Tatsuya Akutsu
Orcid: 0000-0001-9763-797X
According to our database1,
Tatsuya Akutsu
authored at least 299 papers
between 1988 and 2025.
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Bibliography
2025
Unsupervised Dual Deep Hashing With Semantic-Index and Content-Code for Cross-Modal Retrieval.
IEEE Trans. Pattern Anal. Mach. Intell., January, 2025
2024
BMC Bioinform., December, 2024
Distributed Pinning Control: Stabilizing Large Boolean Networks Subjected to Perturbations.
IEEE Trans. Cybern., November, 2024
Molecular Design Based on Integer Programming and Splitting Data Sets by Hyperplanes.
IEEE ACM Trans. Comput. Biol. Bioinform., 2024
Accurate multi-view clustering to seek the cross-viewed yet uniform sample assignment via tensor feature matching.
Inf. Sci., 2024
A Unified Approach to Inferring Chemical Compounds with the Desired Aqueous Solubility.
CoRR, 2024
CoRR, 2024
IEEE Access, 2024
2023
eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio-temporal architectures of cells.
BMC Bioinform., December, 2023
<i>ProsperousPlus</i>: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction.
Briefings Bioinform., September, 2023
Briefings Bioinform., September, 2023
iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities.
Briefings Bioinform., July, 2023
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships.
Bioinform., March, 2023
ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning.
Briefings Bioinform., March, 2023
IEEE Trans. Neural Networks Learn. Syst., February, 2023
Identifying miRNA-Gene Common and Specific Regulatory Modules for Cancer Subtyping by a High-Order Graph Matching Model.
IEEE ACM Trans. Comput. Biol. Bioinform., 2023
IEEE ACM Trans. Comput. Biol. Bioinform., 2023
On the Trade-off between the Number of Nodes and the Number of Trees in a Random Forest.
CoRR, 2023
2022
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites.
Bioinform., November, 2022
IEEE Trans. Neural Networks Learn. Syst., 2022
A Novel Method for Inferring Chemical Compounds With Prescribed Topological Substructures Based on Integer Programming.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022
Guest Editorial for Special Section on the 16th International Conference on Intelligent Computing (ICIC).
IEEE ACM Trans. Comput. Biol. Bioinform., 2022
An FVS-Based Approach to Attractor Detection in Asynchronous Random Boolean Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022
Identification of periodic attractors in Boolean networks using a priori information.
PLoS Comput. Biol., 2022
Comparison of the Representational Power of Random Forests, Binary Decision Diagrams, and Neural Networks.
Neural Comput., 2022
<i>iFeatureOmega: </i> an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets.
Nucleic Acids Res., 2022
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations.
J. Chem. Inf. Model., 2022
Molecular Design Based on Integer Programming and Quadratic Descriptors in a Two-layered Model.
CoRR, 2022
BMC Bioinform., 2022
Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.
Briefings Bioinform., 2022
A new approach to the design of acyclic chemical compounds using skeleton trees and integer linear programming.
Appl. Intell., 2022
Proceedings of the 33rd International Symposium on Algorithms and Computation, 2022
Proceedings of the ICBBB 2022: 12th International Conference on Bioscience, Biochemistry and Bioinformatics, Tokyo, Japan, January 7, 2022
Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies, 2022
2021
Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks.
Briefings Bioinform., July, 2021
PLoS Comput. Biol., 2021
CoRR, 2021
CoRR, 2021
Tree Edit Distance with Variables. Measuring the Similarity between Mathematical Formulas.
CoRR, 2021
BMC Bioinform., 2021
Weighted minimum feedback vertex sets and implementation in human cancer genes detection.
BMC Bioinform., 2021
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy.
Briefings Bioinform., 2021
Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules.
Briefings Bioinform., 2021
Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations.
Briefings Bioinform., 2021
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming.
Algorithms Mol. Biol., 2021
An Improved Integer Programming Formulation for Inferring Chemical Compounds with Prescribed Topological Structures.
Proceedings of the Advances and Trends in Artificial Intelligence. Artificial Intelligence Practices, 2021
Proceedings of the Intelligent Computing Theories and Application, 2021
Molecular Design Based on Artificial Neural Networks, Integer Programming and Grid Neighbor Search.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
2020
Neural Networks, 2020
Comparison of Pseudoknotted RNA Secondary Structures by Topological Centroid Identification and Tree Edit Distance.
J. Comput. Biol., 2020
Improved Hardness of Maximum Common Subgraph Problems on Labeled Graphs of Bounded Treewidth and Bounded Degree.
