Quantifying the recovery process of skeletal muscle on hematoxylin and eosin stained images via learning from label proportion

Yu Yamaoka, Weng Ian Chan, Shigeto Seno, Kanako Iwamori, So-ichiro Fukada, Hideo Matsuda

Scientific Reports　Vol. 14　No. 1　2024/11/07　Research paper (scientific journal)

Effect of applying Lactiplantibacillus plantarum subsp. plantarum N793 to the scalps of men and women with thinning hair: a randomized, double-blind, placebo-controlled, parallel-group study

Ayaka Mori-Ichioka, Yosuke Sunada, Takashi Koikeda, Hideo Matsuda, Shinji Matsuo

Bioscience of Microbiota, Food and Health　Vol. 43　No. 3　p. 192-203　2024/07　Research paper (scientific journal)

Microcirculatory disturbance in acute liver injury is triggered by IFNγ-CD40 axis

Miho Kurokawa, Takeshi Goya, Motoyuki Kohjima, Masatake Tanaka, Sadahiro Iwabuchi, Shigeyuki Shichino, Satoshi Ueha, Tomonobu Hioki, Tomomi Aoyagi, Motoi Takahashi, Koji Imoto, Shigeki Tashiro, Hideo Suzuki, Masaki Kato, Shinichi Hashimoto, Hideo Matsuda, Kouji Matsushima, Yoshihiro Ogawa

Journal of Inflammation　Vol. 21　No. 1　2024/06/21　Research paper (scientific journal)

A Novel Approach to Detection Algorithms for Artifacts in Clinical Endoscopy

Seiryo Watanabe, Hironori Shigeta, Shigeto Seno, Hideo Matsuda

IPSJ Transactions on Bioinformatics　Vol. 17　p. 18-26　2024/04　Research paper (scientific journal)

High HER2 Intratumoral Heterogeneity Is a Predictive Factor for Poor Prognosis in Early-Stage and Locally Advanced HER2-Positive Breast Cancer

Tomonori Tanei, Shigeto Seno, Yoshiaki Sota, Takaaki Hatano, Yuri Kitahara, Kaori Abe, nanae masunaga, Masami Tsukabe, Tetsuhiro Yoshinami, Tomohiro Miyake, Masafumi Shimoda, Hideo Matsuda, Kenzo Shimazu

Cancers　Vol. 16　No. 5　2024/03　Research paper (scientific journal)

Accurate Detection of Fusion Genes in Long-Read Transcriptome Datasets from Multiple Cancer Cell Lines

Keigo Masuda, Yoshiaki Sota, Hideo Matsuda

Proceedings of the 2024 14th International Conference on Bioscience, Biochemistry and Bioinformatics　p. 7-13　2024/03/01　Research paper (international conference proceedings)

Detecting Fusion Genes in Long-Read Transcriptome Sequencing Data with FUGAREC

Keigo Masuda, Yoshiaki Sota, Hideo Matsuda

IPSJ Transactions on Bioinformatics　Vol. 17　p. 1-9　2024/02　Research paper (scientific journal)

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

Bio Systems　Vol. 235　p. 105087-105087　2023/11/19　Research paper (scientific journal)

動画像シミュレータを介した強化学習による 細胞追跡手法

長村徹, 瀬尾茂人, 藤本健二, 繁田浩功, 松田秀雄

情報処理学会論文誌 数理モデル化と応用　Vol. 16　No. 2　p. 11-22　2023/10　Research paper (scientific journal)

Cell Tracking via Reinforcement Learning with Microscopic Image Simulator

Toru Nagamura, Shigeto Seno, Hironori Shigeta, Tomohiro Mashita, Hideo Matsuda

Proceedings of the 2023 13th International Conference on Biomedical Engineering and Technology　p. 16-22　2023/06/15　Research paper (international conference proceedings)

Pseudotime-based Deep Learning of Gene Regulatory Relationships from Single-Cell Expression Data

Koki Nishi, Junko Yoshida, Shigeto Seno, Kyoji Horie, Hideo Matsuda

Proceedings of the 2023 13th International Conference on Biomedical Engineering and Technology　p. 56-62　2023/06/15　Research paper (international conference proceedings)

A Cell Tracking Method for Dynamic Analysis of Immune Cells Based on Deep Learning

Aya Watanabe, Kenji Fujimoto, Hironori Shigeta, Shigeto Seno, Yutaka Uchida, Masaru Ishii, Hideo Matsuda

International Journal of Machine Learning　Vol. 13　No. 2　p. 64-69　2023/04　Research paper (scientific journal)

A Novel Method for Fusion Gene Detection using Both End-Fragment Sequences of Long Reads

Keigo Masuda, Yoshiaki Sota, Hideo Matsuda

Proceedings of the 2022 9th International Conference on Biomedical and Bioinformatics Engineering　p. 88-92　2022/11/10　Research paper (international conference proceedings)

Inference of Cell-Cell Communication for Detecting Immune Disease-Associated Signaling Pathways using Single-Cell RNA-seq

Akihiro Nomura, Hideo Matsuda

Proceedings of the 2022 9th International Conference on Biomedical and Bioinformatics Engineering　p. 74-80　2022/11/10　Research paper (international conference proceedings)

Myeloid cell-specific ablation of Runx2 gene exacerbates post-infarct cardiac remodeling.

Masashi Tomimatsu, Kotaro Matsumoto, Moe Ashizuka, Shohei Kumagai, Shota Tanaka, Takafumi Nakae, Kosei Yokota, Shunsuke Kominami, Ryota Kajiura, Daisuke Okuzaki, Daisuke Motooka, Aki Shiraishi, Takaya Abe, Hideo Matsuda, Yoshiaki Okada, Makiko Maeda, Shigeto Seno, Masanori Obana, Yasushi Fujio

Scientific Reports　Vol. 12　No. 1　p. 16656-16656　2022/10/05　Research paper (scientific journal)

Identification of Lineage Markers for T Cell Immune Dysregulation in Sarcoidosis Using Single-Cell RNA-seq

Akihiro Nomura, Hideo Matsuda

International Journal of Bioscience, Biochemistry and Bioinformatics　Vol. 12　No. 4　p. 63-70　2022/10　Research paper (scientific journal)

MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus.

Naoko Fujiwara, Maki Shigemoto, Mizuki Hirayama, Ken-Ichi Fujita, Shigeto Seno, Hideo Matsuda, Masami Nagahama, Seiji Masuda

Nucleic Acids Research　Vol. 50　No. 15　p. 8779-8806　2022/07/29　Research paper (scientific journal)

A Novel Method for Gene Regulatory Network Inference with Pseudotime Data Using Information Criterion

Shuhei Yao, Kaito Uemura, Shigeto Seno, Hideo Matsuda

International Jounral of Bioscience, Biochemistry and Bioinformatics　Vol. 12　No. 3　p. 43-52　2022/07　Research paper (scientific journal)

Detection of Biomarkers for Epithelial-Mesenchymal Transition with Single-Cell Trajectory Inference

Kosho Murayama, Hideo Matsuda

Frontiers in Bioscience-Landmark　Vol. 27　No. 4　p. 127-127　2022/04/15　Research paper (scientific journal)

A Method for Detection of Markers for Epithelial-Mesenchymal Transition based on Single Cell Transcriptomic Data

Kosho Murayama, Hideo Matsuda

International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB)　p. 57-62　2022/01/07　Research paper (international conference proceedings)

Osteoclasts adapt to physioxia perturbation through DNA demethylation

Keizo Nishikawa, Shigeto Seno, Toshitada Yoshihara, Ayako Narazaki, Yuki Sugiura, Reito Shimizu, Junichi Kikuta, Reiko Sakaguchi, Norio Suzuki, Norihiko Takeda, Hiroaki Semba, Masamichi Yamamoto, Daisuke Okuzaki, Daisuke Motooka, Yasuhiro Kobayashi, Makoto Suematsu, Haruhiko Koseki, Hideo Matsuda, Masayuki Yamamoto, Seiji Tobita, Yasuo Mori, Masaru Ishii

EMBO reports　Vol. 22　No. e53035　2021/10/18　Research paper (scientific journal)

SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization

Mikio Shiga, Shigeto Seno, Makoto Onizuka, Hideo Matsuda

PeerJ　Vol. 9　p. e12087-e12087　2021/08/27　Research paper (scientific journal)

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

Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics　No. 35　p. 1-7　2021/08　Research paper (international conference proceedings)

Detecting Lineage-Specific Marker Genes for Tumor Evolution Based on Single Cell Transcriptome

Kosho Murayama, Hideo Matsuda

International Journal of Bioscience, Biochemistry and Bioinformatics　Vol. 11　No. 3　p. 50-57　2021/07　Research paper (scientific journal)

SLPI is a critical mediator that controls PTH-induced bone formation

Akito Morimoto, Junichi Kikuta, Keizo Nishikawa, Takao Sudo, Maki Uenaka, Masayuki Furuya, Tetsuo Hasegawa, Kunihiko Hashimoto, Hiroyuki Tsukazaki, Shigeto Seno, Akira Nakamura, Daisuke Okuzaki, Fuminori Sugihara, Akinori Ninomiya, Takeshi Yoshimura, Ryoko Takao-Kawabata, Hideo Matsuda, Masaru Ishii

Nature Communications　Vol. 12　No. 1　p. 2136-2136　2021/04　Research paper (scientific journal)

Determining homologous recombination deficiency scores with whole exome sequencing and their association with responses to neoadjuvant chemotherapy in breast cancer

Seung Jin Kim, Yoshiaki Sota, Yasuto Naoi, Keiichiro Honma, Naofumi Kagara, Tomohiro Miyake, Masafumi Shimoda, Tomonori Tanei, Shigeto Seno, Hideo Matsuda, Shinzaburo Noguchi, Kenzo Shimazu

Translational Oncology　Vol. 14　No. 2　p. 100986-100986　2021/02　Research paper (scientific journal)

Glycerol kinase stimulates uncoupling protein 1 expression by regulating fatty acid metabolism in beige adipocytes.

