Tatsuya Akutsu

According to our database1, Tatsuya Akutsu authored at least 285 papers between 1988 and 2024.

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Bibliography

2024
DiCleave: a deep learning model for predicting human Dicer cleavage sites.
BMC Bioinform., December, 2024

2023
eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio-temporal architectures of cells.
BMC Bioinform., December, 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

On the Compressive Power of Boolean Threshold Autoencoders.
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

Common Attractors in Multiple Boolean Networks.
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

Molecular Design Based on Integer Programming and Splitting Data Sets by Hyperplanes.
CoRR, 2023

2022
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites.
Bioinform., November, 2022

On the Distribution of Successor States in Boolean Threshold Networks.
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

Densest subgraph-based methods for protein-protein interaction hot spot prediction.
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

On the Complexity of Tree Edit Distance with Variables.
Proceedings of the 33rd International Symposium on Algorithms and Computation, 2022

A Method for Molecular Design Based on Linear Regression and Integer Programming.
Proceedings of the ICBBB 2022: 12th International Conference on Bioscience, Biochemistry and Bioinformatics, Tokyo, Japan, January 7, 2022

Adjustive Linear Regression and Its Application to the Inverse QSAR.
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

New and improved algorithms for unordered tree inclusion.
Theor. Comput. Sci., 2021

Inhibitory neurons exhibit high controlling ability in the cortical microconnectome.
PLoS Comput. Biol., 2021

Editorial: Inference of Biological Networks.
Frontiers Bioinform., 2021

On the Size and Width of the Decoder of a Boolean Threshold Autoencoder.
CoRR, 2021

A Method for Inferring Polymers Based on Linear Regression and Integer Programming.
CoRR, 2021

An Inverse QSAR Method Based on Linear Regression and Integer Programming.
CoRR, 2021

Tree Edit Distance with Variables. Measuring the Similarity between Mathematical Formulas.
CoRR, 2021

ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites.
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

Discrimination of attractors with noisy nodes in Boolean networks.
Autom., 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

An Inverse QSAR Method Based on Decision Tree and Integer Programming.
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
Extracting boolean and probabilistic rules from trained neural networks.
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

Network control principles for identifying personalized driver genes in cancer.
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

Breast Cancer Subtype by Imbalanced Omics Data through A Deep Learning Fusion Model.
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

Bastion3: a two-layer ensemble predictor of type III secreted effectors.
Bioinform., 2019

Protease target prediction via matrix factorization.
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
Identifying a Probabilistic Boolean Threshold Network From Samples.
IEEE Trans. Neural Networks Learn. Syst., 2018

Computing Minimum Reaction Modifications in a Boolean Metabolic Network.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.
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

Enumerating Chemical Mono-Block 3-Augmented Trees with Two Junctions.
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

Algorithms for Analysis and Control of Boolean Networks.
Proceedings of the Algorithms for Computational Biology - 5th International Conference, 2018

2017
On the parameterized complexity of associative and commutative unification.
Theor. Comput. Sci., 2017

Selected Papers from the 16th International Conference on Bioinformatics (InCoB 2017).
J. Bioinform. Comput. Biol., 2017

New Algorithms for Unordered Tree Inclusion.
CoRR, 2017

An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data.
Bioinform., 2017

Discrimination of singleton and periodic attractors in Boolean networks.
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

Enumerating Naphthalene Isomers of Tree-like Chemical Graphs.
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
Similar Subtree Search Using Extended Tree Inclusion.
IEEE Trans. Knowl. Data Eng., 2015

On the complexity of finding a largest common subtree of bounded degree.
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

On observability of attractors in Boolean Networks.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

2014
Efficient exponential-time algorithms for edit distance between unordered trees.
J. Discrete Algorithms, 2014

Efficient enumeration of monocyclic chemical graphs with given path frequencies.
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

Domain-Based Approaches to Prediction and Analysis of Protein-Protein Interactions.
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

Feature weight estimation for gene selection: a local hyperlinear learning approach.
BMC Bioinform., 2014

Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets.
Bioinform., 2014

Network Completion for Static Gene Expression Data.
Adv. Bioinformatics, 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

Breadth-First Search Approach to Enumeration of Tree-like Chemical Compounds.
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