Int. J. Found. Comput. Sci., 2020
Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information.
Genom. Proteom. Bioinform., 2020
A novel method for inference of chemical compounds with prescribed topological substructures based on integer programming.
CoRR, 2020
Enumerating Chemical Graphs with Two Disjoint Cycles Satisfying Given Path Frequency Specifications.
CoRR, 2020
Enumerating Chemical Graphs with Mono-block 2-Augmented Tree Structure from Given Upper and Lower Bounds on Path Frequencies.
CoRR, 2020
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins.
Bioinform., 2020
DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites.
Bioinform., 2020
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction.
Briefings Bioinform., 2020
Briefings Bioinform., 2020
Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences.
Briefings Bioinform., 2020
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data.
Briefings Bioinform., 2020
A Novel Method for Inference of Chemical Compounds of Cycle Index Two with Desired Properties Based on Artificial Neural Networks and Integer Programming.
Algorithms, 2020
A New Integer Linear Programming Formulation to the Inverse QSAR/QSPR for Acyclic Chemical Compounds Using Skeleton Trees.
Proceedings of the Trends in Artificial Intelligence Theory and Applications. Artificial Intelligence Practices, 2020
Proceedings of the ICBBB 2020: 10th International Conference on Bioscience, 2020
A Method for the Inverse QSAR/QSPR Based on Artificial Neural Networks and Mixed Integer Linear Programming.
Proceedings of the ICBBB 2020: 10th International Conference on Bioscience, 2020
A Novel Method for the Inverse QSAR/QSPR based on Artificial Neural Networks and Mixed Integer Linear Programming with Guaranteed Admissibility.
Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020), 2020
2019
Identification of the Structure of a Probabilistic Boolean Network From Samples Including Frequencies of Outcomes.
IEEE Trans. Neural Networks Learn. Syst., 2019
Resource Cut, a New Bounding Procedure to Algorithms for Enumerating Tree-Like Chemical Graphs.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019
Optimal string clustering based on a Laplace-like mixture and EM algorithm on a set of strings.
J. Comput. Syst. Sci., 2019
Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles.
J. Bioinform. Comput. Biol., 2019
Deep learning with evolutionary and genomic profiles for identifying cancer subtypes.
J. Bioinform. Comput. Biol., 2019
Bioinform., 2019
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework.
Briefings Bioinform., 2019
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.
Briefings Bioinform., 2019
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites.
Briefings Bioinform., 2019
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.
Briefings Bioinform., 2019
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.
Briefings Bioinform., 2019
Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features.
Briefings Bioinform., 2019
2018
IEEE Trans. Neural Networks Learn. Syst., 2018
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
Analysis of Critical and Redundant Vertices in Controlling Directed Complex Networks Using Feedback Vertex Sets.
J. Comput. Biol., 2018
ncRNA-disease association prediction based on sequence information and tripartite network.
BMC Syst. Biol., 2018
Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.
BMC Bioinform., 2018
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.
Bioinform., 2018
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy.
Bioinform., 2018
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.
Bioinform., 2018
Proceedings of the 8th International Conference on Bioscience, 2018
A Simple Linear-Time Algorithm for Computing the Centroid and Canonical Form of a Plane Graph and Its Applications.
Proceedings of the Annual Symposium on Combinatorial Pattern Matching, 2018
Grammar-based Compression for Directed and Undirected Generalized Series-parallel Graphs using Integer Linear Programming.
Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2018), 2018
Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes.
Proceedings of the 18th IEEE International Conference on Bioinformatics and Bioengineering, 2018
Proceedings of the Algorithms for Computational Biology - 5th International Conference, 2018
WorldScientific, ISBN: 9789813233447, 2018
2017
Theor. Comput. Sci., 2017
Selected Papers from the 16th International Conference on Bioinformatics (InCoB 2017).
J. Bioinform. Comput. Biol., 2017
An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data.
Bioinform., 2017
Autom., 2017
2016
Exact Identification of the Structure of a Probabilistic Boolean Network from Samples.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016
Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach.
J. Comput. Biol., 2016
A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models.
Comput. Stat. Data Anal., 2016
Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order.
BMC Bioinform., 2016
LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length.
BMC Bioinform., 2016
Critical evaluation of <i>in silico</i> methods for prediction of coiled-coil domains in proteins.
Briefings Bioinform., 2016
Finding and Analyzing the Minimum Set of Driver Nodes in control of Boolean Networks.
Adv. Complex Syst., 2016
Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016), 2016
Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks.
Proceedings of the 16th IEEE International Conference on Bioinformatics and Bioengineering, 2016
Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network.
