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2020 – today
- 2020
[j163]Jianshen Zhu, Chenxi Wang, Aleksandar Shurbevski
, Hiroshi Nagamochi, Tatsuya Akutsu:
A Novel Method for Inference of Chemical Compounds of Cycle Index Two with Desired Properties Based on Artificial Neural Networks and Integer Programming. Algorithms 13(5): 124 (2020)- [j162]Zhen Chen, Pei Zhao, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Yan Zhu, David R. Powell, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Alexander Ian Smith, Roger J. Daly, Jian Li, Jiangning Song:
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. Briefings Bioinform. 21(3): 1047-1057 (2020) - [j161]Shutao Mei, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Kailin Giam, Nathan P. Croft, Tatsuya Akutsu, Alexander Ian Smith, Jian Li, Jamie Rossjohn, Anthony W. Purcell, Jiangning Song:
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. Briefings Bioinform. 21(4): 1119-1135 (2020) - [j160]Weifeng Guo, Shaowu Zhang, Tao Zeng, Tatsuya Akutsu, Luonan Chen:
Network control principles for identifying personalized driver genes in cancer. Briefings Bioinform. 21(5): 1641-1662 (2020) - [j159]Zhen Chen, Pei Zhao, Fuyi Li, Yanan Wang, Alexander Ian Smith, Geoffrey I. Webb, Tatsuya Akutsu, Abdelkader Baggag, Halima Bensmail, Jiangning Song:
Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences. Briefings Bioinform. 21(5): 1676-1696 (2020) - [j158]Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Alexander Ian Smith, Zongyuan Ge, Jiawei Wang, Trevor Lithgow, Jiangning Song:
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. Bioinform. 36(3): 704-712 (2020) - [j157]Fuyi Li, Jinxiang Chen, André Leier, Tatiana T. Marquez-Lago, Quanzhong Liu, Yanze Wang, Jerico Nico De Leon Revote, Alexander Ian Smith, Tatsuya Akutsu, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song:
DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites. Bioinform. 36(4): 1057-1065 (2020) - [j156]Fuyi Li, André Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, Alexander Ian Smith, Tatiana T. Marquez-Lago, Jian Li, Jiangning Song:
Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information. Genom. Proteom. Bioinform. 18(1): 52-64 (2020) - [j155]Tatsuya Akutsu, Avraham A. Melkman, Takeyuki Tamura:
Improved Hardness of Maximum Common Subgraph Problems on Labeled Graphs of Bounded Treewidth and Bounded Degree. Int. J. Found. Comput. Sci. 31(2): 253-273 (2020) - [j154]Pengyu Liu, Avraham A. Melkman, Tatsuya Akutsu:
Extracting boolean and probabilistic rules from trained neural networks. Neural Networks 126: 300-311 (2020) - [c86]Naveed Ahmed Azam, Rachaya Chiewvanichakorn, Fan Zhang, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu:
A Novel Method for the Inverse QSAR/QSPR based on Artificial Neural Networks and Mixed Integer Linear Programming with Guaranteed Admissibility. BIOINFORMATICS 2020: 101-108 - [c85]Fan Zhang, Jianshen Zhu, Rachaya Chiewvanichakorn, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu:
A New Integer Linear Programming Formulation to the Inverse QSAR/QSPR for Acyclic Chemical Compounds Using Skeleton Trees. IEA/AIE 2020: 433-444 - [i8]Yuui Tamura, Yuhei Nishiyama, Chenxi Wang, Yanming Sun, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu:
Enumerating Chemical Graphs with Mono-block 2-Augmented Tree Structure from Given Upper and Lower Bounds on Path Frequencies. CoRR abs/2004.06367 (2020) - [i7]Kyousuke Yamashita, Ryuji Masui, Xiang Zhou, Chenxi Wang, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu:
Enumerating Chemical Graphs with Two Disjoint Cycles Satisfying Given Path Frequency Specifications. CoRR abs/2004.08381 (2020) - [i6]Avraham A. Melkman, Sini Guo, Wai-Ki Ching, Pengyu Liu, Tatsuya Akutsu:
