Sequential Prolog Machine PEK. - Naoyuki Tamura; Koichi Wada 003; Hideo Matsuda; Yukio Kaneda; Sadao Maekawa (FGCS, 1984)

Parallel Prolog Machine PARK: Its Hardware Structure and Prolog System. - Hideo Matsuda; M. Kohata; T. Masuo; Yukio Kaneda; Sadao Maekawa (LP, 1985)

Sequential Prolog Machine PEK. - Yukio Kaneda; Naoyuki Tamura; Koichi Wada 003; Hideo Matsuda; Shumin Kuo; Sadao Maekawa (New Gener. Comput., 1986)

Implementing Parallel Prolog System on Multiprocessor System PARK. - Hideo Matsuda; M. Kohata; T. Masuo; Yukio Kaneda; Sadao Maekawa (IWDM, 1987)

A Priority Control System for OR-Parallel Prolog and Its Performance Evaluation. - Yukio Kaneda; Hideo Matsuda; Shigeo Suzuka (Parallel Symbolic Computing, 1992)

Fast phylogenetic analysis on a massively parallel machine. - Hideo Matsuda; Gary J. Olsen; Ross A. Overbeek; Yukio Kaneda (International Conference on Supercomputing, 1994)

Overview of the JUMP-1, an MPP prototype for general-purpose parallel computations. - Kei Hiraki; Hideharu Amano; Morihiro Kuga; Toshinori Sueyoshi; Tomohiro Kudoh; Hiroshi Nakashima; Hironori Nakajo; Hideo Matsuda; Takashi Matsumoto 002; Shin-ichiro Mori (ISPAN, 1994)

fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. - Gary J. Olsen; Hideo Matsuda; Ray Hagstrom; Ross A. Overbeek (Comput. Appl. Biosci., 1994)

An Application of an OR-Parallel Prolog Systemto Phylogenetic Analysis. - Hideo Matsuda; Yukio Kaneda (LISP Symb. Comput., 1994)

High Performance I/O System of the Distributed Shared-Memory Massively Parallel Computer JUMP-1. - Hironori Nakajo; Takashi Matsumoto 002; Masaki Kohata; Hideo Matsuda; Kei Hiraki; Yukio Kaneda (Parallel and Distributed Computing and Systems, 1995)

Classifying Molecular Sequences Using a Linkage Graph With Their Pairwise Similarities. - Hideo Matsuda; T. Ishihara; Akihiro Hashimoto (Theor. Comput. Sci., 1999)

A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy. - Yukako Tohsato; Hideo Matsuda; Akihiro Hashimoto (ISMB, 2000)

Hierarchical Approach to Parallel Tree Search for Protein Conformational Analysis. - Makoto Ando; Yutaka Akiyama; Hideo Matsuda (PDPTA, 2000)

Quick selection of representative protein chain sets based on customizable requirements. - Tamotsu Noguchi; Kentaro Onizuka; Makoto Ando; Hideo Matsuda; Yutaka Akiyama (Bioinform., 2000)

An efficient procedure for maintaining materialized views on distributed database systems. - Takeya Kasukawa; Michio Nakanishi; Hideo Matsuda; Akihiro Hashimoto (Syst. Comput. Jpn., 2000)

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB). - Tamotsu Noguchi; Hideo Matsuda; Yutaka Akiyama (Nucleic Acids Res., 2001)

An Application of a Pathway Alignment Method to Comparative Analysis between Genome and Pathways. - Shoko Miyake; Yukako Tohsato; Hideo Matsuda (CSB, 2002)

P-quasi Complete Linkage Analysis for Gene-Expression Data. - Shigeto Seno; Reiji Teramoto; Hideo Matsuda (CSB, 2002)

Using Data Compression for Multidimensional Distribution Analysis. - Kentaro Onizuka; Tamotsu Noguchi; Yutaka Akiyama; Hideo Matsuda (IEEE Intell. Syst., 2002)

Clustering Method for Comparative Analysis between Genomes and Pathways. - Shoko Miyake; Yukako Tohsato; Yoichi Takenaka; Hideo Matsuda (DASFAA, 2003)

MaXML: mouse annotation XML. - Takeya Kasukawa; Hidemasa Bono; Yoshihide Hayashizaki; Yasushi Okazaki; Hideo Matsuda (Silico Biol., 2003)

A Graph Analysis Method to Detect Metabolic Sub-Networks Based on Phylogenetic Profile. - Shoko Miyake; Yoichi Takenaka; Hideo Matsuda (CSB, 2004)