Mari Iwase, Soshi Tokiwa, Shigeto Seno, Takako Mukai, Yu-Sheng Yeh, Haruya Takahashi, Wataru Nomura, Huei-Fen Jheng, Sigenobu Matsumura, Tatsuya Kusudo, Naoki Osato, Hideo Matsuda, Kazuo Inoue, Teruo Kawada, Tsuyoshi Goto

The Journal of biological chemistry　Vol. 295　No. 20　p. 7033-7045　2020/05/15　Research paper (scientific journal)

Anti-Inflammatory and Antioxidative Properties of Isoflavones Provide Renal Protective Effects Distinct from Those of Dietary Soy Proteins against Diabetic Nephropathy.

Huei-Fen Jheng, Kanako Hayashi, Yasuki Matsumura, Teruo Kawada, Shigeto Seno, Hideo Matsuda, Kazuo Inoue, Wataru Nomura, Haruya Takahashi, Tsuyoshi Goto

Molecular nutrition & food research　Vol. 64　No. 10　2020/05　Research paper (scientific journal)

Tracking and Analysis of FUCCI-Labeled Cells Based on Particle Filters and Time-to-Event Analysis

Kenji Fujimoto, Shigeto Seno, Hironori Shigeta, Tomohiro Mashita, Masaru Ishii, Hideo Matsuda

International Journal of Bioscience, Biochemistry and Bioinformatics　Vol. 10　No. 2　p. 94-109　2020/04　Research paper (scientific journal)

In vivo dynamic analysis of BMP-2-induced ectopic bone formation

Kunihiko Hashimoto, Takashi Kaito, Masayuki Furuya, Shigeto Seno, Daisuke Okuzaki, Junichi Kikuta, Hiroyuki Tsukazaki, Hideo Matsuda, Hideki Yoshikawa, Masaru Ishii

Scientific Reports　Vol. 10　No. 1　2020/03/16　Research paper (scientific journal)

Long non-coding RNA 2310069B03Rik functions as a suppressor of Ucp1 expression under prolonged cold exposure in murine beige adipocytes.

Mari Iwase, Shoko Sakai, Shigeto Seno, Yu-Sheng Yeh, Tony Kuo, Haruya Takahashi, Wataru Nomura, Huei-Fen Jheng, Paul Horton, Naoki Osato, Hideo Matsuda, Kazuo Inoue, Teruo Kawada, Tsuyoshi Goto

Bioscience, biotechnology, and biochemistry　Vol. 84　No. 2　p. 305-313　2020/02　Research paper (scientific journal)

URH49 exports mRNA by remodeling complex formation and mediating the NXF1-dependent pathway.

Ken-Ichi Fujita, Tomohiro Yamazaki, Kotaro Harada, Shigeto Seno, Hideo Matsuda, Seiji Masuda

Biochimica et biophysica acta. Gene regulatory mechanisms　Vol. 1863　No. 2　p. 194480-194480　2020/01/07　Research paper (scientific journal)

Thrombomodulin induces anti-inflammatory effects by inhibiting the rolling adhesion of leukocytes in vivo

Shino Nishizawa, Junichi Kikuta, Shigeto Seno, Masahiro Kajiki, Ryuichi Tsujita, Hiroki Mizuno, Takao Sudo, Tomoka Ao, Hideo Matsuda, Masaru Ishii

Journal of Pharmacological Sciences　Vol. 1347-8613　No. 20　p. 30002-30005　2020/01　Research paper (scientific journal)

Single-cell transcriptome analysis of mouse leukocytes in inflammatory stimulation

Naoki Osato, Hironori Shigeta, Shigeto Seno, Yutaka Uchida, Junichi Kikuta, Masaru Ishii, Hideo Matsuda

2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)　p. 1229-1231　2019/11　Research paper (international conference proceedings)

Analyzing Leukocyte Migration Trajectories by Deformable Image Matching

Hironori Shigeta, Shigeto Seno, Shino Nishizawa, Yutaka Uchida, Junichi Kikuta, Masaru Ishii, Hideo Matsuda

IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)　p. 94-98　2019/10　Research paper (international conference proceedings)

生体蛍光観察動画像の深度を考慮した深層学習による細胞追跡精度の改善

嶋田 彩人, 瀬尾 茂人, 繁田 浩功, 間下 以大, 内田 穣, 石井 優, 松田 秀雄

情報処理学会論文誌数理モデル化と応用（TOM）　Vol. 12　No. 2　p. 82-91　2019/07　Research paper (scientific journal)

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, Shinzabro Noguchi, Hideo Matsuda

Journal of Bioinformatics and Computational Biology　Vol. 17　No. 3　p. 1940008-1940008　2019/06　Research paper (scientific journal)

In vivo Multicolor Imaging with Fluorescent Probes Revealed the Dynamics and Function of Osteoclast Proton Pumps

Masafumi Minoshima, Junichi Kikuta, Yuta Omori, Shigeto Seno, Riko Suehara, Hiroki Maeda, Hideo Matsuda, Masaru Ishii, Kazuya Kikuchi

ACS Central Science　Vol. 5　No. 6　p. 1059-1066　2019/06　Research paper (scientific journal)

DNN Models And Postprocessing Thresholds For Endoscopy Artifact Detection In Practice

Seiryo Watanabe, Shigeto Seno, Hideo Matsuda

CEUR Workshop Proceedings: the 2019 Challenge on Endoscopy Artefacts Detection (EAD2019)　2019/05　Research paper (international conference proceedings)

Asymmetric Integration of Single-Cell Transcriptomic Data using Latent Dirichlet Allocation and Procrustes Analysis

Mitsuhiro Eto, Wataru Hirota, Shigeto Seno, Hideo Matsuda

2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)　p. 2129-2135　2018/12　Research paper (international conference proceedings)

Roles of Enhancer RNAs in RANKL-induced Osteoclast Differentiation Identified by Genome-wide Cap-analysis of Gene Expression using CRISPR

Yukako Sakaguchi, Keizo Nishikawa, Shigeto Seno, Hideo Matsuda, Hiroshi Takayanagi, Masaru Ishii

Scientific Reports　Vol. 8　No. 1　2018/12/01　Research paper (scientific journal)

The dipeptidyl peptidase-4 (DPP-4) inhibitor teneligliptin enhances brown adipose tissue function, thereby preventing obesity in mice

Takeda, K., Sawazaki, H., Takahashi, H., Yeh, Y.-S., Jheng, H.-F., Nomura, W., Ara, T., Takahashi, N., Seno, S., Osato, N., Matsuda, H., Kawada, T., Goto, T.

FEBS Open Bio　Vol. 8　No. 11　p. 1782-1793　2018/09　Research paper (scientific journal)

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 Bioinformatics　Vol. 19　No. 89　p. 49-59　2018/05/08　Research paper (scientific journal)

A Phytol-Enriched Diet Activates PPAR-α in the Liver and Brown Adipose Tissue to Ameliorate Obesity-Induced Metabolic Abnormalities

Ji-Yeong An, Huei-Fen Jheng, Hiroyuki Nagai, Kohei Sanada, Haruya Takahashi, Mari Iwase, Natsumi Watanabe, Young-Il Kim, Aki Teraminami, Nobuyuki Takahashi, Rieko Nakata, Hiroyasu Inoue, Shigeto Seno, Hideo Mastuda, Teruo Kawada, Tsuyoshi Goto

Molecular Nutrition and Food Research　Vol. 62　No. 6　2018/03/01　Research paper (scientific journal)

Chromatin 3D reconstruction from chromosomal contacts using a genetic algorithm

Kapilevich, V., Seno, S., Matsuda, H., Takenaka, Y.

IEEE/ACM Transactions on Computational Biology and Bioinformatics　Vol. 16　No. 5　p. 1-1　2018/03　Research paper (scientific journal)

Direct cell-cell contact between mature osteoblasts and osteoclasts dynamically controls their functions in vivo.

