Tatsuya Akutsu and
Alexander Ian Smith and
Jian Li and
Jamie Rossjohn and
Anthony W. Purcell and
Jiangning Song},
title = {A comprehensive review and performance evaluation of bioinformatics
tools for {HLA} class {I} peptide-binding prediction},
journal = {Briefings Bioinform.},
volume = {21},
number = {4},
pages = {1119--1135},
year = {2020},
url = {https://doi.org/10.1093/bib/bbz051},
doi = {10.1093/BIB/BBZ051},
timestamp = {Thu, 16 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MeiLLMGCASLRPS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuoZZAC20,
author = {Weifeng Guo and
Shaowu Zhang and
Tao Zeng and
Tatsuya Akutsu and
Luonan Chen},
title = {Network control principles for identifying personalized driver genes
in cancer},
journal = {Briefings Bioinform.},
volume = {21},
number = {5},
pages = {1641--1662},
year = {2020},
url = {https://doi.org/10.1093/bib/bbz089},
doi = {10.1093/BIB/BBZ089},
timestamp = {Thu, 05 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GuoZZAC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenZLWSWABBS20,
author = {Zhen Chen and
Pei Zhao and
Fuyi Li and
Yanan Wang and
Alexander Ian Smith and
Geoffrey I. Webb and
Tatsuya Akutsu and
Abdelkader Baggag and
Halima Bensmail and
Jiangning Song},
title = {Comprehensive review and assessment of computational methods for predicting
{RNA} post-transcriptional modification sites from {RNA} sequences},
journal = {Briefings Bioinform.},
volume = {21},
number = {5},
pages = {1676--1696},
year = {2020},
url = {https://doi.org/10.1093/bib/bbz112},
doi = {10.1093/BIB/BBZ112},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenZLWSWABBS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangYXLLMASGWL20,
author = {Yanju Zhang and
Sha Yu and
Ruopeng Xie and
Jiahui Li and
Andr{\'{e}} Leier and
Tatiana T. Marquez{-}Lago and
Tatsuya Akutsu and
Alexander Ian Smith and
Zongyuan Ge and
Jiawei Wang and
Trevor Lithgow and
Jiangning Song},
title = {PeNGaRoo, a combined gradient boosting and ensemble learning framework
for predicting non-classical secreted proteins},
journal = {Bioinform.},
volume = {36},
number = {3},
pages = {704--712},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz629},
doi = {10.1093/BIOINFORMATICS/BTZ629},
timestamp = {Fri, 23 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangYXLLMASGWL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiCLMLWRSAWKS20,
author = {Fuyi Li and
Jinxiang Chen and
Andr{\'{e}} Leier and
Tatiana T. Marquez{-}Lago and
Quanzhong Liu and
Yanze Wang and
Jerico Nico De Leon Revote and
Alexander Ian Smith and
Tatsuya Akutsu and
Geoffrey I. Webb and
Lukasz A. Kurgan and
Jiangning Song},
title = {DeepCleave: a deep learning predictor for caspase and matrix metalloprotease
substrates and cleavage sites},
journal = {Bioinform.},
volume = {36},
number = {4},
pages = {1057--1065},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz721},
doi = {10.1093/BIOINFORMATICS/BTZ721},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiCLMLWRSAWKS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/gpb/LiLLWXAWSM0S20,
author = {Fuyi Li and
Andr{\'{e}} Leier and
Quanzhong Liu and
Yanan Wang and
Dongxu Xiang and
Tatsuya Akutsu and
Geoffrey I. Webb and
Alexander Ian Smith and
Tatiana T. Marquez{-}Lago and
Jian Li and
Jiangning Song},
title = {Procleave: Predicting Protease-specific Substrate Cleavage Sites by
Combining Sequence and Structural Information},
journal = {Genom. Proteom. Bioinform.},
volume = {18},
number = {1},
pages = {52--64},
year = {2020},
url = {https://doi.org/10.1016/j.gpb.2019.08.002},
doi = {10.1016/J.GPB.2019.08.002},
timestamp = {Mon, 17 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/gpb/LiLLWXAWSM0S20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijfcs/AkutsuMT20,
author = {Tatsuya Akutsu and
Avraham A. Melkman and
Takeyuki Tamura},
title = {Improved Hardness of Maximum Common Subgraph Problems on Labeled Graphs
of Bounded Treewidth and Bounded Degree},
journal = {Int. J. Found. Comput. Sci.},
volume = {31},
number = {2},
pages = {253--273},
year = {2020},
url = {https://doi.org/10.1142/S0129054120500069},
doi = {10.1142/S0129054120500069},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijfcs/AkutsuMT20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/WangAM20,
author = {Feiqi Wang and
Tatsuya Akutsu and
Tomoya Mori},
title = {Comparison of Pseudoknotted {RNA} Secondary Structures by Topological
Centroid Identification and Tree Edit Distance},
journal = {J. Comput. Biol.},
volume = {27},
number = {9},
pages = {1443--1451},
year = {2020},
url = {https://doi.org/10.1089/cmb.2019.0512},
doi = {10.1089/CMB.2019.0512},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/WangAM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nn/LiuMA20,
author = {Pengyu Liu and
Avraham A. Melkman and
Tatsuya Akutsu},
title = {Extracting boolean and probabilistic rules from trained neural networks},
journal = {Neural Networks},
volume = {126},
pages = {300--311},
year = {2020},
url = {https://doi.org/10.1016/j.neunet.2020.03.024},
doi = {10.1016/J.NEUNET.2020.03.024},
timestamp = {Mon, 16 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nn/LiuMA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/AzamCZSNA20,
author = {Naveed Ahmed Azam and
Rachaya Chiewvanichakorn and
Fan Zhang and
Aleksandar Shurbevski and
Hiroshi Nagamochi and
Tatsuya Akutsu},
editor = {Elisabetta De Maria and
Ana Fred and
Hugo Gamboa},
title = {A Novel Method for the Inverse {QSAR/QSPR} based on Artificial Neural
Networks and Mixed Integer Linear Programming with Guaranteed Admissibility},
booktitle = {Proceedings of the 13th International Joint Conference on Biomedical
Engineering Systems and Technologies {(BIOSTEC} 2020) - Volume 3:
BIOINFORMATICS, Valletta, Malta, February 24-26, 2020},
pages = {101--108},
publisher = {{SCITEPRESS}},
year = {2020},
url = {https://doi.org/10.5220/0008876801010108},
doi = {10.5220/0008876801010108},
timestamp = {Tue, 13 Aug 2024 14:18:07 +0200},
biburl = {https://dblp.org/rec/conf/biostec/AzamCZSNA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbbb/Chiewvanichakorn20,
author = {Rachaya Chiewvanichakorn and
Chenxi Wang and
Zhe Zhang and
Aleksandar Shurbevski and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {A Method for the Inverse {QSAR/QSPR} Based on Artificial Neural Networks
and Mixed Integer Linear Programming},
booktitle = {{ICBBB} 2020: 10th International Conference on Bioscience, Biochemistry
and Bioinformatics, Kyoto, Japan, January, 2020},
pages = {40--46},
publisher = {{ACM}},
year = {2020},
url = {https://doi.org/10.1145/3386052.3386054},
doi = {10.1145/3386052.3386054},
timestamp = {Sun, 17 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbbb/Chiewvanichakorn20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbbb/ZengCA20,
author = {Jingwen Zeng and
Hongmin Cai and
Tatsuya Akutsu},
title = {Breast Cancer Subtype by Imbalanced Omics Data through {A} Deep Learning
Fusion Model},
booktitle = {{ICBBB} 2020: 10th International Conference on Bioscience, Biochemistry
and Bioinformatics, Kyoto, Japan, January, 2020},
pages = {78--83},
publisher = {{ACM}},
year = {2020},
url = {https://doi.org/10.1145/3386052.3386063},
doi = {10.1145/3386052.3386063},
timestamp = {Sun, 17 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbbb/ZengCA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ieaaie/ZhangZCSNA20,
author = {Fan Zhang and
Jianshen Zhu and
Rachaya Chiewvanichakorn and
Aleksandar Shurbevski and
Hiroshi Nagamochi and
Tatsuya Akutsu},
editor = {Hamido Fujita and
Philippe Fournier{-}Viger and
Moonis Ali and
Jun Sasaki},
title = {A New Integer Linear Programming Formulation to the Inverse {QSAR/QSPR}
for Acyclic Chemical Compounds Using Skeleton Trees},
booktitle = {Trends in Artificial Intelligence Theory and Applications. Artificial
Intelligence Practices - 33rd International Conference on Industrial,
Engineering and Other Applications of Applied Intelligent Systems,
{IEA/AIE} 2020, Kitakyushu, Japan, September 22-25, 2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12144},
pages = {433--444},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-55789-8\_38},
doi = {10.1007/978-3-030-55789-8\_38},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ieaaie/ZhangZCSNA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2004-06367,
author = {Yuui Tamura and
Yuhei Nishiyama and
Chenxi Wang and
Yanming Sun and
Aleksandar Shurbevski and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Enumerating Chemical Graphs with Mono-block 2-Augmented Tree Structure
from Given Upper and Lower Bounds on Path Frequencies},
journal = {CoRR},
volume = {abs/2004.06367},
year = {2020},
url = {https://arxiv.org/abs/2004.06367},
eprinttype = {arXiv},
eprint = {2004.06367},
timestamp = {Tue, 21 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2004-06367.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2004-08381,
author = {Kyousuke Yamashita and
Ryuji Masui and
Xiang Zhou and
Chenxi Wang and
Aleksandar Shurbevski and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Enumerating Chemical Graphs with Two Disjoint Cycles Satisfying Given
Path Frequency Specifications},
journal = {CoRR},
volume = {abs/2004.08381},
year = {2020},
url = {https://arxiv.org/abs/2004.08381},
eprinttype = {arXiv},
eprint = {2004.08381},
timestamp = {Tue, 21 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2004-08381.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2004-09735,
author = {Avraham A. Melkman and
Sini Guo and
Wai{-}Ki Ching and
Pengyu Liu and
Tatsuya Akutsu},
title = {On the Compressive Power of Boolean Threshold Autoencoders},
journal = {CoRR},
volume = {abs/2004.09735},
year = {2020},
url = {https://arxiv.org/abs/2004.09735},
eprinttype = {arXiv},
eprint = {2004.09735},
timestamp = {Mon, 16 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2004-09735.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2009-09646,
author = {Naveed Ahmed Azam and
Jianshen Zhu and
Yanming Sun and
Yu Shi and
Aleksandar Shurbevski and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {A Novel Method for Inference of Acyclic Chemical Compounds with Bounded
Branch-height Based on Artificial Neural Networks and Integer Programming},
journal = {CoRR},
volume = {abs/2009.09646},
year = {2020},
url = {https://arxiv.org/abs/2009.09646},
eprinttype = {arXiv},
eprint = {2009.09646},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2009-09646.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2009-13198,
author = {Xiaoqing Cheng and
Wai{-}Ki Ching and
Sini Guo and
Tatsuya Akutsu},
title = {Discrimination of attractors with noisy nodes in Boolean networks},
journal = {CoRR},
volume = {abs/2009.13198},
year = {2020},
url = {https://arxiv.org/abs/2009.13198},
eprinttype = {arXiv},
eprint = {2009.13198},
timestamp = {Wed, 30 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2009-13198.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2010-09203,
author = {Tatsuya Akutsu and
Hiroshi Nagamochi},
title = {A novel method for inference of chemical compounds with prescribed
topological substructures based on integer programming},
journal = {CoRR},
volume = {abs/2010.09203},
year = {2020},
url = {https://arxiv.org/abs/2010.09203},
eprinttype = {arXiv},
eprint = {2010.09203},
timestamp = {Wed, 21 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2010-09203.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SongWLARWC19,
author = {Jiangning Song and
Yanan Wang and
Fuyi Li and
Tatsuya Akutsu and
Neil D. Rawlings and
Geoffrey I. Webb and
Kuo{-}Chen Chou},
title = {iProt-Sub: a comprehensive package for accurately mapping and predicting
protease-specific substrates and cleavage sites},
journal = {Briefings Bioinform.},
volume = {20},
number = {2},
pages = {638--658},
year = {2019},
url = {https://doi.org/10.1093/bib/bby028},
doi = {10.1093/BIB/BBY028},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SongWLARWC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangYAMLWHZHAWS19,
author = {Jiawei Wang and
Bingjiao Yang and
Yi An and
Tatiana T. Marquez{-}Lago and
Andr{\'{e}} Leier and
Jonathan Wilksch and
Qingyang Hong and
Yang Zhang and
Morihiro Hayashida and
Tatsuya Akutsu and
Geoffrey I. Webb and
Richard A. Strugnell and
Jiangning Song and
Trevor Lithgow},
title = {Systematic analysis and prediction of type {IV} secreted effector
proteins by machine learning approaches},
journal = {Briefings Bioinform.},
volume = {20},
number = {3},
pages = {931--951},
year = {2019},
url = {https://doi.org/10.1093/bib/bbx164},
doi = {10.1093/BIB/BBX164},
timestamp = {Fri, 23 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangYAMLWHZHAWS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BaoMTKMHSA19,
author = {Yu Bao and
Simone Marini and
Takeyuki Tamura and
Mayumi Kamada and
Shingo Maegawa and
Hiroshi Hosokawa and
Jiangning Song and
Tatsuya Akutsu},
title = {Toward more accurate prediction of caspase cleavage sites: a comprehensive
review of current methods, tools and features},
journal = {Briefings Bioinform.},
volume = {20},
number = {5},
pages = {1669--1684},
year = {2019},
url = {https://doi.org/10.1093/bib/bby041},
doi = {10.1093/BIB/BBY041},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BaoMTKMHSA19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiWLMLRHRACPPWS19,
author = {Fuyi Li and
Yanan Wang and
Chen Li and
Tatiana T. Marquez{-}Lago and
Andr{\'{e}} Leier and
Neil D. Rawlings and
Gholamreza Haffari and
Jerico Nico De Leon Revote and
Tatsuya Akutsu and
Kuo{-}Chen Chou and
Anthony W. Purcell and
Robert N. Pike and
Geoffrey I. Webb and
Alexander Ian Smith and
Trevor Lithgow and
Roger J. Daly and
James C. Whisstock and
Jiangning Song},
title = {Twenty years of bioinformatics research for protease-specific substrate
and cleavage site prediction: a comprehensive revisit and benchmarking
of existing methods},
journal = {Briefings Bioinform.},
volume = {20},
number = {6},
pages = {2150--2166},
year = {2019},
url = {https://doi.org/10.1093/bib/bby077},
doi = {10.1093/BIB/BBY077},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiWLMLRHRACPPWS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangXWLMAWCS19,
author = {Yanju Zhang and
Ruopeng Xie and
Jiawei Wang and
Andr{\'{e}} Leier and
Tatiana T. Marquez{-}Lago and
Tatsuya Akutsu and
Geoffrey I. Webb and
Kuo{-}Chen Chou and
Jiangning Song},
title = {Computational analysis and prediction of lysine malonylation sites
by exploiting informative features in an integrative machine-learning
framework},
journal = {Briefings Bioinform.},
volume = {20},
number = {6},
pages = {2185--2199},
year = {2019},
url = {https://doi.org/10.1093/bib/bby079},
doi = {10.1093/BIB/BBY079},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangXWLMAWCS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenLLLMLAWXSLC19,
author = {Zhen Chen and
Xuhan Liu and
Fuyi Li and
Chen Li and
Tatiana T. Marquez{-}Lago and
Andr{\'{e}} Leier and
Tatsuya Akutsu and
Geoffrey I. Webb and
Dakang Xu and
Alexander Ian Smith and
Lei Li and
Kuo{-}Chen Chou and
Jiangning Song},
title = {Large-scale comparative assessment of computational predictors for
lysine post-translational modification sites},
journal = {Briefings Bioinform.},
volume = {20},
number = {6},
pages = {2267--2290},
year = {2019},
url = {https://doi.org/10.1093/bib/bby089},
doi = {10.1093/BIB/BBY089},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenLLLMLAWXSLC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MariniVRDA19,
author = {Simone Marini and
Francesca Vitali and
Sara Rampazzi and
Andrea Demartini and
Tatsuya Akutsu},
title = {Protease target prediction via matrix factorization},
journal = {Bioinform.},
volume = {35},
number = {6},
pages = {923--929},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty746},
doi = {10.1093/BIOINFORMATICS/BTY746},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MariniVRDA19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLYXMLHAZCSZ19,
author = {Jiawei Wang and
Jiahui Li and
Bingjiao Yang and
Ruopeng Xie and
Tatiana T. Marquez{-}Lago and
Andr{\'{e}} Leier and
Morihiro Hayashida and
Tatsuya Akutsu and
Yanju Zhang and
Kuo{-}Chen Chou and
Joel Selkrig and
Tieli Zhou and
Jiangning Song and
Trevor Lithgow},
title = {Bastion3: a two-layer ensemble predictor of type {III} secreted effectors},
journal = {Bioinform.},
volume = {35},
number = {12},
pages = {2017--2028},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty914},
doi = {10.1093/BIOINFORMATICS/BTY914},
timestamp = {Fri, 23 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLYXMLHAZCSZ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/LinRLYSSA19,
author = {Chun{-}Yu Lin and
Peiying Ruan and
Ruiming Li and
Jinn{-}Moon Yang and
Simon See and
Jiangning Song and
Tatsuya Akutsu},
title = {Deep learning with evolutionary and genomic profiles for identifying
cancer subtypes},
journal = {J. Bioinform. Comput. Biol.},
volume = {17},
number = {3},
pages = {1940005:1--1940005:15},
year = {2019},
url = {https://doi.org/10.1142/S0219720019400055},
doi = {10.1142/S0219720019400055},
timestamp = {Thu, 05 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/LinRLYSSA19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/MatsubaraOHAN19,
author = {Teppei Matsubara and
Tomoshiro Ochiai and
Morihiro Hayashida and
Tatsuya Akutsu and
Jose C. Nacher},
title = {Convolutional neural network approach to lung cancer classification
integrating protein interaction network and gene expression profiles},
journal = {J. Bioinform. Comput. Biol.},
volume = {17},
number = {3},
pages = {1940007:1--1940007:11},
year = {2019},
url = {https://doi.org/10.1142/S0219720019400079},
doi = {10.1142/S0219720019400079},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/MatsubaraOHAN19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcss/KoyanoHA19,
author = {Hitoshi Koyano and
Morihiro Hayashida and
Tatsuya Akutsu},
title = {Optimal string clustering based on a Laplace-like mixture and {EM}
algorithm on a set of strings},
journal = {J. Comput. Syst. Sci.},
volume = {106},
pages = {94--128},
year = {2019},
url = {https://doi.org/10.1016/j.jcss.2019.07.003},
doi = {10.1016/J.JCSS.2019.07.003},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcss/KoyanoHA19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/NishiyamaSNA19,
author = {Yuhei Nishiyama and
Aleksandar Shurbevski and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Resource Cut, a New Bounding Procedure to Algorithms for Enumerating
Tree-Like Chemical Graphs},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {16},
