Publication of Hideo Matsuda (as of March 31st, 2019)

1. Journal Paper (refereed)

Kenichiro Takeda, Honami Sawazaki, Haruya Takahashi, Yu-Sheng Yeh, Huei-Fen Jheng, Wataru Nomura, Takeshi Ara, Nobuyuki Takahashi, Shigeto Seno, Naoki Osato, Hideo Matsuda, Teruo Kawada, Tsuyoshi Goto,
The dipeptidyl peptidase-4 (DPP-4) inhibitor teneligliptin enhances brown adipose tissue function, thereby preventing obesity in mice,
FEBS Open Bio, Vol.8, No.11, pp.1782-1793, doi: 10.1002/2211-5463.12498 (November, 2018).

Yukako Sakaguchi, Keizo Nishikawa, Shigeto Seno, Hideo Matsuda, Hiroshi Takayanagi, Masaru Ishii,
Roles of enhancer RNAs in RANKL-induced osteoclast differentiation identified by genome-wide cap-analysis of gene expression using CRISPR/Cas9,
Scientific Reports, Vol.8, No.1, 7504, doi: 10.1038/s41598-018-25748-3 (May, 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 Bioinformatics, Vol.19(Suppl.4), No.89, pp.49-59, doi: 10.1186/s12859-018-2072-y (May, 2018).

Viacheslav Kapilevich, Shigeto Seno, Hideo Matsuda, Yoichi Takenaka,
Chromatin 3D reconstruction from chromosomal contacts using a genetic algorithm,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, doi: 10.1109/TCBB.2018.2814995 (March, 2018).

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,
A phytol-enriched diet activates PPAR-alpha in the liver and brown adipose tissue to ameliorate obesity-induced metabolic abnormalities,
Molecular Nutrition & Food Research, Vol.62, No.6, e17000688, doi: 10.1002/mnfr.201700688 (February, 2018).

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,
Direct cell-cell contact between mature osteoblasts and osteoclasts dynamically controls their functions in vivo,
Nature Communications, Vol.9, No.300, pp.1-12, doi: 10.1038/s41467-017-02541-w (January, 2018).

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,
Diagnostic assessment of deep learning algorithms for detection of lymph node metastases in women with breast cancer,
The Journal of the American Medical Association, Vol.318, No.22, pp.2199-2210, doi: 10.1001/jama.2017.14585 (December, 2017).

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,
Journal of Bioinformatics and Computational Biology, Vol.15, No.5, pp.1740004-1 - 1740004-16, doi: 10.1142/S0219720017400042 (September, 2017).

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,
The hepatokine FGF21 is crucial for peroxisome proliferator-activated receptor-α agonist-induced amelioration of metabolic disorders in obese mice,
Journal of Biological Chemistry, Vol.292, No.22, pp.9175-9190, doi: 10.1074/jbc.M116.767590 (June, 2017).

Bei-Wen Ying, Shigeto Seno, Hideo Matsuda, Tetsuya Yomo,
A simple comparison of the extrinsic noise in gene expression between native and foreign regulations in Escherichia coli,
Biochemical and Biophysical Research Communications, Vol.486, No.3, pp.852-857, doi: 10.1016/j.bbrc.2017.03.148 (May, 2017).

Masaomi Kurokawa, Shigeto Seno, Hideo Matsuda, Bei-Wen Ying,
Correlation between genome reduction and bacterial growth,
DNA Research, doi: 10.1093/dnares/dsw035 (July, 2016).

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,
Proinflammatory cytokine interleukin-1 beta suppresses cold-induced thermogenesis in adipocytes,
Cytokine, Vol.77, pp.107-114, doi: 10.1016/j.cyto.2015.11.001 (January, 2016).

Kazuma Yama, Yuki Matsumoto, Yoshie Murakami, Shigeto Seno, Hideo Matsuda, Kazuyoshi Gotoh, Daisuke Motooka, Shota Nakamura, Bei-Wen Ying, Tetsuya Yomo,
Functional specialization in regulation and quality control in thermal adaptive evolution,
Gene to Cells, Vol.20, Issue 11, pp.943-955, doi: 10.1111/gtc.12298 (November, 2015).

Yoichi Takenaka, Shigeto Seno, Hideo Matsuda,
Detecting the shifts of gene regulatory networks during time-course experiments with a single time point temporal resolution,
Journal of Bioinformatics and Computational Biology, Vol.13, No.5, pp.1543002-1 - 1543002-18, doi: 10.1142/S0219720015430027 (October, 2015).

Bei-Wen Ying, Tomoya Honda, Saburo Tsuru, Shigeto Seno, Hideo Matsuda, Yasuaki Kazuta, Tetsuya Yomo,
Evolutionary consequence of a trade-off between growth and maintenance along with ribosomal damages,
PLoS ONE, Vol.10, No.8, e0135639. doi:10.1371/journal.pone.0135639 (August, 2015).

Mari Yoshida, Saburo Tsuru, Naoko Hirata, Shigeto Seno, Hideo Matsuda, Bei-Wen Ying, Tetsuya Yomo,
Directed evolution of cell size in Escherichia coli,
BMC Evolutionary Biology, Vol.14, No.1, 257, doi: 10.1186/s12862-014-0257-1 (December, 2014).