Masayuki Furuya, Junichi Kikuta, Sayumi Fujimori, Shigeto Seno, Hiroki Maeda, Mai Shirazaki, Maki Uenaka, Hiroki Mizuno, Yoriko Iwamoto, Akito Morimoto, Kunihiko Hashimoto, Takeshi Ito, Yukihiro Isogai, Masafumi Kashii, Takashi Kaito, Shinsuke Ohba, Ung-Il Chung, Alexander C Lichtler, Kazuya Kikuchi, Hideo Matsuda, Hideki Yoshikawa, Masaru Ishii

Nature Communications　Vol. 9　No. 1　p. 300-300　2018/01/19　Research paper (scientific journal)

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

PROCEEDINGS 2018 IEEE 18TH INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOENGINEERING (BIBE)　p. 159-162　2018　Research paper (international conference proceedings)

Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer

Babak Ehteshami Bejnordi, Mitko Veta, Paul Johannes van Diest, Bram van Ginneken, Nico Karssemeijer, Geert Litjens, Jeroen A. W. M. van der Laak, Meyke Hermsen, Quirine F Manson, Maschenka Balkenhol, Oscar Geessink, Nikolaos Stathonikos, Marcory CRF van Dijk, Peter Bult, Francisco Beca, Andrew H Beck, Dayong Wang, Aditya Khosla, Rishab Gargeya, Humayun Irshad, Aoxiao Zhong, Qi Dou, Quanzheng Li, Hao Chen, Huang-Jing Lin, Pheng-Ann Heng, Christian Haß, Elia Bruni, Quincy Wong, Ugur Halici, Mustafa Ümit Öner, Rengul Cetin-Atalay, Matt Berseth, Vitali Khvatkov, Alexei Vylegzhanin, Oren Kraus, Muhammad Shaban, Nasir Rajpoot, Ruqayya Awan, Korsuk Sirinukunwattana, Talha Qaiser, Yee-Wah Tsang, David Tellez, Jonas Annuscheit, Peter Hufnagl, Mira Valkonen, Kimmo Kartasalo, Leena Latonen, Pekka Ruusuvuori, Kaisa Liimatainen, Shadi Albarqouni, Bharti Mungal, Ami George, Stefanie Demirci, Nassir Navab, Seiryo Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda, Hady Ahmady Phoulady, Vassili Kovalev, Alexander Kalinovsky, Vitali Liauchuk, Gloria Bueno, M. Milagro Fernandez-Carrobles, Ismael Serrano, Oscar Deniz, Daniel Racoceanu, Rui Venâncio

The Journal of the American Medical Association　Vol. 318　No. 22　p. 2199-2199　2017/12/12　Research paper (scientific journal)

Over-expression of PPAR alpha in obese mice adipose tissue improves insulin sensitivity

Haruya Takahashi, Kohei Sanada, Hiroyuki Nagai, Yongjia Li, Yumeko Aoki, Takeshi Ara, Shigeto Seno, Hideo Matsuda, Rina Yu, Teruo Kawada, Tsuyoshi Goto

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS　Vol. 493　No. 1　p. 108-114　2017/11　Research paper (scientific journal)

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

JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY　Vol. 15　No. 5　p. 1740004-1-1740004-16　2017/10　Research paper (scientific journal)

The hepatokine FGF21 is crucial for peroxisome proliferator-activated receptor-alpha agonist-induced amelioration of metabolic disorders in obese mice

Tsuyoshi Goto, Mariko Hirata, Yumeko Aoki, Mari Iwase, Haruya Takahashi, Minji Kim, Yongjia Li, Huei-Fen Jheng, Wataru Nomura, Nobuyuki Takahashi, Chu-Sook Kim, Rina Yu, Shigeto Seno, Hideo Matsuda, Megumi Aizawa-Abe, Ken Ebihara, Nobuyuki Itoh, Teruo Kawada

JOURNAL OF BIOLOGICAL CHEMISTRY　Vol. 292　No. 22　p. 9175-9190　2017/06　Research paper (scientific journal)

A simple comparison of the extrinsic noise in gene expression between native and foreign regulations in Escherichia coli

Bei-Wen Ying, Shigeto Seno, Hideo Matsuda, Tetsuya Yomo

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS　Vol. 486　No. 3　p. 852-857　2017/05　Research paper (scientific journal)

Correlation between genome reduction and bacterial growth

Masaomi Kurokawa, Shigeto Seno, Hideo Matsuda, Bei-Wen Ying

DNA RESEARCH　Vol. 23　No. 6　p. 517-525　2016/12　Research paper (scientific journal)

A Bone Marrow Cavity Segmentation Method using Wavelet-based Texture Feature

Hironori Shigeta, Tomohiro Mashita, Junichi Kikutat, Shigeto Seno, Haruo Takemura, Hideo Matsuda, Masaru Ishii

2016 23RD INTERNATIONAL CONFERENCE ON PATTERN RECOGNITION (ICPR)　p. 2133-2138　2016　Research paper (international conference proceedings)

Proinflammatory cytokine interleukin-1 beta suppresses cold-induced thermogenesis in adipocytes

Tsuyoshi Goto, Supaporn Naknukool, Rieko Yoshitake, Yuki Hanafusa, Soshi Tokiwa, Yongjia Li, Tomoya Sakamoto, Takahiro Nitta, Minji Kim, Nobuyuki Takahashi, Rina Yu, Hiromi Daiyasu, Shigeto Seno, Hideo Matsuda, Teruo Kawada

CYTOKINE　Vol. 77　p. 107-114　2016/01　Research paper (scientific journal)

Comparative Analysis of Transformation Methods for Gene Expression Profiles in Breast Cancer Datasets

Yoshiaki Sota, Shigeto Seno, Yoichi Takenaka, Shinzaburo Noguchi, Hideo Matsuda

2016 IEEE 16TH INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOENGINEERING (BIBE)　p. 328-333　2016　Research paper (international conference proceedings)

Functional specialization in regulation and quality control in thermal adaptive evolution

Kazuma Yama, Yuki Matsumoto, Yoshie Murakami, Shigeto Seno, Hideo Matsuda, Kazuyoshi Gotoh, Daisuke Motooka, Shota Nakamura, Bei-Wen Ying, Tetsuya Yomo

GENES TO CELLS　Vol. 20　No. 11　p. 943-955　2015/11　Research paper (scientific journal)

Detecting shifts in gene regulatory networks during time-course experiments at single-time-point temporal resolution

Yoichi Takenaka, Shigeto Seno, Hideo Matsuda

Journal of Bioinformatics and Computational Biology　Vol. 13　No. 5　2015/10　Research paper (scientific journal)

Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages

Bei-Wen Ying, Tomoya Honda, Saburo Tsuru, Shigeto Seno, Hideo Matsuda, Yasuaki Kazuta, Tetsuya Yomo

PLOS ONE　Vol. 10　No. 8　2015/08　Research paper (scientific journal)

A Bone Marrow Recognition Method for Bone Tissue Images using Wavelet Transform

Hironori Shigeta, Tomohiro Mashita, Takeshi Kaneko, Junichi Kikuta, Shigeto Senoo, Haruo Takemura, Hideo Matsuda, Masaru Ishii

2015/03　Research paper (bulletin of university, research institution)

A Bone-marrow Space Segmentation Method Using Graph-cuts

Vol. 8　No. 1　p. 18-27　2015/03　Research paper (scientific journal)

Directed evolution of cell size in Escherichia coli

Mari Yoshida, Saburo Tsuru, Naoko Hirata, Shigeto Seno, Hideo Matsuda, Bei-Wen Ying, Tetsuya Yomo

BMC EVOLUTIONARY BIOLOGY　Vol. 14　No. 1　2014/12　Research paper (scientific journal)

A Segmentation Method for Bone Marrow Cavity Image Using Graph-Cuts

Tomohiro Mashita, Jun Usami, Hironori Shigeta, Yoshihiro Kuroda, Junichi Kikuta, Shigeto Senoo, Masaru Ishii, Hideo Matsuda, Haruo Takemura

2014/09　Research paper (international conference proceedings)

Metagenome fragment classification based on multiple motif-occurrence profiles

Naoki Matsushita, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

PEERJ　Vol. 2　No. e559　2014/09　Research paper (scientific journal)

A Graph Cuts Image Segmentation Method for Quantifying Barrier Permeation in Bone Tissue

Hironori Shigeta, Tomohiro Mashita, Takeshi Kaneko, Junichi Kikuta, Shigeto Senoo, Haruo Takemura, Hideo Matsuda, Masaru Ishii

2014 1st Workshop on Pattern Recognition Techniques for Indirect Immunofluorescence Images　p. 16-19　2014/08　Research paper (international conference proceedings)

Inference of TFRNs (2)

Hideo Matsuda

Methods in Molecular Biology　Vol. 2014　p. 97-107　2014/05/06　Part of collection (book)

Gene expression scaled by distance to the genome replication site

Bei-Wen Ying, Saburo Tsuru, Shigeto Seno, Hideo Matsuda, Tetsuya Yomo

MOLECULAR BIOSYSTEMS　Vol. 10　No. 3　p. 375-379　2014　Research paper (scientific journal)

A Robust Method for Estimating Gene Regulatory Networks Using Multiple Time Series Gene Expression Profiles

Vol. Vol.6, No.3, pp.151-162　No. 3　p. 151-162　2013/12

Segmentation and Tracking Method of Cell Nuclei for Time-lapse Fluorescent Microscopy Images Based on Gaussian Mixture Model

Vol. 6　No. 3　p. 140-150　2013/12　Research paper (scientific journal)

Integrative prediction of miRNA-mRNA interactions from high-throughput sequencing data

Tomoshige Ohno, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges 2013　2013/11

An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles

Ryo Araki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

Gene　Vol. 518　No. 1　p. 17-25　2013/04/10　Research paper (scientific journal)

Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome

Bei-Wen Ying, Shigeto Seno, Fuyuro Kaneko, Hideo Matsuda, Tetsuya Yomo

BMC GENOMICS　Vol. 14　2013/01　Research paper (scientific journal)

Estimate Dynamic Gene Regulatory Networks in Adipocyte Differentiation for Detecting Changes of Gene Regulations by Splitting Time Course Data

Tomoyoshi Nakayama, Yoshiyuki Kido, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

23rd International Conference on Genome Informatics (GIW2012)　2012/12　Research paper (international conference proceedings)

Automatic cell tracking for time-lapse fluorescent images of cell cycle

Shigeto Seno, Sakae Maeda, Tomohiro Mashita, Yoichi Takenaka, Masaru Ishii, Hideo Matsuda

2012/10　Research paper (international conference proceedings)

Estimation of Dynamic Gene Regulatory Networks for Cell Differentiation by Splitting Time Course Data

Tomoyoshi Nakayama, Yoshiyuki Kido, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

2012/10

A cell-tracking method for time-lapse multicolor fluorescent images

Shigeto Seno, Tomohiro Mashita, Yoichi Takenaka, Masaru Ishii, Hideo Matsuda

2012/09　Research paper (international conference proceedings)

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

Series on Advances in Bioinformatics and Computational Biology　Vol. 13　2012　Research paper (international conference proceedings)

A method for isoform prediction from RNA-seq data by iterative mapping

Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

IPSJ Transactions on Bioinformatics　Vol. 5　p. 27-33　2012　Research paper (scientific journal)

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 GENOMICS　Vol. 13　No. Suppl.1　2012/01　Research paper (scientific journal)

Inference of S-system models of gene regulatory networks using immune algorithm

Tomoyoshi Nakayama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

Journal of Bioinformatics and Computational Biology　Vol. 9　No. Suppl.1　p. 75-86　2011/12　Research paper (scientific journal)

Perfect Hamming code with a hash table for faster genome mapping

Yoichi Takenaka, Shigeto Seno, Hideo Matsuda

BMC GENOMICS　Vol. 12　2011/11　Research paper (scientific journal)

A Crosstalk Model and an Estimation Method to Find Crosstalk Genes on Cell Differentiation

Hiroshi Yoshizawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

The Information Processing Society of Japan (IPSJ)Transactions on Mathematical Modeling and its Applications (TOM)　2011/11　Research paper (scientific journal)

Exploration of Potential Genomic Portraits Associated with Intrahepatic Recurrence in Human Hepatocellular Carcinoma

Nobuyoshi Kittaka, Ichiro Takemasa, Shigeto Seno, Yutaka Takeda, Shogo Kobayashi, Shigeru Marubashi, Keizo Dono, Koji Umeshita, Hiroaki Nagano, Hideo Matsuda, Morito Monden, Masaki Mori, Yuichiro Doki

ANNALS OF SURGICAL ONCOLOGY　Vol. 17　No. 12　p. 3145-3154　2010/12　Research paper (scientific journal)

A Metadata Management System for Composing Bioinformatics Workflows

Takuya Ishibashi, Yoshiyuki Kido, Takanori Fukumoto, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

9th International Conference on Bioinformatics (InCoB2010)　2010/09　Research paper (international conference proceedings)

Gene Expression Profile Prospectively Predicts Peritoneal Relapse After Curative Surgery of Gastric Cancer

Atsushi Takeno, Ichiro Takemasa, Shigeto Seno, Makoto Yamasaki, Masaaki Motoori, Hiroshi Miyata, Kiyokazu Nakajima, Shuji Takiguchi, Yoshiyuki Fujiwara, Toshiro Nishida, Toshitsugu Okayama, Kenichi Matsubara, Yoichi Takenaka, Hideo Matsuda, Morito Monden, Masaki Mori, Yuichiro Doki

ANNALS OF SURGICAL ONCOLOGY　Vol. 17　No. 4　p. 1033-1042　2010/04　Research paper (scientific journal)

Improved prediction method for protein interactions using both structural and functional characteristics of proteins

Tatsuya Yoshikawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

IPSJ Transactions on Bioinformatics　Vol. 3　No. 2　p. 10-23　2010　Research paper (scientific journal)

A method for efficient execution of bioinformatics workflows.

Seo, J., Kido, Y., Seno, S., Takenaka, Y., Matsuda, H.

Genome informatics. International Conference on Genome Informatics　Vol. 23　No. 1　p. 139-148　2009/12　Research paper (international conference proceedings)

Gendoo: Functional profiling of gene and disease features using MeSH vocabulary

Takeru Nakazato, Hidemasa Bono, Hideo Matsuda, Toshihisa Takagi

NUCLEIC ACIDS RESEARCH　Vol. 37　p. W166-W169　2009/07　Research paper (scientific journal)

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Harukazu Suzuki, Alistair R R Forrest, Erik van Nimwegen, Carsten O Daub, Piotr J Balwierz, Katharine M Irvine, Timo Lassmann, Timothy Ravasi, Yuki Hasegawa, Michiel J L de Hoon, Shintaro Katayama, Kate Schroder, Piero Carninci, Yasuhiro Tomaru, Mutsumi Kanamori-Katayama, Atsutaka Kubosaki, Altuna Akalin, Yoshinari Ando, Erik Arner, Maki Asada, Hiroshi Asahara, Timothy Bailey, Vladimir B Bajic, Denis Bauer, Anthony G Beckhouse, Nicolas Bertin, Johan Björkegren, Frank Brombacher, Erika Bulger, Alistair M Chalk, Joe Chiba, Nicole Cloonan, Adam Dawe, Josee Dostie, Pär G Engström, Magbubah Essack, Geoffrey J Faulkner, J Lynn Fink, David Fredman, Ko Fujimori, Masaaki Furuno, Takashi Gojobori, Julian Gough, Sean M Grimmond, Mika Gustafsson, Megumi Hashimoto, Takehiro Hashimoto, Mariko Hatakeyama, Susanne Heinzel, Winston Hide, Oliver Hofmann, Michael Hörnquist, Lukasz Huminiecki, Kazuho Ikeo, Naoko Imamoto, Satoshi Inoue, Yusuke Inoue, Ryoko Ishihara, Takao Iwayanagi, Anders Jacobsen, Mandeep Kaur, Hideya Kawaji, Markus C Kerr, Ryuichiro Kimura, Syuhei Kimura, Yasumasa Kimura, Hiroaki Kitano, Hisashi Koga, Toshio Kojima, Shinji Kondo, Takeshi Konno, Anders Krogh, Adele Kruger, Ajit Kumar, Boris Lenhard, Andreas Lennartsson, Morten Lindow, Marina Lizio, Cameron Macpherson, Norihiro Maeda, Christopher A Maher, Monique Maqungo, Jessica Mar, Nicholas A Matigian, Hideo Matsuda, John S Mattick, Stuart Meier, Sei Miyamoto, Etsuko Miyamoto-Sato, Kazuhiko Nakabayashi, Yutaka Nakachi, Mika Nakano, Sanne Nygaard, Toshitsugu Okayama, Yasushi Okazaki, Haruka Okuda-Yabukami, Valerio Orlando, Jun Otomo, Mikhail Pachkov, Nikolai Petrovsky, Charles Plessy, John Quackenbush, Aleksandar Radovanovic, Michael Rehli, Rintaro Saito, Albin Sandelin, Sebastian Schmeier, Christian Schönbach, Ariel S Schwartz, Colin A Semple, Miho Sera, Jessica Severin, Katsuhiko Shirahige, Cas Simons, George St Laurent, Masanori Suzuki, Takahiro Suzuki, Matthew J Sweet, Ryan J Taft, Shizu Takeda, Yoichi Takenaka, Kai Tan, Martin S Taylor, Rohan D Teasdale, Jesper Tegnér, Sarah Teichmann, Eivind Valen, Claes Wahlestedt, Kazunori Waki, Andrew Waterhouse, Christine A Wells, Ole Winther, Linda Wu, Kazumi Yamaguchi, Hiroshi Yanagawa, Jun Yasuda, Mihaela Zavolan, David A Hume, Takahiro Arakawa, Shiro Fukuda, Kengo Imamura, Chikatoshi Kai, Ai Kaiho, Tsugumi Kawashima, Chika Kawazu, Yayoi Kitazume, Miki Kojima, Hisashi Miura, Kayoko Murakami, Mitsuyoshi Murata, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Chihiro Ogawa, Takuma Sano, Christophe Simon, Michihira Tagami, Yukari Takahashi, Jun Kawai, Yoshihide Hayashizaki

Nature genetics　Vol. 41　No. 5　p. 553-62　2009/05　Research paper (scientific journal)

An Architecture of Modeling Data Search using Ontology and Meta-Ontology

Yoshiyuki Kido, Yoshiyuki Asai, Taishin Nomura, Yoshihisa Kurachi, Hideo Matsuda

The 3rd MEI International SymposiumPhysiome and Systems Biology for IntegratedLife Sciences and Predictive Medicine　2008/12　Research paper (international conference proceedings)

A Combination Method of the Tanimoto Coefficient and Proximity Measure of Random Forest for Compound Activity Prediction

Gen Kawamura, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

IPSJ Transactions on Bioinformatics　Vol. 49　No. 5　p. 46-57　2008/03　Research paper (scientific journal)

A Distributed-Processing System for Accelerating Biological Research Using Data-Staging

Kido Yoshiyuki, Seno Shigeto, Date Susumu, Takenaka Yoichi, Matsuda Hideo

ipsjdc　Vol. 49　No. 5　p. 58-64　2008/03　Research paper (scientific journal)

Compound-transporter interaction studies using canonical correlation analysis

Masato Kitajima, Yohsuke Minowa, Hideo Matsuda, Yasushi Okuno

Chem-Bio Informatics Journal　Vol. 7　No. 2　p. 24-34　2008/01/12　Research paper (scientific journal)

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

In Silico Biology　Vol. 8　No. 1　p. 53-61　2008　Research paper (scientific journal)

Tissue-specific functions based on information content of gene ontology using cap analysis gene expression

Sami Maekawa, Atsuko Matsumoto, Yoichi Takenaka, Hideo Matsuda

MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING　Vol. 45　No. 11　p. 1029-1036　2007/11　Research paper (scientific journal)

Retrieving Functionally Similar Bioinformatics Workflows using TF-IDF Filtering.