number = {1},
pages = {77--90},
year = {2019},
url = {https://doi.org/10.1109/TCBB.2018.2832061},
doi = {10.1109/TCBB.2018.2832061},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/NishiyamaSNA19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tnn/AkutsuM19,
author = {Tatsuya Akutsu and
Avraham A. Melkman},
title = {Identification of the Structure of a Probabilistic Boolean Network
From Samples Including Frequencies of Outcomes},
journal = {{IEEE} Trans. Neural Networks Learn. Syst.},
volume = {30},
number = {8},
pages = {2383--2396},
year = {2019},
url = {https://doi.org/10.1109/TNNLS.2018.2884454},
doi = {10.1109/TNNLS.2018.2884454},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tnn/AkutsuM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@book{DBLP:books/ws/Akutsu18,
author = {Tatsuya Akutsu},
title = {Algorithms for Analysis, Inference, and Control of Boolean Networks},
publisher = {WorldScientific},
year = {2018},
url = {https://doi.org/10.1142/10801},
doi = {10.1142/10801},
isbn = {9789813233423},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/ws/Akutsu18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SongLLMAHCWP18,
author = {Jiangning Song and
Fuyi Li and
Andr{\'{e}} Leier and
Tatiana T. Marquez{-}Lago and
Tatsuya Akutsu and
Gholamreza Haffari and
Kuo{-}Chen Chou and
Geoffrey I. Webb and
Robert N. Pike},
title = {PROSPERous: high-throughput prediction of substrate cleavage sites
for 90 proteases with improved accuracy},
journal = {Bioinform.},
volume = {34},
number = {4},
pages = {684--687},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx670},
doi = {10.1093/BIOINFORMATICS/BTX670},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SongLLMAHCWP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangYLMHRZACSSL18,
author = {Jiawei Wang and
Bingjiao Yang and
Andr{\'{e}} Leier and
Tatiana T. Marquez{-}Lago and
Morihiro Hayashida and
Andrea Rocker and
Yanju Zhang and
Tatsuya Akutsu and
Kuo{-}Chen Chou and
Richard A. Strugnell and
Jiangning Song and
Trevor Lithgow},
title = {Bastion6: a bioinformatics approach for accurate prediction of type
{VI} secreted effectors},
journal = {Bioinform.},
volume = {34},
number = {15},
pages = {2546--2555},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty155},
doi = {10.1093/BIOINFORMATICS/BTY155},
timestamp = {Fri, 23 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangYLMHRZACSSL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiLMLAPSLDSC18,
author = {Fuyi Li and
Chen Li and
Tatiana T. Marquez{-}Lago and
Andr{\'{e}} Leier and
Tatsuya Akutsu and
Anthony W. Purcell and
Alexander Ian Smith and
Trevor Lithgow and
Roger J. Daly and
Jiangning Song and
Kuo{-}Chen Chou},
title = {Quokka: a comprehensive tool for rapid and accurate prediction of
kinase family-specific phosphorylation sites in the human proteome},
journal = {Bioinform.},
volume = {34},
number = {24},
pages = {4223--4231},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty522},
doi = {10.1093/BIOINFORMATICS/BTY522},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiLMLAPSLDSC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RuanHAV18,
author = {Peiying Ruan and
Morihiro Hayashida and
Tatsuya Akutsu and
Jean{-}Philippe Vert},
title = {Improving prediction of heterodimeric protein complexes using combination
with pairwise kernel},
journal = {{BMC} Bioinform.},
volume = {19-S},
number = {1},
pages = {73--84},
year = {2018},
url = {https://doi.org/10.1186/s12859-018-2017-5},
doi = {10.1186/S12859-018-2017-5},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RuanHAV18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/MoriNHAN18,
author = {Takuya Mori and
Hayliang Ngouv and
Morihiro Hayashida and
Tatsuya Akutsu and
Jose C. Nacher},
title = {ncRNA-disease association prediction based on sequence information
and tripartite network},
journal = {{BMC} Syst. Biol.},
volume = {12},
number = {1},
pages = {41--51},
year = {2018},
url = {https://doi.org/10.1186/s12918-018-0527-4},
doi = {10.1186/S12918-018-0527-4},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/MoriNHAN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BaoHLINA18,
author = {Yu Bao and
Morihiro Hayashida and
Pengyu Liu and
Masayuki Ishitsuka and
Jose C. Nacher and
Tatsuya Akutsu},
title = {Analysis of Critical and Redundant Vertices in Controlling Directed
Complex Networks Using Feedback Vertex Sets},
journal = {J. Comput. Biol.},
volume = {25},
number = {10},
pages = {1071--1090},
year = {2018},
url = {https://doi.org/10.1089/cmb.2018.0019},
doi = {10.1089/CMB.2018.0019},
timestamp = {Mon, 16 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/BaoHLINA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LiNA18,
author = {Jinghui Li and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {15},
number = {2},
pages = {633--646},
year = {2018},
url = {https://doi.org/10.1109/TCBB.2016.2628888},
doi = {10.1109/TCBB.2016.2628888},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LiNA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/TamuraLSA18,
author = {Takeyuki Tamura and
Wei Lu and
Jiangning Song and
Tatsuya Akutsu},
title = {Computing Minimum Reaction Modifications in a Boolean Metabolic Network},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {15},
number = {6},
pages = {1853--1862},
year = {2018},
url = {https://doi.org/10.1109/TCBB.2017.2777456},
doi = {10.1109/TCBB.2017.2777456},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/TamuraLSA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tnn/MelkmanCCA18,
author = {Avraham A. Melkman and
Xiaoqing Cheng and
Wai{-}Ki Ching and
Tatsuya Akutsu},
title = {Identifying a Probabilistic Boolean Threshold Network From Samples},
journal = {{IEEE} Trans. Neural Networks Learn. Syst.},
volume = {29},
number = {4},
pages = {869--881},
year = {2018},
url = {https://doi.org/10.1109/TNNLS.2017.2648039},
doi = {10.1109/TNNLS.2017.2648039},
timestamp = {Mon, 09 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tnn/MelkmanCCA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alcob/Akutsu18,
author = {Tatsuya Akutsu},
editor = {Jesper Jansson and
Carlos Mart{\'{\i}}n{-}Vide and
Miguel A. Vega{-}Rodr{\'{\i}}guez},
title = {Algorithms for Analysis and Control of Boolean Networks},
booktitle = {Algorithms for Computational Biology - 5th International Conference,
AlCoB 2018, Hong Kong, China, June 25-26, 2018, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10849},
pages = {3--7},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-3-319-91938-6\_1},
doi = {10.1007/978-3-319-91938-6\_1},
timestamp = {Tue, 17 May 2022 11:54:28 +0200},
biburl = {https://dblp.org/rec/conf/alcob/Akutsu18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/LinRLYSA18,
author = {Chun{-}Yu Lin and
Peiying Ruan and
Ruiming Li and
Jinn{-}Moon Yang and
Simon See and
Tatsuya Akutsu},
title = {Deep Learning with Evolutionary and Genomic Profiles for Identifying
Cancer Subtypes},
booktitle = {18th {IEEE} International Conference on Bioinformatics and Bioengineering,
{BIBE} 2018, Taichung, Taiwan, October 29-31, 2018},
pages = {147--150},
publisher = {{IEEE}},
year = {2018},
url = {https://doi.org/10.1109/BIBE.2018.00035},
doi = {10.1109/BIBE.2018.00035},
timestamp = {Thu, 05 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bibe/LinRLYSA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/MatsubaraOHAN18,
author = {Teppei Matsubara and
Tomoshiro Ochiai and
Morihiro Hayashida and
Tatsuya Akutsu and
Jose C. Nacher},
title = {Convolutional Neural Network Approach to Lung Cancer Classification
Integrating Protein Interaction Network and Gene Expression Profiles},
booktitle = {18th {IEEE} International Conference on Bioinformatics and Bioengineering,
{BIBE} 2018, Taichung, Taiwan, October 29-31, 2018},
pages = {151--154},
publisher = {{IEEE}},
year = {2018},
url = {https://doi.org/10.1109/BIBE.2018.00036},
doi = {10.1109/BIBE.2018.00036},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bibe/MatsubaraOHAN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/HayashidaKA18,
author = {Morihiro Hayashida and
Hitoshi Koyano and
Tatsuya Akutsu},
editor = {Paul Anderson and
Hugo Gamboa and
Ana L. N. Fred and
Sergi Berm{\'{u}}dez i Badia},
title = {Grammar-based Compression for Directed and Undirected Generalized
Series-parallel Graphs using Integer Linear Programming},
booktitle = {Proceedings of the 11th International Joint Conference on Biomedical
Engineering Systems and Technologies {(BIOSTEC} 2018) - Volume 3:
BIOINFORMATICS, Funchal, Madeira, Portugal, January 19-21, 2018},
pages = {105--111},
publisher = {SciTePress},
year = {2018},
url = {https://doi.org/10.5220/0006583001050111},
doi = {10.5220/0006583001050111},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/biostec/HayashidaKA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/AkutsuHT18,
author = {Tatsuya Akutsu and
Colin de la Higuera and
Takeyuki Tamura},
editor = {Gonzalo Navarro and
David Sankoff and
Binhai Zhu},
title = {A Simple Linear-Time Algorithm for Computing the Centroid and Canonical
Form of a Plane Graph and Its Applications},
booktitle = {Annual Symposium on Combinatorial Pattern Matching, {CPM} 2018, July
2-4, 2018 - Qingdao, China},
series = {LIPIcs},
volume = {105},
pages = {10:1--10:12},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2018},
url = {https://doi.org/10.4230/LIPIcs.CPM.2018.10},
doi = {10.4230/LIPICS.CPM.2018.10},
timestamp = {Wed, 28 Feb 2024 00:16:40 +0100},
biburl = {https://dblp.org/rec/conf/cpm/AkutsuHT18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbbb/TamuraSNA18,
author = {Yuui Tamura and
Aleksandar Shurbevski and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Enumerating Chemical Mono-Block 3-Augmented Trees with Two Junctions},
booktitle = {Proceedings of the 8th International Conference on Bioscience, Biochemistry
and Bioinformatics, {ICBBB} 2018, Tokyo, Japan, January 18-20, 2018},
pages = {48--55},
publisher = {{ACM}},
year = {2018},
url = {https://doi.org/10.1145/3180382.3180384},
doi = {10.1145/3180382.3180384},
timestamp = {Sun, 17 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbbb/TamuraSNA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isaac/AkutsuJLTT18,
author = {Tatsuya Akutsu and
Jesper Jansson and
Ruiming Li and
Atsuhiro Takasu and
Takeyuki Tamura},
editor = {Wen{-}Lian Hsu and
Der{-}Tsai Lee and
Chung{-}Shou Liao},
title = {New and Improved Algorithms for Unordered Tree Inclusion},
booktitle = {29th International Symposium on Algorithms and Computation, {ISAAC}
2018, December 16-19, 2018, Jiaoxi, Yilan, Taiwan},
series = {LIPIcs},
volume = {123},
pages = {27:1--27:12},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2018},
url = {https://doi.org/10.4230/LIPIcs.ISAAC.2018.27},
doi = {10.4230/LIPICS.ISAAC.2018.27},
timestamp = {Tue, 17 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isaac/AkutsuJLTT18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/automatica/ChengTCA17,
author = {Xiaoqing Cheng and
Takeyuki Tamura and
Wai{-}Ki Ching and
Tatsuya Akutsu},
title = {Discrimination of singleton and periodic attractors in Boolean networks},
journal = {Autom.},
volume = {84},
pages = {205--213},
year = {2017},
url = {https://doi.org/10.1016/j.automatica.2017.07.012},
doi = {10.1016/J.AUTOMATICA.2017.07.012},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/automatica/ChengTCA17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KatoMSMHA17,
author = {Yuki Kato and
Tomoya Mori and
Kengo Sato and
Shingo Maegawa and
Hiroshi Hosokawa and
Tatsuya Akutsu},
title = {An accessibility-incorporated method for accurate prediction of {RNA-RNA}
interactions from sequence data},
journal = {Bioinform.},
volume = {33},
number = {2},
pages = {202--209},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btw603},
doi = {10.1093/BIOINFORMATICS/BTW603},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KatoMSMHA17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/Akutsu17,
author = {Tatsuya Akutsu},
title = {Selected Papers from the 16th International Conference on Bioinformatics
(InCoB 2017)},
journal = {J. Bioinform. Comput. Biol.},
volume = {15},
number = {5},
pages = {1702003:1--1702003:2},
year = {2017},
url = {https://doi.org/10.1142/S0219720017020036},
doi = {10.1142/S0219720017020036},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/Akutsu17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AkutsuJTT17,
author = {Tatsuya Akutsu and
Jesper Jansson and
Atsuhiro Takasu and
Takeyuki Tamura},
title = {On the parameterized complexity of associative and commutative unification},
journal = {Theor. Comput. Sci.},
volume = {660},
pages = {57--74},
year = {2017},
url = {https://doi.org/10.1016/j.tcs.2016.11.026},
doi = {10.1016/J.TCS.2016.11.026},
timestamp = {Tue, 17 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/AkutsuJTT17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1712-05517,
author = {Tatsuya Akutsu and
Jesper Jansson and
Ruiming Li and
Atsuhiro Takasu and
Takeyuki Tamura},
title = {New Algorithms for Unordered Tree Inclusion},
journal = {CoRR},
volume = {abs/1712.05517},
year = {2017},
url = {http://arxiv.org/abs/1712.05517},
eprinttype = {arXiv},
eprint = {1712.05517},
timestamp = {Tue, 17 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1712-05517.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/advcs/HouTCA16,
author = {Wenpin Hou and
Takeyuki Tamura and
Wai{-}Ki Ching and
Tatsuya Akutsu},
title = {Finding and Analyzing the Minimum Set of Driver Nodes in control of
Boolean Networks},
journal = {Adv. Complex Syst.},
volume = {19},
number = {3},
pages = {1650006:1--1650006:32},
year = {2016},
url = {https://doi.org/10.1142/S0219525916500065},
doi = {10.1142/S0219525916500065},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/advcs/HouTCA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiCNPHASB16,
author = {Chen Li and
Catherine Ching Han Chang and
Jeremy Nagel and
Benjamin T. Porebski and
Morihiro Hayashida and
Tatsuya Akutsu and
Jiangning Song and
Ashley M. Buckle},
title = {Critical evaluation of \emph{in silico} methods for prediction of
coiled-coil domains in proteins},
journal = {Briefings Bioinform.},
volume = {17},
number = {2},
pages = {270--282},
year = {2016},
url = {https://doi.org/10.1093/bib/bbv047},
doi = {10.1093/BIB/BBV047},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiCNPHASB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Jindalertudomdee16,
author = {Jira Jindalertudomdee and
Morihiro Hayashida and
Yang Zhao and
Tatsuya Akutsu},
title = {Enumeration method for tree-like chemical compounds with benzene rings
and naphthalene rings by breadth-first search order},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {113},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-0962-4},
doi = {10.1186/S12859-016-0962-4},
timestamp = {Wed, 06 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Jindalertudomdee16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BaoHA16,
author = {Yu Bao and
Morihiro Hayashida and
Tatsuya Akutsu},
title = {LBSizeCleav: improved support vector machine (SVM)-based prediction
of Dicer cleavage sites using loop/bulge length},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {487:1--487:11},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1353-6},
doi = {10.1186/S12859-016-1353-6},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BaoHA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/csda/HasegawaNMSYMAI16,
author = {Takanori Hasegawa and
Atsushi Niida and
Tomoya Mori and
Teppei Shimamura and
Rui Yamaguchi and
Satoru Miyano and
Tatsuya Akutsu and
Seiya Imoto},
title = {A likelihood-free filtering method via approximate Bayesian computation
in evaluating biological simulation models},
journal = {Comput. Stat. Data Anal.},
volume = {94},
pages = {63--74},
year = {2016},
url = {https://doi.org/10.1016/j.csda.2015.08.003},
doi = {10.1016/J.CSDA.2015.08.003},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/csda/HasegawaNMSYMAI16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Jindalertudomdee16,
author = {Jira Jindalertudomdee and
Morihiro Hayashida and
Tatsuya Akutsu},
title = {Enumeration Method for Structural Isomers Containing User-Defined
Structures Based on Breadth-First Search Approach},
journal = {J. Comput. Biol.},
volume = {23},
number = {8},
pages = {625--640},
year = {2016},
url = {https://doi.org/10.1089/cmb.2016.0056},
doi = {10.1089/CMB.2016.0056},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/Jindalertudomdee16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ChengMQCA16,
author = {Xiaoqing Cheng and
Tomoya Mori and
Yushan Qiu and
Wai{-}Ki Ching and
Tatsuya Akutsu},
title = {Exact Identification of the Structure of a Probabilistic Boolean Network
from Samples},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {13},
number = {6},
pages = {1107--1116},
year = {2016},
url = {https://doi.org/10.1109/TCBB.2015.2505310},
doi = {10.1109/TCBB.2015.2505310},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/ChengMQCA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/Jindalertudomdee16,
author = {Jira Jindalertudomdee and
Morihiro Hayashida and
Jiangning Song and
Tatsuya Akutsu},
title = {Host-Pathogen Protein Interaction Prediction Based on Local Topology
Structures of a Protein Interaction Network},
booktitle = {16th {IEEE} International Conference on Bioinformatics and Bioengineering,
{BIBE} 2016, Taichung, Taiwan, October 31 - November 2, 2016},
pages = {7--12},
publisher = {{IEEE} Computer Society},
year = {2016},
url = {https://doi.org/10.1109/BIBE.2016.26},
doi = {10.1109/BIBE.2016.26},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibe/Jindalertudomdee16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/TamuraALY16,
author = {Takeyuki Tamura and
Tatsuya Akutsu and
Chun{-}Yu Lin and
Jinn{-}Moon Yang},
title = {Finding Influential Genes Using Gene Expression Data and Boolean Models
of Metabolic Networks},
booktitle = {16th {IEEE} International Conference on Bioinformatics and Bioengineering,
{BIBE} 2016, Taichung, Taiwan, October 31 - November 2, 2016},
pages = {57--63},
publisher = {{IEEE} Computer Society},
year = {2016},
url = {https://doi.org/10.1109/BIBE.2016.25},
doi = {10.1109/BIBE.2016.25},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibe/TamuraALY16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/HeHNA16,
author = {Fei He and
Akiyoshi Hanai and
Hiroshi Nagamochi and
Tatsuya Akutsu},
editor = {James P. Gilbert and
Haim Azhari and
Hesham H. Ali and