Naoki Matsushita, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Metagenome fragment classification based on multiple motif-occurrence profiles,
PeerJ, Vol.2, e559, doi: 10.7717/peerj.559 (September, 2014).

Bei-Wen Ying, Saburo Tsuru, Shigeto Seno, Hideo Matsuda, Tetsuya Yomo,
Gene expression scaled by distance to the genome replication site,
Molecular BioSystems, Vol.10, No.3, pp.375-379, doi: 10.1039/c3mb70254e (November, 2013).

Ryo Araki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles,
Gene, Vol.518, pp.17-25, doi: 10.1016/j.gene.2012.11.090 (April 2013).

Bei-Wen Ying, Shigeto Seno, Fuyuro Kaneko, Hideo Matsuda, Tetsuya Yomo,
Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome,
BMC Genomics, Vol.14, 25, doi: 10.1186/1471-2164-14-25 (January, 2013).

Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A method for isoform prediction from RNA-Seq data by iterative mapping,
IPSJ Transactions on Bioinformatics, Vol.5, pp.27-33, doi: 10.2197/ipsjtbio.5.27 (April 2012).IPSJ Outstanding Paper Award

Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
An estimation method for inference of gene regulatory network using Bayesian network with uniting of partial problems,
BMC Genomics, Vol.13, No.Suppl. 1, S12, doi: 10.1186/1471-2164-13-S1-S12 (January 2012). APBC2012 Best Paper Award

Tomoyoshi Nakayama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Inference of S-system models of gene regulatory networks using immune algorithm,
Journal of Bioinformatics and Computational Biology, Vol.9, No.Suppl. 1, pp.75-86, doi: 10.1142/S0219720011005768 (December, 2011).

Yoichi Takenaka, Shigeto Seno, Hideo Matsuda,
Perfect Hamming code with a hash table for faster genome mapping,
BMC Genomics, Vol.12, No.Suppl. 3, S3 (November, 2011).

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,
Exploration of potential genomic portraits associated with intrahepatic recurrence in human hepatocellular carcinoma,
Annals of Surgical Oncology, Vol.17, No.12, pp.3145-3154 (December, 2010).

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,
Gene expression profile prospectively predicts peritoneal relapse after curative surgery of gastric cancer,
Annals of Surgical Oncology, Vol.17, No.4, pp.1033-1042 (April, 2010).

Tatsuya Yoshikawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Improved prediction method for protein interactions using both structural and functional characteristics of proteins,
IPSJ Transactions on Bioinformatics, Vol.3, pp.10-23 (March, 2010).

Takeru Nakazato, Hidemasa Bono, Hideo Matsuda, Toshihisa Takagi,
Gendoo: Functional profiling of gene and disease features using MeSH vocabulary,
Nucleic Acids Research, Vol.37, No.(Web Server Issue), pp.W166-W169 (June, 2009).

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 Bjoerkegren, Frank Brombacher, Erika Bulger, Alistair M Chalk, Joe Chiba, Nicole Cloonan, Adam Dawe, Josee Dostie, Paer G Engstroem, 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 Heinze, Winston Hide, Oliver Hofmann, Michael Hoernquist, Lukasz Huminieck, Kazuho Ikeo, Naoko Imamoto, Satoshi Inoue, Yusuke Inoue, Ryoko Ishihara, Takao Iwayanagi, Anders Jacobsen, Mandeep Kaur, Hideya Kawaji, Markus C Kerr1, 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 Schoenbach, 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 Tegne'r, 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,
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line,
Nature Genetics, Vol.41, No.5, pp.553-562 (May, 2009).

Yoshiyuki Kido, Shigeto Seno, Susumu Date, Yoichi Takenaka, Hideo Matsuda,
A Distributed-Processing System for Accelerating Biological Research using Data-Staging,
IPSJ Transactions on Bioinformatics, Vol.49, No.SIG5(TBIO4), pp.58-64 (March, 2008).

Gen Kawamura, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Combination Method of the Tanimoto Coefficient and Proximity Measure of Random Forest for Compound Activity Prediction,
IPSJ Transactions on Bioinformatics, Vol.49, No.SIG5(TBIO4), pp.46-57 (March, 2008).

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,
In Silico Biology, Vol.8, pp.53-61 (January, 2008).

Masato Kitajima, Yohsuke Minowa, Hideo Matsuda, Yasushi Okuno,
Compound-Transporter Interaction Studies using Canonical Correlation Analysis,
Chem-Bio Informatics Journal, Vol.7, No.2, pp.24-34 (December, 2007).

Sami Maekawa, Atsuko Matsumoto, Yoichi Takenaka, Hideo Matsuda,
Tissue-specific functions based on information content of gene ontology using cap analysis gene expression,
Medical and Biological Engineering and Computing, Vol.45, No.11, pp.1029-1036 (November, 2007).

Junya Seo, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Retrieving Functionally Similar Bioinformatics Workflows using TF-IDF Filtering,
IPSJ Transactions on Bioinformatics, Vol.48, No.SIG5(TBIO2), pp.20-29 (March, 2007).

Shigeto Seno, Yoichi Takenaka, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Hideo Matsuda,
A Method for Similarity Search of Genomic Positional Expression Using CAGE,
PLoS Genetics, Vol.2, No.4, pp.578-586 (April, 2006).

Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y
The transcriptional landscape of the mammalian genome,
Science, Vol.309, No.5740, pp.1559-1563 (September, 2005).

Susumu Date, Kazutoshi Fujikawa, Hideo Matsuda, Haruki Nakamura, Shinji Shimojo,
An Empirical Study of Grid Applications in Life Science - Lesson learnt from Biogrid Project in Japan -,
International Journal of Information Technology, Vol. 11, No. 3, pp.16-28 (August, 2005).

Takahiro Kosaka, Yukako Tohsato, Susumu Date, Hideo Matsuda, Shinji Shimojo,
An OGSA-based Integration of Life Science Resources,
Methods of Information in Medicine, Vol.44, No.2, pp.257-261 (June, 2005).

Yoji Nakamura, Takeshi Itoh, Hideo Matsuda, Takashi Gojobori,
Biased biological functions of horizontally transferred genes in prokaryotic genomes,
Nature Genetics, Vol.36, No.7, pp.760-766 (July, 2004).

Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda JI, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Md M, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, R Gopinath G, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.,
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones,
PLoS Biology, Vol.2, No.6 (June, 2004).

Haruki Nakamura, Susumu Date, Hideo Matsuda, Shinji Shimojo,
A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science,
New Generation Computing, Vol.22, No.2, pp.157-166, Ohmsha and Springer-Verlag (February, 2004).

Hideya Kawaji, Yoichi Takenaka, Hideo Matsuda,
Graph-based clustering for finding distant relationships in a large set of protein sequences,
Bioinformatics, Vol.20, No.2, pp.243-252 (January, 2004).

Takeshi Nagashima, Hideo Matsuda, Diego G. Silva, Nikolai Petrovsky, RIKEN GER Group, GSL Members, Akihiko Konagaya, Christian Schoenbach,
FREP: a database of functional repeats in mouse cDNAs,
Nucleic Acids Research, Vol.32, No.(DB issue), pp.D471-D475 (January, 2004).

Takeya Kasukawa, Hidemasa Bono, Yoshihide Hayashizaki, Yasushi Okazaki, Hideo Matsuda,
MaXML: mouse annotation XML,
In Silico Biology, Vol.4, No.3, pp.7-15 (January, 2004).

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 and GSL Members, Zheng Yuan,
Mouse Proteome Analysis,
Genome Research, Vol.13, No.6B, pp.1335-1344 (June, 2003).

Takeya Kasukawa, Masaaki Furuno, Itoshi Nikaido, Hidemasa Bono, David A. Hume, Carol Bult, David P. Hill, Richard Baldarelli, Julian Gough, Alexander Kanapin, Hideo Matsuda, Lynn M. Schriml, Yoshihide Hayashizaki, Yasushi Okazaki, John Quackenbush,
Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System,
Genome Research, Vol.13, No.6B, pp.1542-1551 (June, 2003).

Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schonbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y.
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
Nature, Vol.420, No.6915, pp.563-573 (December, 2002).

Kentaro Onizuka, Tamotsu Noguchi, Yutaka Akiyama, Hideo Matsuda,
Using Data Compression for Multidimensional Distribution Analysis,
IEEE Intelligent Systems, Vol.17, No.3, pp.48-54 (May/June, 2002).

Hideya Kawaji, Christian Schoenbach, Yo Matsuo, Jun Kawai, Yasushi Okazaki, Yoshihide Hayashizaki, Hideo Matsuda,
Exploration of Novel Motifs derived from Mouse cDNA sequences,
Genome Research, Vol.12, No.3, pp.367-378 (March, 2002).

Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto,
An Application of a Pathway Alignment Method to the Analysis of Metabolic Pathways,
Research Communications in Biochemistry, Cell and Molecular Biology, Vol.15, Nos.3/4, pp.179-191 (2001).

Makoto Ando, Yutaka Akiyama, Hideo Matsuda,
Peptide Conformation Prediction by High-Speed Parallel Tree Search on a Massively Parallel Computer,
Research Communications in Biochemistry, Cell and Molecular Biology, Vol.15, Nos.1/2, pp.95-114 (2001).

Tamotsu Noguchi, Masahiro Ito, Hideo Matsuda, Yutaka Akiyama, Ken Nishikawa,
Prediction of Protein Secondary Structure Using the Threading Algorithm and Local Sequence Similarity,
Research Communications in Biochemistry, Cell and Molecular Biology, Vol.15, Nos.1/2, pp.115-131 (2001).