Junya Seo, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

IPSJ Transactions on Bioinformatics　Vol. 2007　No. 128　p. 259-266　2007/03　Research paper (scientific journal)

GO based tissue specific functions of mouse using countable gene expression profiles

Yoichi Takenaka, Akit Matsumoto, Hideo Matsuda

GENOME INFORMATICS 2007, VOL 19　Vol. 19　p. 154-+　2007　Research paper (international conference proceedings)

Inference of transcriptional regulatory networks using CAGE transcriptome dataset of Mus musculus

Kohei Taki, Yoichi Takenaka, Hideo Matsuda

WORLD CONGRESS ON MEDICAL PHYSICS AND BIOMEDICAL ENGINEERING 2006, VOL 14, PTS 1-6　Vol. 14　p. 187-190　2007　Research paper (international conference proceedings)

A method for exploring Tissue-Specific Functions based on Information Content of Gene Ontology Terms using CAGE tags

Sami Maekawa, Atsuko Matsumoto, Yoichi Takenaka, Hideo Matsuda

WORLD CONGRESS ON MEDICAL PHYSICS AND BIOMEDICAL ENGINEERING 2006, VOL 14, PTS 1-6　Vol. 14　p. 163-+　2007　Research paper (international conference proceedings)

nference of Gene Regulatory Networks from Gene-expression Profiles with Utilization of Biclustering Results

Kohei Taki, Yoichi Takenaka, Hideo Matsuda

IPSJ Transactions on Mathematical Modeling and Its Applications　Vol. 47　No. 14　p. 118-128　2006/10　Research paper (scientific journal)

Extraction of Functionally Similar Bioinformatics Workflows

Junya Seo, Shigeto Senoo, Yoichi Takenaka, Hideo Matsuda

6th International Workshop on Distibuted Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics (NETTAB 2006)　2006/07　Research paper (international conference proceedings)

A method for similarity search of genomic positional expression using CAGE

Shigeto Seno, Yoichi Takenaka, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Hideo Matsuda

PLOS GENETICS　Vol. 2　No. 4　p. 578-586　2006/04　Research paper (scientific journal)

A framework for biological analysis on the grid

Toshiyuki Okumura, Susumu Date, Yoichi Takenaka, Hideo Matsuda

GRID COMPUTING IN LIFE SCIENCES　p. 79-+　2006　Research paper (international conference proceedings)

Do grid technologies help life sciences? Lessons learnt from biogrid project in Japan

Susumu Date, Kazutoshi Fujikawa, Hideo Matsuda, Haruki Nakamura, Shinji Shimojo

GRID COMPUTING IN LIFE SCIENCES　p. 65-+　2006　Research paper (international conference proceedings)

The transcriptional landscape of the mammalian genome

P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, R Oyama, T Ravasi, B Lenhard, C Wells, R Kodzius, K Shimokawa, VB Bajic, SE Brenner, S Batalov, ARR Forrest, M Zavolan, MJ Davis, LG Wilming, Aidinis, V, JE Allen, Ambesi-Impiombato, X, R Apweiler, RN Aturaliya, TL Bailey, M Bansal, L Baxter, KW Beisel, T Bersano, H Bono, AM Chalk, KP Chiu, Choudhary, V, A Christoffels, DR Clutterbuck, ML Crowe, E Dalla, BP Dalrymple, B de Bono, G Della Gatta, D di Bernardo, T Down, P Engstrom, M Fagiolini, G Faulkner, CF Fletcher, T Fukushima, M Furuno, S Futaki, M Gariboldi, P Georgii-Hemming, TR Gingeras, T Gojobori, RE Green, S Gustincich, M Harbers, Y Hayashi, TK Hensch, N Hirokawa, D Hill, L Huminiecki, M Iacono, K Ikeo, A Iwama, T Ishikawa, M Jakt, A Kanapin, M Katoh, Y Kawasawa, J Kelso, H Kitamura, H Kitano, G Kollias, SPT Krishnan, A Kruger, SK Kummerfeld, Kurochkin, IV, LF Lareau, D Lazarevic, L Lipovich, J Liu, S Liuni, S McWilliam, MM Babu, M Madera, L Marchionni, H Matsuda, S Matsuzawa, H Miki, F Mignone, S Miyake, K Morris, S Mottagui-Tabar, N Mulder, N Nakano, H Nakauchi, P Ng, R Nilsson, S Nishiguchi, S Nishikawa, F Nori, O Ohara, Y Okazaki, Orlando, V, KC Pang, WJ Pavan, G Pavesi, G Pesole, N Petrovsky, S Piazza, J Reed, JF Reid, BZ Ring, M Ringwald, B Rost, Y Ruan, SL Salzberg, A Sandelin, C Schneider, C Schonbach, K Sekiguchi, CAM Semple, S Seno, L Sessa, Y Sheng, Y Shibata, H Shimada, K Shimada, D Silva, B Sinclair, S Sperling, E Stupka, K Sugiura, R Sultana, Y Takenaka, K Taki, K Tammoja, SL Tan, S Tang, MS Taylor, J Tegner, SA Teichmann, HR Ueda, E van Nimwegen, R Verardo, CL Wei, K Yagi, H Yamanishi, E Zabarovsky, S Zhu, A Zimmer, W Hide, C Bult, SM Grimmond, RD Teasdale, ET Liu, Brusic, V, J Quackenbush, C Wahlestedt, JS Mattick, DA Hume, C Kai, D Sasaki, Y Tomaru, S Fukuda, M Kanamori-Katayama, M Suzuki, J Aoki, T Arakawa, J Iida, K Imamura, M Itoh, T Kato, H Kawaji, N Kawagashira, T Kawashima, M Kojima, S Kondo, H Konno, K Nakano, N Ninomiya, T Nishio, M Okada, C Plessy, K Shibata, T Shiraki, S Suzuki, M Tagami, K Waki, A Watahiki, Y Okamura-Oho, H Suzuki, J Kawai, Y Hayashizaki

SCIENCE　Vol. 309　No. 5740　p. 1559-1563　2005/09　Research paper (scientific journal)

An Empirical Study of Grid Applications in Life Science - Lesson learnt from Biogrid Project in Japan -

Susumu Date, Kazutoshi Fujikawa, Hideo Matsuda, Haruki Nakamura, Shinji Shimojo

International Journal of Information Technology　Vol. 11　No. 3　p. 16-28　2005/08　Research paper (scientific journal)

Heterogeneous database federation using grid technology for drug discovery process

Y Tohsato, T Kosaka, S Date, S Shimojo, H Matsuda

GRID COMPUTING IN LIFE SCIENCE　Vol. 3370　p. 43-52　2005　Research paper (scientific journal)

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

Proceedings - International Workshop on Biomedical Data Engineering, BMDE2005　Vol. 2005　2005　Research paper (international conference proceedings)

Inference method of gene regulatory networks using gene functional classification

Kohei Taki, Reiji Teramoto, Yoichi Takenaka, Hideo Matsuda

Information Technology Letters　2004/09　Research paper (scientific journal)

Biased biological functions of horizontally transferred genes in prokaryotic genomes

Y Nakamura, T Itoh, H Matsuda, T Gojobori

NATURE GENETICS　Vol. 36　No. 7　p. 760-766　2004/07　Research paper (scientific journal)

Interaction Seach Between Proteins and Ligands by Database Integration with Grid Technology, 2nd International Conference "Genomics, Proteomics and Bioinformatics for Medicine

Masato Kitajima, Yukako Tohsato, Takahiro Kosaka, Kazuto Yamazaki, Reiji Teramoto, Susumu Date, Shinji Shimojo, Hideo Matsuda

2nd International Conference on Genomics, Proteomics and Bioinformatics for Medicine　2004/07

Heterogeneous Database Federation using Grid Technology for Drug Discovery Process

Yukako Tohsato, Takahiro Kosaka, Susumu Date, Shinji Shimojo, Hideo Matsuda

Proceedings of First International Workshop on Life Science Grid (LSGRID2004)　2004/05

A graph analysis method to detect metabolic sub-networks based on phylogenetic profile