Carla Quint{\~{a}}o and
Jan Sliwa and
Carolina Ruiz and
Ana L. N. Fred and
Hugo Gamboa},
title = {Enumerating Naphthalene Isomers of Tree-like Chemical Graphs},
booktitle = {Proceedings of the 9th International Joint Conference on Biomedical
Engineering Systems and Technologies {(BIOSTEC} 2016) - Volume 3:
BIOINFORMATICS, Rome, Italy, February 21-23, 2016},
pages = {258--265},
publisher = {SciTePress},
year = {2016},
url = {https://doi.org/10.5220/0005783902580265},
doi = {10.5220/0005783902580265},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/biostec/HeHNA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icde/MoriTJHTA16,
author = {Tomoya Mori and
Atsuhiro Takasu and
Jesper Jansson and
Jaewook Hwang and
Takeyuki Tamura and
Tatsuya Akutsu},
title = {Similar subtree search using extended tree inclusion},
booktitle = {32nd {IEEE} International Conference on Data Engineering, {ICDE} 2016,
Helsinki, Finland, May 16-20, 2016},
pages = {1558--1559},
publisher = {{IEEE} Computer Society},
year = {2016},
url = {https://doi.org/10.1109/ICDE.2016.7498424},
doi = {10.1109/ICDE.2016.7498424},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icde/MoriTJHTA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhaoHCHA15,
author = {Yang Zhao and
Morihiro Hayashida and
Yue Cao and
Jaewook Hwang and
Tatsuya Akutsu},
title = {Grammar-based compression approach to extraction of common rules among
multiple trees of glycans and RNAs},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {128:1--128:13},
year = {2015},
url = {https://doi.org/10.1186/s12859-015-0558-4},
doi = {10.1186/S12859-015-0558-4},
timestamp = {Wed, 06 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhaoHCHA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/HasegawaMYSMIA15,
author = {Takanori Hasegawa and
Tomoya Mori and
Rui Yamaguchi and
Teppei Shimamura and
Satoru Miyano and
Seiya Imoto and
Tatsuya Akutsu},
title = {Genomic data assimilation using a higher moment filtering technique
for restoration of gene regulatory networks},
journal = {{BMC} Syst. Biol.},
volume = {9},
pages = {14},
year = {2015},
url = {https://doi.org/10.1186/s12918-015-0154-2},
doi = {10.1186/S12918-015-0154-2},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/HasegawaMYSMIA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/MoriFKAK15,
author = {Tomoya Mori and
Max Fl{\"{o}}ttmann and
Marcus Krantz and
Tatsuya Akutsu and
Edda Klipp},
title = {Stochastic simulation of Boolean rxncon models: towards quantitative
analysis of large signaling networks},
journal = {{BMC} Syst. Biol.},
volume = {9},
pages = {45},
year = {2015},
url = {https://doi.org/10.1186/s12918-015-0193-8},
doi = {10.1186/S12918-015-0193-8},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/MoriFKAK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/ChangTCA15,
author = {Chia{-}Jung Chang and
Takeyuki Tamura and
Kun{-}Mao Chao and
Tatsuya Akutsu},
title = {A Fixed-Parameter Algorithm for Detecting a Singleton Attractor in
an {AND/OR} Boolean Network with Bounded Treewidth},
journal = {{IEICE} Trans. Fundam. Electron. Commun. Comput. Sci.},
volume = {98-A},
number = {1},
pages = {384--390},
year = {2015},
url = {https://doi.org/10.1587/transfun.E98.A.384},
doi = {10.1587/TRANSFUN.E98.A.384},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/ChangTCA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/LuTSA15,
author = {Wei Lu and
Takeyuki Tamura and
Jiangning Song and
Tatsuya Akutsu},
title = {Computing Smallest Intervention Strategies for Multiple Metabolic
Networks in a Boolean Model},
journal = {J. Comput. Biol.},
volume = {22},
number = {2},
pages = {85--110},
year = {2015},
url = {https://doi.org/10.1089/cmb.2014.0274},
doi = {10.1089/CMB.2014.0274},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/LuTSA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jip/CongA15,
author = {Xiao Cong and
Tatsuya Akutsu},
title = {Matrix Network: {A} New Data Structure for Efficient Enumeration of
Microstates of a Genetic Regulatory Network},
journal = {J. Inf. Process.},
volume = {23},
number = {6},
pages = {804--813},
year = {2015},
url = {https://doi.org/10.2197/ipsjjip.23.804},
doi = {10.2197/IPSJJIP.23.804},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jip/CongA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AkutsuTMT15,
author = {Tatsuya Akutsu and
Takeyuki Tamura and
Avraham A. Melkman and
Atsuhiro Takasu},
title = {On the complexity of finding a largest common subtree of bounded degree},
journal = {Theor. Comput. Sci.},
volume = {590},
pages = {2--16},
year = {2015},
url = {https://doi.org/10.1016/j.tcs.2014.10.012},
doi = {10.1016/J.TCS.2014.10.012},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/AkutsuTMT15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tkde/MoriTJHTA15,
author = {Tomoya Mori and
Atsuhiro Takasu and
Jesper Jansson and
Jaewook Hwang and
Takeyuki Tamura and
Tatsuya Akutsu},
title = {Similar Subtree Search Using Extended Tree Inclusion},
journal = {{IEEE} Trans. Knowl. Data Eng.},
volume = {27},
number = {12},
pages = {3360--3373},
year = {2015},
url = {https://doi.org/10.1109/TKDE.2015.2457922},
doi = {10.1109/TKDE.2015.2457922},
timestamp = {Tue, 17 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tkde/MoriTJHTA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/QiuCCJA15,
author = {Yushan Qiu and
Xiaoqing Cheng and
Wai{-}Ki Ching and
Hao Jiang and
Tatsuya Akutsu},
editor = {Jun Huan and
Satoru Miyano and
Amarda Shehu and
Xiaohua Tony Hu and
Bin Ma and
Sanguthevar Rajasekaran and
Vijay K. Gombar and
Matthieu{-}P. Schapranow and
Illhoi Yoo and
Jiayu Zhou and
Brian Chen and
Vinay Pai and
Brian G. Pierce},
title = {On observability of attractors in Boolean Networks},
booktitle = {2015 {IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2015, Washington, DC, USA, November 9-12, 2015},
pages = {263--266},
publisher = {{IEEE} Computer Society},
year = {2015},
url = {https://doi.org/10.1109/BIBM.2015.7359690},
doi = {10.1109/BIBM.2015.7359690},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/QiuCCJA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/abi/NakajimaA14,
author = {Natsu Nakajima and
Tatsuya Akutsu},
title = {Network Completion for Static Gene Expression Data},
journal = {Adv. Bioinformatics},
volume = {2014},
pages = {382452:1--382452:9},
year = {2014},
url = {https://doi.org/10.1155/2014/382452},
doi = {10.1155/2014/382452},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/abi/NakajimaA14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangZTAWS14,
author = {Mingjun Wang and
Xing{-}Ming Zhao and
Hao Tan and
Tatsuya Akutsu and
James C. Whisstock and
Jiangning Song},
title = {Cascleave 2.0, a new approach for predicting caspase and granzyme
cleavage targets},
journal = {Bioinform.},
volume = {30},
number = {1},
pages = {71--80},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt603},
doi = {10.1093/BIOINFORMATICS/BTT603},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangZTAWS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CaiRNA14,
author = {Hongmin Cai and
Peiying Ruan and
Michael Kwok{-}Po Ng and
Tatsuya Akutsu},
title = {Feature weight estimation for gene selection: a local hyperlinear
learning approach},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {70},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-70},
doi = {10.1186/1471-2105-15-70},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CaiRNA14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RuanHMA14,
author = {Peiying Ruan and
Morihiro Hayashida and
Osamu Maruyama and
Tatsuya Akutsu},
title = {Prediction of heterotrimeric protein complexes by two-phase learning
using neighboring kernels},
journal = {{BMC} Bioinform.},
volume = {15},
number = {{S-2}},
pages = {S6},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-S2-S6},
doi = {10.1186/1471-2105-15-S2-S6},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RuanHMA14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/QiuTCA14,
author = {Yushan Qiu and
Takeyuki Tamura and
Wai{-}Ki Ching and
Tatsuya Akutsu},
title = {On control of singleton attractors in multiple Boolean networks: integer
programming-based method},
journal = {{BMC} Syst. Biol.},
volume = {8},
number = {{S-1}},
pages = {S7},
year = {2014},
url = {https://doi.org/10.1186/1752-0509-8-S1-S7},
doi = {10.1186/1752-0509-8-S1-S7},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/QiuTCA14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/compnet/NacherA14,
author = {Jose C. Nacher and
Tatsuya Akutsu},
title = {Analysis of critical and redundant nodes in controlling directed and
undirected complex networks using dominating sets},
journal = {J. Complex Networks},
volume = {2},
number = {4},
pages = {394--412},
year = {2014},
url = {https://doi.org/10.1093/comnet/cnu029},
doi = {10.1093/COMNET/CNU029},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/compnet/NacherA14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijkdb/HayashidaA14,
author = {Morihiro Hayashida and
Tatsuya Akutsu},
title = {Domain-Based Approaches to Prediction and Analysis of Protein-Protein
Interactions},
journal = {Int. J. Knowl. Discov. Bioinform.},
volume = {4},
number = {1},
pages = {24--41},
year = {2014},
url = {https://doi.org/10.4018/ijkdb.2014010103},
doi = {10.4018/IJKDB.2014010103},
timestamp = {Thu, 18 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijkdb/HayashidaA14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/HasegawaMYIMA14,
author = {Takanori Hasegawa and
Tomoya Mori and
Rui Yamaguchi and
Seiya Imoto and
Satoru Miyano and
Tatsuya Akutsu},
title = {An Efficient Data Assimilation Schema for Restoration and Extension
of Gene Regulatory Networks Using Time-Course Observation Data},
journal = {J. Comput. Biol.},
volume = {21},
number = {11},
pages = {785--798},
year = {2014},
url = {https://doi.org/10.1089/cmb.2014.0171},
doi = {10.1089/CMB.2014.0171},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/HasegawaMYIMA14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/SuzukiNA14,
author = {Masaki Suzuki and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Efficient enumeration of monocyclic chemical graphs with given path
frequencies},
journal = {J. Cheminformatics},
volume = {6},
number = {1},
pages = {31},
year = {2014},
url = {https://doi.org/10.1186/1758-2946-6-31},
doi = {10.1186/1758-2946-6-31},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/SuzukiNA14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jda/AkutsuTFT14,
author = {Tatsuya Akutsu and
Takeyuki Tamura and
Daiji Fukagawa and
Atsuhiro Takasu},
title = {Efficient exponential-time algorithms for edit distance between unordered
trees},
journal = {J. Discrete Algorithms},
volume = {25},
pages = {79--93},
year = {2014},
url = {https://doi.org/10.1016/j.jda.2013.09.001},
doi = {10.1016/J.JDA.2013.09.001},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jda/AkutsuTFT14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwpec/AkutsuJTT14,
author = {Tatsuya Akutsu and
Jesper Jansson and
Atsuhiro Takasu and
Takeyuki Tamura},
editor = {Marek Cygan and
Pinar Heggernes},
title = {On the Parameterized Complexity of Associative and Commutative Unification},
booktitle = {Parameterized and Exact Computation - 9th International Symposium,
{IPEC} 2014, Wroclaw, Poland, September 10-12, 2014. Revised Selected
Papers},
series = {Lecture Notes in Computer Science},
volume = {8894},
pages = {15--27},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-13524-3\_2},
doi = {10.1007/978-3-319-13524-3\_2},
timestamp = {Tue, 17 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iwpec/AkutsuJTT14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithms/AkutsuT13,
author = {Tatsuya Akutsu and
Takeyuki Tamura},
title = {A Polynomial-Time Algorithm for Computing the Maximum Common Connected
Edge Subgraph of Outerplanar Graphs of Bounded Degree},
journal = {Algorithms},
volume = {6},
number = {1},
pages = {119--135},
year = {2013},
url = {https://doi.org/10.3390/a6010119},
doi = {10.3390/A6010119},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithms/AkutsuT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhaoTAV13,
author = {Yang Zhao and
Takeyuki Tamura and
Tatsuya Akutsu and
Jean{-}Philippe Vert},
title = {Flux balance impact degree: a new definition of impact degree to properly
treat reversible reactions in metabolic networks},
journal = {Bioinform.},
volume = {29},
number = {17},
pages = {2178--2185},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt364},
doi = {10.1093/BIOINFORMATICS/BTT364},
timestamp = {Wed, 06 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoTAV13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/HayashidaKSA13,
author = {Morihiro Hayashida and
Mayumi Kamada and
Jiangning Song and
Tatsuya Akutsu},
title = {Prediction of protein-RNA residue-base contacts using two-dimensional
conditional random field with the lasso},
journal = {{BMC} Syst. Biol.},
volume = {7},
number = {{S-2}},
pages = {S15},
year = {2013},
url = {https://doi.org/10.1186/1752-0509-7-S2-S15},
doi = {10.1186/1752-0509-7-S2-S15},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/HayashidaKSA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/JiangTCA13,
author = {Hao Jiang and
Takeyuki Tamura and
Wai{-}Ki Ching and
Tatsuya Akutsu},
title = {On the Complexity of Inference and Completion of Boolean Networks
from Given Singleton Attractors},
journal = {{IEICE} Trans. Fundam. Electron. Commun. Comput. Sci.},
volume = {96-A},
number = {11},
pages = {2265--2274},
year = {2013},
url = {https://doi.org/10.1587/transfun.E96.A.2265},
doi = {10.1587/TRANSFUN.E96.A.2265},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/JiangTCA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijdmb/ChenATC13,
author = {Xi Chen and
Tatsuya Akutsu and
Takeyuki Tamura and
Wai{-}Ki Ching},
title = {Finding optimal control policy in probabilistic Boolean Networks with
hard constraints by using integer programming and dynamic programming},
journal = {Int. J. Data Min. Bioinform.},
volume = {7},
number = {3},
pages = {321--343},
year = {2013},
url = {https://doi.org/10.1504/IJDMB.2013.053306},
doi = {10.1504/IJDMB.2013.053306},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijdmb/ChenATC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/ZhaoHJNA13,
author = {Yang Zhao and
Morihiro Hayashida and
Jira Jindalertudomdee and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Breadth-First Search Approach to Enumeration of Tree-like Chemical
Compounds},
journal = {J. Bioinform. Comput. Biol.},
volume = {11},
number = {6},
year = {2013},
url = {https://doi.org/10.1142/S0219720013430075},
doi = {10.1142/S0219720013430075},
timestamp = {Wed, 06 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/ZhaoHJNA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/MelkmanA13,
author = {Avraham A. Melkman and
Tatsuya Akutsu},
title = {An Improved Satisfiability Algorithm for Nested Canalyzing Functions
and its Application to Determining a Singleton Attractor of a Boolean
Network},
journal = {J. Comput. Biol.},
volume = {20},
number = {12},
pages = {958--969},
year = {2013},
url = {https://doi.org/10.1089/cmb.2013.0060},
doi = {10.1089/CMB.2013.0060},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/MelkmanA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AkutsuFHTT13,
author = {Tatsuya Akutsu and
Daiji Fukagawa and
Magn{\'{u}}s M. Halld{\'{o}}rsson and
Atsuhiro Takasu and
Keisuke Tanaka},
title = {Approximation and parameterized algorithms for common subtrees and
edit distance between unordered trees},
journal = {Theor. Comput. Sci.},
volume = {470},
pages = {10--22},
year = {2013},
url = {https://doi.org/10.1016/j.tcs.2012.11.017},
doi = {10.1016/J.TCS.2012.11.017},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/AkutsuFHTT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cisis/NakajimaA13,
author = {Natsu Nakajima and
Tatsuya Akutsu},
editor = {Leonard Barolli and
Fatos Xhafa and
Hsing{-}Chung Chen and
Antonio Fernandez G{\'{o}}mez{-}Skarmeta and
Farooq Hussain},
title = {Network Completion for Time Varying Genetic Networks},
booktitle = {Seventh International Conference on Complex, Intelligent, and Software
Intensive Systems, {CISIS} 2013, Taichung, Taiwan, July 3-5, 2013},
pages = {553--558},
publisher = {{IEEE} Computer Society},
year = {2013},
url = {https://doi.org/10.1109/CISIS.2013.100},
doi = {10.1109/CISIS.2013.100},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cisis/NakajimaA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fct/AkutsuTMT13,
author = {Tatsuya Akutsu and
Takeyuki Tamura and
Avraham A. Melkman and
Atsuhiro Takasu},
editor = {Leszek Gasieniec and
Frank Wolter},
title = {On the Complexity of Finding a Largest Common Subtree of Bounded Degree},
booktitle = {Fundamentals of Computation Theory - 19th International Symposium,
{FCT} 2013, Liverpool, UK, August 19-21, 2013. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8070},
pages = {4--15},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-40164-0\_4},
doi = {10.1007/978-3-642-40164-0\_4},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fct/AkutsuTMT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sitis/NacherA13,
author = {Jose C. Nacher and
Tatsuya Akutsu},
editor = {Kokou Y{\'{e}}tongnon and
Albert Dipanda and
Richard Chbeir},
title = {Analysis on critical nodes in controlling complex networks using dominating
sets},
booktitle = {Ninth International Conference on Signal-Image Technology {\&}
Internet-Based Systems, {SITIS} 2013, Kyoto, Japan, December 2-5,
2013},
pages = {649--654},
publisher = {{IEEE} Computer Society},
year = {2013},
url = {https://doi.org/10.1109/SITIS.2013.106},
doi = {10.1109/SITIS.2013.106},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sitis/NacherA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/AkutsuTT13,
author = {Tatsuya Akutsu and
Takeyuki Tamura and
Atsuhiro Takasu},
title = {On the Parameterized Complexity of Associative and Commutative Unification},
journal = {CoRR},
volume = {abs/1310.0919},
year = {2013},
url = {http://arxiv.org/abs/1310.0919},
eprinttype = {arXiv},
eprint = {1310.0919},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/AkutsuTT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SatoKAAS12,
author = {Kengo Sato and
Yuki Kato and
Tatsuya Akutsu and
Kiyoshi Asai and
Yasubumi Sakakibara},
title = {{DAFS:} simultaneous aligning and folding of {RNA} sequences via dual
decomposition},
journal = {Bioinform.},
volume = {28},
