| 2022 | ISAAC | On the Complexity of Tree Edit Distance with Variables. | Tatsuya Akutsu, Tomoya Mori, Naotoshi Nakamura, Satoshi Kozawa, Yuhei Ueno, Thomas N. Sato |
| 2018 | BIBE | Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes. | Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Tatsuya Akutsu |
| 2018 | BIBE | Convolutional Neural Network Approach to Lung Cancer Classification Integrating Protein Interaction Network and Gene Expression Profiles. | Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher |
| 2018 | CPM | A Simple Linear-Time Algorithm for Computing the Centroid and Canonical Form of a Plane Graph and Its Applications. | Tatsuya Akutsu, Colin de la Higuera, Takeyuki Tamura |
| 2018 | ISAAC | New and Improved Algorithms for Unordered Tree Inclusion. | Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura |
| 2016 | BIBE | Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network. | Jira Jindalertudomdee, Morihiro Hayashida, Jiangning Song, Tatsuya Akutsu |
| 2016 | BIBE | Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks. | Takeyuki Tamura, Tatsuya Akutsu, Chun-Yu Lin, Jinn-Moon Yang |
| 2016 | ICDE | Similar subtree search using extended tree inclusion. | Tomoya Mori, Atsuhiro Takasu, Jesper Jansson, Jaewook Hwang, Takeyuki Tamura, Tatsuya Akutsu |
| 2013 | CISIS | Network Completion for Time Varying Genetic Networks. | Natsu Nakajima, Tatsuya Akutsu |
| 2013 | FCT | On the Complexity of Finding a Largest Common Subtree of Bounded Degree. | Tatsuya Akutsu, Takeyuki Tamura, Avraham A. Melkman, Atsuhiro Takasu |
| 2012 | CPM | Efficient Exponential Time Algorithms for Edit Distance between Unordered Trees. | Tatsuya Akutsu, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu |
| 2012 | ISAAC | On the Complexity of the Maximum Common Subgraph Problem for Partial k-Trees of Bounded Degree. | Tatsuya Akutsu, Takeyuki Tamura |
| 2012 | MFCS | A Polynomial-Time Algorithm for Computing the Maximum Common Subgraph of Outerplanar Graphs of Bounded Degree. | Tatsuya Akutsu, Takeyuki Tamura |
| 2011 | CISIS | An Improved Clique-Based Method for Computing Edit Distance between Unordered Trees and Its Application to Comparison of Glycan Structures. | Tatsuya Akutsu, Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita |
| 2010 | ICPR | A Variational Bayesian EM Algorithm for Tree Similarity. | Atsuhiro Takasu, Daiji Fukagawa, Tatsuya Akutsu |
| 2010 | PSB | Dynamic Programming Algorithms for RNA Structure Prediction with Binding Sites. | Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu |
| 2009 | ALT | Completing Networks Using Observed Data. | Tatsuya Akutsu, Takeyuki Tamura, Katsuhisa Horimoto |
| 2009 | CIKM | Efficient computation of impact degrees for multiple reactions in metabolic networks with cycles. | Yang Cong, Takeyuki Tamura, Tatsuya Akutsu, Wai-Ki Ching |
| 2009 | CISIS | Measuring Structural Robustness of Metabolic Networks under a Boolean Model Using Integer Programming and Feedback Vertex Sets. | Takeyuki Tamura, Kazuhiro Takemoto, Tatsuya Akutsu |
| 2009 | DIS | Latent Topic Extraction from Relational Table for Record Matching. | Atsuhiro Takasu, Daiji Fukagawa, Tatsuya Akutsu |
| 2009 | ISAAC | Enumerating Stereoisomers of Tree Structured Molecules Using Dynamic Programming. | Tomoki Imada, Shunsuke Ota, Hiroshi Nagamochi, Tatsuya Akutsu |
| 2009 | SPIRE | Constant Factor Approximation of Edit Distance of Bounded Height Unordered Trees. | Daiji Fukagawa, Tatsuya Akutsu, Atsuhiro Takasu |
| 2008 | APBC | Preface. | Alvis Brazma, Satoru Miyano, Tatsuya Akutsu |
| 2008 | APBC | Image Compression-based Approach to Measuring the Similarity of Protein Structures. | Morihiro Hayashida, Tatsuya Akutsu |
| 2007 | APBC | Inferring a Chemical Structure from a Feature Vector Based on Frequency of Labeled Paths and Small Fragments. | Tatsuya Akutsu, Daiji Fukagawa |
| 2007 | APBC | A Novel Clustering Method for Analysis of Biological Networks using Maximal Components of Graphs. | Morihiro Hayashida, Tatsuya Akutsu, Hiroshi Nagamochi |
| 2007 | FCT | An O(1.787 | Takeyuki Tamura, Tatsuya Akutsu |
| 2007 | ICDM | Statistical Learning Algorithm for Tree Similarity. | Atsuhiro Takasu, Daiji Fukagawa, Tatsuya Akutsu |
| 2007 | TAMC | An Efficient Algorithm for Generating Colored Outerplanar Graphs. | Jiexun Wang, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu |
| 2006 | APBC | On the Complexity of Finding Control Strategies for Boolean Networks. | Tatsuya Akutsu, Morihiro Hayashida, Wai-Ki Ching, Michael K. Ng |