Proceedings of the 16th IEEE International Conference on Bioinformatics and Bioengineering, 2016
2015
IEEE Trans. Knowl. Data Eng., 2015
Theor. Comput. Sci., 2015
Matrix Network: A New Data Structure for Efficient Enumeration of Microstates of a Genetic Regulatory Network.
J. Inf. Process., 2015
Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model.
J. Comput. Biol., 2015
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., 2015
Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks.
BMC Syst. Biol., 2015
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks.
BMC Syst. Biol., 2015
Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs.
BMC Bioinform., 2015
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
2014
J. Discrete Algorithms, 2014
J. Cheminformatics, 2014
An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data.
J. Comput. Biol., 2014
Int. J. Knowl. Discov. Bioinform., 2014
Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets.
J. Complex Networks, 2014
On control of singleton attractors in multiple Boolean networks: integer programming-based method.
BMC Syst. Biol., 2014
Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels.
BMC Bioinform., 2014
BMC Bioinform., 2014
Bioinform., 2014
2013
Approximation and parameterized algorithms for common subtrees and edit distance between unordered trees.
Theor. Comput. Sci., 2013
An Improved Satisfiability Algorithm for Nested Canalyzing Functions and its Application to Determining a Singleton Attractor of a Boolean Network.
J. Comput. Biol., 2013
J. Bioinform. Comput. Biol., 2013
Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming.
Int. J. Data Min. Bioinform., 2013
On the Complexity of Inference and Completion of Boolean Networks from Given Singleton Attractors.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2013
CoRR, 2013
Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso.
BMC Syst. Biol., 2013
Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks.
Bioinform., 2013
A Polynomial-Time Algorithm for Computing the Maximum Common Connected Edge Subgraph of Outerplanar Graphs of Bounded Degree.
Algorithms, 2013
Proceedings of the Ninth International Conference on Signal-Image Technology & Internet-Based Systems, 2013
Proceedings of the Seventh International Conference on Complex, 2013
2012
IEEE ACM Trans. Comput. Biol. Bioinform., 2012
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming.
Nucleic Acids Res., 2012
A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees.
J. Comput. Biol., 2012
Inf. Process. Lett., 2012
Protein complex prediction via improved verification methods using constrained domain-domain matching.
Int. J. Bioinform. Res. Appl., 2012
Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks.
IEICE Trans. Inf. Syst., 2012
Integr. Comput. Aided Eng., 2012
Bioinform., 2012
Finding Conserved Regions in Protein Structures Using Support Vector Machines and Structure Alignment.
Proceedings of the Pattern Recognition in Bioinformatics, 2012
A Polynomial-Time Algorithm for Computing the Maximum Common Subgraph of Outerplanar Graphs of Bounded Degree.
Proceedings of the Mathematical Foundations of Computer Science 2012, 2012
Predicting protein-RNA residue-base contacts using two-dimensional conditional random field.
Proceedings of the 6th IEEE International Conference on Systems Biology, 2012
On the Complexity of the Maximum Common Subgraph Problem for Partial k-Trees of Bounded Degree.
Proceedings of the Algorithms and Computation - 23rd International Symposium, 2012
2011
Theor. Comput. Sci., 2011
Efficient Enumeration of Stereoisomers of Outerplanar Chemical Graphs Using Dynamic Programming.
J. Chem. Inf. Model., 2011
Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions.
J. Comput. Biol., 2011
J. Bioinform. Comput. Biol., 2011
J. Bioinform. Comput. Biol., 2011
An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles.
IEICE Trans. Inf. Syst., 2011
IEICE Trans. Inf. Syst., 2011
IEICE Trans. Inf. Syst., 2011
Conditional random field approach to prediction of protein-protein interactions using domain information.
BMC Syst. Biol., 2011
Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies.
BMC Bioinform., 2011
A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures.
BMC Bioinform., 2011
Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features.
BMC Bioinform., 2011
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.
Bioinform., 2011
An Improved Clique-Based Method for Computing Edit Distance between Unordered Trees and Its Application to Comparison of Glycan Structures.
Proceedings of the International Conference on Complex, 2011
2010
Branch-and-Bound Algorithms for Enumerating Treelike Chemical Graphs with Given Path Frequency Using Detachment-Cut.
J. Chem. Inf. Model., 2010
Determining a singleton attractor of an AND/OR Boolean network in O(1.587<sup>n</sup>) time.
Inf. Process. Lett., 2010
Inf. Process. Lett., 2010
Prediction of Protein Folding Rates from Structural Topology and Complex Network Properties.