On the Parameterized Complexity of Associative and Commutative Unification.
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

Analysis on critical nodes in controlling complex networks using dominating sets.
Proceedings of the Ninth International Conference on Signal-Image Technology & Internet-Based Systems, 2013

Network Completion for Time Varying Genetic Networks.
Proceedings of the Seventh International Conference on Complex, 2013

2012
Finding a Periodic Attractor of a Boolean Network.
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

Singleton and 2-periodic attractors of sign-definite Boolean networks.
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

A quadsection algorithm for grammar-based image compression.
Integr. Comput. Aided Eng., 2012

Inferring a graph from path frequency.
Discret. Appl. Math., 2012

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.
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
Exact algorithms for computing the tree edit distance between unordered trees.
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

Bioinformatic Approaches for Predicting substrates of Proteases.
J. Bioinform. Comput. Biol., 2011

Using binding Profiles to Predict binding sites of Target RNAs.
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

Measuring the Similarity of Protein Structures Using Image Compression Algorithms.
IEICE Trans. Inf. Syst., 2011

Kernel Methods for Chemical Compounds: From Classification to Design.
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

A bisection algorithm for grammar-based compression of ordered trees.
Inf. Process. Lett., 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

Tree Edit Distance Problems: Algorithms and Applications to Bioinformatics.
IEICE Trans. Inf. Syst., 2010

Comparing biological networks via graph compression.
BMC Syst. Biol., 2010

Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures.
BMC Bioinform., 2010

The role of internal duplication in the evolution of multi-domain proteins.
Biosyst., 2010

Cascleave: towards more accurate prediction of caspase substrate cleavage sites.
Bioinform., 2010

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming.
Bioinform., 2010

Approximating Tree Edit Distance through String Edit Distance.
Algorithmica, 2010

Dynamic Programming Algorithms for RNA Structure Prediction with Binding Sites.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

A Variational Bayesian EM Algorithm for Tree Similarity.
Proceedings of the 20th International Conference on Pattern Recognition, 2010

2009
A grammatical approach to RNA-RNA interaction prediction.
Pattern Recognit., 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

Detecting a Singleton Attractor in a Boolean Network Utilizing SAT Algorithms.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2009

On Finding a Fixed Point in a Boolean Network with Maximum Indegree 2.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2009

Prediction of RNA secondary structure with pseudoknots using integer programming.
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

Constant Factor Approximation of Edit Distance of Bounded Height Unordered Trees.
Proceedings of the String Processing and Information Retrieval, 2009

Enumerating Stereoisomers of Tree Structured Molecules Using Dynamic Programming.
Proceedings of the Algorithms and Computation, 20th International Symposium, 2009

Latent Topic Extraction from Relational Table for Record Matching.
Proceedings of the Discovery Science, 12th International Conference, 2009

A Bipartite Graph Based Model of Protein Domain Networks.
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

Completing Networks Using Observed Data.
Proceedings of the Algorithmic Learning Theory, 20th International Conference, 2009

2008
Bioinformatics.
Proceedings of the Wiley Encyclopedia of Computer Science and Engineering, 2008

Enumerating Treelike Chemical Graphs with Given Path Frequency.
J. Chem. Inf. Model., 2008

Improved approximation of the largest common subtree of two unordered trees of bounded height.
Inf. Process. Lett., 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

Origin of structural difference in metabolic networks with respect to temperature.
BMC Syst. Biol., 2008

HSEpred: predict half-sphere exposure from protein sequences.
Bioinform., 2008

Prediction of Protein Beta-Sheets: Dynamic Programming versus Grammatical Approach.
Proceedings of the Pattern Recognition in Bioinformatics, 2008

Image Compression-based Approach to Measuring the Similarity of Protein Structures.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

Preface.
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

Algorithms for Inference, Analysis and Control of Boolean Networks.
Proceedings of the Algebraic Biology, Third International Conference, 2008

2007
Topological aspects of protein networks.
Proceedings of the Emergent Intelligence of Networked Agents, 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

Algorithms for Finding Small Attractors in Boolean Networks.
EURASIP J. Bioinform. Syst. Biol., 2007

Genetic Regulatory Networks.
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