number = {24},
pages = {3218--3224},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts612},
doi = {10.1093/BIOINFORMATICS/BTS612},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SatoKAAS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/AkutsuFJS12,
author = {Tatsuya Akutsu and
Daiji Fukagawa and
Jesper Jansson and
Kunihiko Sadakane},
title = {Inferring a graph from path frequency},
journal = {Discret. Appl. Math.},
volume = {160},
number = {10-11},
pages = {1416--1428},
year = {2012},
url = {https://doi.org/10.1016/j.dam.2012.02.002},
doi = {10.1016/J.DAM.2012.02.002},
timestamp = {Tue, 17 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dam/AkutsuFJS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/icae/HayashidaRA12,
author = {Morihiro Hayashida and
Peiying Ruan and
Tatsuya Akutsu},
title = {A quadsection algorithm for grammar-based image compression},
journal = {Integr. Comput. Aided Eng.},
volume = {19},
number = {1},
pages = {23--38},
year = {2012},
url = {https://doi.org/10.3233/ICA-2012-0389},
doi = {10.3233/ICA-2012-0389},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/icae/HayashidaRA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/AkutsuZHT12,
author = {Tatsuya Akutsu and
Yang Zhao and
Morihiro Hayashida and
Takeyuki Tamura},
title = {Integer Programming-Based Approach to Attractor Detection and Control
of Boolean Networks},
journal = {{IEICE} Trans. Inf. Syst.},
volume = {95-D},
number = {12},
pages = {2960--2970},
year = {2012},
url = {https://doi.org/10.1587/transinf.E95.D.2960},
doi = {10.1587/TRANSINF.E95.D.2960},
timestamp = {Wed, 06 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/AkutsuZHT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijbra/ZhaoHNNA12,
author = {Yang Zhao and
Morihiro Hayashida and
Jose C. Nacher and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Protein complex prediction via improved verification methods using
constrained domain-domain matching},
journal = {Int. J. Bioinform. Res. Appl.},
volume = {8},
number = {3/4},
pages = {210--227},
year = {2012},
url = {https://doi.org/10.1504/IJBRA.2012.048970},
doi = {10.1504/IJBRA.2012.048970},
timestamp = {Wed, 06 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijbra/ZhaoHNNA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/AkutsuMT12,
author = {Tatsuya Akutsu and
Avraham A. Melkman and
Takeyuki Tamura},
title = {Singleton and 2-periodic attractors of sign-definite Boolean networks},
journal = {Inf. Process. Lett.},
volume = {112},
number = {1-2},
pages = {35--38},
year = {2012},
url = {https://doi.org/10.1016/j.ipl.2011.10.002},
doi = {10.1016/J.IPL.2011.10.002},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/AkutsuMT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/MoriTFTTA12,
author = {Tomoya Mori and
Takeyuki Tamura and
Daiji Fukagawa and
Atsuhiro Takasu and
Etsuji Tomita and
Tatsuya Akutsu},
title = {A Clique-Based Method Using Dynamic Programming for Computing Edit
Distance Between Unordered Trees},
journal = {J. Comput. Biol.},
volume = {19},
number = {10},
pages = {1089--1104},
year = {2012},
url = {https://doi.org/10.1089/cmb.2012.0133},
doi = {10.1089/CMB.2012.0133},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/MoriTFTTA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KatoSAA12,
author = {Yuki Kato and
Kengo Sato and
Kiyoshi Asai and
Tatsuya Akutsu},
title = {Rtips: fast and accurate tools for {RNA} 2D structure prediction using
integer programming},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Web-Server-Issue},
pages = {29--34},
year = {2012},
url = {https://doi.org/10.1093/nar/gks412},
doi = {10.1093/NAR/GKS412},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KatoSAA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/AkutsuKMT12,
author = {Tatsuya Akutsu and
Sven Kosub and
Avraham A. Melkman and
Takeyuki Tamura},
title = {Finding a Periodic Attractor of a Boolean Network},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {5},
pages = {1410--1421},
year = {2012},
url = {https://doi.org/10.1109/TCBB.2012.87},
doi = {10.1109/TCBB.2012.87},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/AkutsuKMT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/AkutsuTFT12,
author = {Tatsuya Akutsu and
Takeyuki Tamura and
Daiji Fukagawa and
Atsuhiro Takasu},
editor = {Juha K{\"{a}}rkk{\"{a}}inen and
Jens Stoye},
title = {Efficient Exponential Time Algorithms for Edit Distance between Unordered
Trees},
booktitle = {Combinatorial Pattern Matching - 23rd Annual Symposium, {CPM} 2012,
Helsinki, Finland, July 3-5, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7354},
pages = {360--372},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-31265-6\_29},
doi = {10.1007/978-3-642-31265-6\_29},
timestamp = {Tue, 21 Mar 2023 21:02:12 +0100},
biburl = {https://dblp.org/rec/conf/cpm/AkutsuTFT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isaac/AkutsuT12,
author = {Tatsuya Akutsu and
Takeyuki Tamura},
editor = {Kun{-}Mao Chao and
Tsan{-}sheng Hsu and
Der{-}Tsai Lee},
title = {On the Complexity of the Maximum Common Subgraph Problem for Partial
k-Trees of Bounded Degree},
booktitle = {Algorithms and Computation - 23rd International Symposium, {ISAAC}
2012, Taipei, Taiwan, December 19-21, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7676},
pages = {146--155},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-35261-4\_18},
doi = {10.1007/978-3-642-35261-4\_18},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isaac/AkutsuT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isb/HayashidaKSA12,
author = {Morihiro Hayashida and
Mayumi Kamada and
Jiangning Song and
Tatsuya Akutsu},
title = {Predicting protein-RNA residue-base contacts using two-dimensional
conditional random field},
booktitle = {6th {IEEE} International Conference on Systems Biology, {ISB} 2012,
Xian, China, August 18-20, 2012},
pages = {152--157},
publisher = {{IEEE}},
year = {2012},
url = {https://doi.org/10.1109/ISB.2012.6314128},
doi = {10.1109/ISB.2012.6314128},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isb/HayashidaKSA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mfcs/AkutsuT12,
author = {Tatsuya Akutsu and
Takeyuki Tamura},
editor = {Branislav Rovan and
Vladimiro Sassone and
Peter Widmayer},
title = {A Polynomial-Time Algorithm for Computing the Maximum Common Subgraph
of Outerplanar Graphs of Bounded Degree},
booktitle = {Mathematical Foundations of Computer Science 2012 - 37th International
Symposium, {MFCS} 2012, Bratislava, Slovakia, August 27-31, 2012.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7464},
pages = {76--87},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-32589-2\_10},
doi = {10.1007/978-3-642-32589-2\_10},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/mfcs/AkutsuT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/prib/AkutsuHT12,
author = {Tatsuya Akutsu and
Morihiro Hayashida and
Takeyuki Tamura},
editor = {Tetsuo Shibuya and
Hisashi Kashima and
Jun Sese and
Shandar Ahmad},
title = {Finding Conserved Regions in Protein Structures Using Support Vector
Machines and Structure Alignment},
booktitle = {Pattern Recognition in Bioinformatics - 7th {IAPR} International Conference,
{PRIB} 2012, Tokyo, Japan, November 8-10, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7632},
pages = {233--242},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-34123-6\_21},
doi = {10.1007/978-3-642-34123-6\_21},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/prib/AkutsuHT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SatoKHAA11,
author = {Kengo Sato and
Yuki Kato and
Michiaki Hamada and
Tatsuya Akutsu and
Kiyoshi Asai},
title = {IPknot: fast and accurate prediction of {RNA} secondary structures
with pseudoknots using integer programming},
journal = {Bioinform.},
volume = {27},
number = {13},
pages = {85--93},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr215},
doi = {10.1093/BIOINFORMATICS/BTR215},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SatoKHAA11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Demir-KavukKAK11,
author = {Ozgur Demir{-}Kavuk and
Mayumi Kamada and
Tatsuya Akutsu and
Ernst{-}Walter Knapp},
title = {Prediction using step-wise L1, {L2} regularization and feature selection
for small data sets with large number of features},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {412},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-412},
doi = {10.1186/1471-2105-12-412},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Demir-KavukKAK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FukagawaTTTA11,
author = {Daiji Fukagawa and
Takeyuki Tamura and
Atsuhiro Takasu and
Etsuji Tomita and
Tatsuya Akutsu},
title = {A clique-based method for the edit distance between unordered trees
and its application to analysis of glycan structures},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-1}},
pages = {S13},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-S1-S13},
doi = {10.1186/1471-2105-12-S1-S13},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FukagawaTTTA11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShimizuNA11,
author = {Masaaki Shimizu and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Enumerating tree-like chemical graphs with given upper and lower bounds
on path frequencies},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-14}},
pages = {S3},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-S14-S3},
doi = {10.1186/1471-2105-12-S14-S3},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ShimizuNA11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/HayashidaKSA11,
author = {Morihiro Hayashida and
Mayumi Kamada and
Jiangning Song and
Tatsuya Akutsu},
title = {Conditional random field approach to prediction of protein-protein
interactions using domain information},
journal = {{BMC} Syst. Biol.},
volume = {5},
number = {{S-1}},
pages = {S8},
year = {2011},
url = {https://doi.org/10.1186/1752-0509-5-S1-S8},
doi = {10.1186/1752-0509-5-S1-S8},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/HayashidaKSA11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/AkutsuN11,
author = {Tatsuya Akutsu and
Hiroshi Nagamochi},
title = {Kernel Methods for Chemical Compounds: From Classification to Design},
journal = {{IEICE} Trans. Inf. Syst.},
volume = {94-D},
number = {10},
pages = {1846--1853},
year = {2011},
url = {https://doi.org/10.1587/transinf.E94.D.1846},
doi = {10.1587/TRANSINF.E94.D.1846},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/AkutsuN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/TamuraCAC11,
author = {Takeyuki Tamura and
Yang Cong and
Tatsuya Akutsu and
Wai{-}Ki Ching},
title = {An Efficient Method of Computing Impact Degrees for Multiple Reactions
in Metabolic Networks with Cycles},
journal = {{IEICE} Trans. Inf. Syst.},
volume = {94-D},
number = {12},
pages = {2393--2399},
year = {2011},
url = {https://doi.org/10.1587/transinf.E94.D.2393},
doi = {10.1587/TRANSINF.E94.D.2393},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/TamuraCAC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/HayashidaA11,
author = {Morihiro Hayashida and
Tatsuya Akutsu},
title = {Measuring the Similarity of Protein Structures Using Image Compression
Algorithms},
journal = {{IEICE} Trans. Inf. Syst.},
volume = {94-D},
number = {12},
pages = {2468--2478},
year = {2011},
url = {https://doi.org/10.1587/transinf.E94.D.2468},
doi = {10.1587/TRANSINF.E94.D.2468},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/HayashidaA11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/SongTBSMWAWP11,
author = {Jiangning Song and
Hao Tan and
Sarah E. Boyd and
Hong{-}Bin Shen and
Khalid Mahmood and
Geoffrey I. Webb and
Tatsuya Akutsu and
James C. Whisstock and
Robert N. Pike},
title = {Bioinformatic Approaches for Predicting substrates of Proteases},
journal = {J. Bioinform. Comput. Biol.},
volume = {9},
number = {1},
pages = {149--178},
year = {2011},
url = {https://doi.org/10.1142/S0219720011005288},
doi = {10.1142/S0219720011005288},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/SongTBSMWAWP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/PoolsapKSA11,
author = {Unyanee Poolsap and
Yuki Kato and
Kengo Sato and
Tatsuya Akutsu},
title = {Using binding Profiles to Predict binding sites of Target RNAs},
journal = {J. Bioinform. Comput. Biol.},
volume = {9},
number = {6},
pages = {697--713},
year = {2011},
url = {https://doi.org/10.1142/S0219720011005628},
doi = {10.1142/S0219720011005628},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/PoolsapKSA11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/AkutsuMTY11,
author = {Tatsuya Akutsu and
Avraham A. Melkman and
Takeyuki Tamura and
Masaki Yamamoto},
title = {Determining a Singleton Attractor of a Boolean Network with Nested
Canalyzing Functions},
journal = {J. Comput. Biol.},
volume = {18},
number = {10},
pages = {1275--1290},
year = {2011},
url = {https://doi.org/10.1089/cmb.2010.0281},
doi = {10.1089/CMB.2010.0281},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/AkutsuMTY11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ImadaONA11,
author = {Tomoki Imada and
Shunsuke Ota and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Efficient Enumeration of Stereoisomers of Outerplanar Chemical Graphs
Using Dynamic Programming},
journal = {J. Chem. Inf. Model.},
volume = {51},
number = {11},
pages = {2788--2807},
year = {2011},
url = {https://doi.org/10.1021/ci200084b},
doi = {10.1021/CI200084B},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/ImadaONA11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AkutsuFTT11,
author = {Tatsuya Akutsu and
Daiji Fukagawa and
Atsuhiro Takasu and
Takeyuki Tamura},
title = {Exact algorithms for computing the tree edit distance between unordered
trees},
journal = {Theor. Comput. Sci.},
volume = {412},
number = {4-5},
pages = {352--364},
year = {2011},
url = {https://doi.org/10.1016/j.tcs.2010.10.002},
doi = {10.1016/J.TCS.2010.10.002},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/AkutsuFTT11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cisis/AkutsuMTFTT11,
author = {Tatsuya Akutsu and
Tomoya Mori and
Takeyuki Tamura and
Daiji Fukagawa and
Atsuhiro Takasu and
Etsuji Tomita},
title = {An Improved Clique-Based Method for Computing Edit Distance between
Unordered Trees and Its Application to Comparison of Glycan Structures},
booktitle = {International Conference on Complex, Intelligent and Software Intensive
Systems, {CISIS} 2011, June 30 - July 2, 2011, Korean Bible University,
Seoul, Korea},
pages = {536--540},
publisher = {{IEEE} Computer Society},
year = {2011},
url = {https://doi.org/10.1109/CISIS.2011.88},
doi = {10.1109/CISIS.2011.88},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cisis/AkutsuMTFTT11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithmica/AkutsuFT10,
author = {Tatsuya Akutsu and
Daiji Fukagawa and
Atsuhiro Takasu},
title = {Approximating Tree Edit Distance through String Edit Distance},
journal = {Algorithmica},
volume = {57},
number = {2},
pages = {325--348},
year = {2010},
url = {https://doi.org/10.1007/s00453-008-9213-z},
doi = {10.1007/S00453-008-9213-Z},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithmica/AkutsuFT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SongTSMBWAW10,
author = {Jiangning Song and
Hao Tan and
Hong{-}Bin Shen and
Khalid Mahmood and
Sarah E. Boyd and
Geoffrey I. Webb and
Tatsuya Akutsu and
James C. Whisstock},
title = {Cascleave: towards more accurate prediction of caspase substrate cleavage
sites},
journal = {Bioinform.},
volume = {26},
number = {6},
pages = {752--760},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq043},
doi = {10.1093/BIOINFORMATICS/BTQ043},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SongTSMBWAW10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KatoSHWAA10,
author = {Yuki Kato and
Kengo Sato and
Michiaki Hamada and
Yoshihide Watanabe and
Kiyoshi Asai and
Tatsuya Akutsu},
title = {RactIP: fast and accurate prediction of {RNA-RNA} interaction using
integer programming},
journal = {Bioinform.},
volume = {26},
number = {18},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq372},
doi = {10.1093/BIOINFORMATICS/BTQ372},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KatoSHWAA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biosystems/NacherHA10,
author = {Jose C. Nacher and
Morihiro Hayashida and
Tatsuya Akutsu},
title = {The role of internal duplication in the evolution of multi-domain
proteins},
journal = {Biosyst.},
volume = {101},
number = {2},
pages = {127--135},
year = {2010},
url = {https://doi.org/10.1016/j.biosystems.2010.05.005},
doi = {10.1016/J.BIOSYSTEMS.2010.05.005},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biosystems/NacherHA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhaoHA10,
author = {Yang Zhao and
Morihiro Hayashida and
Tatsuya Akutsu},
title = {Integer programming-based method for grammar-based tree compression
and its application to pattern extraction of glycan tree structures},
journal = {{BMC} Bioinform.},
volume = {11},
number = {{S-11}},
pages = {S4},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-S11-S4},
doi = {10.1186/1471-2105-11-S11-S4},
timestamp = {Wed, 06 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhaoHA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/HayashidaA10,
author = {Morihiro Hayashida and
Tatsuya Akutsu},
title = {Comparing biological networks via graph compression},
journal = {{BMC} Syst. Biol.},
volume = {4},
number = {{S-2}},
pages = {S13},
year = {2010},
url = {https://doi.org/10.1186/1752-0509-4-S2-S13},
doi = {10.1186/1752-0509-4-S2-S13},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/HayashidaA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/Akutsu10,
author = {Tatsuya Akutsu},
title = {Tree Edit Distance Problems: Algorithms and Applications to Bioinformatics},
journal = {{IEICE} Trans. Inf. Syst.},
volume = {93-D},
number = {2},
pages = {208--218},
year = {2010},
url = {https://doi.org/10.1587/transinf.E93.D.208},
doi = {10.1587/TRANSINF.E93.D.208},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/Akutsu10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/TamuraA10,
author = {Takeyuki Tamura and
Tatsuya Akutsu},
title = {Exact Algorithms for Finding a Minimum Reaction Cut under a Boolean
Model of Metabolic Networks},
journal = {{IEICE} Trans. Fundam. Electron. Commun. Comput. Sci.},
volume = {93-A},
number = {8},
pages = {1497--1507},
year = {2010},
url = {https://doi.org/10.1587/transfun.E93.A.1497},
