Hideo Matsuda

Publication Activity (10 Years)

Years Active: 1984-2024
Publications (10 Years): 18

Top Topics

Segmentation Method

Escherichia Coli

Expression Profiles

Top Venues

J. Bioinform. Comput. Biol.

Publications

Keigo Masuda, Yoshiaki Sota, Hideo Matsuda
Accurate Detection of Fusion Genes in Long-Read Transcriptome Datasets from Multiple Cancer Cell Lines. ICBBB (2024)
Kazufumi Hosoda, Shigeto Seno, Naomi Murakami, Hideo Matsuda, Yutaka Osada, Rikuto Kamiura, Michio Kondoh
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach. Biosyst. 235 (2024)
Koki Nishi, Junko Yoshida, Shigeto Seno, Kyoji Horie, Hideo Matsuda
Pseudotime-based Deep Learning of Gene Regulatory Relationships from Single-Cell Expression Data. ICBET (2023)
Toru Nagamura, Shigeto Seno, Hironori Shigeta, Tomohiro Mashita, Hideo Matsuda
Cell Tracking via Reinforcement Learning with Microscopic Image Simulator. ICBET (2023)
Kosho Murayama, Hideo Matsuda
A Method for Detection of Markers for Epithelial-Mesenchymal Transition based on Single Cell Transcriptomic Data. ICBBB (2022)
Akihiro Nomura, Hideo Matsuda
Inference of Cell-Cell Communication for Detecting Immune Disease-Associated Signaling Pathways using Single-Cell RNA-seq. ICBBE (2022)
Keigo Masuda, Yoshiaki Sota, Hideo Matsuda
A Novel Method for Fusion Gene Detection using Both End-Fragment Sequences of Long Reads. ICBBE (2022)
Kenji Fujimoto, Tsubasa Mizugaki, Utkrisht Rajkumar, Hironori Shigeta, Shigeto Seno, Yutaka Uchida, Masaru Ishii, Vineet Bafna, Hideo Matsuda
A CNN-based cell tracking method for multi-slice intravital imaging data. BCB (2021)
Viacheslav Kapilevich, Shigeto Seno, Hideo Matsuda, Yoichi Takenaka
Chromatin 3D Reconstruction from Chromosomal Contacts Using a Genetic Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (5) (2019)
Yoshiaki Sota, Shigeto Seno, Hironori Shigeta, Naoki Osato, Masafumi Shimoda, Shinzaburo Noguchi, Hideo Matsuda
Improvement of detection performance of fusion genes from RNA-seq data by clustering short reads. J. Bioinform. Comput. Biol. 17 (3) (2019)
Naoki Osato, Hironori Shigeta, Shigeto Seno, Yutaka Uchida, Junichi Kikuta, Masaru Ishii, Hideo Matsuda
Single-cell Transcriptome Analysis of Mouse Leukocytes in Inflammatory Stimulation. BIBM (2019)
Hironori Shigeta, Shigeto Seno, Shino Nishizawa, Yutaka Uchida, Junichi Kikuta, Masaru Ishii, Hideo Matsuda
Analyzing Leukocyte Migration Trajectories by Deformable Image Matching. BIBE (2019)
Mitsuhiro Eto, Wataru Hirota, Shigeto Seno, Hideo Matsuda
Asymmetric Integration of Single-Cell Transcriptomic Data using Latent Dirichlet Allocation and Procrustes Analysis. BIBM (2018)
Yoichi Takenaka, Kazuma Mikami, Shigeto Seno, Hideo Matsuda
Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells. BMC Bioinform. (4) (2018)
Yoshiaki Sota, Shigeto Seno, Hironori Shigeta, Naoki Osato, Masafumi Shimoda, Shinzaburo Noguchi, Hideo Matsuda
Detection of Fusion Genes from Human Breast Cancer Cell-Line RNA-Seq Data Using Shifted Short Read Clustering. BIBE (2018)
Hironori Shigeta, Tomohiro Mashita, Junichi Kikuta, Shigeto Seno, Haruo Takemura, Masaru Ishii, Hideo Matsuda
Bone marrow cavity segmentation using graph-cuts with wavelet-based texture feature. J. Bioinform. Comput. Biol. 15 (5) (2017)
Yoshiaki Sota, Shigeto Seno, Yoichi Takenaka, Shinzaburo Noguchi, Hideo Matsuda