Shoko Miyake, Yoichi Takenaka, Hideo Matsuda

Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004　p. 634-635　2004　Research paper (international conference proceedings)

Inference of gene regulatory network based on module network model with gene functional classifications

K Taki, R Teramoto, Y Takenaka, H Matsuda

2004 IEEE COMPUTATIONAL SYSTEMS BIOINFORMATICS CONFERENCE, PROCEEDINGS　p. 632-633　2004　Research paper (international conference proceedings)

MaXML: Mouse annotation XML

Takeya Kasukawa, Hidemasa Bono, Yoshihide Hayashizaki, Yasushi Okazaki, Hideo Matsuda

In Silico Biology　Vol. 4　No. 1　p. 7-15　2004　Research paper (scientific journal)

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, Roberto A. Barrero, Takuro Tamura, Yumi Yamaguchi-Kabata, Motohiko Tanino, Kei Yura, Satoru Miyazaki, Kazuho Ikeo, Keiichi Homma, Arek Kasprzyk, Tetsuo Nishikawa, Mika Hirakawa, Jean Thierry-Mieg, Danielle Thierry-Mieg, Jennifer Ashurst, Libin Jia, Mitsuteru Nakao, Michael A. Thomas, Nicola Mulder, Youla Karavidopoulou, Lihua Jin, Sangsoo Kim, Tomohiro Yasuda, Boris Lenhard, Eric Eveno, Yoshiyuki Suzuki, Chisato Yamasaki, Jun-Ichi Takeda, Craig Gough, Phillip Hilton, Yasuyuki Fujii, Hiroaki Sakai, Susumu Tanaka, Clara Amid, Matthew Bellgard, Maria de Fatima Bonaldo, Hidemasa Bono, Susan K. Bromberg, Anthony J. Brookes, Elspeth Bruford, Piero Carninci, Claude Chelala, Christine Couillault, Sandro J. de Souza, Marie-Anne Debily, Marie-Dominique Devignes, Inna Dubchak, Toshinori Endo, Anne Estreicher, Eduardo Eyras, Kaoru Fukami-Kobayashi, Gopal R. Gopinath, Esther Graudens, Yoonsoo Hahn, Michael Han, Ze-Guang Han, Kousuke Hanada, Hideki Hanaoka, Erimi Harada, Katsuyuki Hashimoto, Ursula Hinz, Momoki Hirai, Teruyoshi Hishiki, Ian Hopkinson, Sandrine Imbeaud, Hidetoshi Inoko, Alexander Kanapin, Yayoi Kaneko, Takeya Kasukawa, Janet Kelso, Paul Kersey, Reiko Kikuno, Kouichi Kimura, Bernhard Korn, Vladimir Kuryshev, Izabela Makalowska, Takashi Makino, Shuhei Mano, Regine Mariage-Samson, Jun Mashima, Hideo Matsuda, Hans-Werner Mewes, Shinsei Minoshima, Keiichi Nagai, Hideki Nagasaki, Naoki Nagata, Rajni Nigam, Osamu Ogasawara, Osamu Ohara, Masafumi Ohtsubo, Norihiro Okada, Toshihisa Okido, Satoshi Oota, Motonori Ota, Toshio Ota, Tetsuji Otsuki, Dominique Piatier-Tonneau, Annemarie Poustka, Shuang-Xi Ren, Naruya Saitou, Katsunaga Sakai, Shigetaka Sakamoto, Ryuichi Sakate, Ingo Schupp, Florence Servant, Stephen Sherry, Rie Shiba, Nobuyoshi Shimizu, Mary Shimoyama, Andrew J. Simpson, Bento Soares, Charles Steward, Makiko Suwa, Mami Suzuki, Aiko Takahashi, Gen Tamiya, Hiroshi Tanaka, Todd Taylor, Joseph D. Terwilliger, Per Unneberg, Vamsi Veeramachaneni, Shinya Watanabe, Laurens Wilming, Norikazu Yasuda, Sook Hyang-Yoo, Marvin Stodolsky, Wojciech Makalowski, Mitiko Go, Kenta Nakai, Toshihisa Takagi, Minoru Kanehisa, Yoshiyuki Sakaki, John Quackenbush, Yasushi Okazaki, Yoshihide Hayashizaki, Winston Hide, Ranajit Chakraborty, Ken Nishikawa, Hideaki Sugawara, Yoshio Tateno, Zhu Chen, Michio Oishi, Peter Tonellato, Rolf Apweiler, Kousaku Okubo, Lukas Wagner, Stefan Wiemann, Robert L. Strausberg, Takao Isogai, Charles Auffray, Nobuo Nomura, Takashi Gojobori, Sumio Sugano

PLoS Biology　Vol. 2　No. 6　2004　Research paper (scientific journal)

FREP: a database of functional repeats in mouse cDNAs

T Nagashima, H Matsuda, DG Silva, N Petrovsky, A Konagaya, C Schonbach

NUCLEIC ACIDS RESEARCH　Vol. 32　p. D471-D475　2004/01　Research paper (scientific journal)

Architecture of a grid-enabled research platform with location-transparency for bioinformatics.

Kido Y, Date S, Takeda S, Hatano S, Ma J, Shimojo S, Matsuda H

Genome informatics. International Conference on Genome Informatics　Vol. 15　No. 2　p. 3-12　2004　Research paper (scientific journal)

A method for clustering gene expression data based on graph structure.

Seno S, Teramoto R, Takenaka Y, Matsuda H

Genome informatics. International Conference on Genome Informatics　Vol. 15　No. 2　p. 151-160　2004　Research paper (scientific journal)

A challenge towards next-generation research infrastructure for advanced life science

H Nakamura, S Date, H Matsuda, S Shimojo

NEW GENERATION COMPUTING　Vol. 22　No. 2　p. 157-166　2004　Research paper (scientific journal)

Graph-based clustering for finding distant relationships in a large set of protein sequences

H Kawaji, Y Takenaka, H Matsuda

BIOINFORMATICS　Vol. 20　No. 2　p. 243-252　2004/01　Research paper (scientific journal)

Development of a database system for drug discovery by employing grid technology

M Kitajima, Y Tohsato, T Kosaka, K Yamazaki, R Teramoto, S Date, S Shimojo, H Matsuda

SEVENTH INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING AND GRID IN ASIA PACIFIC REGION, PROCEEDINGS　p. 365-369　2004　Research paper (international conference proceedings)

Analysis of gene expression profiles based on clustering

Y Takenaka, H Matsuda

GENOME RESEARCH　Vol. 13　No. 6B　p. 1558-1558　2003/06　Research paper (scientific journal)

Development and evaluation of an automated annotation pipeline and cDNA annotation system

T Kasukawa, M Furuno, Nikaido, I, H Bono, DA Hume, C Bult, DP Hill, R Baldarelli, J Gough, A Kanapin, H Matsuda, LM Schriml, Y Hayashizaki, Y Okazaki, J Quackenbush

GENOME RESEARCH　Vol. 13　No. 6B　p. 1542-1551　2003/06　Research paper (scientific journal)

Mouse Proteome Analysis

Alexander Kanapin, Serge Batalov, Melissa J. Davis, Julian Gough, Sean Grimmond, Hideya Kawaji, Michele Magrane, Hideo Matsuda, Christian Schoenbach, Rohan D. Teasdale, RIKEN GER Group, GSL Members, Zheng Yuan

Genome Research, 13, 6B, 1335-1344　Vol. 13　No. 6B　p. 1335-44　2003/06　Research paper (scientific journal)

BioGrid project in Kansai: towards a Grid technology for advanced life science

Shinji Shimojo, Susumu Date, Toyokazu Akiyama, Toshiyuki Okumura, Hideo Matsuda, Haruki Nakamura

Grid Computing and e-Science　2003/06　Research paper (other academic)

A clustering method for comparative analysis between genomes and pathways

S Miyake, Y Tohsato, Y Takenaka, H Matsuda

EIGHTH INTERNATIONAL CONFERENCE ON DATABASE SYSTEMS FOR ADVANCED APPLICATIONS, PROCEEDINGS　p. 327-334　2003　Research paper (international conference proceedings)