Kawai, J., Shinagawa, A., Shibata, K., Yoshino, M., Itoh, M., Ishii, Y., Arakawa, T., Hara, A., Fukunishi, Y., Konno, H., Adachi, J., Fukuda, S., Aizawa, K., Izawa, M., Nishi, K., Kiyosawa, H., Kondo, S., Yamanaka, I., Saito, T., Okazaki, Y., Gojobori, T., Bono, H., Kasukawa, T., Saito, R., Kadota, K., Matsuda, H., Ashburner, M., Batalov, S., Casavant, T., Fleischmann, W., Gaasterland, T., Gissi, C., King, B., Kochiwa, H., Kuehl, P., Lewis, S., Matsuo, Y., Nikaido, I., Pesole, G., Quackenbush, J., Schriml, L. M., Staubli, F., Suzuki, R., Tomita, M., Wagner, L., Washio, T., Sakai, K., Okido, T., Furuno, M., Aono, H., Baldarelli, R., Barsh G., Blake, J., Boffelli, D., Bojunga, N., Carninci, P., de Bonaldo, M. F., Brownstein, M. J., Bult, C., Fletcher, C., Fujita, M., Gariboldi, M., Gustincich, S., Hill, D., Hofmann, M., Hume, D. A., Kamiya, M., Lee, NH., Lyons, P., Marchionni, L., Mashima, J., Mazzarelli, J., Mombaerts, P., Nordone, P., Ring, B., Ringwald, M., Rodriguez, I., Sakamoto, N., Sasaki, H., Sato, K., Schoenbach, C., Seya, T., Shibata, Y., Storch, K. F., Suzuki, H., Toyo-oka, K., Wang, K. H., Weitz, C., Whittaker, C., Wilming, L., Wynshaw-Boris, A., Yoshida, K., Hasegawa, Y., Kawaji, H., Kohtsuki, S., Hayashizaki, Y.,
Functional Annotation of a Full-Length Mouse cDNA Collection,
Nature, Vol.409, No.6821, pp.685-690 (February, 2001).

Tamotsu Noguchi, Hideo Matsuda, Yutaka Akiyama,
PDB-REPRDB: database of representative protein chains from the Protein Data Bank (PDB),
Nucleic Acids Research, Vol.29, No.1, pp.219-220 (January, 2001).

Wataru Fujibuchi, Hiroyuki Ogata, Hideo Matsuda, Minoru Kanehisa,
Automatic Detection of Conserved Gene Clusters in Multiple Genomes by Graph Comparison and P-quasi Grouping,
Nucleic Acids Research, Vol.28, No.20, pp.4029-4036 (October, 2000).

Tamotsu Noguchi, Kentaro Onizuka, Makoto Ando, Hideo Matsuda, Yutaka Akiyama,
Quick Selection of Representative Protein Chain Sets based on Customizable Requirements,
Bioinformatics, Vol.16, No.6, pp.520-526 (June, 2000).

Hideo Matsuda,
Detection of Conserved Domains in Protein Sequences using a Maximum-Density Subgraph Algorithm,
IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, Vol.E83-A, No.4, pp.713-721 (April, 2000).

Yoshihiro Yamamoto, Koichi Murata, Hideo Matsuda, Takahisa Hosoda, Kazuo Tamura, Jun-ichi Furuyama,
Determination of the Complete Nucleotide Sequence and Haplotypes in the D-loop Region of the Mitochondorial Genome in the Oriental White Stork, Ciconia boyciana,
Genes and Genetic Systems, Vol.75, No.1, pp.25-32 (February, 2000).

Takeshi Itoh, Hideo Matsuda, Hirotada Mori,
Phylogenetic Analysis of the Third Hsp70 Homolog in Escherichia coli; a Novel Member of the Hsc66 Subfamily and Its Possible Cochaperon,
DNA Research, Vol.6, No.5, pp.299-305 (October, 1999).

Aaron J. Stokes, Hideo Matsuda, Akihiro Hashimoto,
GXML: A Novel Method for Exchanging and Querying Complete Genomes by Representing them as Structured Documents,
IPSJ Transactions on Databases, Vol.40, No.TOD3, pp.66-78 (August, 1999).

Hideo Matsuda, Hiroyuki Yamanaka, Akihiro Hashimoto,
An Approximation Algorithm for Genome Rearrangements with Reversals and Transpositions,
IPSJ Transactions on Mathematical Modeling and Its Applications, Vol.40, No.SIG2(TOM1), pp.82-90 (February, 1999).

Hideo Matsuda, Takashi Imai, Michio Nakanishi, Akihiro Hashimoto,
Querying Molecular Biology Databases by Integration using Multiagents,
IEICE Transactions on Information and Systems, Vol.E82-D, No.1, pp.199-207 (January, 1999).

Hideo Matsuda, Tatsuya Ishihara, Akihiro Hashimoto,
Classifying Molecular Sequences using a Linkage Graph with Their Pairwise Similarities,
Theoretical Computer Science, Vol.210, No.2, pp.305-325 (January, 1999).

Hideo Matsuda, Toru Kawabata, Yukio Kaneda,
Implementation of a Parallel Prolog System on a Distributed Memory Parallel Computer,
IEICE Transactions on Information and Systems, Vol.E80-D, No.4, pp.504-509 (April, 1997).

Hideo Matsuda, Yukio Kaneda,
An Application of an OR-Parallel Prolog System to Phylogenetic Analysis,
Lisp and Symbolic Computation, Vol.7, Nos.2/3, pp.211-229, Kluwer Academic Publishers, Boston (December, 1994).

Gary J. Olsen, Hideo Matsuda, Ray Hagstrom, Ross Overbeek,
fastDNAml: A Tool for Construction of Phylogenetic Trees of DNA Sequences using Maximum Likelihood,
Computer Applications in the Biosciences, Vol.10, No.1, pp.41-48, Oxford University Press (February, 1994).