Correlation between structure and temperature in prokaryotic metabolic networks.
BMC Bioinform., 2007

An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks.
Bioinform., 2007

An Efficient Algorithm for Generating Colored Outerplanar Graphs.
Proceedings of the Theory and Applications of Models of Computation, 2007

Statistical Learning Algorithm for Tree Similarity.
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
A Control Model for Markovian Genetic Regulatory Networks.
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

Fast Algorithms for Comparison of Similar Unordered Trees.
Int. J. Found. Comput. Sci., 2006

Algorithms for Point Set Matching with K-differences.
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

Optimizing amino acid substitution matrices with a local alignment kernel.
BMC Bioinform., 2006

Identification of metabolic units induced by environmental signals.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

On the Complexity of Finding Control Strategies for Boolean Networks.
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

Performance analysis of a greedy algorithm for inferring Boolean functions.
Inf. Process. Lett., 2005

On construction of stochastic genetic networks based on gene expression sequences.
Int. J. Neural Syst., 2005

Fast and accurate database homology search using upper bounds of local alignment scores.
Bioinform., 2005

A score matrix to reveal the hidden links in glycans.
Bioinform., 2005

A linear control model for gene intervention in a genetic regulatory network.
Proceedings of the 2005 IEEE International Conference on Granular Computing, 2005

Inferring a Graph from Path Frequency.
Proceedings of the Combinatorial Pattern Matching, 16th Annual Symposium, 2005

Clique-based algorithms for protein threading with profiles and constraints.
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005

2004
Managing and Analyzing Carbohydrate Data.
SIGMOD Rec., 2004

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.
Nucleic Acids Res., 2004

Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data.
J. Comput. Biol., 2004

Clustering under the line graph transformation: application to reaction network.
BMC Bioinform., 2004

Protein homology detection using string alignment kernels.
Bioinform., 2004

Optimizing substitution matrices by separating score distributions.
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

Extensions of marginalized graph kernels.
Proceedings of the Machine Learning, 2004

Protein Threading with Profiles and Constraints.
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

Point matching under non-uniform distortions.
Discret. Appl. Math., 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

Computational and Statistical Methods in Bioinformatics.
Proceedings of the Active Mining, Second International Workshop, 2003

2002
On the Complexity of Deriving Position Specific Score Matrices from Examples.
Proceedings of the Combinatorial Pattern Matching, 13th Annual Symposium, 2002

Inferring a Union of Halfspaces from Examples.
Proceedings of the Computing and Combinatorics, 8th Annual International Conference, 2002

2000
On the approximation of largest common subtrees and largest common point sets.
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

Inferring qualitative relations in genetic networks and metabolic pathways.
Bioinform., 2000

On approximation algorithms for local multiple alignment.
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
On the Approximation of Protein Threading.
Theor. Comput. Sci., 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

On determining the congruence of point sets in d dimensions.
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
Rapid protein fragment search using hash functions based on the Fourier transform.
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

Approximating Minimum Keys and Optimal Substructure Screens.
Proceedings of the Computing and Combinatorics, Second Annual International Conference, 1996

1995
Approximate String Matching with don't Care Characters.
Inf. Process. Lett., 1995

A Parallel Algorithm for Determining the Congruence of Point Sets in Three-Dimensions.
IEICE Trans. Inf. Syst., 1995

New hashing techniques and their application to a protein structure database system.
Proceedings of the 28th Annual Hawaii International Conference on System Sciences (HICSS-28), 1995

1994
On PAC Learnability of Functional Depencies.
New Gener. Comput., 1994

On Determining the Congruity of Point Sets in Higher Dimensions.
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
Knowledge-based system for computer-aided drug design.
Knowl. Based Syst., 1993

A Linear Time Pattern Matching Algorithm Between a String and a Tree.
Proceedings of the Combinatorial Pattern Matching, 4th Annual Symposium, 1993

1992
Algorithms for Determining the Geometrical Congruity in Two and Three Dimensions.
Proceedings of the Algorithms and Computation, Third International Symposium, 1992

On PAC Learnability of Functional Dependencies.
Proceedings of the Algorithmic Learning Theory, Third Workshop, 1992

1991
Logic-based approach to expert systems in chemistry.
Knowl. Based Syst., 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


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