doi = {10.1587/TRANSFUN.E93.A.1497},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/TamuraA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijkdb/TamuraTA10,
author = {Takeyuki Tamura and
Kazuhiro Takemoto and
Tatsuya Akutsu},
title = {Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean
Model Using Integer Programming and Feedback Vertex Sets},
journal = {Int. J. Knowl. Discov. Bioinform.},
volume = {1},
number = {1},
pages = {14--31},
year = {2010},
url = {https://doi.org/10.4018/jkdb.2010100202},
doi = {10.4018/JKDB.2010100202},
timestamp = {Thu, 18 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijkdb/TamuraTA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/imt/SongTSTGA10,
author = {Jiangning Song and
Kazuhiro Takemoto and
Hongbin Shen and
Hao Tan and
M. Michael Gromiha and
Tatsuya Akutsu},
title = {Prediction of Protein Folding Rates from Structural Topology and Complex
Network Properties},
journal = {Inf. Media Technol.},
volume = {5},
number = {3},
pages = {980--993},
year = {2010},
url = {https://doi.org/10.11185/imt.5.980},
doi = {10.11185/IMT.5.980},
timestamp = {Wed, 04 Sep 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/imt/SongTSTGA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/MelkmanTA10,
author = {Avraham A. Melkman and
Takeyuki Tamura and
Tatsuya Akutsu},
title = {Determining a singleton attractor of an {AND/OR} Boolean network in
O(1.587\({}^{\mbox{n}}\)) time},
journal = {Inf. Process. Lett.},
volume = {110},
number = {14-15},
pages = {565--569},
year = {2010},
url = {https://doi.org/10.1016/j.ipl.2010.05.001},
doi = {10.1016/J.IPL.2010.05.001},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/MelkmanTA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/Akutsu10,
author = {Tatsuya Akutsu},
title = {A bisection algorithm for grammar-based compression of ordered trees},
journal = {Inf. Process. Lett.},
volume = {110},
number = {18-19},
pages = {815--820},
year = {2010},
url = {https://doi.org/10.1016/j.ipl.2010.07.004},
doi = {10.1016/J.IPL.2010.07.004},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/Akutsu10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/IshidaKZNA10,
author = {Yusuke Ishida and
Yuki Kato and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Branch-and-Bound Algorithms for Enumerating Treelike Chemical Graphs
with Given Path Frequency Using Detachment-Cut},
journal = {J. Chem. Inf. Model.},
volume = {50},
number = {5},
pages = {934--946},
year = {2010},
url = {https://doi.org/10.1021/ci900447z},
doi = {10.1021/CI900447Z},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/IshidaKZNA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/ChenATC10,
author = {Xi Chen and
Tatsuya Akutsu and
Takeyuki Tamura and
Wai{-}Ki Ching},
editor = {Taesung Park and
Stephen Kwok{-}Wing Tsui and
Luonan Chen and
Michael K. Ng and
Limsoon Wong and
Xiaohua Hu},
title = {Finding optimal control policy in Probabilistic Boolean Networks with
hard constraints by using integer programming and dynamic programming},
booktitle = {2010 {IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2010, Hong Kong, China, December 18-21, 2010, Proceedings},
pages = {240--246},
publisher = {{IEEE} Computer Society},
year = {2010},
url = {https://doi.org/10.1109/BIBM.2010.5706570},
doi = {10.1109/BIBM.2010.5706570},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/ChenATC10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fgit/HayashidaRA10,
author = {Morihiro Hayashida and
Peiying Ruan and
Tatsuya Akutsu},
editor = {Tai{-}Hoon Kim and
Young{-}Hoon Lee and
Byeong Ho Kang and
Dominik Slezak},
title = {A Quadsection Algorithm for Grammar-Based Image Compression},
booktitle = {Future Generation Information Technology - Second International Conference,
{FGIT} 2010, Jeju Island, Korea, December 13-15, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6485},
pages = {234--248},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-17569-5\_24},
doi = {10.1007/978-3-642-17569-5\_24},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fgit/HayashidaRA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpr/TakasuFA10,
author = {Atsuhiro Takasu and
Daiji Fukagawa and
Tatsuya Akutsu},
title = {A Variational Bayesian {EM} Algorithm for Tree Similarity},
booktitle = {20th International Conference on Pattern Recognition, {ICPR} 2010,
Istanbul, Turkey, 23-26 August 2010},
pages = {1056--1059},
publisher = {{IEEE} Computer Society},
year = {2010},
url = {https://doi.org/10.1109/ICPR.2010.264},
doi = {10.1109/ICPR.2010.264},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icpr/TakasuFA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/PoolsapKA10,
author = {Unyanee Poolsap and
Yuki Kato and
Tatsuya Akutsu},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Dynamic Programming Algorithms for {RNA} Structure Prediction with
Binding Sites},
booktitle = {Biocomputing 2010: Proceedings of the Pacific Symposium, Kamuela,
Hawaii, USA, 4-8 January 2010},
pages = {98--107},
publisher = {World Scientific Publishing},
year = {2010},
url = {http://psb.stanford.edu/psb-online/proceedings/psb10/poolsap.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/PoolsapKA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biosystems/NacherHA09,
author = {Jose C. Nacher and
Morihiro Hayashida and
Tatsuya Akutsu},
title = {Emergence of scale-free distribution in protein-protein interaction
networks based on random selection of interacting domain pairs},
journal = {Biosyst.},
volume = {95},
number = {2},
pages = {155--159},
year = {2009},
url = {https://doi.org/10.1016/j.biosystems.2008.10.002},
doi = {10.1016/J.BIOSYSTEMS.2008.10.002},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biosystems/NacherHA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BrownA09,
author = {J. B. Brown and
Tatsuya Akutsu},
title = {Identification of novel {DNA} repair proteins via primary sequence,
secondary structure, and homology},
journal = {{BMC} Bioinform.},
volume = {10},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-25},
doi = {10.1186/1471-2105-10-25},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BrownA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PoolsapKA09,
author = {Unyanee Poolsap and
Yuki Kato and
Tatsuya Akutsu},
title = {Prediction of {RNA} secondary structure with pseudoknots using integer
programming},
journal = {{BMC} Bioinform.},
volume = {10},
number = {{S-1}},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-S1-S38},
doi = {10.1186/1471-2105-10-S1-S38},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PoolsapKA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/TamuraA09,
author = {Takeyuki Tamura and
Tatsuya Akutsu},
title = {Detecting a Singleton Attractor in a Boolean Network Utilizing {SAT}
Algorithms},
journal = {{IEICE} Trans. Fundam. Electron. Commun. Comput. Sci.},
volume = {92-A},
number = {2},
pages = {493--501},
year = {2009},
url = {https://doi.org/10.1587/transfun.E92.A.493},
doi = {10.1587/TRANSFUN.E92.A.493},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/TamuraA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/AkutsuT09,
author = {Tatsuya Akutsu and
Takeyuki Tamura},
title = {On Finding a Fixed Point in a Boolean Network with Maximum Indegree
2},
journal = {{IEICE} Trans. Fundam. Electron. Commun. Comput. Sci.},
volume = {92-A},
number = {8},
pages = {1771--1778},
year = {2009},
url = {https://doi.org/10.1587/transfun.E92.A.1771},
doi = {10.1587/TRANSFUN.E92.A.1771},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/AkutsuT09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/imt/AkutsuHZC009,
author = {Tatsuya Akutsu and
Morihiro Hayashida and
Shuqin Zhang and
Wai{-}Ki Ching and
Michael K. Ng},
title = {Analyses and Algorithms for Predecessor and Control Problems for Boolean
Networks of Bounded Indegree},
journal = {Inf. Media Technol.},
volume = {4},
number = {2},
pages = {338--349},
year = {2009},
url = {https://doi.org/10.11185/imt.4.338},
doi = {10.11185/IMT.4.338},
timestamp = {Thu, 05 Sep 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/imt/AkutsuHZC009.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/KatoAS09,
author = {Yuki Kato and
Tatsuya Akutsu and
Hiroyuki Seki},
title = {Dynamic Programming Algorithms and Grammatical Modeling for Protein
Beta-Sheet Prediction},
journal = {J. Comput. Biol.},
volume = {16},
number = {7},
pages = {945--957},
year = {2009},
url = {https://doi.org/10.1089/cmb.2008.0228},
doi = {10.1089/CMB.2008.0228},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/KatoAS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mics/TamuraA09,
author = {Takeyuki Tamura and
Tatsuya Akutsu},
title = {Algorithms for Singleton Attractor Detection in Planar and Nonplanar
{AND/OR} Boolean Networks},
journal = {Math. Comput. Sci.},
volume = {2},
number = {3},
pages = {401--420},
year = {2009},
url = {https://doi.org/10.1007/s11786-008-0063-5},
doi = {10.1007/S11786-008-0063-5},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mics/TamuraA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pr/KatoAS09,
author = {Yuki Kato and
Tatsuya Akutsu and
Hiroyuki Seki},
title = {A grammatical approach to {RNA-RNA} interaction prediction},
journal = {Pattern Recognit.},
volume = {42},
number = {4},
pages = {531--538},
year = {2009},
url = {https://doi.org/10.1016/j.patcog.2008.08.004},
doi = {10.1016/J.PATCOG.2008.08.004},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pr/KatoAS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alt/AkutsuTH09,
author = {Tatsuya Akutsu and
Takeyuki Tamura and
Katsuhisa Horimoto},
editor = {Ricard Gavald{\`{a}} and
G{\'{a}}bor Lugosi and
Thomas Zeugmann and
Sandra Zilles},
title = {Completing Networks Using Observed Data},
booktitle = {Algorithmic Learning Theory, 20th International Conference, {ALT}
2009, Porto, Portugal, October 3-5, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5809},
pages = {126--140},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04414-4\_14},
doi = {10.1007/978-3-642-04414-4\_14},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/alt/AkutsuTH09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cdc/AkutsuHT09,
author = {Tatsuya Akutsu and
Morihiro Hayashida and
Takeyuki Tamura},
title = {Integer programming-based methods for attractor detection and control
of boolean networks},
booktitle = {Proceedings of the 48th {IEEE} Conference on Decision and Control,
{CDC} 2009, combined withe the 28th Chinese Control Conference, December
16-18, 2009, Shanghai, China},
pages = {5610--5617},
publisher = {{IEEE}},
year = {2009},
url = {https://doi.org/10.1109/CDC.2009.5400017},
doi = {10.1109/CDC.2009.5400017},
timestamp = {Fri, 04 Mar 2022 13:27:41 +0100},
biburl = {https://dblp.org/rec/conf/cdc/AkutsuHT09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cikm/CongTAC09,
author = {Yang Cong and
Takeyuki Tamura and
Tatsuya Akutsu and
Wai{-}Ki Ching},
editor = {Doheon Lee and
Russ B. Altman and
Min Song and
Jun Huan},
title = {Efficient computation of impact degrees for multiple reactions in
metabolic networks with cycles},
booktitle = {Proceeding of the 3rd International Workshop on Data and Text Mining
in Bioinformatics, {DTMBIO} 2009, Hong Kong, China, November 6, 2009},
pages = {67--70},
publisher = {{ACM}},
year = {2009},
url = {https://doi.org/10.1145/1651318.1651332},
doi = {10.1145/1651318.1651332},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cikm/CongTAC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cisis/TamuraTA09,
author = {Takeyuki Tamura and
Kazuhiro Takemoto and
Tatsuya Akutsu},
editor = {Leonard Barolli and
Fatos Xhafa and
Hui{-}Huang Hsu},
title = {Measuring Structural Robustness of Metabolic Networks under a Boolean
Model Using Integer Programming and Feedback Vertex Sets},
booktitle = {2009 International Conference on Complex, Intelligent and Software
Intensive Systems, {CISIS} 2009, Fukuoka, Japan, March 16-19, 2009},
pages = {819--824},
publisher = {{IEEE} Computer Society},
year = {2009},
url = {https://doi.org/10.1109/CISIS.2009.49},
doi = {10.1109/CISIS.2009.49},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cisis/TamuraTA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/complex/NacherOHA09,
author = {Jose C. Nacher and
Tomoshiro Ochiai and
Morihiro Hayashida and
Tatsuya Akutsu},
editor = {Jie Zhou},
title = {A Bipartite Graph Based Model of Protein Domain Networks},
booktitle = {Complex Sciences, First International Conference, Complex 2009, Shanghai,
China, February 23-25, 2009. Revised Papers, Part 1},
series = {Lecture Notes of the Institute for Computer Sciences, Social Informatics
and Telecommunications Engineering},
volume = {4},
pages = {525--535},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02466-5\_50},
doi = {10.1007/978-3-642-02466-5\_50},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/complex/NacherOHA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dis/TakasuFA09,
author = {Atsuhiro Takasu and
Daiji Fukagawa and
Tatsuya Akutsu},
editor = {Jo{\~{a}}o Gama and
V{\'{\i}}tor Santos Costa and
Al{\'{\i}}pio M{\'{a}}rio Jorge and
Pavel Brazdil},
title = {Latent Topic Extraction from Relational Table for Record Matching},
booktitle = {Discovery Science, 12th International Conference, {DS} 2009, Porto,
Portugal, October 3-5, 2009},
series = {Lecture Notes in Computer Science},
volume = {5808},
pages = {449--456},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04747-3\_38},
doi = {10.1007/978-3-642-04747-3\_38},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/dis/TakasuFA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isaac/ImadaONA09,
author = {Tomoki Imada and
Shunsuke Ota and
Hiroshi Nagamochi and
Tatsuya Akutsu},
editor = {Yingfei Dong and
Ding{-}Zhu Du and
Oscar H. Ibarra},
title = {Enumerating Stereoisomers of Tree Structured Molecules Using Dynamic
Programming},
booktitle = {Algorithms and Computation, 20th International Symposium, {ISAAC}
2009, Honolulu, Hawaii, USA, December 16-18, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5878},
pages = {14--23},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-10631-6\_4},
doi = {10.1007/978-3-642-10631-6\_4},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isaac/ImadaONA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spire/FukagawaAT09,
author = {Daiji Fukagawa and
Tatsuya Akutsu and
Atsuhiro Takasu},
editor = {Jussi Karlgren and
Jorma Tarhio and
Heikki Hyyr{\"{o}}},
title = {Constant Factor Approximation of Edit Distance of Bounded Height Unordered
Trees},
booktitle = {String Processing and Information Retrieval, 16th International Symposium,
{SPIRE} 2009, Saariselk{\"{a}}, Finland, August 25-27, 2009,
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5721},
pages = {7--17},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-03784-9\_2},
doi = {10.1007/978-3-642-03784-9\_2},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/spire/FukagawaAT09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SongTTA08,
author = {Jiangning Song and
Hao Tan and
Kazuhiro Takemoto and
Tatsuya Akutsu},
title = {HSEpred: predict half-sphere exposure from protein sequences},
journal = {Bioinform.},
volume = {24},
number = {13},
pages = {1489--1497},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn222},
doi = {10.1093/BIOINFORMATICS/BTN222},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SongTTA08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/TakemotoA08,
author = {Kazuhiro Takemoto and
Tatsuya Akutsu},
title = {Origin of structural difference in metabolic networks with respect
to temperature},
journal = {{BMC} Syst. Biol.},
volume = {2},
pages = {82},
year = {2008},
url = {https://doi.org/10.1186/1752-0509-2-82},
doi = {10.1186/1752-0509-2-82},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/TakemotoA08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ejbsb/HayashidaTAZC08,
author = {Morihiro Hayashida and
Takeyuki Tamura and
Tatsuya Akutsu and
Shuqin Zhang and
Wai{-}Ki Ching},
title = {Algorithms and Complexity Analyses for Control of Singleton Attractors
in Boolean Networks},
journal = {{EURASIP} J. Bioinform. Syst. Biol.},
volume = {2008},
year = {2008},
url = {https://doi.org/10.1155/2008/521407},
doi = {10.1155/2008/521407},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ejbsb/HayashidaTAZC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijbra/HayashidaSAHA08,
author = {Morihiro Hayashida and
Fuyan Sun and
Sachiyo Aburatani and
Katsuhisa Horimoto and
Tatsuya Akutsu},
title = {Integer programming-based approach to allocation of reporter genes
for cell array analysis},
journal = {Int. J. Bioinform. Res. Appl.},
volume = {4},
number = {4},
pages = {385--399},
year = {2008},
url = {https://doi.org/10.1504/IJBRA.2008.021201},
doi = {10.1504/IJBRA.2008.021201},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijbra/HayashidaSAHA08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/imt/HayashidaAN08,
author = {Morihiro Hayashida and
Tatsuya Akutsu and
Hiroshi Nagamochi},
title = {A Clustering Method for Analysis of Sequence Similarity Networks of
Proteins Using Maximal Components of Graphs},
journal = {Inf. Media Technol.},
volume = {3},
number = {2},
pages = {341--350},
year = {2008},
url = {https://doi.org/10.11185/imt.3.341},
doi = {10.11185/IMT.3.341},
timestamp = {Wed, 28 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/imt/HayashidaAN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/AkutsuFT08,
author = {Tatsuya Akutsu and
Daiji Fukagawa and
Atsuhiro Takasu},
title = {Improved approximation of the largest common subtree of two unordered
trees of bounded height},
journal = {Inf. Process. Lett.},
volume = {109},
number = {2},
pages = {165--170},
year = {2008},
url = {https://doi.org/10.1016/j.ipl.2008.09.025},
doi = {10.1016/J.IPL.2008.09.025},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/AkutsuFT08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FujiwaraWZNA08,
author = {Hiroki Fujiwara and
Jiexun Wang and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
title = {Enumerating Treelike Chemical Graphs with Given Path Frequency},
journal = {J. Chem. Inf. Model.},
volume = {48},
number = {7},
pages = {1345--1357},
year = {2008},
url = {https://doi.org/10.1021/ci700385a},
doi = {10.1021/CI700385A},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/FujiwaraWZNA08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ab/AkutsuHT08,
author = {Tatsuya Akutsu and
Morihiro Hayashida and
Takeyuki Tamura},
editor = {Katsuhisa Horimoto and
Georg Regensburger and
