Detour Queries in Geographical Databases for Navigation and Related Algorithm Animations. - Tetsuo Shibuya; Hiroshi Imai; Shigeki Nishimura; Hiroshi Shimoura; Kenji Tenmoku (CODAS, 1996)

A Package for Triangulations. - Tsuyoshi Ono; Yoshiaki Kyoda; Tomonari Masada; Kazuyoshi Hayase; Tetsuo Shibuya; Motoki Nakade; Mary Inaba; Hiroshi Imai; Keiko Imai; David Avis (SCG, 1996)

New Flexible Approaches for Multiple Sequence Alignment. - Tetsuo Shibuya; Hiroshi Imai (J. Comput. Biol., 1997)

Computing the n × m Shortest Paths Efficently. - Tetsuo Shibuya (ALENEX, 1999)

Optimal On-line Algorithms for an Electronic Commerce Money Distribution System. - Hiroshi Kawazoe; Tetsuo Shibuya; Takeshi Tokuyama (SODA, 1999)

Computing the nxm Shortest Paths Efficiently. - Tetsuo Shibuya (ACM J. Exp. Algorithmics, 2000)

Optimal Online Algorithms for an Electronic Commerce Money Distribution System. - Hiroshi Kawazoe; Tetsuo Shibuya; Takeshi Tokuyama (Algorithmica, 2002)

Match Chaining Algorithms for cDNA Mapping. - Tetsuo Shibuya; Igor Kurochkin (WABI, 2003)

Constructing the Suffix Tree of a Tree with a Large Alphabet. - Tetsuo Shibuya (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2003)

The web server of IBM's Bioinformatics and Pattern Discovery group. - Tien Huynh; Isidore Rigoutsos; Laxmi Parida; Daniel E. Platt; Tetsuo Shibuya (Nucleic Acids Res., 2003)

Generalization of a Suffix Tree for RNA Structural Pattern Matching. - Tetsuo Shibuya (Algorithmica, 2004)

Efficient filtering methods for clustering cDNAs with spliced sequence alignment. - Tetsuo Shibuya; Hisashi Kashima; Akihiko Konagaya (Bioinform., 2004)

Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures. - Tetsuo Shibuya (CPM, 2006)

Prefix-Shuffled Geometric Suffix Tree. - Tetsuo Shibuya (SPIRE, 2007)

Efficient Substructure RMSD Query Algorithms. - Tetsuo Shibuya (J. Comput. Biol., 2007)

Lazy Suffix Array: The Data Structure for Online Construction and Pattern Searching. - Ben Hachimori; Tetsuo Shibuya (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2009)

Linear-time protein 3-D structure searching with insertions and deletions. - Tetsuo Shibuya; Jesper Jansson 001; Kunihiko Sadakane (Algorithms Mol. Biol., 2010)

Geometric suffix tree: Indexing protein 3-D structures. - Tetsuo Shibuya (J. ACM, 2010)

Searching Protein 3-D Structures in Linear Time. - Tetsuo Shibuya (J. Comput. Biol., 2010)

Searching Protein Three-Dimensional Structures in Faster Than Linear Time. - Tetsuo Shibuya (J. Comput. Biol., 2010)

Fast Hinge Detection Algorithms for Flexible Protein Structures. - Tetsuo Shibuya (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

An Index Structure for Spaced Seed Search. - Taku Onodera; Tetsuo Shibuya (ISAAC, 2011)

A Subpath Kernel for Rooted Unordered Trees. - Daisuke Kimura; Tetsuji Kuboyama; Tetsuo Shibuya; Hisashi Kashima (PAKDD (1), 2011)

Succinct de Bruijn Graphs. - Alexander Bowe; Taku Onodera; Kunihiko Sadakane; Tetsuo Shibuya (WABI, 2012)

Population Model-Based Inter-Diplotype Similarity Measure for Accurate Diplotype Clustering. - Ritsuko Onuki; Ryo Yamada; Rui Yamaguchi; Minoru Kanehisa; Tetsuo Shibuya (J. Comput. Biol., 2012)

LB3D: A Protein Three-Dimensional Substructure Search Program Based on the Lower Bound of a Root Mean Square Deviation Value. - Genki Terashi; Tetsuo Shibuya; Mayuko Takeda-Shitaka (J. Comput. Biol., 2012)

Max-Shift BM and Max-Shift Horspool: Practical Fast Exact String Matching Algorithms. - Mohammed Sahli; Tetsuo Shibuya (J. Inf. Process., 2012)

The Gapped Spectrum Kernel for Support Vector Machines. - Taku Onodera; Tetsuo Shibuya (MLDM, 2013)

Detecting Superbubbles in Assembly Graphs. - Taku Onodera; Kunihiko Sadakane; Tetsuo Shibuya (WABI, 2013)

SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints. - Tomohiko Ohtsuki; Naoki Nariai; Kaname Kojima; Takahiro Mimori; Yukuto Sato; Yosuke Kawai; Yumi Yamaguchi-Kabata; Tetsuo Shibuya; Masao Nagasaki (AlCoB, 2014)

Improving miRNA Classification Using an Exhaustive Set of Features. - Sherin M. ElGokhy; Tetsuo Shibuya; Amin A. Shoukry (PACBB, 2014)

Editorial. - Tetsuo Shibuya; Chuan Yi Tang; Paul Horton; Kiyoshi Asai (J. Bioinform. Comput. Biol., 2014)

Malphite: A convolutional neural network and ensemble learning based protein secondary structure predictor. - Yang Li; Tetsuo Shibuya (BIBM, 2015)

Locating controlling regions of neural networks using constrained evolutionary computation. - Mohammad A. Eita; Tetsuo Shibuya; Amin A. Shoukry (CEC, 2015)

Guest Editorial for the 25th International Conference on Genome Informatics (GIW/ISCB-Asia 2014). - Tetsuo Shibuya; Chuan Yi Tang; Paul Horton; Kiyoshi Asai (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

An O(m, log m)-Time Algorithm for Detecting Superbubbles. - Wing-Kin Sung; Kunihiko Sadakane; Tetsuo Shibuya; Abha Belorkar; Iana Pyrogova (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Fast Classification of Protein Structures by an Alignment-Free Kernel. - Taku Onodera; Tetsuo Shibuya (SPIRE, 2016)

Succinct Oblivious RAM. - Taku Onodera; Tetsuo Shibuya (STACS, 2018)

Efficient Approximate 3-Dimensional Point Set Matching Using Root-Mean-Square Deviation Score. - Yoichi Sasaki 002; Tetsuo Shibuya; Kimihito Ito; Hiroki Arimura (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2019)

Preface for the Special Issue on the Project "Foundation of Innovative Algorithms for Big Data". - Naoki Katoh; Yuya Higashikawa; Hiro Ito; Shun Kataoka; Takuya Kida; Toshiki Saitoh; Tetsuo Shibuya; Kazuyuki Tanaka; Yushi Uno (Rev. Socionetwork Strateg., 2019)

Application-Oriented Succinct Data Structures for Big Data. - Tetsuo Shibuya (Rev. Socionetwork Strateg., 2019)

Transfer Learning for Biomedical Question Answering. - Arda Akdemir; Tetsuo Shibuya (CLEF (Working Notes), 2020)

Subword Contextual Embeddings for Languages with Rich Morphology. - Arda Akdemir; Tetsuo Shibuya; Tunga Güngör (ICMLA, 2020)

Wear Leveling Revisited. - Taku Onodera; Tetsuo Shibuya (ISAAC, 2020)

Hierarchical Multi Task Learning with Subword Contextual Embeddings for Languages with Rich Morphology. - Arda Akdemir; Tetsuo Shibuya; Tunga Güngör (CoRR, 2020)

Analyzing the Effect of Multi-task Learning for Biomedical Named Entity Recognition. - Arda Akdemir; Tetsuo Shibuya (CoRR, 2020)

Nanopore basecalling from a perspective of instance segmentation. - Yao-zhong Zhang; Arda Akdemir; Georg Tremmel; Seiya Imoto; Satoru Miyano; Tetsuo Shibuya; Rui Yamaguchi (BMC Bioinform., 2020)

Differentially Private Linkage Analysis with TDT - the case of two affected children per family. - Akito Yamamoto; Tetsuo Shibuya (BIBM, 2021)

UDON: Unsupervised Data SelectiON for Biomedical Entity Recognition. - Arda Akdemir; Tetsuo Shibuya (ICCBD, 2021)

Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition. - Kazushi Kitaya; Tetsuo Shibuya (WABI, 2021)

Counting on a Rainbow Connection (text not included). - Robert D. Barish; Tetsuo Shibuya (ICTCS, 2022)

Counting 2-Factors of 4-Regular Bipartite Graphs is #P-Complete. - Robert D. Barish; Tetsuo Shibuya (JCDCGGG, 2022)

Developing Language Resources and NLP Tools for the North Korean Language. - Arda Akdemir; Yeojoo Jeon; Tetsuo Shibuya (LREC, 2022)

Efficient and Highly Accurate Differentially Private Statistical Genomic Analysis using Discrete Fourier Transform. - Akito Yamamoto; Tetsuo Shibuya (TrustCom, 2022)

(ε, k)-Randomized Anonymization: ε-Differentially Private Data Sharing with k-Anonymity. - Akito Yamamoto; Eizen Kimura; Tetsuo Shibuya (HEALTHINF, 2023)