Comparative Analysis of Transformation Methods for Gene Expression Profiles in Breast Cancer Datasets. BIBE (2016)
Hironori Shigeta, Tomohiro Mashita, Junichi Kikuta, Shigeto Seno, Haruo Takemura, Hideo Matsuda, Masaru Ishii
A bone marrow cavity segmentation method using wavelet-based texture feature. ICPR (2016)
Yoichi Takenaka, Shigeto Seno, Hideo Matsuda
Detecting shifts in gene regulatory networks during time-course experiments at single-time-point temporal resolution. J. Bioinform. Comput. Biol. 13 (5) (2015)
Tomohiro Mashita, Jun Usam, Hironori Shigeta, Yoshihiro Kuroda, Junichi Kikuta, Shigeto Seno, Masaru Ishii, Hideo Matsuda, Haruo Takemura
A Segmentation Method for Bone Marrow Cavity Imaging Using Graph Cuts. I3A@ICPR (2014)
Hironori Shigeta, Tomohiro Mashita, Takeshi Kaneko, Junichi Kikuta, Shigeto Seno, Haruo Takemura, Hideo Matsuda, Masaru Ishii
A Graph Cuts Image Segmentation Method for Quantifying Barrier Permeation in Bone Tissue. I3A@ICPR (2014)
Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
An estimation method for inference of gene regulatory net-work using Bayesian network with uniting of partial problems. BMC Genom. 13 (S-1) (2012)
Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
A Method for Isoform Prediction from RNA-Seq Data by Iterative Mapping. Inf. Media Technol. 7 (2) (2012)
Takeru Nakazato, Hidemasa Bono, Hideo Matsuda, Toshihisa Takagi
Gendoo: Functional profiling of gene and disease features using MeSH vocabulary. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Takeru Nakazato, Toru Takinaka, Hironori Mizuguchi, Hideo Matsuda, Hidemasa Bono, Minoru Asogawa
BioCompass: A Novel Functional Inference Tool that Utilizes MeSH Hierarchy to Analyze Groups of Genes. Silico Biol. 8 (1) (2008)
Sami Maekawa, Atsuko Matsumoto, Yoichi Takenaka, Hideo Matsuda
Tissue-specific functions based on information content of gene ontology using cap analysis gene expression. Medical Biol. Eng. Comput. 45 (11) (2007)
Takahiro Kosaka, Susumu Date, Hideo Matsuda, Shinji Shimojo
Designing a Rule-Based Environment to Interoperate Life-Scientific Ontologies for Drug Discovery. SAINT Workshops (2005)
Hideo Matsuda
A Grid Environment for Data Integration of Scientific Databases. e-Science (2005)
Gen Kawamura, Masato Kitajima, Kentaro Wakatsuki, Takehiro Furudate, Takahiro Kosaka, Kazuto Yamazaki, Reiji Teramoto, Susumu Date, Shinji Shimojo, Hideo Matsuda
A Grid-based Information Integration System for Drug Discovery. ICDE Workshops (2005)
Shoko Miyake, Yoichi Takenaka, Hideo Matsuda
A Graph Analysis Method to Detect Metabolic Sub-Networks Based on Phylogenetic Profile. CSB (2004)
Takeshi Nagashima, Hideo Matsuda, Diego G. Silva, Nikolai Petrovsky, Akihiko Konagaya, Christian Schönbach
FREP: a database of functional repeats in mouse cDNAs. Nucleic Acids Res. 32 (Database-Issue) (2004)
Hideya Kawaji, Yoichi Takenaka, Hideo Matsuda
Graph-based clustering for finding distant relationships in a large set of protein sequences. Bioinform. 20 (2) (2004)
Yukako Tohsato, Takahiro Kosaka, Susumu Date, Shinji Shimojo, Hideo Matsuda
Heterogeneous Database Federation Using Grid Technology for Drug Discovery Process. LSGRID (2004)
Haruki Nakamura, Susumu Date, Hideo Matsuda, Shinji Shimojo
A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science. New Gener. Comput. 22 (2) (2004)
Kohei Taki, Reiji Teramoto, Yoichi Takenaka, Hideo Matsuda
