# Tatsuya Akutsu

According to our database

Collaborative distances:

^{1}, Tatsuya Akutsu authored at least 222 papers between 1988 and 2018.Collaborative distances:

## Timeline

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## Bibliography

2018

Identifying a Probabilistic Boolean Threshold Network From Samples.

IEEE Trans. Neural Netw. Learning Syst., 2018

Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.

IEEE/ACM Trans. Comput. Biology Bioinform., 2018

ncRNA-disease association prediction based on sequence information and tripartite network.

BMC Systems Biology, 2018

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.

BMC Bioinformatics, 2018

Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.

Bioinformatics, 2018

PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy.

Bioinformatics, 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

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. Bioinformatics and Computational Biology, 2017

New Algorithms for Unordered Tree Inclusion.

CoRR, 2017

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

Bioinformatics, 2017

Discrimination of singleton and periodic attractors in Boolean networks.

Automatica, 2017

2016

Exact Identification of the Structure of a Probabilistic Boolean Network from Samples.

IEEE/ACM Trans. Comput. Biology Bioinform., 2016

Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach.

Journal of Computational Biology, 2016

A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models.

Computational Statistics & Data Analysis, 2016

Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order.

BMC Bioinformatics, 2016

LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length.

BMC Bioinformatics, 2016

Critical evaluation of

*in silico*methods for prediction of coiled-coil domains in proteins.
Briefings in Bioinformatics, 2016

Finding and Analyzing the Minimum Set of Driver Nodes in control of Boolean Networks.

Advances in Complex Systems, 2016

Similar subtree search using extended tree inclusion.

Proceedings of the 32nd IEEE International Conference on Data Engineering, 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.

JIP, 2015

Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model.

Journal of Computational Biology, 2015

A Fixed-Parameter Algorithm for Detecting a Singleton Attractor in an AND/OR Boolean Network with Bounded Treewidth.

IEICE Transactions, 2015

Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks.

BMC Systems Biology, 2015

Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks.

BMC Systems Biology, 2015

Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs.

BMC Bioinformatics, 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.

Journal of Computational Biology, 2014

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

IJKDB, 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 Systems Biology, 2014

Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels.

BMC Bioinformatics, 2014

Feature weight estimation for gene selection: a local hyperlinear learning approach.

BMC Bioinformatics, 2014

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

Bioinformatics, 2014

Network Completion for Static Gene Expression Data.

Adv. Bioinformatics, 2014

On the Parameterized Complexity of Associative and Commutative Unification.

Proceedings of the Parameterized and Exact Computation - 9th International Symposium, 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.

Journal of Computational Biology, 2013

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

J. Bioinformatics and Computational Biology, 2013

Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming.

IJDMB, 2013

On the Complexity of Inference and Completion of Boolean Networks from Given Singleton Attractors.

IEICE Transactions, 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 Systems Biology, 2013

Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks.

Bioinformatics, 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

On the Complexity of Finding a Largest Common Subtree of Bounded Degree.

Proceedings of the Fundamentals of Computation Theory - 19th International Symposium, 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. Biology Bioinform., 2012

Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming.

Nucleic Acids Research, 2012

A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees.

Journal of Computational Biology, 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.

IJBRA, 2012

Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks.

IEICE Transactions, 2012

A quadsection algorithm for grammar-based image compression.

Integrated Computer-Aided Engineering, 2012

Inferring a graph from path frequency.

Discrete Applied Mathematics, 2012

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.

Bioinformatics, 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

Efficient Exponential Time Algorithms for Edit Distance between Unordered Trees.

Proceedings of the Combinatorial Pattern Matching - 23rd Annual 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.

Journal of Chemical Information and Modeling, 2011

Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions.

Journal of Computational Biology, 2011

Bioinformatic Approaches for Predicting substrates of Proteases.

J. Bioinformatics and Computational Biology, 2011

Using binding Profiles to Predict binding sites of Target RNAs.

J. Bioinformatics and Computational Biology, 2011

An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles.

IEICE Transactions, 2011

Measuring the Similarity of Protein Structures Using Image Compression Algorithms.

IEICE Transactions, 2011

Kernel Methods for Chemical Compounds: From Classification to Design.

IEICE Transactions, 2011

Conditional random field approach to prediction of protein-protein interactions using domain information.

BMC Systems Biology, 2011

Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies.

BMC Bioinformatics, 2011

A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures.

BMC Bioinformatics, 2011

Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features.

BMC Bioinformatics, 2011

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.

Bioinformatics [ISMB/ECCB], 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.

Journal of Chemical Information and Modeling, 2010

Determining a singleton attractor of an AND/OR Boolean network in O(1.587

^{n}) 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.

IJKDB, 2010

Exact Algorithms for Finding a Minimum Reaction Cut under a Boolean Model of Metabolic Networks.

IEICE Transactions, 2010

Tree Edit Distance Problems: Algorithms and Applications to Bioinformatics.

IEICE Transactions, 2010

Comparing biological networks via graph compression.

BMC Systems Biology, 2010

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

BMC Bioinformatics, 2010

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

Biosystems, 2010

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

Bioinformatics, 2010

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

Bioinformatics, 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

A Quadsection Algorithm for Grammar-Based Image Compression.