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Y Okazaki, M Furuno, T Kasukawa, J Adachi, H Bono, S Kondo, Nikaido, I, N Osato, R Saito, H Suzuki, Yamanaka, I, H Kiyosawa, K Yagi, Y Tomaru, Y Hasegawa, A Nogami, C Schonbach, T Gojobori, R Baldarelli, DP Hill, C Bult, DA Hume, J Quackenbush, LM Schriml, A Kanapin, H Matsuda, S Batalov, KW Beisel, JA Blake, D Bradt, Brusic, V, C Chothia, LE Corbani, S Cousins, E Dalla, TA Dragani, CF Fletcher, A Forrest, KS Frazer, T Gaasterland, M Gariboldi, C Gissi, A Godzik, J Gough, S Grimmond, S Gustincich, N Hirokawa, IJ Jackson, ED Jarvis, A Kanai, H Kawaji, Y Kawasawa, RM Kedzierski, BL King, A Konagaya, Kurochkin, IV, Y Lee, B Lenhard, PA Lyons, DR Maglott, L Maltais, L Marchionni, L McKenzie, H Miki, T Nagashima, K Numata, T Okido, WJ Pavan, G Pertea, G Pesole, N Petrovsky, R Pillai, JU Pontius, D Qi, S Ramachandran, T Ravasi, JC Reed, DJ Reed, J Reid, BZ Ring, M Ringwald, A Sandelin, C Schneider, CAM Semple, M Setou, K Shimada, R Sultana, Y Takenaka, MS Taylor, RD Teasdale, M Tomita, R Verardo, L Wagner, C Wahlestedt, Y Wang, Y Watanabe, C Wells, LG Wilming, A Wynshaw-Boris, M Yanagisawa, Yang, I, L Yang, Z Yuan, M Zavolan, Y Zhu, A Zimmer, P Carninci, N Hayatsu, T Hirozane-Kishikawa, H Konno, M Nakamura, N Sakazume, K Sato, T Shiraki, K Waki, J Kawai, K Aizawa, T Arakawa, S Fukuda, A Hara, W Hashizume, K Imotani, Y Ishii, M Itoh, Kagawa, I, A Miyazaki, K Sakai, D Sasaki, K Shibata, A Shinagawa, A Yasunishi, M Yoshino, R Waterston, ES Lander, J Rogers, E Birney, Y Hayashizaki

NATURE　Vol. 420　No. 6915　p. 563-573　2002/12　Research paper (scientific journal)

Using data compression for multidimensional distribution analysis

K Onizuka, T Noguchi, Y Akiyama, H Matsuda

IEEE INTELLIGENT SYSTEMS　Vol. 17　No. 3　p. 48-54　2002/05　Research paper (scientific journal)

Exploration of novel motifs derived from mouse cDNA sequences

H Kawaji, C Schonbach, Y Matsuo, J Kawai, Y Okazaki, Y Hayashizaki, H Matsuda

GENOME RESEARCH　Vol. 12　No. 3　p. 367-378　2002/03　Research paper (scientific journal)

An application of a pathway alignment method to comparative analysis between genome and pathways

S. Miyake, Y. Tahsato, H. Matsuda

Proceedings - IEEE Computer Society Bioinformatics Conference, CSB 2002　2002　Research paper (international conference proceedings)

P-quasi complete linkage analysis for gene-expression data

S. Seno, R. Teramoto, H. Matsuda

Proceedings - IEEE Computer Society Bioinformatics Conference, CSB 2002　2002　Research paper (international conference proceedings)

Using Data Compression for Multidimensional Distribution Analysis

Yutaka Akiyama, Tamotsu Noguchi, Kentaro Onizuka, Hideo Matsuda

IEEE Intelligent Systems　Vol. 17　No. 3　p. 48-54　2002　Research paper (scientific journal)

An Application of a Pathway Alignment Method to the Analysis of Metabolic Pathways

Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto

Research Communications in Biochemistry, Cell and Molecular Biology, 15, 3/4, 179-191　2001/12　Research paper (scientific journal)

Prediction of Protein Secondary Structure Using the Threading Algorithm and Local Sequence Similarity

Tamotsu Noguchi, Masahiro Ito, Hideo Matsuda, Yutaka Akiyama, Ken Nishikawa

Research Communications in Biochemistry and Cell and Molecular Biology　Vol. 5　No. 1-2　2001/10　Research paper (scientific journal)

Peptide Conformation Prediction by High-Speed Parallel Tree Search on a Massively Parallel Computer

Makoto Ando, Yutaka Akiyama, Hideo Matsuda

Research Communications in Biochemistry and Cell and Molecular Biology　Vol. 5　No. 1-2　2001/10　Research paper (scientific journal)

Functional annotation of a full-length mouse cDNA collection

J Kawai, A Shinagawa, K Shibata, M Yoshino, M Itoh, Y Ishii, T Arakawa, A Hara, Y Fukunishi, H Konno, J Adachi, S Fukuda, K Aizawa, M Izawa, K Nishi, H Kiyosawa, S Kondo, Yamanaka, I, T Saito, Y Okazaki, T Gojobori, H Bono, T Kasukawa, R Saito, K Kadota, H Matsuda, M Ashburner, S Batalov, T Casavant, W Fleischmann, T Gaasterland, C Gissi, B King, H Kochiwa, P Kuehl, S Lewis, Y Matsuo, Nikaido, I, G Pesole, J Quackenbush, LM Schriml, F Staubli, R Suzuki, M Tomita, L Wagner, T Washio, K Sakai, T Okido, M Furuno, H Aono, R Baldarelli, G Barsh, J Blake, D Boffelli, N Bojunga, P Carninci, MF de Bonaldo, MJ Brownstein, C Bult, C Fletcher, M Fujita, M Gariboldi, S Gustincich, D Hill, M Hofmann, DA Hume, M Kamiya, NH Lee, P Lyons, L Marchionni, J Mashima, J Mazzarelli, P Mombaerts, P Nordone, B Ring, M Ringwald, Rodriguez, I, N Sakamoto, H Sasaki, K Sato, C Schonbach, T Seya, Y Shibata, KF Storch, H Suzuki, K Toyo-oka, KH Wang, C Weitz, C Whittaker, L Wilming, A Wynshaw-Boris, K Yoshida, Y Hasegawa, H Kawaji, S Kohtsuki, Y Hayashizaki

NATURE　Vol. 409　No. 6821　p. 685-690　2001/02　Research paper (scientific journal)

Conformational Search and Potential Energy Analysis of Protein β-Hairpin Formations by Parallel Exhaustive Tree Search

Ando Makoto, Akiyama Yutaka, Matsuda Hideo

GI　Vol. 12　p. 362-363　2001

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)

T Noguchi, H Matsuda, Y Akiyama

NUCLEIC ACIDS RESEARCH　Vol. 29　No. 1　p. 219-220　2001/01　Research paper (scientific journal)

A graph-based clustering method for a large set of sequences using a graph partitioning algorithm.

Kawaji H, Yamaguchi Y, Matsuda H, Hashimoto A, Genome informatics. International Conference on Genome Informatics

GI　Vol. 12　p. 93-102　2001

An Information Content Maximization Alignment Algorithm for Metabolic Pathway Analysis

Yukako Tosato, Hideo Matsuda, Akihiro Hashimoto

Vol. 41　No. 7　p. 41-48　2000/11　Research paper (scientific journal)

Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping

Wataru Fujibuchi, Hiroyuki Ogata, Hideo Matsuda, Minoru Kanehisa

Nucleic Acids Research　Vol. 28　No. 20　p. 4029-4036　2000/10/15　Research paper (scientific journal)

A Multiple Alignment Algorithm for Metabolic Pathway Analysis using Enzyme Hierarchy

Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto

Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology, 2000　p. 376-383　2000/08

Quick selection of representative protein chain sets based on customizable requirements

T Noguchi, K Onizuka, M Ando, H Matsuda, Y Akiyama

BIOINFORMATICS　Vol. 16　No. 6　p. 520-526　2000/06　Research paper (scientific journal)

Determination of the complete nucleotide sequence and haplotypes in the D-loop region of the mitochondrial genome in the Oriental white stork, Ciconia boyciana

Yoshihiro Yamamoto, Koichi Murata, Hideo Matsuda, Takahisa Hosoda, Kazuo Tamura, Jun-Ichi Furuyama

Genes and Genetic Systems　Vol. 75　No. 1　p. 25-32　2000/02　Research paper (scientific journal)

Detection of conserved domains in protein sequences using a maximum-density subgraph algorithm

Matsuda, H.

IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences　Vol. E83-A　No. 4　2000　Research paper (scientific journal)

An Application of a Pathway Alignment Method to the Analysis of Amino Acid Biosynthesis

Tohsato Yukako, Matsuda Hideo, Hashimoto Akihiro

GI　Vol. 11　p. 284-285　2000

Representing Functional Annotations of Mouse cDNA Sequences in XML

Kasukawa Takeya, Bono Hidemasa, Matsuda Hideo, Okazaki Yasushi, Kohtsuki Shotaro, Hayashizaki Yoshihide

GI　Vol. 11　p. 376-377　2000

Hierarchical Approach to Parallel Tree Search for Protein Conformational Analysis.

