SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. - Yasuo Tabei; Koji Tsuda; Taishin Kin; Kiyoshi Asai (Bioinform., 2006)

Murlet: a practical multiple alignment tool for structural RNA sequences. - Hisanori Kiryu; Yasuo Tabei; Taishin Kin; Kiyoshi Asai (Bioinform., 2007)

A fast structural multiple alignment method for long RNA sequences. - Yasuo Tabei; Hisanori Kiryu; Taishin Kin; Kiyoshi Asai (BMC Bioinform., 2008)

Software.ncrna.org: web servers for analyses of RNA sequences. - Kiyoshi Asai; Hisanori Kiryu; Michiaki Hamada; Yasuo Tabei; Kengo Sato; Hiroshi Matsui; Yasubumi Sakakibara; Goro Terai; Toutai Mituyama (Nucleic Acids Res., 2008)

A local multiple alignment method for detection of non-coding RNA sequences. - Yasuo Tabei; Kiyoshi Asai (Bioinform., 2009)

Single versus Multiple Sorting in All Pairs Similarity Search. - Yasuo Tabei; Takeaki Uno; Masashi Sugiyama; Koji Tsuda (ACML, 2010)

LGM: Mining Frequent Subgraphs from Linear Graphs. - Yasuo Tabei; Daisuke Okanohara; Shuichi Hirose; Koji Tsuda (PAKDD (2), 2011)

Kernel-based Similarity Search in Massive Graph Databases with Wavelet Trees. - Yasuo Tabei; Koji Tsuda (SDM, 2011)

Variable-Length Codes for Space-Efficient Grammar-Based Compression. - Yoshimasa Takabatake; Yasuo Tabei; Hiroshi Sakamoto (SPIRE, 2012)

Succinct Multibit Tree: Compact Representation of Multibit Trees by Using Succinct Data Structures in Chemical Fingerprint Searches. - Yasuo Tabei (WABI, 2012)

Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers. - Yasuo Tabei; Edouard Pauwels; Véronique Stoven; Kazuhiro Takemoto; Yoshihiro Yamanishi (Bioinform., 2012)

PoSSuM: a database of similar protein-ligand binding and putative pockets. - Jun-Ichi Ito; Yasuo Tabei; Kana Shimizu; Koji Tsuda; Kentaro Tomii (Nucleic Acids Res., 2012)

A Succinct Grammar Compression. - Yasuo Tabei; Yoshimasa Takabatake; Hiroshi Sakamoto (CPM, 2013)

Succinct interval-splitting tree for scalable similarity search of compound-protein pairs with property constraints. - Yasuo Tabei; Akihiro Kishimoto; Masaaki Kotera; Yoshihiro Yamanishi (KDD, 2013)

Fully-Online Grammar Compression. - Shirou Maruyama; Yasuo Tabei; Hiroshi Sakamoto; Kunihiko Sadakane (SPIRE, 2013)

Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets. - Masaaki Kotera; Yasuo Tabei; Yoshihiro Yamanishi; Toshiaki Tokimatsu; Susumu Goto (Bioinform., 2013)

Inferring protein domains associated with drug side effects based on drug-target interaction network. - Hiroaki Iwata; Sayaka Mizutani; Yasuo Tabei; Masaaki Kotera; Susumu Goto; Yoshihiro Yamanishi (BMC Syst. Biol., 2013)

KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. - Masaaki Kotera; Yasuo Tabei; Yoshihiro Yamanishi; Yuki Moriya; Toshiaki Tokimatsu; Minoru Kanehisa; Susumu Goto (BMC Syst. Biol., 2013)

Scalable prediction of compound-protein interactions using minwise hashing. - Yasuo Tabei; Yoshihiro Yamanishi (BMC Syst. Biol., 2013)

Fully Online Grammar Compression in Constant Space. - Shirou Maruyama; Yasuo Tabei (DCC, 2014)

Finding Ambiguous Patterns on Grammar Compressed String. - Koji Maeda; Yoshimasa Takabatake; Yasuo Tabei; Hiroshi Sakamoto (JSAI-isAI Workshops, 2014)

Online Pattern Matching for String Edit Distance with Moves. - Yoshimasa Takabatake; Yasuo Tabei; Hiroshi Sakamoto (SPIRE, 2014)

Improved ESP-index: A Practical Self-index for Highly Repetitive Texts. - Yoshimasa Takabatake; Yasuo Tabei; Hiroshi Sakamoto (SEA, 2014)

Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach. - Masaaki Kotera; Yasuo Tabei; Yoshihiro Yamanishi; Ai Muto; Yuki Moriya; Toshiaki Tokimatsu; Susumu Goto (Bioinform., 2014)

Rank, select and access in grammar-compressed strings. - Djamal Belazzougui; Simon J. Puglisi; Yasuo Tabei (CoRR, 2014)

Queries on LZ-Bounded Encodings. - Djamal Belazzougui; Travis Gagie; Pawel Gawrychowski; Juha Kärkkäinen; Alberto Ordóñez Pereira; Simon J. Puglisi; Yasuo Tabei (DCC, 2015)

Access, Rank, and Select in Grammar-compressed Strings. - Djamal Belazzougui; Patrick Hagge Cording; Simon J. Puglisi; Yasuo Tabei (ESA, 2015)

Online Self-Indexed Grammar Compression. - Yoshimasa Takabatake; Yasuo Tabei; Hiroshi Sakamoto (SPIRE, 2015)

Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments. - Yoshihiro Yamanishi; Yasuo Tabei; Masaaki Kotera (Bioinform., 2015)

Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices. - Yasuo Tabei; Hiroto Saigo; Yoshihiro Yamanishi; Simon J. Puglisi (KDD, 2016)

siEDM: An Efficient String Index and Search Algorithm for Edit Distance with Moves. - Yoshimasa Takabatake; Kenta Nakashima; Tetsuji Kuboyama; Yasuo Tabei; Hiroshi Sakamoto (Algorithms, 2016)

Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction. - Yasuo Tabei; Yoshihiro Yamanishi; Masaaki Kotera (Bioinform., 2016)

Bayesian Dynamic Mode Decomposition. - Naoya Takeishi; Yoshinobu Kawahara; Yasuo Tabei; Takehisa Yairi (IJCAI, 2017)

Scalable Similarity Search for Molecular Descriptors. - Yasuo Tabei; Simon J. Puglisi (SISAP, 2017)

A Dynamic Compressed Self-Index for Highly Repetitive Text Collections. - Takaaki Nishimoto; Yoshimasa Takabatake; Yasuo Tabei (DCC, 2018)

Entire Regularization Path for Sparse Nonnegative Interaction Model. - Mirai Takayanagi; Yasuo Tabei; Hiroto Saigo (ICDM, 2018)

Scalable Machine Learning on Compact Data Representations. - Yasuo Tabei (ISITA, 2018)

Scalable Alignment Kernels via Space-Efficient Feature Maps. - Yasuo Tabei; Yoshihiro Yamanishi; Rasmus Pagh (CoRR, 2018)

b-Bit Sketch Trie: Scalable Similarity Search on Integer Sketches. - Shunsuke Kanda; Yasuo Tabei (IEEE BigData, 2019)

Conversion from RLBWT to LZ77. - Takaaki Nishimoto; Yasuo Tabei (CPM, 2019)

Statistically Discriminative Sub-trajectory Mining with Multiple Testing Correction. - Vo Nguyen Le Duy; Takuto Sakuma; Taiju Ishiyama; Hiroki Toda; Kazuya Arai; Masayuki Karasuyama; Yuta Okubo; Masayuki Sunaga; Yasuo Tabei; Ichiro Takeuchi (SIGSPATIAL/GIS, 2019)

Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm. - Michio Iwata; Longhao Yuan; Qibin Zhao; Yasuo Tabei; Francois Berenger; Ryusuke Sawada; Sayaka Akiyoshi; Momoko Hamano; Yoshihiro Yamanishi (Bioinform., 2019)

Network-based characterization of drug-protein interaction signatures with a space-efficient approach. - Yasuo Tabei; Masaaki Kotera; Ryusuke Sawada; Yoshihiro Yamanishi (BMC Syst. Biol., 2019)

Approximate-Closed-Itemset Mining for Streaming Data Under Resource Constraint. - Yoshitaka Yamamoto; Yasuo Tabei; Koji Iwanuma (CoRR, 2019)

Statistically Discriminative Sub-trajectory Mining. - Vo Nguyen Le Duy; Takuto Sakuma; Taiju Ishiyama; Hiroki Toda; Kazuya Nishi; Masayuki Karasuyama; Yuta Okubo; Masayuki Sunaga; Yasuo Tabei; Ichiro Takeuchi (CoRR, 2019)

Succinct Trit-array Trie for Scalable Trajectory Similarity Search. - Shunsuke Kanda; Koh Takeuchi 001; Keisuke Fujii 001; Yasuo Tabei (SIGSPATIAL/GIS, 2020)