Yukio Kaneda, Hideo Matsuda, Katsuki Akiyoshi,
Introduction of dosim Predicate to Prolog,
New Generation Computing, Vol.8, No.2, pp.163-181, Ohmsha and Springer-Verlag (February, 1990).

Yukio Kaneda, Naoyuki Tamura, Koichi Wada, Hideo Matsuda, Shumin Kuo, Sadao Maekawa,
Sequential Prolog Machine PEK,
New Generation Computing, Vol.4, No.1, pp.51-66, Ohmsha and Springer-Verlag (April, 1986).

2. Invited Talk

Hideo Matsuda,
Reconstruction of Gene Regulatory Networks for Drug Target Discovery,
The 3rd National Seminar and Workshop on Computer Aided-Drug Design: Virtual Screening (CADD2010), Gurney Hotel, Penang, Malaysia (December 3, 2010) (Keynote Talk).

Hideo Matsuda,
Inference of Gene Regulatory Network for Cell Differentiations,
The Korean Society for Bioinformatics and Systems Biology (KSBSB) Summer School 2010, Soongsil University, Seoul, Korea (July 2, 2010) (Plenary Talk).

Hideo Matsuda,
A Plan of Data Grid Federation using Resource Namespace Service,
The 22nd Open Grid Forum (OGF22), Cambridge, USA (February 27, 2008).

Hideo Matsuda,
Experiences in NAREGI Project,
EGEE Workshop on Management of Rights in Production Grids, Paris (June 19, 2006).

Hideo Matsuda,
Bioinformatics Data Integration,
The 17th Global Grid Forum (GGF17), Tokyo (May 12, 2006).

Hideo Matsuda,
Data Integration of Life Science Databases using Grid Technology,
International Workshop on the Interoperability of Biological Information Resources (IBIR), Tokyo (March 17, 2006).

Hideo Matsuda,
Integration of Genomic and Biochemical Databases with Grid,
International Chemical Congress of Pacific Basin Societies (PacifiChem 2005), Program No.185, Honolulu, Hawaii (December 16, 2005).

Hideo Matsuda,
A Grid Environment for Data Integration of Scientific Databases,
First IEEE International Conference on e-Science and Grid Computing, p.3, Melbourne, Australia (December 7, 2005) (Keynote Talk).

Hideo Matsuda,
Bridging Life Science Databases with Globus 3/OGSA-DAI for Supporting Drug Discovery,
GlobusWorld, San Farncisco (January 23, 2004).

Hideo Matsuda,
Development of Bio-Information Environment on the Grid,
GlobusWorld, San Diego (January 16, 2003).

Hideo Matsuda,
Exploration of Novel Motifs in Mouse Full-Length cDNA Sequences,
Waterfront Symposium of Human Genome Science (WASH), Tokyo (March 2-3, 2002).

3. Conference Proceedings (refereed)

Yoshiaki Sota, Shigeto Seno, Yoichi Takenaka, Shinzaburo Noguchi, Hideo Matsuda,
Comparative analysis of transformation methods for gene expression profiles in breast cancer datasets,
IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE 2016), Splendor Hotel, Taichung, Taiwan, pp.328-333, doi: 10.1109/BIBE.2016.51 (October 31-November 2, 2016).

Hironori Shigeta, Tomohiro Mashita, Takeshi Kaneko, Junichi Kikuta, Shigeto Senoo, Haruo Takemura, Hideo Matsuda, Masaru Ishii,
A graph cuts image segmentation method for quantifying barrier permeation in bone tissue,
2014 1st workshop on Pattern Recognition Techniques for Indirect Immunofluorescence Images (I3A), Stockholm Waterfront Congress Centre, Sweden, pp. 16-19 (August 24,2014).

Tomohiro Mashita, Jun Usami, Hironori Shigeta, Yoshihiro Kuroda, Junichi Kikuta, Shigeto Senoo, Masaru Ishii, Hideo Matsuda, Haruo Takemura,
A Segmentation Method for Bone Marrow Cavity Image Using Graph-Cuts,
2014 1st workshop on Pattern Recognition Techniques for Indirect Immunofluorescence Images (I3A), Stockholm Waterfront Congress Centre, Sweden, pp. 20-23 (August 24,2014).

Tomoyoshi Nakayama, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Reconstruction of dynamic gene regulatory networks for cell differentiation by separation of time-course data,
2013 International Conference on Bioinformatics and Computational Biology (BIOCOMP'13), New Tropicana Hotel , Las Vegas, Nevada, USA (July 25, 2013)

Kensuke Suzuki, Daisuke Ueta, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A method of sequence analysis for high-throughput sequence data based on shifted short read clustering,
2013 International Conference on Bioinformatics and Computational Biology (BIOCOMP'13), New Tropicana Hotel , Las Vegas, Nevada, USA (July 25, 2013)

Yuta Okuma, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Gene set enrichment analysis for a long time series gene expression profile,
2013 International Conference on Bioinformatics and Computational Biology (BIOCOMP'13), New Tropicana Hotel , Las Vegas, Nevada, USA (July 25, 2013)

Ryo Araki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles,
23rd International Conference on Genome Informatics (GIW2012), National Cheng Kung University, Tainan, Taiwan (December 13, 2012).(Accepted for Oral Presentation)