Markus Rosenkranz and
Hiroshi Yoshida},
title = {Algorithms for Inference, Analysis and Control of Boolean Networks},
booktitle = {Algebraic Biology, Third International Conference, {AB} 2008, Castle
of Hagenberg, Austria, July 31-August 2, 2008, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5147},
pages = {1--15},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-85101-1\_1},
doi = {10.1007/978-3-540-85101-1\_1},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ab/AkutsuHT08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ab/TamuraA08,
author = {Takeyuki Tamura and
Tatsuya Akutsu},
editor = {Katsuhisa Horimoto and
Georg Regensburger and
Markus Rosenkranz and
Hiroshi Yoshida},
title = {An Improved Algorithm for Detecting a Singleton Attractor in a Boolean
Network Consisting of {AND/OR} Nodes},
booktitle = {Algebraic Biology, Third International Conference, {AB} 2008, Castle
of Hagenberg, Austria, July 31-August 2, 2008, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5147},
pages = {216--229},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-85101-1\_16},
doi = {10.1007/978-3-540-85101-1\_16},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ab/TamuraA08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/BrazmaMA08,
author = {Alvis Brazma and
Satoru Miyano and
Tatsuya Akutsu},
editor = {Alvis Brazma and
Satoru Miyano and
Tatsuya Akutsu},
title = {Preface},
booktitle = {Proceedings of the 6th Asia-Pacific Bioinformatics Conference, {APBC}
2008, 14-17 January 2008, Kyoto, Japan},
series = {Advances in Bioinformatics and Computational Biology},
volume = {6},
publisher = {Imperial College Press},
year = {2008},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2008/apbc08preface.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/apbc/BrazmaMA08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/HayashidaA08,
author = {Morihiro Hayashida and
Tatsuya Akutsu},
editor = {Alvis Brazma and
Satoru Miyano and
Tatsuya Akutsu},
title = {Image Compression-based Approach to Measuring the Similarity of Protein
Structures},
booktitle = {Proceedings of the 6th Asia-Pacific Bioinformatics Conference, {APBC}
2008, 14-17 January 2008, Kyoto, Japan},
series = {Advances in Bioinformatics and Computational Biology},
volume = {6},
pages = {221--230},
publisher = {Imperial College Press},
year = {2008},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2008/apbc055a.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/apbc/HayashidaA08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/prib/KatoAS08,
author = {Yuki Kato and
Tatsuya Akutsu and
Hiroyuki Seki},
editor = {Madhu Chetty and
Alioune Ngom and
Shandar Ahmad},
title = {Prediction of Protein Beta-Sheets: Dynamic Programming versus Grammatical
Approach},
booktitle = {Pattern Recognition in Bioinformatics, Third {IAPR} International
Conference, {PRIB} 2008, Melbourne, Australia, October 15-17, 2008.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5265},
pages = {66--77},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-88436-1\_6},
doi = {10.1007/978-3-540-88436-1\_6},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/prib/KatoAS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/wiley/Akutsu08,
author = {Tatsuya Akutsu},
editor = {Benjamin W. Wah},
title = {Bioinformatics},
booktitle = {Wiley Encyclopedia of Computer Science and Engineering},
publisher = {John Wiley {\&} Sons, Inc.},
year = {2008},
url = {https://doi.org/10.1002/9780470050118.ecse042},
doi = {10.1002/9780470050118.ECSE042},
timestamp = {Tue, 16 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/wiley/Akutsu08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/apbc/2008,
editor = {Alvis Brazma and
Satoru Miyano and
Tatsuya Akutsu},
title = {Proceedings of the 6th Asia-Pacific Bioinformatics Conference, {APBC}
2008, 14-17 January 2008, Kyoto, Japan},
series = {Advances in Bioinformatics and Computational Biology},
volume = {6},
publisher = {Imperial College Press},
year = {2008},
isbn = {978-1-84816-108-5},
timestamp = {Mon, 15 Sep 2008 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/apbc/2008.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChingZNA07,
author = {Wai{-}Ki Ching and
Shuqin Zhang and
Michael K. Ng and
Tatsuya Akutsu},
title = {An approximation method for solving the steady-state probability distribution
of probabilistic Boolean networks},
journal = {Bioinform.},
volume = {23},
number = {12},
pages = {1511--1518},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm142},
doi = {10.1093/BIOINFORMATICS/BTM142},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChingZNA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TakemotoNA07,
author = {Kazuhiro Takemoto and
Jose C. Nacher and
Tatsuya Akutsu},
title = {Correlation between structure and temperature in prokaryotic metabolic
networks},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-303},
doi = {10.1186/1471-2105-8-303},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TakemotoNA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TamuraA07,
author = {Takeyuki Tamura and
Tatsuya Akutsu},
title = {Subcellular location prediction of proteins using support vector machines
with alignment of block sequences utilizing amino acid composition},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-466},
doi = {10.1186/1471-2105-8-466},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TamuraA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/AkutsuBMO07,
author = {Tatsuya Akutsu and
Hideo Bannai and
Satoru Miyano and
Sascha Ott},
title = {On the complexity of deriving position specific score matrices from
positive and negative sequences},
journal = {Discret. Appl. Math.},
volume = {155},
number = {6-7},
pages = {676--685},
year = {2007},
url = {https://doi.org/10.1016/j.dam.2004.10.011},
doi = {10.1016/J.DAM.2004.10.011},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dam/AkutsuBMO07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ejbsb/DoughertyACT07,
author = {Edward R. Dougherty and
Tatsuya Akutsu and
Paul Dan Cristea and
Ahmed H. Tewfik},
title = {Genetic Regulatory Networks},
journal = {{EURASIP} J. Bioinform. Syst. Biol.},
volume = {2007},
year = {2007},
url = {https://doi.org/10.1155/2007/17321},
doi = {10.1155/2007/17321},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ejbsb/DoughertyACT07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ejbsb/ZhangHACN07,
author = {Shuqin Zhang and
Morihiro Hayashida and
Tatsuya Akutsu and
Wai{-}Ki Ching and
Michael Kwok{-}Po Ng},
title = {Algorithms for Finding Small Attractors in Boolean Networks},
journal = {{EURASIP} J. Bioinform. Syst. Biol.},
volume = {2007},
year = {2007},
url = {https://doi.org/10.1155/2007/20180},
doi = {10.1155/2007/20180},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ejbsb/ZhangHACN07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/TamuraA07,
author = {Takeyuki Tamura and
Tatsuya Akutsu},
title = {Approximation Algorithms for Optimal {RNA} Secondary Structures Common
to Multiple Sequences},
journal = {{IEICE} Trans. Fundam. Electron. Commun. Comput. Sci.},
volume = {90-A},
number = {5},
pages = {917--923},
year = {2007},
url = {https://doi.org/10.1093/ietfec/e90-a.5.917},
doi = {10.1093/IETFEC/E90-A.5.917},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/TamuraA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijdmb/ZhangCNA07,
author = {Shuqin Zhang and
Wai{-}Ki Ching and
Michael K. Ng and
Tatsuya Akutsu},
title = {Simulation study in Probabilistic Boolean Network models for genetic
regulatory networks},
journal = {Int. J. Data Min. Bioinform.},
volume = {1},
number = {3},
pages = {217--240},
year = {2007},
url = {https://doi.org/10.1504/IJDMB.2007.011610},
doi = {10.1504/IJDMB.2007.011610},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijdmb/ZhangCNA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/imt/AkutsuAS07,
author = {Tatsuya Akutsu and
Hiroki Arimura and
Shinichi Shimozono},
title = {Hardness Results on Local Multiple Alignment of Biological Sequences},
journal = {Inf. Media Technol.},
volume = {2},
number = {2},
pages = {514--522},
year = {2007},
url = {https://doi.org/10.11185/imt.2.514},
doi = {10.11185/IMT.2.514},
timestamp = {Tue, 27 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/imt/AkutsuAS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/AkutsuF07,
author = {Tatsuya Akutsu and
Daiji Fukagawa},
editor = {David Sankoff and
Lusheng Wang and
Francis Y. L. Chin},
title = {Inferring a Chemical Structure from a Feature Vector Based on Frequency
of Labeled Paths and Small Fragments},
booktitle = {Proceedings of 5th Asia-Pacific Bioinformatics Conference, {APBC}
2007, 15-17 January 2007, Hong Kong, China},
series = {Advances in Bioinformatics and Computational Biology},
volume = {5},
pages = {165--174},
publisher = {Imperial College Press},
year = {2007},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2007/apbc118a.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/apbc/AkutsuF07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/HayashidaAN07,
author = {Morihiro Hayashida and
Tatsuya Akutsu and
Hiroshi Nagamochi},
editor = {David Sankoff and
Lusheng Wang and
Francis Y. L. Chin},
title = {A Novel Clustering Method for Analysis of Biological Networks using
Maximal Components of Graphs},
booktitle = {Proceedings of 5th Asia-Pacific Bioinformatics Conference, {APBC}
2007, 15-17 January 2007, Hong Kong, China},
series = {Advances in Bioinformatics and Computational Biology},
volume = {5},
pages = {257--266},
publisher = {Imperial College Press},
year = {2007},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2007/apbc119a.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/apbc/HayashidaAN07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fct/TamuraA07,
author = {Takeyuki Tamura and
Tatsuya Akutsu},
editor = {Erzs{\'{e}}bet Csuhaj{-}Varj{\'{u}} and
Zolt{\'{a}}n {\'{E}}sik},
title = {An O(1.787\({}^{\mbox{n}}\))-Time Algorithm for Detecting a Singleton
Attractor in a Boolean Network Consisting of {AND/OR} Nodes},
booktitle = {Fundamentals of Computation Theory, 16th International Symposium,
{FCT} 2007, Budapest, Hungary, August 27-30, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4639},
pages = {494--505},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-74240-1\_43},
doi = {10.1007/978-3-540-74240-1\_43},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fct/TamuraA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icdm/TakasuFA07,
author = {Atsuhiro Takasu and
Daiji Fukagawa and
Tatsuya Akutsu},
title = {Statistical Learning Algorithm for Tree Similarity},
booktitle = {Proceedings of the 7th {IEEE} International Conference on Data Mining
{(ICDM} 2007), October 28-31, 2007, Omaha, Nebraska, {USA}},
pages = {667--672},
publisher = {{IEEE} Computer Society},
year = {2007},
url = {https://doi.org/10.1109/ICDM.2007.38},
doi = {10.1109/ICDM.2007.38},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icdm/TakasuFA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/tamc/WangZNA07,
author = {Jiexun Wang and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu},
editor = {Jin{-}yi Cai and
S. Barry Cooper and
Hong Zhu},
title = {An Efficient Algorithm for Generating Colored Outerplanar Graphs},
booktitle = {Theory and Applications of Models of Computation, 4th International
Conference, {TAMC} 2007, Shanghai, China, May 22-25, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4484},
pages = {573--583},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-72504-6\_52},
doi = {10.1007/978-3-540-72504-6\_52},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/tamc/WangZNA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:series/sci/NacherHA07,
author = {Jose C. Nacher and
Morihiro Hayashida and
Tatsuya Akutsu},
editor = {Akira Namatame and
Satoshi Kurihara and
Hideyuki Nakashima},
title = {Topological aspects of protein networks},
booktitle = {Emergent Intelligence of Networked Agents},
series = {Studies in Computational Intelligence},
volume = {56},
pages = {147--158},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-71075-2\_12},
doi = {10.1007/978-3-540-71075-2\_12},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/series/sci/NacherHA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SaigoVA06,
author = {Hiroto Saigo and
Jean{-}Philippe Vert and
Tatsuya Akutsu},
title = {Optimizing amino acid substitution matrices with a local alignment
kernel},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {246},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-246},
doi = {10.1186/1471-2105-7-246},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SaigoVA06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/AkutsuHBTSH06,
author = {Tatsuya Akutsu and
Morihiro Hayashida and
Dukka Bahadur and
Etsuji Tomita and
Jun'ichi Suzuki and
Katsuhisa Horimoto},
title = {Dynamic Programming and Clique Based Approaches for Protein Threading
with Profiles and Constraints},
journal = {{IEICE} Trans. Fundam. Electron. Commun. Comput. Sci.},
volume = {89-A},
number = {5},
pages = {1215--1222},
year = {2006},
url = {https://doi.org/10.1093/ietfec/e89-a.5.1215},
doi = {10.1093/IETFEC/E89-A.5.1215},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/AkutsuHBTSH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijfcs/FukagawaA06,
author = {Daiji Fukagawa and
Tatsuya Akutsu},
title = {Fast Algorithms for Comparison of Similar Unordered Trees},
journal = {Int. J. Found. Comput. Sci.},
volume = {17},
number = {3},
pages = {703--729},
year = {2006},
url = {https://doi.org/10.1142/S0129054106004054},
doi = {10.1142/S0129054106004054},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijfcs/FukagawaA06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijfcs/Akutsu06,
author = {Tatsuya Akutsu},
title = {Algorithms for Point Set Matching with K-differences},
journal = {Int. J. Found. Comput. Sci.},
volume = {17},
number = {4},
pages = {903--918},
year = {2006},
url = {https://doi.org/10.1142/S0129054106004170},
doi = {10.1142/S0129054106004170},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijfcs/Akutsu06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/Akutsu06,
author = {Tatsuya Akutsu},
title = {A relation between edit distance for ordered trees and edit distance
for Euler strings},
journal = {Inf. Process. Lett.},
volume = {100},
number = {3},
pages = {105--109},
year = {2006},
url = {https://doi.org/10.1016/j.ipl.2006.06.002},
doi = {10.1016/J.IPL.2006.06.002},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/Akutsu06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/DukkaTSHA06,
author = {K. C. Dukka Bahadur and
Etsuji Tomita and
Jun'ichi Suzuki and
Katsuhisa Horimoto and
Tatsuya Akutsu},
title = {Protein Threading with Profiles and Distance Constraints Using Clique
Based Algorithms},
journal = {J. Bioinform. Comput. Biol.},
volume = {4},
number = {1},
pages = {19--42},
year = {2006},
url = {https://doi.org/10.1142/S0219720006001680},
doi = {10.1142/S0219720006001680},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/DukkaTSHA06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcsb/NgZCA06,
author = {Michael K. Ng and
Shuqin Zhang and
Wai{-}Ki Ching and
Tatsuya Akutsu},
title = {A Control Model for Markovian Genetic Regulatory Networks},
journal = {Trans. Comp. Sys. Biology},
volume = {5},
pages = {36--48},
year = {2006},
url = {https://doi.org/10.1007/11790105\_4},
doi = {10.1007/11790105\_4},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcsb/NgZCA06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/AkutsuHCN06,
author = {Tatsuya Akutsu and
Morihiro Hayashida and
Wai{-}Ki Ching and
Michael K. Ng},
editor = {Tao Jiang and
Ueng{-}Cheng Yang and
Yi{-}Ping Phoebe Chen and
Limsoon Wong},
title = {On the Complexity of Finding Control Strategies for Boolean Networks},
booktitle = {Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February
2006, Taipei, Taiwan},
pages = {99--108},
publisher = {Imperial College Press, London},
year = {2006},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2006/155.pdf},
timestamp = {Wed, 03 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/apbc/AkutsuHCN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isaac/AkutsuFT06,
author = {Tatsuya Akutsu and
Daiji Fukagawa and
Atsuhiro Takasu},
editor = {Tetsuo Asano},
title = {Approximating Tree Edit Distance Through String Edit Distance},
booktitle = {Algorithms and Computation, 17th International Symposium, {ISAAC}
2006, Kolkata, India, December 18-20, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4288},
pages = {90--99},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11940128\_11},
doi = {10.1007/11940128\_11},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isaac/AkutsuFT06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/NacherSKA06,
author = {Jose C. Nacher and
Jean{-}Marc Schwartz and
Minoru Kanehisa and
Tatsuya Akutsu},
title = {Identification of metabolic units induced by environmental signals},
booktitle = {Proceedings 14th International Conference on Intelligent Systems for
Molecular Biology 2006, Fortaleza, Brazil, August 6-10, 2006},
pages = {375--383},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl202},
doi = {10.1093/BIOINFORMATICS/BTL202},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/NacherSKA06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ItohGAK05,
author = {Masumi Itoh and
Susumu Goto and
Tatsuya Akutsu and
Minoru Kanehisa},
title = {Fast and accurate database homology search using upper bounds of local
alignment scores},
journal = {Bioinform.},
volume = {21},
number = {7},
pages = {912--921},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti076},
doi = {10.1093/BIOINFORMATICS/BTI076},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ItohGAK05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AokiMAK05,
author = {Kiyoko F. Aoki and
Hiroshi Mamitsuka and
Tatsuya Akutsu and
Minoru Kanehisa},
title = {A score matrix to reveal the hidden links in glycans},
journal = {Bioinform.},
volume = {21},
number = {8},
pages = {1457--1463},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti193},
doi = {10.1093/BIOINFORMATICS/BTI193},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AokiMAK05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijns/ChingNFA05,
author = {Wai{-}Ki Ching and
Michael K. Ng and
Eric S. Fung and
Tatsuya Akutsu},
title = {On construction of stochastic genetic networks based on gene expression
sequences},
journal = {Int. J. Neural Syst.},
volume = {15},
number = {4},