Inf. Media Technol., 2010
Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets.
Int. J. Knowl. Discov. Bioinform., 2010
Exact Algorithms for Finding a Minimum Reaction Cut under a Boolean Model of Metabolic Networks.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2010
IEICE Trans. Inf. Syst., 2010
Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures.
BMC Bioinform., 2010
Biosyst., 2010
Bioinform., 2010
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming.
Bioinform., 2010
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010
Proceedings of the 20th International Conference on Pattern Recognition, 2010
2009
Algorithms for Singleton Attractor Detection in Planar and Nonplanar AND/OR Boolean Networks.
Math. Comput. Sci., 2009
Dynamic Programming Algorithms and Grammatical Modeling for Protein Beta-Sheet Prediction.
J. Comput. Biol., 2009
Analyses and Algorithms for Predecessor and Control Problems for Boolean Networks of Bounded Indegree.
Inf. Media Technol., 2009
IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2009
IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2009
BMC Bioinform., 2009
Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology.
BMC Bioinform., 2009
Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs.
Biosyst., 2009
Proceedings of the String Processing and Information Retrieval, 2009
Proceedings of the Algorithms and Computation, 20th International Symposium, 2009
Proceedings of the Discovery Science, 12th International Conference, 2009
Proceedings of the Complex Sciences, 2009
Measuring Structural Robustness of Metabolic Networks under a Boolean Model Using Integer Programming and Feedback Vertex Sets.
Proceedings of the 2009 International Conference on Complex, 2009
Efficient computation of impact degrees for multiple reactions in metabolic networks with cycles.
Proceedings of the Proceeding of the 3rd International Workshop on Data and Text Mining in Bioinformatics, 2009
Integer programming-based methods for attractor detection and control of boolean networks.
Proceedings of the 48th IEEE Conference on Decision and Control, 2009
Proceedings of the Algorithmic Learning Theory, 20th International Conference, 2009
2008
Proceedings of the Wiley Encyclopedia of Computer Science and Engineering, 2008
J. Chem. Inf. Model., 2008
Improved approximation of the largest common subtree of two unordered trees of bounded height.
Inf. Process. Lett., 2008
A Clustering Method for Analysis of Sequence Similarity Networks of Proteins Using Maximal Components of Graphs.
Inf. Media Technol., 2008
Integer programming-based approach to allocation of reporter genes for cell array analysis.
Int. J. Bioinform. Res. Appl., 2008
Algorithms and Complexity Analyses for Control of Singleton Attractors in Boolean Networks.
EURASIP J. Bioinform. Syst. Biol., 2008
BMC Syst. Biol., 2008
Proceedings of the Pattern Recognition in Bioinformatics, 2008
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008
An Improved Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes.
Proceedings of the Algebraic Biology, Third International Conference, 2008
Proceedings of the Algebraic Biology, Third International Conference, 2008
2007
Proceedings of the Emergent Intelligence of Networked Agents, 2007
Inf. Media Technol., 2007
Simulation study in Probabilistic Boolean Network models for genetic regulatory networks.
Int. J. Data Min. Bioinform., 2007
Approximation Algorithms for Optimal RNA Secondary Structures Common to Multiple Sequences.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2007
EURASIP J. Bioinform. Syst. Biol., 2007
On the complexity of deriving position specific score matrices from positive and negative sequences.
Discret. Appl. Math., 2007
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition.
BMC Bioinform., 2007
BMC Bioinform., 2007
An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks.
Bioinform., 2007
Proceedings of the Theory and Applications of Models of Computation, 2007
Proceedings of the 7th IEEE International Conference on Data Mining (ICDM 2007), 2007
An O(1.787<sup>n</sup>)-Time Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes.
Proceedings of the Fundamentals of Computation Theory, 16th International Symposium, 2007
A Novel Clustering Method for Analysis of Biological Networks using Maximal Components of Graphs.
Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007
Inferring a Chemical Structure from a Feature Vector Based on Frequency of Labeled Paths and Small Fragments.
Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007
2006
Trans. Comp. Sys. Biology, 2006
Protein Threading with Profiles and Distance Constraints Using Clique Based Algorithms.
J. Bioinform. Comput. Biol., 2006
A relation between edit distance for ordered trees and edit distance for Euler strings.
Inf. Process. Lett., 2006
Int. J. Found. Comput. Sci., 2006
Int. J. Found. Comput. Sci., 2006
Dynamic Programming and Clique Based Approaches for Protein Threading with Profiles and Constraints.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2006
BMC Bioinform., 2006
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006
Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, 2006
2005
A Probabilistic Model for Mining Labeled Ordered Trees: Capturing Patterns in Carbohydrate Sugar Chains.