Dynamic Similarity Search on Integer Sketches. - Shunsuke Kanda; Yasuo Tabei (ICDM, 2020)

Automatically mining Relevant Variable Interactions Via Sparse Bayesian Learning. - Ryoichiro Yafune; Daisuke Sakuma; Mirai Takayanagi; Yasuo Tabei; Noritaka Saito; Hiroto Saigo (ICPR, 2020)

Enumeration of LCP values, LCP intervals and Maximal repeats in BWT-runs Bounded Space. - Takaaki Nishimoto; Yasuo Tabei (CoRR, 2020)

Faster Queries on BWT-runs Compressed Indexes. - Takaaki Nishimoto; Yasuo Tabei (CoRR, 2020)

Space-Efficient Feature Maps for String Alignment Kernels. - Yasuo Tabei; Yoshihiro Yamanishi; Rasmus Pagh (Data Sci. Eng., 2020)

A compressed dynamic self-index for highly repetitive text collections. - Takaaki Nishimoto; Yoshimasa Takabatake; Yasuo Tabei (Inf. Comput., 2020)

Dynamic Path-decomposed Tries. - Shunsuke Kanda; Dominik Köppl; Yasuo Tabei; Kazuhiro Morita; Masao Fuketa (ACM J. Exp. Algorithmics, 2020)

PARASOL: a hybrid approximation approach for scalable frequent itemset mining in streaming data. - Yoshitaka Yamamoto; Yasuo Tabei; Koji Iwanuma (J. Intell. Inf. Syst., 2020)

R-enum: Enumeration of Characteristic Substrings in BWT-runs Bounded Space. - Takaaki Nishimoto; Yasuo Tabei (CPM, 2021)

Fréchet Kernel for Trajectory Data Analysis. - Koh Takeuchi 001; Masaaki Imaizumi; Shunsuke Kanda; Yasuo Tabei; Keisuke Fujii 001; Ken Yoda; Masakazu Ishihata; Takuya Maekawa (SIGSPATIAL/GIS, 2021)

Optimal-Time Queries on BWT-Runs Compressed Indexes. - Takaaki Nishimoto; Yasuo Tabei (ICALP, 2021)

Sparse Nonnegative Interaction Models. - Mirai Takayanagi; Yasuo Tabei; Einoshin Suzuki; Hiroto Saigo (IEEE Access, 2021)

Block trees. - Djamal Belazzougui; Manuel Cáceres; Travis Gagie; Pawel Gawrychowski; Juha Kärkkäinen; Gonzalo Navarro 001; Alberto Ordóñez Pereira; Simon J. Puglisi; Yasuo Tabei (J. Comput. Syst. Sci., 2021)

DyFT: a dynamic similarity search method on integer sketches. - Shunsuke Kanda; Yasuo Tabei (Knowl. Inf. Syst., 2021)

An Optimal-Time RLBWT Construction in BWT-Runs Bounded Space. - Takaaki Nishimoto; Shunsuke Kanda; Yasuo Tabei (ICALP, 2022)

LZRR: LZ77 parsing with right reference. - Takaaki Nishimoto; Yasuo Tabei (Inf. Comput., 2022)

Stat-DSM: Statistically Discriminative Sub-Trajectory Mining With Multiple Testing Correction. - Vo Nguyen Le Duy; Takuto Sakuma; Taiju Ishiyama; Hiroki Toda; Kazuya Arai; Masayuki Karasuyama; Yuta Okubo; Masayuki Sunaga; Hiroyuki Hanada; Yasuo Tabei; Ichiro Takeuchi (IEEE Trans. Knowl. Data Eng., 2022)

Multi-agent statistical discriminative sub-trajectory mining and an application to NBA basketball. - Rory P. Bunker; Vo Nguyen Le Duy; Yasuo Tabei; Ichiro Takeuchi; Keisuke Fujii 001 (CoRR, 2023)

A Branch-and-Bound Approach to Efficient Classification and Retrieval of Documents. - Kotaro Ii; Hiroto Saigo; Yasuo Tabei (ICPRAM, 2024)

Dynamic Suffix Array in Optimal Compressed Space. - Takaaki Nishimoto; Yasuo Tabei (CoRR, 2024)

Dynamic r-index: An Updatable Self-Index for Highly Repetitive Strings. - Takaaki Nishimoto; Yasuo Tabei (CoRR, 2025)