On the Compressive Power of Boolean Threshold Autoencoders. CoRR abs/2004.09735 (2020) - [i5]Naveed Ahmed Azam, Jianshen Zhu, Yanming Sun, Yu Shi, Aleksandar Shurbevski, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu:
A Novel Method for Inference of Acyclic Chemical Compounds with Bounded Branch-height Based on Artificial Neural Networks and Integer Programming. CoRR abs/2009.09646 (2020) - [i4]Xiaoqing Cheng, Wai-Ki Ching, Sini Guo, Tatsuya Akutsu:
Discrimination of attractors with noisy nodes in Boolean networks. CoRR abs/2009.13198 (2020) - [i3]Tatsuya Akutsu, Hiroshi Nagamochi:
A novel method for inference of chemical compounds with prescribed topological substructures based on integer programming. CoRR abs/2010.09203 (2020)
2010 – 2019
- 2019
- [j153]Jiangning Song, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Neil D. Rawlings, Geoffrey I. Webb, Kuo-Chen Chou:
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites. Briefings Bioinform. 20(2): 638-658 (2019) - [j152]Jiawei Wang, Bingjiao Yang, Yi An, Tatiana T. Marquez-Lago, André Leier, Jonathan Wilksch, Qingyang Hong, Yang Zhang, Morihiro Hayashida, Tatsuya Akutsu, Geoffrey I. Webb, Richard A. Strugnell, Jiangning Song, Trevor Lithgow:
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. Briefings Bioinform. 20(3): 931-951 (2019) - [j151]Yu Bao, Simone Marini, Takeyuki Tamura, Mayumi Kamada, Shingo Maegawa, Hiroshi Hosokawa, Jiangning Song, Tatsuya Akutsu:
Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features. Briefings Bioinform. 20(5): 1669-1684 (2019) - [j150]Fuyi Li, Yanan Wang, Chen Li, Tatiana T. Marquez-Lago, André Leier, Neil D. Rawlings, Gholamreza Haffari, Jerico Nico De Leon Revote, Tatsuya Akutsu, Kuo-Chen Chou, Anthony W. Purcell, Robert N. Pike, Geoffrey I. Webb, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, James C. Whisstock, Jiangning Song:
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. Briefings Bioinform. 20(6): 2150-2166 (2019) - [j149]Yanju Zhang, Ruopeng Xie, Jiawei Wang, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Jiangning Song:
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework. Briefings Bioinform. 20(6): 2185-2199 (2019) - [j148]Zhen Chen, Xuhan Liu, Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Geoffrey I. Webb, Dakang Xu, Alexander Ian Smith, Lei Li, Kuo-Chen Chou, Jiangning Song:
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. Briefings Bioinform. 20(6): 2267-2290 (2019) - [j147]Simone Marini, Francesca Vitali, Sara Rampazzi, Andrea Demartini, Tatsuya Akutsu:
Protease target prediction via matrix factorization. Bioinform. 35(6): 923-929 (2019) - [j146]Jiawei Wang, Jiahui Li, Bingjiao Yang, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Morihiro Hayashida, Tatsuya Akutsu, Yanju Zhang, Kuo-Chen Chou, Joel Selkrig, Tieli Zhou, Jiangning Song, Trevor Lithgow:
Bastion3: a two-layer ensemble predictor of type III secreted effectors. Bioinform. 35(12): 2017-2028 (2019) - [j145]Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Jiangning Song, Tatsuya Akutsu:
Deep learning with evolutionary and genomic profiles for identifying cancer subtypes. J. Bioinform. Comput. Biol. 17(3): 1940005 (2019) - [j144]Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher:
Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles. J. Bioinform. Comput. Biol. 17(3): 1940007 (2019) - [j143]Hitoshi Koyano, Morihiro Hayashida, Tatsuya Akutsu:
Optimal string clustering based on a Laplace-like mixture and EM algorithm on a set of strings. J. Comput. Syst. Sci. 106: 94-128 (2019) - [j142]Yuhei Nishiyama, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu:
Resource Cut, a New Bounding Procedure to Algorithms for Enumerating Tree-Like Chemical Graphs. IEEE ACM Trans. Comput. Biol. Bioinform. 16(1): 77-90 (2019) - [j141]Tatsuya Akutsu, Avraham A. Melkman:
Identification of the Structure of a Probabilistic Boolean Network From Samples Including Frequencies of Outcomes. IEEE Trans. Neural Networks Learn. Syst. 30(8): 2383-2396 (2019) - 2018