pages = {297--310},
year = {2005},
url = {https://doi.org/10.1142/S0129065705000256},
doi = {10.1142/S0129065705000256},
timestamp = {Wed, 03 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijns/ChingNFA05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/FukagawaA05,
author = {Daiji Fukagawa and
Tatsuya Akutsu},
title = {Performance analysis of a greedy algorithm for inferring Boolean functions},
journal = {Inf. Process. Lett.},
volume = {93},
number = {1},
pages = {7--12},
year = {2005},
url = {https://doi.org/10.1016/j.ipl.2004.09.017},
doi = {10.1016/J.IPL.2004.09.017},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/FukagawaA05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/BahadurTSA05,
author = {K. C. Dukka Bahadur and
Etsuji Tomita and
Jun'ichi Suzuki and
Tatsuya Akutsu},
title = {Protein Side-chain Packing Problem: a Maximum Edge-weight Clique Algorithmic
Approach},
journal = {J. Bioinform. Comput. Biol.},
volume = {3},
number = {1},
pages = {103--126},
year = {2005},
url = {https://doi.org/10.1142/S0219720005000904},
doi = {10.1142/S0219720005000904},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/BahadurTSA05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MaheUAPV05,
author = {Pierre Mah{\'{e}} and
Nobuhisa Ueda and
Tatsuya Akutsu and
Jean{-}Luc Perret and
Jean{-}Philippe Vert},
title = {Graph Kernels for Molecular Structure-Activity Relationship Analysis
with Support Vector Machines},
journal = {J. Chem. Inf. Model.},
volume = {45},
number = {4},
pages = {939--951},
year = {2005},
url = {https://doi.org/10.1021/ci050039t},
doi = {10.1021/CI050039T},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/MaheUAPV05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tkde/UedaAYAM05,
author = {Nobuhisa Ueda and
Kiyoko F. Aoki{-}Kinoshita and
Atsuko Yamaguchi and
Tatsuya Akutsu and
Hiroshi Mamitsuka},
title = {A Probabilistic Model for Mining Labeled Ordered Trees: Capturing
Patterns in Carbohydrate Sugar Chains},
journal = {{IEEE} Trans. Knowl. Data Eng.},
volume = {17},
number = {8},
pages = {1051--1064},
year = {2005},
url = {https://doi.org/10.1109/TKDE.2005.117},
doi = {10.1109/TKDE.2005.117},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tkde/UedaAYAM05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/BahadurTSHA05,
author = {Dukka Bahadur and
Etsuji Tomita and
Jun'ichi Suzuki and
Katsuhisa Horimoto and
Tatsuya Akutsu},
editor = {Yi{-}Ping Phoebe Chen and
Limsoon Wong},
title = {Clique-based algorithms for protein threading with profiles and constraints},
booktitle = {Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January
2005, Singapore},
pages = {51--64},
publisher = {Imperial College Press, London},
year = {2005},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2005/camera-ready/146.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/apbc/BahadurTSHA05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/AkutsuF05,
author = {Tatsuya Akutsu and
Daiji Fukagawa},
editor = {Alberto Apostolico and
Maxime Crochemore and
Kunsoo Park},
title = {Inferring a Graph from Path Frequency},
booktitle = {Combinatorial Pattern Matching, 16th Annual Symposium, {CPM} 2005,
Jeju Island, Korea, June 19-22, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3537},
pages = {371--382},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11496656\_32},
doi = {10.1007/11496656\_32},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/AkutsuF05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/grc/ZhangNCA05,
author = {Shuqin Zhang and
Michael K. Ng and
Wai{-}Ki Ching and
Tatsuya Akutsu},
editor = {Xiaohua Hu and
Qing Liu and
Andrzej Skowron and
Tsau Young Lin and
Ronald R. Yager and
Bo Zhang},
title = {A linear control model for gene intervention in a genetic regulatory
network},
booktitle = {2005 {IEEE} International Conference on Granular Computing, Beijing,
China, July 25-27, 2005},
pages = {354--358},
publisher = {{IEEE}},
year = {2005},
url = {https://doi.org/10.1109/GRC.2005.1547303},
doi = {10.1109/GRC.2005.1547303},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/grc/ZhangNCA05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HouraiAA04,
author = {Yuichiro Hourai and
Tatsuya Akutsu and
Yutaka Akiyama},
title = {Optimizing substitution matrices by separating score distributions},
journal = {Bioinform.},
volume = {20},
number = {6},
pages = {863--873},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/btg494},
doi = {10.1093/BIOINFORMATICS/BTG494},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HouraiAA04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SaigoVUA04,
author = {Hiroto Saigo and
Jean{-}Philippe Vert and
Nobuhisa Ueda and
Tatsuya Akutsu},
title = {Protein homology detection using string alignment kernels},
journal = {Bioinform.},
volume = {20},
number = {11},
pages = {1682--1689},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth141},
doi = {10.1093/BIOINFORMATICS/BTH141},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SaigoVUA04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NacherUYKA04,
author = {Jose C. Nacher and
Nobuhisa Ueda and
Takuji Yamada and
Minoru Kanehisa and
Tatsuya Akutsu},
title = {Clustering under the line graph transformation: application to reaction
network},
journal = {{BMC} Bioinform.},
volume = {5},
pages = {207},
year = {2004},
url = {https://doi.org/10.1186/1471-2105-5-207},
doi = {10.1186/1471-2105-5-207},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/NacherUYKA04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Akutsu04,
author = {Tatsuya Akutsu},
title = {Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction
Data},
journal = {J. Comput. Biol.},
volume = {11},
number = {2/3},
pages = {449--462},
year = {2004},
url = {https://doi.org/10.1089/1066527041410337},
doi = {10.1089/1066527041410337},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/Akutsu04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AokiYUAMGK04,
author = {Kiyoko F. Aoki and
Atsuko Yamaguchi and
Nobuhisa Ueda and
Tatsuya Akutsu and
Hiroshi Mamitsuka and
Susumu Goto and
Minoru Kanehisa},
title = {KCaM {(KEGG} Carbohydrate Matcher): a software tool for analyzing
the structures of carbohydrate sugar chains},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Web-Server-Issue},
pages = {267--272},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh473},
doi = {10.1093/NAR/GKH473},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/AokiYUAMGK04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sigmod/AokiUYAKM04,
author = {Kiyoko F. Aoki and
Nobuhisa Ueda and
Atsuko Yamaguchi and
Tatsuya Akutsu and
Minoru Kanehisa and
Hiroshi Mamitsuka},
title = {Managing and Analyzing Carbohydrate Data},
journal = {{SIGMOD} Rec.},
volume = {33},
number = {2},
pages = {33--38},
year = {2004},
url = {https://doi.org/10.1145/1024694.1024700},
doi = {10.1145/1024694.1024700},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/sigmod/AokiUYAKM04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/BahadurATS04,
author = {Dukka Bahadur and
Tatsuya Akutsu and
Etsuji Tomita and
Tomokazu Seki},
editor = {Yi{-}Ping Phoebe Chen},
title = {Protein Side-chain Packing Problem: {A} Maximum Edge-weight Clique
Algorithmic Approach},
booktitle = {Second Asia-Pacific Bioinformatics Conference {(APBC} 2004), January
18-22, 2004, Dunedin, New Zealand},
series = {{CRPIT}},
volume = {29},
pages = {191--200},
publisher = {Australian Computer Society},
year = {2004},
url = {http://crpit.scem.westernsydney.edu.au/abstracts/CRPITV29Dukka.html},
timestamp = {Thu, 25 Jul 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/apbc/BahadurATS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/AkutsuHTSH04,
author = {Tatsuya Akutsu and
Morihiro Hayashida and
Etsuji Tomita and
Jun'ichi Suzuki and
Katsuhisa Horimoto},
title = {Protein Threading with Profiles and Constraints},
booktitle = {4th {IEEE} International Symposium on BioInformatics and BioEngineering
{(BIBE} 2004), 19-21 March 2004, Taichung, Taiwan},
pages = {537--544},
publisher = {{IEEE} Computer Society},
year = {2004},
url = {https://doi.org/10.1109/BIBE.2004.1317389},
doi = {10.1109/BIBE.2004.1317389},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibe/AkutsuHTSH04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cocoon/Akutsu04,
author = {Tatsuya Akutsu},
editor = {Kyung{-}Yong Chwa and
J. Ian Munro},
title = {Algorithms for Point Set Matching with k-Differences},
booktitle = {Computing and Combinatorics, 10th Annual International Conference,
{COCOON} 2004, Jeju Island, Korea, August 17-20, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3106},
pages = {249--258},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-27798-9\_28},
doi = {10.1007/978-3-540-27798-9\_28},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cocoon/Akutsu04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/MaheUAPV04,
author = {Pierre Mah{\'{e}} and
Nobuhisa Ueda and
Tatsuya Akutsu and
Jean{-}Luc Perret and
Jean{-}Philippe Vert},
editor = {Carla E. Brodley},
title = {Extensions of marginalized graph kernels},
booktitle = {Machine Learning, Proceedings of the Twenty-first International Conference
{(ICML} 2004), Banff, Alberta, Canada, July 4-8, 2004},
series = {{ACM} International Conference Proceeding Series},
volume = {69},
publisher = {{ACM}},
year = {2004},
url = {https://doi.org/10.1145/1015330.1015446},
doi = {10.1145/1015330.1015446},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icml/MaheUAPV04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isaac/FukagawaA04,
author = {Daiji Fukagawa and
Tatsuya Akutsu},
editor = {Rudolf Fleischer and
Gerhard Trippen},
title = {Fast Algorithms for Comparison of Similar Unordered Trees},
booktitle = {Algorithms and Computation, 15th International Symposium, {ISAAC}
2004, Hong Kong, China, December 20-22, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3341},
pages = {452--463},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30551-4\_40},
doi = {10.1007/978-3-540-30551-4\_40},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isaac/FukagawaA04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/AokiUYKAM04,
author = {Kiyoko F. Aoki and
Nobuhisa Ueda and
Atsuko Yamaguchi and
Minoru Kanehisa and
Tatsuya Akutsu and
Hiroshi Mamitsuka},
title = {Application of a new probabilistic model for recognizing complex patterns
in glycans},
booktitle = {Proceedings Twelfth International Conference on Intelligent Systems
for Molecular Biology/Third European Conference on Computational Biology
2004, Glasgow, UK, July 31-August 4, 2004},
pages = {6--14},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth916},
doi = {10.1093/BIOINFORMATICS/BTH916},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/AokiUYKAM04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/AkutsuKOF03,
author = {Tatsuya Akutsu and
Kyotetsu Kanaya and
Akira Ohyama and
Asao Fujiyama},
title = {Point matching under non-uniform distortions},
journal = {Discret. Appl. Math.},
volume = {127},
number = {1},
pages = {5--21},
year = {2003},
url = {https://doi.org/10.1016/S0166-218X(02)00282-2},
doi = {10.1016/S0166-218X(02)00282-2},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dam/AkutsuKOF03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AkutsuMK03,
author = {Tatsuya Akutsu and
Satoru Miyano and
Satoru Kuhara},
title = {A simple greedy algorithm for finding functional relations: efficient
implementation and average case analysis},
journal = {Theor. Comput. Sci.},
volume = {292},
number = {2},
pages = {481--495},
year = {2003},
url = {https://doi.org/10.1016/S0304-3975(02)00183-4},
doi = {10.1016/S0304-3975(02)00183-4},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/AkutsuMK03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AkutsuKMM03,
author = {Tatsuya Akutsu and
Satoru Kuhara and
Osamu Maruyama and
Satoru Miyano},
title = {Identification of genetic networks by strategic gene disruptions and
gene overexpressions under a boolean model},
journal = {Theor. Comput. Sci.},
volume = {298},
number = {1},
pages = {235--251},
year = {2003},
url = {https://doi.org/10.1016/S0304-3975(02)00425-5},
doi = {10.1016/S0304-3975(02)00425-5},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/AkutsuKMM03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amining/Akutsu03,
author = {Tatsuya Akutsu},
editor = {Shusaku Tsumoto and
Takahira Yamaguchi and
Masayuki Numao and
Hiroshi Motoda},
title = {Computational and Statistical Methods in Bioinformatics},
booktitle = {Active Mining, Second International Workshop, {AM} 2003, Maebashi,
Japan, October 28, 2003, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {3430},
pages = {11--33},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/11423270\_2},
doi = {10.1007/11423270\_2},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amining/Akutsu03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dis/FukagawaA03,
author = {Daiji Fukagawa and
Tatsuya Akutsu},
editor = {Gunter Grieser and
Yuzuru Tanaka and
Akihiro Yamamoto},
title = {Performance Analysis of a Greedy Algorithm for Inferring Boolean Functions},
booktitle = {Discovery Science, 6th International Conference, {DS} 2003, Sapporo,
Japan, October 17-19,2003, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2843},
pages = {114--127},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/978-3-540-39644-4\_11},
doi = {10.1007/978-3-540-39644-4\_11},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/dis/FukagawaA03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/HayashidaUA03,
author = {Morihiro Hayashida and
Nobuhisa Ueda and
Tatsuya Akutsu},
title = {Inferring strengths of protein-protein interactions from experimental
data using linear programming},
booktitle = {Proceedings of the European Conference on Computational Biology {(ECCB}
2003), September 27-30, 2003, Paris, France},
pages = {58--65},
year = {2003},
timestamp = {Mon, 27 Oct 2003 15:56:17 +0100},
biburl = {https://dblp.org/rec/conf/eccb/HayashidaUA03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/ShinozakiAM03,
author = {Daisuke Shinozaki and
Tatsuya Akutsu and
Osamu Maruyama},
title = {Finding optimal degenerate patterns in {DNA} sequences},
booktitle = {Proceedings of the European Conference on Computational Biology {(ECCB}
2003), September 27-30, 2003, Paris, France},
pages = {206--214},
year = {2003},
timestamp = {Mon, 27 Oct 2003 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eccb/ShinozakiAM03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/Akutsu03,
author = {Tatsuya Akutsu},
editor = {Martin Vingron and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman and
Webb Miller},
title = {Efficient extraction of mapping rules of atoms from enzymatic reaction
data},
booktitle = {Proceedings of the Sventh Annual International Conference on Computational
Biology, {RECOMB} 2003, Berlin, Germany, April 10-13, 2003},
pages = {1--8},
publisher = {{ACM}},
year = {2003},
url = {https://doi.org/10.1145/640075.640076},
doi = {10.1145/640075.640076},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/Akutsu03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cocoon/AkutsuO02,
author = {Tatsuya Akutsu and
Sascha Ott},
editor = {Oscar H. Ibarra and
Louxin Zhang},
title = {Inferring a Union of Halfspaces from Examples},
booktitle = {Computing and Combinatorics, 8th Annual International Conference,
{COCOON} 2002, Singapore, August 15-17, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2387},
pages = {117--126},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45655-4\_14},
doi = {10.1007/3-540-45655-4\_14},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cocoon/AkutsuO02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/AkutsuBMO02,
author = {Tatsuya Akutsu and
Hideo Bannai and
Satoru Miyano and
Sascha Ott},
editor = {Alberto Apostolico and
Masayuki Takeda},
title = {On the Complexity of Deriving Position Specific Score Matrices from
Examples},
booktitle = {Combinatorial Pattern Matching, 13th Annual Symposium, {CPM} 2002,
Fukuoka, Japan, July 3-5, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2373},
pages = {168--177},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45452-7\_15},
doi = {10.1007/3-540-45452-7\_15},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/AkutsuBMO02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AkutsuMK00,
author = {Tatsuya Akutsu and
Satoru Miyano and
Satoru Kuhara},
title = {Inferring qualitative relations in genetic networks and metabolic
pathways},
journal = {Bioinform.},
volume = {16},
number = {8},
pages = {727--734},
year = {2000},
url = {https://doi.org/10.1093/bioinformatics/16.8.727},
doi = {10.1093/BIOINFORMATICS/16.8.727},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AkutsuMK00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/Akutsu00,
author = {Tatsuya Akutsu},
title = {Dynamic programming algorithms for {RNA} secondary structure prediction
with pseudoknots},
journal = {Discret. Appl. Math.},
volume = {104},
number = {1-3},
pages = {45--62},
year = {2000},
url = {https://doi.org/10.1016/S0166-218X(00)00186-4},
doi = {10.1016/S0166-218X(00)00186-4},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dam/Akutsu00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/AkutsuMK00,
author = {Tatsuya Akutsu and
Satoru Miyano and
Satoru Kuhara},
title = {Algorithms for Identifying Boolean Networks and Related Biological
Networks Based on Matrix Multiplication and Fingerprint Function},
journal = {J. Comput. Biol.},
volume = {7},
number = {3-4},
pages = {331--343},
year = {2000},
url = {https://doi.org/10.1089/106652700750050817},
doi = {10.1089/106652700750050817},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/AkutsuMK00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AkutsuH00,
author = {Tatsuya Akutsu and
Magn{\'{u}}s M. Halld{\'{o}}rsson},
title = {On the approximation of largest common subtrees and largest common
point sets},
journal = {Theor. Comput. Sci.},
volume = {233},
number = {1-2},
pages = {33--50},
year = {2000},
url = {https://doi.org/10.1016/S0304-3975(97)00278-8},
doi = {10.1016/S0304-3975(97)00278-8},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/AkutsuH00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dis/AkutsuMK00,
author = {Tatsuya Akutsu and
Satoru Miyano and
Satoru Kuhara},
editor = {Setsuo Arikawa and
Shinichi Morishita},
title = {A Simple Greedy Algorithm for Finding Functional Relations: Efficient
Implementation and Average Case Anaylsis},
booktitle = {Discovery Science, Third International Conference, {DS} 2000, Kyoto,