Proceedings of the Future Generation Information Technology, 2010

Finding optimal control policy in Probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming.

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2009

A grammatical approach to RNA-RNA interaction prediction.

Pattern Recognition, 2009

Algorithms for Singleton Attractor Detection in Planar and Nonplanar AND/OR Boolean Networks.

Mathematics in Computer Science, 2009

Dynamic Programming Algorithms and Grammatical Modeling for Protein Beta-Sheet Prediction.

Journal of Computational Biology, 2009

Detecting a Singleton Attractor in a Boolean Network Utilizing SAT Algorithms.

IEICE Transactions, 2009

On Finding a Fixed Point in a Boolean Network with Maximum Indegree 2.

IEICE Transactions, 2009

Prediction of RNA secondary structure with pseudoknots using integer programming.

BMC Bioinformatics, 2009

Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology.

BMC Bioinformatics, 2009

Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs.

Biosystems, 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.

Journal of Chemical Information and Modeling, 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.

IJBRA, 2008

Algorithms and Complexity Analyses for Control of Singleton Attractors in Boolean Networks.

EURASIP J. Bioinformatics and Systems Biology, 2008

Origin of structural difference in metabolic networks with respect to temperature.

BMC Systems Biology, 2008

HSEpred: predict half-sphere exposure from protein sequences.

Bioinformatics, 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.

IJDMB, 2007

Approximation Algorithms for Optimal RNA Secondary Structures Common to Multiple Sequences.

IEICE Transactions, 2007

Algorithms for Finding Small Attractors in Boolean Networks.

EURASIP J. Bioinformatics and Systems Biology, 2007

Genetic Regulatory Networks.

EURASIP J. Bioinformatics and Systems Biology, 2007

On the complexity of deriving position specific score matrices from positive and negative sequences.

Discrete Applied Mathematics, 2007

Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition.

BMC Bioinformatics, 2007

Correlation between structure and temperature in prokaryotic metabolic networks.

BMC Bioinformatics, 2007

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

Bioinformatics, 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

^{n})-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.

, 2006

Protein Threading with Profiles and Distance Constraints Using Clique Based Algorithms.

J. Bioinformatics and Computational Biology, 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 Transactions, 2006

Optimizing amino acid substitution matrices with a local alignment kernel.

BMC Bioinformatics, 2006

Identification of metabolic units induced by environmental signals.

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

Approximating Tree Edit Distance Through String Edit Distance.

Proceedings of the Algorithms and Computation, 17th International Symposium, 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.

Journal of Chemical Information and Modeling, 2005

Protein Side-chain Packing Problem: a Maximum Edge-weight Clique Algorithmic Approach.

J. Bioinformatics and Computational Biology, 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.

Bioinformatics, 2005

A score matrix to reveal the hidden links in glycans.

Bioinformatics, 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 Record, 2004

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.

Nucleic Acids Research, 2004

Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data.

Journal of Computational Biology, 2004

Clustering under the line graph transformation: application to reaction network.

BMC Bioinformatics, 2004

Protein homology detection using string alignment kernels.

Bioinformatics, 2004

Optimizing substitution matrices by separating score distributions.

Bioinformatics, 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

Fast Algorithms for Comparison of Similar Unordered Trees.

Proceedings of the Algorithms and Computation, 15th International Symposium, 2004

Extensions of marginalized graph kernels.

Proceedings of the Machine Learning, 2004

Algorithms for Point Set Matching with k-Differences.

Proceedings of the Computing and Combinatorics, 10th Annual International Conference, 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.

Discrete Applied Mathematics, 2003

Efficient extraction of mapping rules of atoms from enzymatic reaction data.

Proceedings of the Sventh Annual International Conference on Computational Biology, 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

Performance Analysis of a Greedy Algorithm for Inferring Boolean Functions.

Proceedings of the Discovery Science, 6th International Conference, 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.

Journal of Computational Biology, 2000

Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots.

Discrete Applied Mathematics, 2000

Inferring qualitative relations in genetic networks and metabolic pathways.

Bioinformatics, 2000

Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function.

Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 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.

Discrete & Computational Geometry, 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

Approximation and Exact Algorithms for RNA Secondary Structure Prediction and Recognition of Stochastic Context-Free Languages.

Proceedings of the Algorithms and Computation, 9th International Symposium, 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.

Computer Applications in the Biosciences, 1997

On the approximation of protein threading.

Proceedings of the First Annual International Conference on Research in Computational Molecular Biology, 1997

Distribution of Distances and Triangles in a Point Set and Algorithms for Computing the Largest Common Point Sets.

Proceedings of the Thirteenth Annual Symposium on Computational Geometry, 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 Transactions, 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 Generation Comput., 1994

On the Approximation of Largest Common Subtrees and Largest Common Point Sets.

Proceedings of the Algorithms and Computation, 5th International Symposium, 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

Approximate String Matching with Don't Care Characters.

Proceedings of the Combinatorial Pattern Matching, 5th Annual Symposium, 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.

Journal of Chemical Information and Computer Sciences, 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.

FGCS, 1988