Inference of Gene Regulatory Network Based on Module Network Model with Gene Functional Classifications. CSB (2004)
Takeya Kasukawa, Hidemasa Bono, Yoshihide Hayashizaki, Yasushi Okazaki, Hideo Matsuda
MaXML: mouse annotation XML. Silico Biol. 4 (1) (2003)
Shoko Miyake, Yukako Tohsato, Yoichi Takenaka, Hideo Matsuda
Clustering Method for Comparative Analysis between Genomes and Pathways. DASFAA (2003)
Shoko Miyake, Yukako Tohsato, Hideo Matsuda
An Application of a Pathway Alignment Method to Comparative Analysis between Genome and Pathways. CSB (2002)
Shigeto Seno, Reiji Teramoto, Hideo Matsuda
P-quasi Complete Linkage Analysis for Gene-Expression Data. CSB (2002)
Kentaro Onizuka, Tamotsu Noguchi, Yutaka Akiyama, Hideo Matsuda
Using Data Compression for Multidimensional Distribution Analysis. IEEE Intell. Syst. 17 (3) (2002)
Tamotsu Noguchi, Hideo Matsuda, Yutaka Akiyama
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB). Nucleic Acids Res. 29 (1) (2001)
Tamotsu Noguchi, Kentaro Onizuka, Makoto Ando, Hideo Matsuda, Yutaka Akiyama
Quick selection of representative protein chain sets based on customizable requirements. Bioinform. 16 (6) (2000)
Makoto Ando, Yutaka Akiyama, Hideo Matsuda
Hierarchical Approach to Parallel Tree Search for Protein Conformational Analysis. PDPTA (2000)
Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto
A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy. ISMB (2000)
Takeya Kasukawa, Michio Nakanishi, Hideo Matsuda, Akihiro Hashimoto
An efficient procedure for maintaining materialized views on distributed database systems. Systems and Computers in Japan 31 (5) (2000)
Hideo Matsuda, T. Ishihara, Akihiro Hashimoto
Classifying Molecular Sequences Using a Linkage Graph With Their Pairwise Similarities. Theor. Comput. Sci. 210 (2) (1999)
Hironori Nakajo, Takashi Matsumoto, Masaki Kohata, Hideo Matsuda, Kei Hiraki, Yukio Kaneda
High Performance I/O System of the Distributed Shared-Memory Massively Parallel Computer JUMP-1. Parallel and Distributed Computing and Systems (1995)
Kei Hiraki, Hideharu Amano, Morihiro Kuga, Toshinori Sueyoshi, Tomohiro Kudoh, Hiroshi Nakashima, Hironori Nakajo, Hideo Matsuda, Takashi Matsumoto, Shin-ichiro Mori
Overview of the JUMP-1, an MPP prototype for general-purpose parallel computations. ISPAN (1994)
Hideo Matsuda, Yukio Kaneda
An Application of an OR-Parallel Prolog Systemto Phylogenetic Analysis. LISP Symb. Comput. 7 (2-3) (1994)
Gary J. Olsen, Hideo Matsuda, Ray Hagstrom, Ross A. Overbeek
fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10 (1) (1994)
Hideo Matsuda, Gary J. Olsen, Ross A. Overbeek, Yukio Kaneda
Fast phylogenetic analysis on a massively parallel machine. International Conference on Supercomputing (1994)
Yukio Kaneda, Hideo Matsuda, Shigeo Suzuka
A Priority Control System for OR-Parallel Prolog and Its Performance Evaluation. Parallel Symbolic Computing (1992)
Hideo Matsuda, M. Kohata, T. Masuo, Yukio Kaneda, Sadao Maekawa
Implementing Parallel Prolog System on Multiprocessor System PARK. IWDM (1987)
Yukio Kaneda, Naoyuki Tamura, Koichi Wada, Hideo Matsuda, Shumin Kuo, Sadao Maekawa
Sequential Prolog Machine PEK. New Gener. Comput. 4 (1) (1986)
Hideo Matsuda, M. Kohata, T. Masuo, Yukio Kaneda, Sadao Maekawa
Parallel Prolog Machine PARK: Its Hardware Structure and Prolog System. LP (1985)
Naoyuki Tamura, Koichi Wada, Hideo Matsuda, Yukio Kaneda, Sadao Maekawa
Sequential Prolog Machine PEK. FGCS (1984)