Inference of Gene Regulatory Network Based on Module Network Model with Gene Functional Classifications. - Kohei Taki; Reiji Teramoto; Yoichi Takenaka; Hideo Matsuda (CSB, 2004)

Heterogeneous Database Federation Using Grid Technology for Drug Discovery Process. - Yukako Tohsato; Takahiro Kosaka; Susumu Date; Shinji Shimojo; Hideo Matsuda (LSGRID, 2004)

Graph-based clustering for finding distant relationships in a large set of protein sequences. - Hideya Kawaji; Yoichi Takenaka; Hideo Matsuda (Bioinform., 2004)

FREP: a database of functional repeats in mouse cDNAs. - Takeshi Nagashima; Hideo Matsuda; Diego G. Silva; Nikolai Petrovsky; Akihiko Konagaya; Christian Schönbach (Nucleic Acids Res., 2004)

A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science. - Haruki Nakamura; Susumu Date; Hideo Matsuda; Shinji Shimojo (New Gener. Comput., 2004)

A Grid Environment for Data Integration of Scientific Databases. - Hideo Matsuda (e-Science, 2005)

A Grid-based Information Integration System for Drug Discovery. - Gen Kawamura; Masato Kitajima; Kentaro Wakatsuki; Takehiro Furudate; Takahiro Kosaka; Kazuto Yamazaki; Reiji Teramoto; Susumu Date; Shinji Shimojo; Hideo Matsuda (ICDE Workshops, 2005)

Designing a Rule-Based Environment to Interoperate Life-Scientific Ontologies for Drug Discovery. - Takahiro Kosaka; Susumu Date; Hideo Matsuda; Shinji Shimojo (SAINT Workshops, 2005)

Tissue-specific functions based on information content of gene ontology using cap analysis gene expression. - Sami Maekawa; Atsuko Matsumoto; Yoichi Takenaka; Hideo Matsuda (Medical Biol. Eng. Comput., 2007)

BioCompass: A Novel Functional Inference Tool that Utilizes MeSH Hierarchy to Analyze Groups of Genes. - Takeru Nakazato; Toru Takinaka; Hironori Mizuguchi; Hideo Matsuda; Hidemasa Bono; Minoru Asogawa (Silico Biol., 2008)

Gendoo: Functional profiling of gene and disease features using MeSH vocabulary. - Takeru Nakazato; Hidemasa Bono; Hideo Matsuda; Toshihisa Takagi (Nucleic Acids Res., 2009)

Improved Prediction Method for Protein Interactions Using Both Structural and Functional Characteristics of Proteins. - Tatsuya Yoshikawa; Shigeto Seno; Yoichi Takenaka; Hideo Matsuda (Inf. Media Technol., 2010)

An estimation method for inference of gene regulatory net-work using Bayesian network with uniting of partial problems. - Yukito Watanabe; Shigeto Seno; Yoichi Takenaka; Hideo Matsuda (BMC Genom., 2012)

A Method for Isoform Prediction from RNA-Seq Data by Iterative Mapping. - Tomoshige Ohno; Shigeto Seno; Yoichi Takenaka; Hideo Matsuda (Inf. Media Technol., 2012)

A Segmentation Method for Bone Marrow Cavity Imaging Using Graph Cuts. - Tomohiro Mashita; Jun Usam; Hironori Shigeta; Yoshihiro Kuroda; Junichi Kikuta; Shigeto Seno; Masaru Ishii; Hideo Matsuda; Haruo Takemura (I3A@ICPR, 2014)

A Graph Cuts Image Segmentation Method for Quantifying Barrier Permeation in Bone Tissue. - Hironori Shigeta; Tomohiro Mashita; Takeshi Kaneko; Junichi Kikuta; Shigeto Seno; Haruo Takemura; Hideo Matsuda; Masaru Ishii (I3A@ICPR, 2014)

Detecting shifts in gene regulatory networks during time-course experiments at single-time-point temporal resolution. - Yoichi Takenaka; Shigeto Seno; Hideo Matsuda (J. Bioinform. Comput. Biol., 2015)

Comparative Analysis of Transformation Methods for Gene Expression Profiles in Breast Cancer Datasets. - Yoshiaki Sota; Shigeto Seno; Yoichi Takenaka; Shinzaburo Noguchi; Hideo Matsuda (BIBE, 2016)

A bone marrow cavity segmentation method using wavelet-based texture feature. - Hironori Shigeta; Tomohiro Mashita; Junichi Kikuta; Shigeto Seno; Haruo Takemura; Hideo Matsuda; Masaru Ishii (ICPR, 2016)