Daisuke Ueta, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Mutation-aware clustering with error correction for short-read genome mapping,
2011 Joint Conference of CBI and JSBi (CBI/JSBi2011), JSBi-27, Kobe International Conference Center, Kobe (November 9, 2011).(Accepted for Oral Presentation)

Tomoshige Ohno, Motokazu Ishikawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
An Improved RNA-Seq Analysis Method for Isoform Prediction by Iterative Mapping,
2010 International Conference on Genome Informatics (GIW2010), No.8, Hangzhou (December 16, 2010).(Accepted for Oral Presentation, Best Poster Award)

Takuya Ishibashi, Yoshiyuki Kido, Takanori Fukumoto, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Metadata Management System for Composing Bioinformatics Workflows,
9th International Conference on Bioinformatics (InCoB2010), No.187, International Conference Center, Waseda University, Tokyo (September 28, 2010).

Junya Seo, Yoshiyuki Kido, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Method for Efficient Execution of Bioinformatics Workflows,
Genome Informatics, Vol.23, pp.139-148, Yokohama, (December 16, 2009).

Takeru Nakazato, Hidemasa Bono, Hideo Matsuda, Toshihisa Takagi,
Functional profiling of OMIM data using MeSH vocabulary,
2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008), P070/T07, Senri-Chuo (December 15, 2008).

Masahiko Hamada, Yoshiyuki Kido, Shigeto Seno, Hiromi Daiyasu, Yoichi Takenaka, Hideo Matsuda,
A Method for Making a New Reference Set of PDB Entries for Retrieving Protein 3D Structures with Structural Annotations,
2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008), P074/T02, Senri-Chuo (December 15, 2008).

Takashi Shimizu, Yoshiyuki Kido, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Method for Reducing Bounds of Compound Search by Dividing Structure Key,
2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008), P077/T01, Senri-Chuo (December 16, 2008).

Yoichi Takenaka, Akiko Matsumoto, Hideo Matsuda,
GO based Tissue Specific Functions of Mouse using Countable Gene Expression Profiles,
Genome Informatics, Vol.19, pp.154-165, Singapore (December 4, 2007).

Hideo Matsuda, Yoshiyuku Kido, Kentaro Wakatsuki,
Grid Interoperation on Data Management between NAREGI and EGEE gLite,
EGEE User Forum, Manchester (May 11, 2007) .

Sami Maekawa, Atsuko Matsumoto, Yoichi Takenaka, Hideo Matsuda,
A Method for Exploring Tissue-Specific Functions based on Information Content of Gene Ontology Terms using CAGE Tags,
World Congress on Medical Physics and Biomedical Engineering, Seoul (August 30, 2006).

Kohei Taki, Yoichi Takenaka, Hideo Matsuda,
Inference of Transcriptional Regulatory Networks using CAGE Transcriptome Dataset of Mus musculus,
World Congress on Medical Physics and Biomedical Engineering, Seoul (August 30, 2006).

Junya Seo, Shigeto Senoo, Yoichi Takenaka, Hideo Matsuda,
Extraction of Functionally Similar Bioinformatics Workflows,
6th International Workshop on Distibuted Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics (NETTAB 2006), pp.70-74, S. Margherita di Pula, Cagliali, Italy (July 11, 2006).

Takahiro Kosaka, Susumu Date, Hideo Matsuda, Shinji Shimojo,
A heuristic query optimization for distributed inference on life-science ontologies,
IEEE Workshop on Knowledge Acquisition from Distributed, Autonomous, Semantically Heterogeneous Data and Knowledge Sources, Houston, Texas (November 27, 2005).

Gen Kawamura, Masato Kitajima, Takahiro Kosaka, Susumu Date, Shinji Shimojo, Hideo Matsuda,
A Grid-based Information Integration System for Drug Discovery by using Freely Accessible Compound Databases,
International CBI Conference (CBI2005), Yokohama (August 26, 2005).

Toshiyuki Okumura, Susumu Date, Yoichi Takenaka, Hideo Matsuda,
A Framework for Biological Analysis on the Grid,
Lifescience Grid Workshop, Singapore (May 5, 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,
International Workshop on Biomedical Data Engineering (BMDE 2005), pp.121-128, Tokyo (April 4th, 2005).

Yukako Tohsato, Takahiro Kosaka, Susumu Date, Shinji Shimojo, Hideo Matsuda,
Heterogeneous Database Federation using Grid Technology for Drug Discovery Process,
In Akihiro Konagaya (ed.), Grid Computing in Life Science: First International Life Science Grid Workshop, LSGRID 2004
Lecture Notes in Bioinformatics, vol.3370, pp.43-52 (February, 2005).

Takahiro Kosaka, Susumu Date, Hideo Matsuda, Shinji Shimojo,
Designing a Rule-Based Environment to Interoperate Life-Scientific Ontologies for Drug Discovery,
2005 Symposium on Applications and the Internet Workshops (SAINTWKSP 2005) January 31-Feruary 4, Trento, Italy (January, 2005).