Makoto Ando, Yutaka Akiyama, Hideo Matsuda

Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications(PDPTA)　2000　Research paper (international conference proceedings)

ESCAPE 2.0: Parallel exhaustive conformational search system of peptides with conformational libraries as building blocks

M. Ando, Y. Akiyama, H. Matsuda

Proceedings - 4th International Conference/Exhibition on High Performance Computing in the Asia-Pacific Region, HPC-Asia 2000　Vol. 2　p. 1097-1102　2000　Research paper (international conference proceedings)

GXML: A Novel Method for Exchanging and Querying Complete Genomes by Representing them as Structured Documents

AARONJ.STOKES, HIDEO MATSUDA, AKIHIRO HASHIMOTO

IPSJ Trans. on Database　Vol. 40　No. 6　p. 66-78　1999/08/15

Implementing a Molecular Phylojenetic Tree Database with Retrieval Function For Similar Structure

YOSHIKAWA TAKANOBU, TABE TOMOHIRO, KISHINAMI RISA, MATSUDA HIDEO, HASHIMOTO AKIHIRO

Vol. 40　No. 6　p. 54-65　1999/08/15

New method for maintaining semi-structured data described in XML

Takeya Kasukawa, Hideo Matsuda, Michio Nakanishi, Akihiro Hashimoto

IEEE Pacific RIM Conference on Communications, Computers, and Signal Processing - Proceedings　p. 258-261　1999　Research paper (scientific journal)

Application to Gene Cluster Analysis of Inductive Inference of Languages over Patterns with Conceptual Hierarchy

Tohsato Yukako, Matsuda Hideo, Hashimoto Akihiro

GI　Vol. 10　p. 324-325　1999

Making High-level Queries on Diverse Genome Data: A Structured Genome Document Database System Based on GXML and GQL

Stokes Aaron, Matsuda Hideo, Hashimoto Akihiro

GI　Vol. 10　p. 176-185　1999

Phylogenetic analysis of the third Hsp70 homolog in Escherichia coli; a novel member of the Hsc66 subfamily and its possible Co-chaperone

Takeshi Itoh, Hideo Matsuda, Hirotada Mori

DNA Research　Vol. 6　No. 5　p. 299-305　1999　Research paper (scientific journal)

Querying molecular biology databases by integration using multiagents

H Matsuda, T Imai, M Nakanishi, A Hashimoto

IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS　Vol. E82D　No. 1　p. 199-207　1999/01　Research paper (scientific journal)

Classifying molecular sequences using a linkage graph with their pairwise similarities

H Matsuda, T Ishihara, A Hashimoto

THEORETICAL COMPUTER SCIENCE　Vol. 210　No. 2　p. 305-325　1999/01　Research paper (scientific journal)

An Efficient Procedure for Maintaining Materialized Views on Distributed Database Systems

KASUKAWA Takeya, NAKANISHI Michio, MATSUDA Hideo, HASHIMOTO Akihiro

The Transactions of the Institute of Electronics,Information and Communication Engineers.　Vol. 81　No. 8　p. 1003-1013　1998/08

Automatic Detection of Gene Clusters by P-Quasi Complete Linkage Grouping

Fujibuchi Wataru, Ogata Hiroyuki, Matsuda Hideo, Kanehisa Minoru

GI　Vol. 9　p. 300-301　1998

A Method for Querying Complete Genomes by Viewing Them as Structured Documents

Stokes Aaron J., Matsuda Hideo, Hashimoto Akihiro

GI　Vol. 9　p. 314-315　1998

Implementation of a parallel Prolog system on a distributed memory parallel computer

H Matsuda, T Kawabata, Y Kaneda

IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS　Vol. E80D　No. 4　p. 504-509　1997/04　Research paper (scientific journal)

An approach to detection of protein structural motifs using an encoding scheme of backbone conformations.

Matsuda, H., Taniguchi, F., Hashimoto, A.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing　1997　Research paper (scientific journal)

Implementing an integrated system for heterogeneous molecular biology databases with intelligent agents

T Imai, H Matsuda, T Sekihara, M Nakanishi, A Hashimoto

1997 IEEE PACIFIC RIM CONFERENCE ON COMMUNICATIONS, COMPUTERS AND SIGNAL PROCESSING, VOLS 1 AND 2　p. 807-810　1997　Research paper (international conference proceedings)

分散共有メモリ型超並列計算機JUMP-1におけるスケーラブルI/Oサブシステムの構成

中條拓伯, 中野智行, 松本尚, 小畑正貴, 松田秀雄, 平木敬, 金田悠紀夫

情報処理学会論文誌　Vol. 37　No. 7　p. 1429-1439　1996/07/15

遺伝的アルゴリズムによる分子系統樹の作成

川本芳久, 松田秀雄, 橋本昭洋

情報処理学会論文誌　Vol. 37　No. 6　p. 1107-1116　1996/06/15

Protein phylogenetic inference using maximum likelihood with a genetic algorithm.

Matsuda, H.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing　1996　Research paper (scientific journal)

Construction of Phylogenetic Trees from Amino Acid Sequences using a Genetic Algorithm

Matsuda Hideo

GI　Vol. 6　p. 19-28　1995

High Performance I/O System of the Distributed Shared-Memory Massively Parallel Computer JUMP-1.

Hironori Nakajo, Takashi Matsumoto, Masaki Kohata, Hideo Matsuda, Kei Hiraki, Yukio Kaneda

Proceedings of the Seventh IASTED/ISMM International Conference on Parallel and Distributed Computing and Systems, Washington, D.C., USA, October 19-21, 1995　p. 470-473　1995

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, Shin-ichiro Mori

Proc. Intl. Symp. Parallel Architectures, Algorithms and Networks　p. 427-434　1994/12　Research paper (international conference proceedings)

Fast phylogenetic analysis on a massively parallel machine

Hideo Matsuda, Gary J. Olsen, Ross Overbeek, Yukio Kaneda

Proceedings of the International Conference on Supercomputing　Vol. 129421　p. 297-302　1994/07/16　Research paper (international conference proceedings)

An application of an OR-Parallel Prolog system to phylogenetic analysis

Hideo Matsuda, Yukio Kaneda

LISP and Symbolic Computation　Vol. 7　No. 2-3　p. 211-229　1994/06　Research paper (scientific journal)

An Application of an OR-Parallel Prolog System with a Priority Control Mechanism to Molecular Phylogenetic Tree Construction

MATSUDA Hideo, KANEDA Yukio

Vol. 35　No. 4　p. 658-665　1994/04　Research paper (scientific journal)

FASTDNAML - A TOOL FOR CONSTRUCTION OF PHYLOGENETIC TREES OF DNA-SEQUENCES USING MAXIMUM-LIKELIHOOD

GJ OLSEN, H MATSUDA, R HAGSTROM, R OVERBEEK

COMPUTER APPLICATIONS IN THE BIOSCIENCES　Vol. 10　No. 1　p. 41-48　1994/02　Research paper (scientific journal)

Molecular Phylogenetic Analysis using both DNA and Amino Acid Sequence Data and Its Parallelization

Matsuda Hideo, Yamashita Hiroshi, Kaneda Yukio

GI　Vol. 5　p. 120-129　1994

Efficient Query Processing on Genomic Database using Data-Parallel Logic Programming Language

Hideo Matsuda

Genome Informatics　Vol. 4　p. 17-24　1993/12　Research paper (international conference proceedings)

IMPLEMENTATION OF A PARALLEL-PROCESSING SYSTEM FOR INFERENCE OF PHYLOGENETIC TREES

Hideo Matsuda, Gary J. Olsen, Ray Hagstrom, Ross Overbeek, Yukio Kaneda

IEEE PACIFIC RIM CONFERENCE ON COMMUNICATIONS, COMPUTERS AND SIGNAL PROCESSING : PROCEEDINGS　p. 280-283　1993/05　Research paper (international conference proceedings)

A Priority Control System for OR-Parallel Prolog and Its Application

Hideo Matsuda, Shigeo Suzuka, Yukio Kaneda

Vol. 34　No. 4　p. 773-781　1993/04　Research paper (scientific journal)

INTRODUCTION OF DOSIM PREDICATE TO PROLOG

Y KANEDA, H MATSUDA

NEW GENERATION COMPUTING　Vol. 8　No. 2　p. 163-181　1990　Research paper (scientific journal)

密結合マルチプロセッサ上でのFGHC処理系の実現

松田秀雄, 石田英雄, 金田悠紀夫, 前川禎男

情報処理学会論文誌　Vol. 30　No. 10　p. 1289-1297　1989/10　Research paper (scientific journal)

A Study on Distributed Simulation for Flexible Manufacturing Systems

Susumu Fujii, Hiroaki Sandoh, Hideo Matsuda, Mitsunobu Tasaka

Proceedings of the IFAC/IFORS/IMACS Symposium on Information Control Problems in Manufacturing Technology　p. 27-32　1989/09　Research paper (international conference proceedings)

A Study on Collision-Free Path Planning for a Robot Manipulator

Susumu Fujii, Hiroaki Sandoh, Hideo Matsuda, Kazuhiro Kumamoto

Proceedings of the USA-Japan Symposium on Flexible Automation　p. 301-306　1988/07　Research paper (international conference proceedings)

Implementing Parallel Prolog System on Multiprocessor System PARK

Transactions on Information Processing Society on Japan　Vol. 29　No. 1　p. 38-46　1988/01　Research paper (scientific journal)

Sequential Prolog machine PEK

Yukio Kaneda, Naoyuki Tamura, Koichi Wada, Hideo Matsuda, Shumin Kuo, Sadao Maekawa

New Generation Computing　Vol. 4　No. 1　p. 51-66　1986/03　Research paper (scientific journal)

PARALLEL PROLOG MACHINE PARK - ITS HARDWARE STRUCTURE AND PROLOG SYSTEM

H MATSUDA, M KOHATA, T MASUO, Y KANEDA, S MAEKAWA

LECTURE NOTES IN COMPUTER SCIENCE　Vol. 221　p. 35-43　1986　Research paper (scientific journal)

Implementing Parallel Prolog System"k - Prolog"

MATSUDA HIDEO, TAMURA NAOYUKI, KOHATA MASAKI, KANEDA YUKIO, MAEKAWA SADAO

IPSJ Journal　Vol. 26　No. 2　p. 296-303　1985/03/15　Research paper (scientific journal)