Bone marrow cavity segmentation using graph-cuts with wavelet-based texture feature. - Hironori Shigeta; Tomohiro Mashita; Junichi Kikuta; Shigeto Seno; Haruo Takemura; Masaru Ishii; Hideo Matsuda (J. Bioinform. Comput. Biol., 2017)

Detection of Fusion Genes from Human Breast Cancer Cell-Line RNA-Seq Data Using Shifted Short Read Clustering. - Yoshiaki Sota; Shigeto Seno; Hironori Shigeta; Naoki Osato; Masafumi Shimoda; Shinzaburo Noguchi; Hideo Matsuda (BIBE, 2018)

Asymmetric Integration of Single-Cell Transcriptomic Data using Latent Dirichlet Allocation and Procrustes Analysis. - Mitsuhiro Eto; Wataru Hirota; Shigeto Seno; Hideo Matsuda (BIBM, 2018)

Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells. - Yoichi Takenaka; Kazuma Mikami; Shigeto Seno; Hideo Matsuda (BMC Bioinform., 2018)

Analyzing Leukocyte Migration Trajectories by Deformable Image Matching. - Hironori Shigeta; Shigeto Seno; Shino Nishizawa; Yutaka Uchida; Junichi Kikuta; Masaru Ishii; Hideo Matsuda (BIBE, 2019)

Single-cell Transcriptome Analysis of Mouse Leukocytes in Inflammatory Stimulation. - Naoki Osato; Hironori Shigeta; Shigeto Seno; Yutaka Uchida; Junichi Kikuta; Masaru Ishii; Hideo Matsuda (BIBM, 2019)

Improvement of detection performance of fusion genes from RNA-seq data by clustering short reads. - Yoshiaki Sota; Shigeto Seno; Hironori Shigeta; Naoki Osato; Masafumi Shimoda; Shinzaburo Noguchi; Hideo Matsuda (J. Bioinform. Comput. Biol., 2019)

Chromatin 3D Reconstruction from Chromosomal Contacts Using a Genetic Algorithm. - Viacheslav Kapilevich; Shigeto Seno; Hideo Matsuda; Yoichi Takenaka (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

A CNN-based cell tracking method for multi-slice intravital imaging data. - Kenji Fujimoto; Tsubasa Mizugaki; Utkrisht Rajkumar; Hironori Shigeta; Shigeto Seno; Yutaka Uchida; Masaru Ishii; Vineet Bafna; Hideo Matsuda (BCB, 2021)

A Method for Detection of Markers for Epithelial-Mesenchymal Transition based on Single Cell Transcriptomic Data. - Kosho Murayama; Hideo Matsuda (ICBBB, 2022)

A Novel Method for Fusion Gene Detection using Both End-Fragment Sequences of Long Reads. - Keigo Masuda; Yoshiaki Sota; Hideo Matsuda (ICBBE, 2022)

Inference of Cell-Cell Communication for Detecting Immune Disease-Associated Signaling Pathways using Single-Cell RNA-seq. - Akihiro Nomura 003; Hideo Matsuda (ICBBE, 2022)

Cell Tracking via Reinforcement Learning with Microscopic Image Simulator. - Toru Nagamura; Shigeto Seno; Hironori Shigeta; Tomohiro Mashita; Hideo Matsuda (ICBET, 2023)

Pseudotime-based Deep Learning of Gene Regulatory Relationships from Single-Cell Expression Data. - Koki Nishi; Junko Yoshida; Shigeto Seno; Kyoji Horie; Hideo Matsuda (ICBET, 2023)

Accurate Detection of Fusion Genes in Long-Read Transcriptome Datasets from Multiple Cancer Cell Lines. - Keigo Masuda; Yoshiaki Sota; Hideo Matsuda (ICBBB, 2024)

Communication Analysis between Human Hair-Follicles and Immune Cells with Single-cell RNA-seq. - Ayaka Mori-Ichioka; Hironori Shigeta; Shigeto Seno; Hideo Matsuda (ICBBE, 2024)

Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach. - Kazufumi Hosoda; Shigeto Seno; Naomi Murakami; Hideo Matsuda; Yutaka Osada; Rikuto Kamiura; Michio Kondoh (Biosyst., 2024)

Learning from Similarity Proportion Loss for Classifying Skeletal Muscle Recovery Stages. - Yu Yamaoka; Weng Ian Chan; Shigeto Seno; Soichiro Fukada; Hideo Matsuda (CoRR, 2025)