IEEE Trans. Knowl. Data Eng., 2005
Graph Kernels for Molecular Structure-Activity Relationship Analysis with Support Vector Machines.
J. Chem. Inf. Model., 2005
Protein Side-chain Packing Problem: a Maximum Edge-weight Clique Algorithmic Approach.
J. Bioinform. Comput. Biol., 2005
Inf. Process. Lett., 2005
Int. J. Neural Syst., 2005
Fast and accurate database homology search using upper bounds of local alignment scores.
Bioinform., 2005
Proceedings of the 2005 IEEE International Conference on Granular Computing, 2005
Proceedings of the Combinatorial Pattern Matching, 16th Annual Symposium, 2005
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005
2004
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.
Nucleic Acids Res., 2004
J. Comput. Biol., 2004
BMC Bioinform., 2004
Application of a new probabilistic model for recognizing complex patterns in glycans.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004
Proceedings of the 4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 2004
Protein Side-chain Packing Problem: A Maximum Edge-weight Clique Algorithmic Approach.
Proceedings of the Second Asia-Pacific Bioinformatics Conference (APBC 2004), 2004
2003
A simple greedy algorithm for finding functional relations: efficient implementation and average case analysis.
Theor. Comput. Sci., 2003
Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model.
Theor. Comput. Sci., 2003
Finding optimal degenerate patterns in DNA sequences.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003
Inferring strengths of protein-protein interactions from experimental data using linear programming.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003
Proceedings of the Active Mining, Second International Workshop, 2003
2002
Proceedings of the Combinatorial Pattern Matching, 13th Annual Symposium, 2002
Proceedings of the Computing and Combinatorics, 8th Annual International Conference, 2002
2000
Theor. Comput. Sci., 2000
Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function.
J. Comput. Biol., 2000
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots.
Discret. Appl. Math., 2000
Bioinform., 2000
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000
A Simple Greedy Algorithm for Finding Functional Relations: Efficient Implementation and Average Case Anaylsis.
Proceedings of the Discovery Science, 2000
1999
Approximation and Exact Algorithms for RNA Secondary Structure Prediction and Recognition of Stochastic Context-free Languages.
J. Comb. Optim., 1999
Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model.
Proceedings of the 4th Pacific Symposium on Biocomputing, 1999
Matching of Spots in 2D Electrophoresis Images. Point Matching Under Non-uniform Distortions.
Proceedings of the Combinatorial Pattern Matching, 10th Annual Symposium, 1999
1998
Distribution of Distances and Triangles in a Point Set and Algorithms for Computing the Largest Common Point Sets.
Discret. Comput. Geom., 1998
Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions.
Proceedings of the Ninth Annual ACM-SIAM Symposium on Discrete Algorithms, 1998
On the Complexity of Deriving Score Functions from Examples for Problems in Molecular Biology.
Proceedings of the Automata, Languages and Programming, 25th International Colloquium, 1998
1997
Comput. Appl. Biosci., 1997
1996
Sampling Effectiveness in Discovering Functional Relationships in Databases.
Proceedings of the Industrial and Engineering Applications of Artificial Intelligence and Expert Systems, 1996
Proceedings of the Computing and Combinatorics, Second Annual International Conference, 1996
1995
A Parallel Algorithm for Determining the Congruence of Point Sets in Three-Dimensions.
IEICE Trans. Inf. Syst., 1995
Proceedings of the 28th Annual Hawaii International Conference on System Sciences (HICSS-28), 1995
1994
Proceedings of the Algorithms and Computation, 5th International Symposium, 1994
Efficient and Robust Three-Dimensional Pattern Matching Algorithms Using Hashing and Dynamic Programming Techniques.
Proceedings of the 27th Annual Hawaii International Conference on System Sciences (HICSS-27), 1994
1993
Proceedings of the Combinatorial Pattern Matching, 4th Annual Symposium, 1993
1992
Proceedings of the Algorithms and Computation, Third International Symposium, 1992
Proceedings of the Algorithmic Learning Theory, Third Workshop, 1992
1991
A new method of computer representation of stereochemistry. Transforming a stereochemical structure into a graph.
J. Chem. Inf. Comput. Sci., 1991
Development and comparison of search algorithms for robot motion planning in the configuration space.
Proceedings of the IEEE/RSJ International Conference on Intelligent Robots and Systems, 1991
1988
CHEMILOG - A Logic Programming Language/System for Chemical Information Processing.
Proceedings of the International Conference on Fifth Generation Computer Systems, 1988