| 2006 | ISAAC | Approximating Tree Edit Distance Through String Edit Distance. | Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu |
| 2006 | ISMB | Identification of metabolic units induced by environmental signals. | Jose C. Nacher, Jean-Marc Schwartz, Minoru Kanehisa, Tatsuya Akutsu |
| 2005 | APBC | Clique-based algorithms for protein threading with profiles and constraints. | Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, Tatsuya Akutsu |
| 2005 | CPM | Inferring a Graph from Path Frequency. | Tatsuya Akutsu, Daiji Fukagawa |
| 2005 | GRC | A linear control model for gene intervention in a genetic regulatory network. | Shuqin Zhang, Michael K. Ng, Wai-Ki Ching, Tatsuya Akutsu |
| 2004 | APBC | Protein Side-chain Packing Problem: A Maximum Edge-weight Clique Algorithmic Approach. | Dukka Bahadur, Tatsuya Akutsu, Etsuji Tomita, Tomokazu Seki |
| 2004 | BIBE | Protein Threading with Profiles and Constraints. | Tatsuya Akutsu, Morihiro Hayashida, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto |
| 2004 | COCOON | Algorithms for Point Set Matching with k-Differences. | Tatsuya Akutsu |
| 2004 | ICML | Extensions of marginalized graph kernels. | Pierre Mah, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert |
| 2004 | ISAAC | Fast Algorithms for Comparison of Similar Unordered Trees. | Daiji Fukagawa, Tatsuya Akutsu |
| 2004 | ISMB | Application of a new probabilistic model for recognizing complex patterns in glycans. | Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, Hiroshi Mamitsuka |
| 2003 | DIS | Performance Analysis of a Greedy Algorithm for Inferring Boolean Functions. | Daiji Fukagawa, Tatsuya Akutsu |
| 2003 | ECCB | Inferring strengths of protein-protein interactions from experimental data using linear programming. | Morihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu |
| 2003 | ECCB | Finding optimal degenerate patterns in DNA sequences. | Daisuke Shinozaki, Tatsuya Akutsu, Osamu Maruyama |
| 2003 | RECOMB | Efficient extraction of mapping rules of atoms from enzymatic reaction data. | Tatsuya Akutsu |
| 2002 | COCOON | Inferring a Union of Halfspaces from Examples. | Tatsuya Akutsu, Sascha Ott |
| 2002 | CPM | On the Complexity of Deriving Position Specific Score Matrices from Examples. | Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott |
| 2000 | DIS | A Simple Greedy Algorithm for Finding Functional Relations: Efficient Implementation and Average Case Anaylsis. | Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara |
| 2000 | RECOMB | On approximation algorithms for local multiple alignment. | Tatsuya Akutsu, Hiroki Arimura, Shinichi Shimozono |
| 2000 | RECOMB | Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. | Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara |
| 1999 | CPM | Matching of Spots in 2D Electrophoresis Images. Point Matching Under Non-uniform Distortions. | Tatsuya Akutsu, Kyotetsu Kanaya, Akira Ohyama, Asao Fujiyama |
| 1999 | PSB | Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model. | Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara |
| 1998 | ICALP | On the Complexity of Deriving Score Functions from Examples for Problems in Molecular Biology. | Tatsuya Akutsu, Mutsunori Yagiura |
| 1998 | ISAAC | Approximation and Exact Algorithms for RNA Secondary Structure Prediction and Recognition of Stochastic Context-Free Languages. | Tatsuya Akutsu |
| 1998 | SODA | Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions. | Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano |
| 1997 | RECOMB | On the approximation of protein threading. | Tatsuya Akutsu, Satoru Miyano |
| 1996 | COCOON | Approximating Minimum Keys and Optimal Substructure Screens. | Tatsuya Akutsu, Feng Bao |
| 1994 | CPM | Approximate String Matching with Don't Care Characters. | Tatsuya Akutsu |
| 1994 | ISAAC | On Determining the Congruity of Point Sets in Higher Dimensions. | Tatsuya Akutsu |
| 1994 | ISAAC | On the Approximation of Largest Common Subtrees and Largest Common Point Sets. | Tatsuya Akutsu, Magns M. Halldrsson |
| 1993 | CPM | A Linear Time Pattern Matching Algorithm Between a String and a Tree. | Tatsuya Akutsu |
| 1992 | ALT | On PAC Learnability of Functional Dependencies. | Tatsuya Akutsu, Atsuhiro Takasu |
| 1992 | ISAAC | Algorithms for Determining the Geometrical Congruity in Two and Three Dimensions. | Tatsuya Akutsu |
| 1991 | IROS | Development and comparison of search algorithms for robot motion planning in the configuration space. | Tatsuya Akutsu, Satoshi Yaoi, Kazunari Sato, Susumu Enomoto |