The Fine-Grained Complexity of Approximately Counting Proper Connected Colorings (Extended Abstract). - Robert D. Barish; Tetsuo Shibuya (COCOA (2), 2023)

Privacy-Preserving Genomic Statistical Analysis Under Local Differential Privacy. - Akito Yamamoto; Tetsuo Shibuya (DBSec, 2023)

A Joint Permute-and-Flip and Its Enhancement for Large-Scale Genomic Statistical Analysis. - Akito Yamamoto; Tetsuo Shibuya (ICDM (Workshops), 2023)

Unbiased Locally Private Estimator for Polynomials of Laplacian Variables. - Quentin Hillebrand; Vorapong Suppakitpaisarn; Tetsuo Shibuya (KDD, 2023)

Privacy-Preserving Publication of GWAS Statistics using Smooth Sensitivity. - Akito Yamamoto; Tetsuo Shibuya (PST, 2023)

Hardness of Bounding Influence via Graph Modification. - Robert D. Barish; Tetsuo Shibuya (SOFSEM, 2023)

Communication Cost Reduction for Subgraph Counting under Local Differential Privacy via Hash Functions. - Quentin Hillebrand; Vorapong Suppakitpaisarn; Tetsuo Shibuya (CoRR, 2023)

Privacy-Preserving Statistical Analysis of Genomic Data Using Compressive Mechanism with Haar Wavelet Transform. - Akito Yamamoto; Tetsuo Shibuya (J. Comput. Biol., 2023)

Genetic algorithm-based feature selection with manifold learning for cancer classification using microarray data. - Zixuan Wang; Yi Zhou; Tatsuya Takagi; Jiangning Song; Yu-Shi Tian; Tetsuo Shibuya (BMC Bioinform., 2023)

Polyhedral roll-connected colorings of partial tilings. - Robert D. Barish; Tetsuo Shibuya (CCCG, 2024)

Fair Selection of Clearing Schemes for Kidney Exchange Markets. - Robert D. Barish; Tetsuo Shibuya (COCOA (2), 2024)

Differentially Private Selection using Smooth Sensitivity. - Akito Yamamoto; Tetsuo Shibuya (IPCCC, 2024)

Privacy-Optimized Randomized Response for Sharing Multi-Attribute Data. - Akito Yamamoto; Tetsuo Shibuya (ISCC, 2024)

Enhancing Convergence in Variational Quantum Eigensolver Using CoolMomentum. - Daisuke Tsukayama; Jun-ichi Shirakashi; Tetsuo Shibuya; Hiroshi Imai (QCE, 2024)

Generalization and Enhancement of Piecewise Mechanism for Collecting Multidimensional Data. - Akito Yamamoto; Tetsuo Shibuya (SpaCCS, 2024)

Recognition and Proper Coloring of Unit Segment Intersection Graphs. - Robert D. Barish; Tetsuo Shibuya (SWAT, 2024)

Counting on Rainbow k-Connections. - Robert D. Barish; Tetsuo Shibuya (TAMC, 2024)

String editing under pattern constraints. - Robert D. Barish; Tetsuo Shibuya (Theor. Comput. Sci., 2024)

Proper colorability of segment intersection graphs. - Robert D. Barish; Tetsuo Shibuya (J. Comb. Optim., 2024)

Direction-Oriented Smooth Sensitivity and Its Application to Genomic Statistical Analysis. - Akito Yamamoto; Tetsuo Shibuya (ACISP (3), 2025)

Packing Dimers to Maximum Occupancy Under Soft-Core Constraints. - Robert D. Barish; Tetsuo Shibuya (CIAC (2), 2025)

Efficient and Accurate Approximation Algorithms for Protein Structure Alignment. - Masahito Tsukahara; Tetsuo Shibuya (ISBRA (1), 2025)

Cycle Counting Under Local Differential Privacy for Degeneracy-Bounded Graphs. - Quentin Hillebrand; Vorapong Suppakitpaisarn; Tetsuo Shibuya (STACS, 2025)

Linear-Space Subquadratic-Time String Alignment Algorithm for Arbitrary Scoring Matrices. - Ryosuke Yamano; Tetsuo Shibuya (WABI, 2025)

Faster and More Accurate Estimation of Protein Hinges Based on Information Criteria. - Bunsho Koyano; Tetsuo Shibuya (J. Comput. Biol., 2025)

Affine optimal k-proper connected edge colorings. - Robert D. Barish; Tetsuo Shibuya (Optim. Lett., 2025)

Communication-Efficient Publication of Sparse Vectors under Differential Privacy. - Quentin Hillebrand; Vorapong Suppakitpaisarn; Tetsuo Shibuya (CoRR, 2025)