- [j140]Jiangning Song, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Gholamreza Haffari, Kuo-Chen Chou, Geoffrey I. Webb, Robert N. Pike:
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy. Bioinform. 34(4): 684-687 (2018) - [j139]Jiawei Wang, Bingjiao Yang, André Leier, Tatiana T. Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Yanju Zhang, Tatsuya Akutsu, Kuo-Chen Chou, Richard A. Strugnell, Jiangning Song, Trevor Lithgow:
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. Bioinform. 34(15): 2546-2555 (2018) - [j138]Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Anthony W. Purcell, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, Jiangning Song, Kuo-Chen Chou:
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome. Bioinform. 34(24): 4223-4231 (2018) - [j137]Peiying Ruan, Morihiro Hayashida, Tatsuya Akutsu, Jean-Philippe Vert:
Improving prediction of heterodimeric protein complexes using combination with pairwise kernel. BMC Bioinform. 19-S(1): 73-84 (2018) - [j136]Takuya Mori, Hayliang Ngouv, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher:
ncRNA-disease association prediction based on sequence information and tripartite network. BMC Syst. Biol. 12(1): 41-51 (2018) - [j135]Yu Bao, Morihiro Hayashida, Pengyu Liu, Masayuki Ishitsuka, Jose C. Nacher, Tatsuya Akutsu:
Analysis of Critical and Redundant Vertices in Controlling Directed Complex Networks Using Feedback Vertex Sets. J. Comput. Biol. 25(10): 1071-1090 (2018) - [j134]Jinghui Li, Hiroshi Nagamochi, Tatsuya Akutsu:
Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs. IEEE ACM Trans. Comput. Biol. Bioinform. 15(2): 633-646 (2018) - [j133]Takeyuki Tamura, Wei Lu, Jiangning Song, Tatsuya Akutsu:
Computing Minimum Reaction Modifications in a Boolean Metabolic Network. IEEE ACM Trans. Comput. Biol. Bioinform. 15(6): 1853-1862 (2018) - [j132]Avraham A. Melkman, Xiaoqing Cheng, Wai-Ki Ching, Tatsuya Akutsu:
Identifying a Probabilistic Boolean Threshold Network From Samples. IEEE Trans. Neural Networks Learn. Syst. 29(4): 869-881 (2018) - [c84]Tatsuya Akutsu:
Algorithms for Analysis and Control of Boolean Networks. AlCoB 2018: 3-7 - [c83]Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Tatsuya Akutsu:
Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes. BIBE 2018: 147-150 - [c82]Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher:
Convolutional Neural Network Approach to Lung Cancer Classification Integrating Protein Interaction Network and Gene Expression Profiles. BIBE 2018: 151-154 - [c81]Morihiro Hayashida, Hitoshi Koyano, Tatsuya Akutsu:
Grammar-based Compression for Directed and Undirected Generalized Series-parallel Graphs using Integer Linear Programming. BIOINFORMATICS 2018: 105-111 - [c80]Tatsuya Akutsu, Colin de la Higuera, Takeyuki Tamura:
A Simple Linear-Time Algorithm for Computing the Centroid and Canonical Form of a Plane Graph and Its Applications. CPM 2018: 10:1-10:12 - [c79]Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura:
New and Improved Algorithms for Unordered Tree Inclusion. ISAAC 2018: 27:1-27:12 - 2017
- [j131]Xiaoqing Cheng, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu:
Discrimination of singleton and periodic attractors in Boolean networks. Autom. 84: 205-213 (2017) - [j130]Yuki Kato, Tomoya Mori, Kengo Sato, Shingo Maegawa, Hiroshi Hosokawa, Tatsuya Akutsu:
An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data. Bioinform. 33(2): 202-209 (2017) - [j129]Tatsuya Akutsu:
Selected Papers from the 16th International Conference on Bioinformatics (InCoB 2017). J. Bioinform. Comput. Biol. 15(5): 1-2 (2017) - [j128]Tatsuya Akutsu, Jesper Jansson, Atsuhiro Takasu, Takeyuki Tamura:
On the parameterized complexity of associative and commutative unification. Theor. Comput. Sci. 660: 57-74 (2017) - [i2]Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura:
New Algorithms for Unordered Tree Inclusion. CoRR abs/1712.05517 (2017) - 2016
- [j127]Wenpin Hou, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu:
Finding and Analyzing the Minimum Set of Driver Nodes in control of Boolean Networks. Adv. Complex Syst. 19(3): 1-32 (2016) - [j126]Chen Li, Catherine Ching Han Chang, Jeremy Nagel, Benjamin T. Porebski, Morihiro Hayashida, Tatsuya Akutsu, Jiangning Song, Ashley M. Buckle:
Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. Briefings Bioinform. 17(2): 270-282 (2016) - [j125]Jira Jindalertudomdee, Morihiro Hayashida, Yang Zhao, Tatsuya Akutsu:
Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order. BMC Bioinform. 17: 113 (2016) - [j124]Yu Bao, Morihiro Hayashida, Tatsuya Akutsu:
LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length. BMC Bioinform. 17: 487:1-487:11 (2016) - [j123]Takanori Hasegawa, Atsushi Niida, Tomoya Mori, Teppei Shimamura, Rui Yamaguchi, Satoru Miyano, Tatsuya Akutsu, Seiya Imoto:
A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models. Comput. Stat. Data Anal. 94: 63-74 (2016) - [j122]Jira Jindalertudomdee, Morihiro Hayashida, Tatsuya Akutsu:
Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach. J. Comput. Biol. 23(8): 625-640 (2016) - [j121]Xiaoqing Cheng, Tomoya Mori, Yushan Qiu, Wai-Ki Ching, Tatsuya Akutsu:
Exact Identification of the Structure of a Probabilistic Boolean Network from Samples. IEEE ACM Trans. Comput. Biol. Bioinform. 13(6): 1107-1116 (2016) - [c78]Jira Jindalertudomdee, Morihiro Hayashida, Jiangning Song, Tatsuya Akutsu:
Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network. BIBE 2016: 7-12 - [c77]Takeyuki Tamura, Tatsuya Akutsu, Chun-Yu Lin, Jinn-Moon Yang:
Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks. BIBE 2016: 57-63 - [c76]Fei He, Akiyoshi Hanai, Hiroshi Nagamochi, Tatsuya Akutsu:
Enumerating Naphthalene Isomers of Tree-like Chemical Graphs. BIOINFORMATICS 2016: 258-265 - [c75]Tomoya Mori, Atsuhiro Takasu, Jesper Jansson, Jaewook Hwang, Takeyuki Tamura, Tatsuya Akutsu:
Similar subtree search using extended tree inclusion. ICDE 2016: 1558-1559 - 2015
- [j120]Yang Zhao, Morihiro Hayashida, Yue Cao, Jaewook Hwang, Tatsuya Akutsu:
Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs. BMC Bioinform. 16: 128:1-128:13 (2015) - [j119]Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Teppei Shimamura, Satoru Miyano, Seiya Imoto, Tatsuya Akutsu:
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. BMC Syst. Biol. 9: 14 (2015) - [j118]Tomoya Mori, Max Flöttmann, Marcus Krantz, Tatsuya Akutsu, Edda Klipp:
Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks. BMC Syst. Biol. 9: 45 (2015) - [j117]Chia-Jung Chang, Takeyuki Tamura, Kun-Mao Chao, Tatsuya Akutsu:
A Fixed-Parameter Algorithm for Detecting a Singleton Attractor in an AND/OR Boolean Network with Bounded Treewidth. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 98-A(1): 384-390 (2015) - [j116]Wei Lu, Takeyuki Tamura, Jiangning Song, Tatsuya Akutsu:
Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model. J. Comput. Biol. 22(2): 85-110 (2015) - [j115]Xiao Cong, Tatsuya Akutsu:
Matrix Network: A New Data Structure for Efficient Enumeration of Microstates of a Genetic Regulatory Network. J. Inf. Process. 23(6): 804-813 (2015) - [j114]Tatsuya Akutsu, Takeyuki Tamura, Avraham A. Melkman, Atsuhiro Takasu:
On the complexity of finding a largest common subtree of bounded degree. Theor. Comput. Sci. 590: 2-16 (2015) - [j113]Tomoya Mori, Atsuhiro Takasu, Jesper Jansson, Jaewook Hwang, Takeyuki Tamura, Tatsuya Akutsu:
Similar Subtree Search Using Extended Tree Inclusion. IEEE Trans. Knowl. Data Eng. 27(12): 3360-3373 (2015) - [c74]Yushan Qiu, Xiaoqing Cheng, Wai-Ki Ching, Hao Jiang, Tatsuya Akutsu:
On observability of attractors in Boolean Networks. BIBM 2015: 263-266 - 2014
- [j112]Natsu Nakajima, Tatsuya Akutsu:
Network Completion for Static Gene Expression Data. Adv. Bioinformatics 2014: 382452:1-382452:9 (2014) - [j111]Mingjun Wang, Xing-Ming Zhao, Hao Tan, Tatsuya Akutsu, James C. Whisstock, Jiangning Song:
Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. Bioinform. 30(1): 71-80 (2014) - [j110]Hongmin Cai, Peiying Ruan, Michael Kwok-Po Ng, Tatsuya Akutsu:
Feature weight estimation for gene selection: a local hyperlinear learning approach. BMC Bioinform. 15: 70 (2014) - [j109]Peiying Ruan, Morihiro Hayashida, Osamu Maruyama, Tatsuya Akutsu:
Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels. BMC Bioinform. 15(S-2): S6 (2014) - [j108]Yushan Qiu, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu:
On control of singleton attractors in multiple Boolean networks: integer programming-based method. BMC Syst. Biol. 8(S-1): S7 (2014) - [j107]Jose C. Nacher, Tatsuya Akutsu:
Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets. J. Complex Networks 2(4): 394-412 (2014) - [j106]Morihiro Hayashida, Tatsuya Akutsu:
Domain-Based Approaches to Prediction and Analysis of Protein-Protein Interactions. Int. J. Knowl. Discov. Bioinform. 4(1): 24-41 (2014) - [j105]Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tatsuya Akutsu:
An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data. J. Comput. Biol. 21(11): 785-798 (2014) - [j104]Masaki Suzuki, Hiroshi Nagamochi, Tatsuya Akutsu:
Efficient enumeration of monocyclic chemical graphs with given path frequencies. J. Cheminformatics 6(1): 31 (2014) - [j103]Tatsuya Akutsu, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu:
Efficient exponential-time algorithms for edit distance between unordered trees. J. Discrete Algorithms 25: 79-93 (2014) - [c73]Tatsuya Akutsu, Jesper Jansson, Atsuhiro Takasu, Takeyuki Tamura:
On the Parameterized Complexity of Associative and Commutative Unification. IPEC 2014: 15-27 - 2013
- [j102]Tatsuya Akutsu, Takeyuki Tamura:
A Polynomial-Time Algorithm for Computing the Maximum Common Connected Edge Subgraph of Outerplanar Graphs of Bounded Degree. Algorithms 6(1): 119-135 (2013) - [j101]Yang Zhao, Takeyuki Tamura, Tatsuya Akutsu, Jean-Philippe Vert:
Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. Bioinform. 29(17): 2178-2185 (2013) - [j100]Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu:
Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso. BMC Syst. Biol. 7(S-2): S15 (2013) - [j99]Hao Jiang, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu:
On the Complexity of Inference and Completion of Boolean Networks from Given Singleton Attractors. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 96-A(11): 2265-2274 (2013) - [j98]Xi Chen, Tatsuya Akutsu, Takeyuki Tamura, Wai-Ki Ching:
Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming. Int. J. Data Min. Bioinform. 7(3): 321-343 (2013) - [j97]Yang Zhao, Morihiro Hayashida, Jira Jindalertudomdee, Hiroshi Nagamochi, Tatsuya Akutsu:
Breadth-First Search Approach to Enumeration of Tree-like Chemical Compounds. J. Bioinform. Comput. Biol. 11(6) (2013) - [j96]Avraham A. Melkman, Tatsuya Akutsu:
An Improved Satisfiability Algorithm for Nested Canalyzing Functions and its Application to Determining a Singleton Attractor of a Boolean Network. J. Comput. Biol. 20(12): 958-969 (2013) - [j95]Tatsuya Akutsu, Daiji Fukagawa, Magnús M. Halldórsson, Atsuhiro Takasu, Keisuke Tanaka:
Approximation and parameterized algorithms for common subtrees and edit distance between unordered trees. Theor. Comput. Sci. 470: 10-22 (2013) - [c72]Natsu Nakajima, Tatsuya Akutsu:
Network Completion for Time Varying Genetic Networks. CISIS 2013: 553-558 - [c71]Tatsuya Akutsu, Takeyuki Tamura, Avraham A. Melkman, Atsuhiro Takasu:
On the Complexity of Finding a Largest Common Subtree of Bounded Degree. FCT 2013: 4-15 - [c70]Jose C. Nacher, Tatsuya Akutsu:
Analysis on critical nodes in controlling complex networks using dominating sets. SITIS 2013: 649-654 - [i1]Tatsuya Akutsu, Takeyuki Tamura, Atsuhiro Takasu:
On the Parameterized Complexity of Associative and Commutative Unification. CoRR abs/1310.0919 (2013) - 2012
- [j94]Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara:
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. Bioinform. 28(24): 3218-3224 (2012) - [j93]Tatsuya Akutsu, Daiji Fukagawa, Jesper Jansson, Kunihiko Sadakane:
Inferring a graph from path frequency. Discret. Appl. Math. 160(10-11): 1416-1428 (2012) - [j92]Morihiro Hayashida, Peiying Ruan, Tatsuya Akutsu:
A quadsection algorithm for grammar-based image compression. Integr. Comput. Aided Eng. 19(1): 23-38 (2012) - [j91]Tatsuya Akutsu, Yang Zhao, Morihiro Hayashida, Takeyuki Tamura:
Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks. IEICE Trans. Inf. Syst. 95-D(12): 2960-2970 (2012) - [j90]Yang Zhao, Morihiro Hayashida, Jose C. Nacher, Hiroshi Nagamochi, Tatsuya Akutsu:
Protein complex prediction via improved verification methods using constrained domain-domain matching. Int. J. Bioinform. Res. Appl. 8(3/4): 210-227 (2012) - [j89]Tatsuya Akutsu, Avraham A. Melkman, Takeyuki Tamura:
Singleton and 2-periodic attractors of sign-definite Boolean networks. Inf. Process. Lett. 112(1-2): 35-38 (2012) - [j88]Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu:
A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees. J. Comput. Biol. 19(10): 1089-1104 (2012) - [j87]Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu:
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming. Nucleic Acids Res. 40(Web-Server-Issue): 29-34 (2012) - [j86]Tatsuya Akutsu, Sven Kosub, Avraham A. Melkman, Takeyuki Tamura:
Finding a Periodic Attractor of a Boolean Network. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1410-1421 (2012) - [c69]Tatsuya Akutsu, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu:
Efficient Exponential Time Algorithms for Edit Distance between Unordered Trees. CPM 2012: 360-372 - [c68]Tatsuya Akutsu, Takeyuki Tamura:
On the Complexity of the Maximum Common Subgraph Problem for Partial k-Trees of Bounded Degree. ISAAC 2012: 146-155 - [c67]Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu:
Predicting protein-RNA residue-base contacts using two-dimensional conditional random field. ISB 2012: 152-157 - [c66]Tatsuya Akutsu, Takeyuki Tamura:
A Polynomial-Time Algorithm for Computing the Maximum Common Subgraph of Outerplanar Graphs of Bounded Degree. MFCS 2012: 76-87 - [c65]Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura:
Finding Conserved Regions in Protein Structures Using Support Vector Machines and Structure Alignment. PRIB 2012: 233-242 - 2011
- [j85]Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai:
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinform. 27(13): 85-93 (2011) - [j84]Ozgur Demir-Kavuk, Mayumi Kamada, Tatsuya Akutsu, Ernst-Walter Knapp:
Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features. BMC Bioinform. 12: 412 (2011) - [j83]Daiji Fukagawa, Takeyuki Tamura, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu:
A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures. BMC Bioinform. 12(S-1): S13 (2011) - [j82]Masaaki Shimizu, Hiroshi Nagamochi, Tatsuya Akutsu:
Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies. BMC Bioinform. 12(S-14): S3 (2011) - [j81]Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu:
Conditional random field approach to prediction of protein-protein interactions using domain information. BMC Syst. Biol. 5(S-1): S8 (2011) - [j80]Tatsuya Akutsu, Hiroshi Nagamochi:
Kernel Methods for Chemical Compounds: From Classification to Design. IEICE Trans. Inf. Syst. 94-D(10): 1846-1853 (2011) - [j79]