Yoshiyuki Kido, Susumu Date, Shingo Takeda, Shoji Hatano, Juncai Ma, Shinji Shimojo, Hideo Matsuda,
Architecture of a Grid-Enabled Research Platform with Location-Transparency for Bioinformatics,
Genome Informatics, Vol.15, No.2, pp.3-12 (December, 2004).

Shigeto Seno, Reiji Teramoto, Yoichi Takenaka, Hideo Matsuda,
A Method for Clustering Expression Data Based on Graph Structure,
Genome Informatics, Vol.15, No.2, pp.151-160 (December, 2004).

Masato Kitajima, Yukako Tohsato, Takahiro Kosaka, Kazuto Yamazaki, Reiji Teramoto, Susumu Date, Shinji Shimojo, Hideo Matsuda,
Development of a database system for drug discovery by employing grid technology,
HPC Asia 2004 Biogrid Workshop, pp.365-369, July 21, Ohmiya (July, 2004).

Yukako Tohsato, Takahiro Kosaka, Susumu Date, Shinji Shimojo, Hideo Matsuda,
Heterogeneous Database Federation using Grid Technology for Drug Discovery Process,
First International Workshop on Life Science Grid (LSGRID2004), May 31st-June 1st, Kanazawa (June, 2004).

Shoko Miyake, Yukako Tohsato, Yoichi Takenaka, Hideo Matsuda,
A Clustering Method for Comparative Analysis between Genomes and Pathways,
8th International Conference on Database Systems for Advanced Applications (DASFAA 2003), pp.327-334 (March 28, 2003)

Hideo Matsuda,
Unifying Bio-Information on the Grid,
3rd Pacific Rim Applications and Grid Middleware Assembly Workshop (PRAGMA), Fukuoka (January 23, 2003).

Hideya Kawaji, Yosuke Yamaguchi, Hideo Matsuda, Akihiro Hashimoto,
A Graph-based Clustering Method for a Large Set of Sequences using a Graph Partitioning Algorithm,
Genome Informatics, 12, pp.93-102 (December, 2001).

Takeya Kasukawa, Hideo Matsuda, Hidemasa Bono, Yasushi Okazaki, Shotaro Kohtsuki, Yoshihide Hayashizaki, Akihiro Hashimoto,
MaXML: Functional Annotation of Mouse cDNA Sequences in XML,
Workshops on CORBA and XML: Towards a Bioinformatics Integrated Network Environment (NETTAB 2001), pp.52-56 (May, 2001).

Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto,
A Multiple Alignment Algorithm for Metabolic Pathway Analysis using Enzyme Hierarchy,
8th International Conference on Intelligent Systems for Molecular Biology (ISMB 2000), pp.376-383 (August, 2000).

Makoto Ando, Yutaka Akiyama, Hideo Matsuda,
Hierarchical Approach to Parallel Tree Search for Protein Conformational Analysis,
International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA2000), pp.643-649 (June, 2000).

Makoto Ando, Yutaka Akiyama, Hideo Matsuda,
ESCAPE 2.0: Parallel Exaustive Conformational Search System of Peptides with Conformational Libraries as Building Blocks,
4th International Conference/Exhibition on High Performance Computing in Asia-Pacific Region (HPC-ASIA 2000), pp.1097-1102, IEEE Press (May, 2000).

Aaron J. Stokes, Hideo Matsuda, Akihiro Hashimoto,
Making High-level Queries on Diverse Genome Data: A Structured Genome Document Database System based on GXML and GQL,
Genome Informatics, Vol.10, pp.176-185, Universal Academy Press (December, 1999).

Takeya Kasukawa, Hideo Matsuda, Michio Nakanishi, Akihiro Hashimoto,
A New Method for Maintaining Semi-Structured Data Described in XML,
IEEE Pacific Rim Conference on Communications, Computers, and Signal Processing, pp.258-261 (August, 1999).

Takanobu Yoshikawa, Tomohiro Tabe, Risa Kishinami, Hideo Matsuda, Akihiro Hashimoto,
On the Implementation of a Phylogenetic Tree Database,
IEEE Pacific Rim Conference on Communications, Computers, and Signal Processing, pp.42-45 (August, 1999).

Sivasundaram Suharnan, Takeshi Itou, Hideo Matsuda, Hirotada Mori,
Clustering Molecular Sequences with Their Components,
Genome Informatics, No.8, pp.125-134, Universal Academy Press (December, 1997).

Yoshihisa Kawamoto, Akihiro Inoue, Yoshihiko Tamada, Hideo Matsuda, Michio Nakanishi, Akihiro Hashimoto:
A Method for Retrieving Relevant Entries of Molecular Biology Databases using Word Cooccurrence Frequency,
International Symposium on Digital Media Information Base (DMIB'97), pp.96-100 (November, 1997).

Hideo Matsuda, Takashi Imai, Toshiko Sekihara, Michio Nakanishi, Akihiro Hashimoto,
Integrating Heterogeneous Molecular Biology Databases with Multiagents,
IPSJ International Symposium on Information Systems and Technologies for Network Society, pp.265-268 (September, 1997).

Takashi Imai, Hideo Matsuda, Toshiko Sekihara, Michio Nakanishi, Akihiro Hashimoto,
Implementing an Integrated System for Heterogeneous Molecular Biology Databases with Intelligent Agents,
IEEE Pacific Rim Conference on Communications, Computers, and Signal Processing, pp.807-810 (August, 1997).