Japan, December 4-6, 2000, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1967},
pages = {86--98},
publisher = {Springer},
year = {2000},
url = {https://doi.org/10.1007/3-540-44418-1\_8},
doi = {10.1007/3-540-44418-1\_8},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/dis/AkutsuMK00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/AkutsuAS00,
author = {Tatsuya Akutsu and
Hiroki Arimura and
Shinichi Shimozono},
editor = {Ron Shamir and
Satoru Miyano and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {On approximation algorithms for local multiple alignment},
booktitle = {Proceedings of the Fourth Annual International Conference on Computational
Molecular Biology, {RECOMB} 2000, Tokyo, Japan, April 8-11, 2000},
pages = {1--7},
publisher = {{ACM}},
year = {2000},
url = {https://doi.org/10.1145/332306.332311},
doi = {10.1145/332306.332311},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/AkutsuAS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/AkutsuMK00,
author = {Tatsuya Akutsu and
Satoru Miyano and
Satoru Kuhara},
editor = {Ron Shamir and
Satoru Miyano and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {Algorithms for identifying Boolean networks and related biological
networks based on matrix multiplication and fingerprint function},
booktitle = {Proceedings of the Fourth Annual International Conference on Computational
Molecular Biology, {RECOMB} 2000, Tokyo, Japan, April 8-11, 2000},
pages = {8--14},
publisher = {{ACM}},
year = {2000},
url = {https://doi.org/10.1145/332306.332317},
doi = {10.1145/332306.332317},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/AkutsuMK00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jco/Akutsu99,
author = {Tatsuya Akutsu},
title = {Approximation and Exact Algorithms for {RNA} Secondary Structure Prediction
and Recognition of Stochastic Context-free Languages},
journal = {J. Comb. Optim.},
volume = {3},
number = {2-3},
pages = {321--336},
year = {1999},
url = {https://doi.org/10.1023/A:1009898029639},
doi = {10.1023/A:1009898029639},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jco/Akutsu99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AkutsuM99,
author = {Tatsuya Akutsu and
Satoru Miyano},
title = {On the Approximation of Protein Threading},
journal = {Theor. Comput. Sci.},
volume = {210},
number = {2},
pages = {261--275},
year = {1999},
url = {https://doi.org/10.1016/S0304-3975(98)00089-9},
doi = {10.1016/S0304-3975(98)00089-9},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/AkutsuM99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/AkutsuKOF99,
author = {Tatsuya Akutsu and
Kyotetsu Kanaya and
Akira Ohyama and
Asao Fujiyama},
editor = {Maxime Crochemore and
Mike Paterson},
title = {Matching of Spots in 2D Electrophoresis Images. Point Matching Under
Non-uniform Distortions},
booktitle = {Combinatorial Pattern Matching, 10th Annual Symposium, {CPM} 99, Warwick
University, UK, July 22-24, 1999, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1645},
pages = {212--222},
publisher = {Springer},
year = {1999},
url = {https://doi.org/10.1007/3-540-48452-3\_16},
doi = {10.1007/3-540-48452-3\_16},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/AkutsuKOF99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/AkutsuMK99,
author = {Tatsuya Akutsu and
Satoru Miyano and
Satoru Kuhara},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {Identification of Genetic Networks from a Small Number of Gene Expression
Patterns Under the Boolean Network Model},
booktitle = {Proceedings of the 4th Pacific Symposium on Biocomputing, {PSB} 1999,
The Orchid at Mauna Lani, Big Island of Hawaii, USA, January 4-9,
1999},
pages = {17--28},
year = {1999},
url = {http://psb.stanford.edu/psb-online/proceedings/psb99/Akutsu.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/AkutsuMK99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/comgeo/Akutsu98,
author = {Tatsuya Akutsu},
title = {On determining the congruence of point sets in d dimensions},
journal = {Comput. Geom.},
volume = {9},
number = {4},
pages = {247--256},
year = {1998},
url = {https://doi.org/10.1016/S0925-7721(97)00010-2},
doi = {10.1016/S0925-7721(97)00010-2},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/comgeo/Akutsu98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dcg/AkutsuTT98,
author = {Tatsuya Akutsu and
Hisao Tamaki and
Takeshi Tokuyama},
title = {Distribution of Distances and Triangles in a Point Set and Algorithms
for Computing the Largest Common Point Sets},
journal = {Discret. Comput. Geom.},
volume = {20},
number = {3},
pages = {307--331},
year = {1998},
url = {https://doi.org/10.1007/PL00009388},
doi = {10.1007/PL00009388},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dcg/AkutsuTT98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icalp/AkutsuY98,
author = {Tatsuya Akutsu and
Mutsunori Yagiura},
editor = {Kim Guldstrand Larsen and
Sven Skyum and
Glynn Winskel},
title = {On the Complexity of Deriving Score Functions from Examples for Problems
in Molecular Biology},
booktitle = {Automata, Languages and Programming, 25th International Colloquium,
ICALP'98, Aalborg, Denmark, July 13-17, 1998, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1443},
pages = {832--843},
publisher = {Springer},
year = {1998},
url = {https://doi.org/10.1007/BFb0055106},
doi = {10.1007/BFB0055106},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icalp/AkutsuY98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isaac/Akutsu98,
author = {Tatsuya Akutsu},
editor = {Kyung{-}Yong Chwa and
Oscar H. Ibarra},
title = {Approximation and Exact Algorithms for {RNA} Secondary Structure Prediction
and Recognition of Stochastic Context-Free Languages},
booktitle = {Algorithms and Computation, 9th International Symposium, {ISAAC} '98,
Taejon, Korea, December 14-16, 1998, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1533},
pages = {337--346},
publisher = {Springer},
year = {1998},
url = {https://doi.org/10.1007/3-540-49381-6\_36},
doi = {10.1007/3-540-49381-6\_36},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isaac/Akutsu98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/soda/AkutsuKMM98,
author = {Tatsuya Akutsu and
Satoru Kuhara and
Osamu Maruyama and
Satoru Miyano},
editor = {Howard J. Karloff},
title = {Identification of Gene Regulatory Networks by Strategic Gene Disruptions
and Gene Overexpressions},
booktitle = {Proceedings of the Ninth Annual {ACM-SIAM} Symposium on Discrete Algorithms,
25-27 January 1998, San Francisco, California, {USA}},
pages = {695--702},
publisher = {{ACM/SIAM}},
year = {1998},
url = {http://dl.acm.org/citation.cfm?id=314613.315050},
timestamp = {Thu, 05 Jul 2018 07:29:49 +0200},
biburl = {https://dblp.org/rec/conf/soda/AkutsuKMM98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AkutsuOI97,
author = {Tatsuya Akutsu and
Kentaro Onizuka and
Masato Ishikawa},
title = {Rapid protein fragment search using hash functions based on the Fourier
transform},
journal = {Comput. Appl. Biosci.},
volume = {13},
number = {4},
pages = {357--364},
year = {1997},
url = {https://doi.org/10.1093/bioinformatics/13.4.357},
doi = {10.1093/BIOINFORMATICS/13.4.357},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AkutsuOI97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/compgeom/AkutsuTT97,
author = {Tatsuya Akutsu and
Hisao Tamaki and
Takeshi Tokuyama},
editor = {Jean{-}Daniel Boissonnat},
title = {Distribution of Distances and Triangles in a Point Set and Algorithms
for Computing the Largest Common Point Sets},
booktitle = {Proceedings of the Thirteenth Annual Symposium on Computational Geometry,
Nice, France, June 4-6, 1997},
pages = {314--323},
publisher = {{ACM}},
year = {1997},
url = {https://doi.org/10.1145/262839.262989},
doi = {10.1145/262839.262989},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/compgeom/AkutsuTT97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/AkutsuM97,
author = {Tatsuya Akutsu and
Satoru Miyano},
editor = {Michael S. Waterman},
title = {On the approximation of protein threading},
booktitle = {Proceedings of the First Annual International Conference on Research
in Computational Molecular Biology, {RECOMB} 1997, Santa Fe, NM, USA,
January 20-23, 1997},
pages = {3--8},
publisher = {{ACM}},
year = {1997},
url = {https://doi.org/10.1145/267521.267523},
doi = {10.1145/267521.267523},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/AkutsuM97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cocoon/AkutsuB96,
author = {Tatsuya Akutsu and
Feng Bao},
editor = {Jin{-}yi Cai and
C. K. Wong},
title = {Approximating Minimum Keys and Optimal Substructure Screens},
booktitle = {Computing and Combinatorics, Second Annual International Conference,
{COCOON} '96, Hong Kong, June 17-19, 1996, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1090},
pages = {290--299},
publisher = {Springer},
year = {1996},
url = {https://doi.org/10.1007/3-540-61332-3\_163},
doi = {10.1007/3-540-61332-3\_163},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cocoon/AkutsuB96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ieaaie/TakasuAA96,
author = {Atsuhiro Takasu and
Tatsuya Akutsu and
Moonis Ali},
editor = {Takushi Tanaka and
Setsuo Ohsuga and
Moonis Ali},
title = {Sampling Effectiveness in Discovering Functional Relationships in
Databases},
booktitle = {Industrial and Engineering Applications of Artificial Intelligence
and Expert Systems, Proceedings of the Ninth International Conference,
Fukuoka, Japan, June 4-7, 1996},
pages = {455--460},
publisher = {Gordon and Breach Science Publishers},
year = {1996},
timestamp = {Fri, 03 Jul 2009 15:24:06 +0200},
biburl = {https://dblp.org/rec/conf/ieaaie/TakasuAA96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/Akutsu95,
author = {Tatsuya Akutsu},
title = {A Parallel Algorithm for Determining the Congruence of Point Sets
in Three-Dimensions},
journal = {{IEICE} Trans. Inf. Syst.},
volume = {78-D},
number = {4},
pages = {321--325},
year = {1995},
url = {http://search.ieice.org/bin/summary.php?id=e78-d\_4\_321},
timestamp = {Sat, 11 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/Akutsu95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/Akutsu95,
author = {Tatsuya Akutsu},
title = {Approximate String Matching with don't Care Characters},
journal = {Inf. Process. Lett.},
volume = {55},
number = {5},
pages = {235--239},
year = {1995},
url = {https://doi.org/10.1016/0020-0190(95)00111-O},
doi = {10.1016/0020-0190(95)00111-O},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/Akutsu95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hicss/AkutsuOI95,
author = {Tatsuya Akutsu and
Kentaro Onizuka and
Masato Ishikawa},
title = {New hashing techniques and their application to a protein structure
database system},
booktitle = {28th Annual Hawaii International Conference on System Sciences (HICSS-28),
January 3-6, 1995, Kihei, Maui, Hawaii, {USA}},
pages = {197--206},
publisher = {{IEEE} Computer Society},
year = {1995},
url = {https://doi.org/10.1109/HICSS.1995.375337},
doi = {10.1109/HICSS.1995.375337},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/hicss/AkutsuOI95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ngc/AkutsuT94,
author = {Tatsuya Akutsu and
Atsuhiro Takasu},
title = {On {PAC} Learnability of Functional Depencies},
journal = {New Gener. Comput.},
volume = {12},
number = {4},
pages = {359--374},
year = {1994},
url = {https://doi.org/10.1007/BF03037352},
doi = {10.1007/BF03037352},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ngc/AkutsuT94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/Akutsu94,
author = {Tatsuya Akutsu},
editor = {Maxime Crochemore and
Dan Gusfield},
title = {Approximate String Matching with Don't Care Characters},
booktitle = {Combinatorial Pattern Matching, 5th Annual Symposium, {CPM} 94, Asilomar,
California, USA, June 5-8, 1994, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {807},
pages = {240--249},
publisher = {Springer},
year = {1994},
url = {https://doi.org/10.1007/3-540-58094-8\_21},
doi = {10.1007/3-540-58094-8\_21},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/Akutsu94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hicss/Akutsu94,
author = {Tatsuya Akutsu},
title = {Efficient and Robust Three-Dimensional Pattern Matching Algorithms
Using Hashing and Dynamic Programming Techniques},
booktitle = {27th Annual Hawaii International Conference on System Sciences (HICSS-27),
January 4-7, 1994, Maui, Hawaii, {USA}},
pages = {225--234},
publisher = {{IEEE} Computer Society},
year = {1994},
timestamp = {Mon, 04 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/hicss/Akutsu94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isaac/Akutsu94,
author = {Tatsuya Akutsu},
editor = {Ding{-}Zhu Du and
Xiang{-}Sun Zhang},
title = {On Determining the Congruity of Point Sets in Higher Dimensions},
booktitle = {Algorithms and Computation, 5th International Symposium, {ISAAC} '94,
Beijing, P. R. China, August 25-27, 1994, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {834},
pages = {38--46},
publisher = {Springer},
year = {1994},
url = {https://doi.org/10.1007/3-540-58325-4\_164},
doi = {10.1007/3-540-58325-4\_164},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isaac/Akutsu94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isaac/AkutsuH94,
author = {Tatsuya Akutsu and
Magn{\'{u}}s M. Halld{\'{o}}rsson},
editor = {Ding{-}Zhu Du and
Xiang{-}Sun Zhang},
title = {On the Approximation of Largest Common Subtrees and Largest Common
Point Sets},
booktitle = {Algorithms and Computation, 5th International Symposium, {ISAAC} '94,
Beijing, P. R. China, August 25-27, 1994, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {834},
pages = {405--413},
publisher = {Springer},
year = {1994},
url = {https://doi.org/10.1007/3-540-58325-4\_205},
doi = {10.1007/3-540-58325-4\_205},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isaac/AkutsuH94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/kbs/SuzukiAO93,
author = {Einoshin Suzuki and
Tatsuya Akutsu and
Setsuo Ohsuga},
title = {Knowledge-based system for computer-aided drug design},
journal = {Knowl. Based Syst.},
volume = {6},
number = {2},
pages = {114--126},
year = {1993},
url = {https://doi.org/10.1016/0950-7051(93)90026-P},
doi = {10.1016/0950-7051(93)90026-P},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/kbs/SuzukiAO93.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/Akutsu93,
author = {Tatsuya Akutsu},
editor = {Alberto Apostolico and
Maxime Crochemore and
Zvi Galil and
Udi Manber},
title = {A Linear Time Pattern Matching Algorithm Between a String and a Tree},
booktitle = {Combinatorial Pattern Matching, 4th Annual Symposium, {CPM} 93, Padova,
Italy, June 2-4, 1993, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {684},
pages = {1--10},
publisher = {Springer},
year = {1993},
url = {https://doi.org/10.1007/BFb0029792},
doi = {10.1007/BFB0029792},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/Akutsu93.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alt/AkutsuT92,
author = {Tatsuya Akutsu and
Atsuhiro Takasu},
editor = {Shuji Doshita and
Koichi Furukawa and
Klaus P. Jantke and
Toyoaki Nishida},
title = {On {PAC} Learnability of Functional Dependencies},
booktitle = {Algorithmic Learning Theory, Third Workshop, {ALT} '92, Tokyo, Japan,
October 20-22, 1992, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {743},
pages = {229--239},
publisher = {Springer},
year = {1992},
url = {https://doi.org/10.1007/3-540-57369-0\_42},
doi = {10.1007/3-540-57369-0\_42},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/alt/AkutsuT92.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isaac/Akutsu92,
author = {Tatsuya Akutsu},
editor = {Toshihide Ibaraki and
Yasuyoshi Inagaki and
Kazuo Iwama and
Takao Nishizeki and
Masafumi Yamashita},
title = {Algorithms for Determining the Geometrical Congruity in Two and Three
Dimensions},
booktitle = {Algorithms and Computation, Third International Symposium, {ISAAC}
'92, Nagoya, Japan, December 16-18, 1992, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {650},
pages = {279--288},
publisher = {Springer},
year = {1992},
url = {https://doi.org/10.1007/3-540-56279-6\_81},
doi = {10.1007/3-540-56279-6\_81},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isaac/Akutsu92.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/Akutsu91,
author = {Tatsuya Akutsu},
title = {A new method of computer representation of stereochemistry. Transforming
a stereochemical structure into a graph},
journal = {J. Chem. Inf. Comput. Sci.},
volume = {31},
number = {3},
pages = {414--417},
year = {1991},
url = {https://doi.org/10.1021/ci00003a008},
doi = {10.1021/CI00003A008},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/Akutsu91.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/kbs/AkutsuSO91,
author = {Tatsuya Akutsu and
Einoshin Suzuki and
Setsuo Ohsuga},
title = {Logic-based approach to expert systems in chemistry},
journal = {Knowl. Based Syst.},
volume = {4},
number = {2},
pages = {103--116},
year = {1991},
url = {https://doi.org/10.1016/0950-7051(91)90014-S},
doi = {10.1016/0950-7051(91)90014-S},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/kbs/AkutsuSO91.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iros/AkutsuYSE91,
author = {Tatsuya Akutsu and
Satoshi Yaoi and
Kazunari Sato and
Susumu Enomoto},
title = {Development and comparison of search algorithms for robot motion planning
in the configuration space},
booktitle = {Proceedings of the {IEEE/RSJ} International Conference on Intelligent
Robots and Systems, {IROS} 1991, Osaka, Japan, November 3-5, 1991},
pages = {429--434},
publisher = {{IEEE}},
year = {1991},
url = {https://doi.org/10.1109/IROS.1991.174506},
doi = {10.1109/IROS.1991.174506},
timestamp = {Wed, 16 Oct 2019 14:14:51 +0200},
biburl = {https://dblp.org/rec/conf/iros/AkutsuYSE91.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fgcs/AkutsuO88,
author = {Tatsuya Akutsu and
Setsuo Ohsuga},
title = {{CHEMILOG} - {A} Logic Programming Language/System for Chemical Information
Processing},
booktitle = {Proceedings of the International Conference on Fifth Generation Computer
Systems, {FGCS} 1988, Tokyo, Japan, November 28-December 2, 1988},
pages = {1176--1183},
publisher = {{OHMSHA} Ltd. Tokyo and Springer-Verlag},
year = {1988},
timestamp = {Mon, 05 Aug 2019 17:00:40 +0200},
biburl = {https://dblp.org/rec/conf/fgcs/AkutsuO88.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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