Hideo Matsuda, Fumihiro Taniguchi, Akihiro Hashimoto,
An Approach to Detection of Protein Structural Motifs using an Encoding Scheme of Backbone Conformations,
2nd Pacific Symposium on Biocomputing, pp.280-291, World Scientific (January, 1997).

Hideo Matsuda, Tatsuya Ishihara, Akihiro Hashimoto,
A Clustering Method for Molecular Sequences based on Pairwise Similarity,
Genome Informatics, No.7, pp.23-32, Universal Academy Press (December, 1996).

Hideo Matsuda,
Protein Phylogenetic Inference using Maximum Likelihood With A Genetic Algorithm,
1st Pacific Symposium on Biocomputing, pp.512-523, World Scientific (January, 1996).

Hideo Matsuda,
Construction of Phylogenetic Trees from Amino Acid Sequences using a Genetic Algorithm,
Genome Informatics, No.6, pp.19-28, Universal Academy Press (December, 1995).

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,
7th IASTED - ISMM International Conference on Parallel and Distributed Computing and Systems, pp.470-473, IASTED - ACTA PRESS, (October, 1995).

Hideo Matsuda,
Querying Genomic Database by using a Parallel Logic Programming System on Distributed Computing Environment,
IEEE Pacific Rim Conference on Communications, Computers, and Signal Processing, pp.333-336 (May, 1995).

Hideo Matsuda, Hiroshi Yamashita, Yukio Kaneda,
Molecular Phylogenetic Analysis using both DNA and Amino Acid Sequence Data and Its Parallelization,
Genome Informatics, No.5, pp.120-129, Universal Academy Press (December, 1994).

Hideo Matsuda, Gary J. Olsen, Ross Overbeek, Yukio Kaneda,
Fast Phylogenetic Analysis on a Massively Parallel Machine,
8th ACM International Conference on Supercomputing, pp.297-302 (July, 1994).

Yukio Kaneda, Hideo Matsuda,
A Priority Control System for OR-Parallel Prolog and Its Performance Evaluation,
Lecture Notes in Computer Science, Vol.748, pp.42-53, Springer-Verlag (December, 1993).

Hideo Matsuda,
Efficient Query Processing on Genomic Database using Data-Parallel Logic Programming Language,
Genome Informatics, No.4, pp.17-24, Universal Academy Press (December, 1993).

Hideo Matsuda, Gary J. Olsen, Ray Hagstrom, Ross Overbeek, Yukio Kaneda,
Implementation of a Parallel Processing System for Inference of Phylogenetic Trees,
IEEE Pacific Rim Conference on Communications, Computers and Signal Processing, pp.280-283 (May, 1993).

Yukio Kaneda, Hideo Matsuda,
A Priority Control Systems for Or-Parallel Prolog,
Parallel Symbolic Computing: Languages, Systems, and Applications, pp.14.1-14.12 (October, 1992).

Susumu Fujii, Hiroaki Sandoh, Hideo Matsuda, Mitsunobu Tasaka,
A Study on Distributed Simulation for Flexible Manufacturing Systems,
IFAC/IFORS/IMACS Symposium on Information Control Problems in Manufacturing Technology, pp.27-32 (September, 1989).

Susumu Fujii, Hiroaki Sandoh, Hideo Matsuda, Kazuhiro Kumamoto,
A Study on Collision-Free Path Planning for a Robot Manipulator,
USA-Japan Symposium on Flexible Automation, pp.301-306 (July, 1988).

Hideo Matsuda, Masaki Kohata, Tsuyoshi Masuo, Yukio Kaneda, Sadao Maekawa,
Implementing Parallel Prolog System on Multiprocessor System PARK,
5th International Workshop on Database Machines, pp.640-653 (October, 1987).

Hideo Matsuda, Masaki Kohata, Tsuyoshi Masuo, Yukio Kaneda, Sadao Maekawa,
Parallel Prolog Machine PARK: Its Hardware Structure and Prolog Systems,
Lecture Notes in Computer Science, Vol.221, pp.35-43, Springer-Verlag (May, 1986).

Yukio Kaneda, Naoyuki Tamura, Koichi Wada, Hideo Matsuda, Shumin Kuo, Sadao Maekawa,
Sequential Prolog Machine PEK and Its Performance Evaluation,
Mini and Microcomputers and Their Applications, pp.190-193 (June, 1985).

Naoyuki Tamura, Koichi Wada, Hideo Matsuda, Yukio Kaneda, Sadao Maekawa,
Sequential Prolog Machine PEK,
International Conference on Fifth Generation Computer Systems, ICOT, pp.542-550 (November, 1984).

Yukio Kaneda, Naoyki Tamura, Koichi Wada, Hideo Matsuda,
Sequential Prolog Machine PEK: Architecture and Software System,
International Workshop on High-Level Computer Architecture, pp.4.1-4.6 (May, 1984).

4. Book

Hideo Matsuda, Satoru Miyano, Toshihisa Takagi, Limsoon Wong (eds):
Genome Informatics 2001,
Universal Academy Press, Tokyo (December 17, 2001).

5. Poster Presentation

Kazumasa Saito, Shigeto Seno, Hideo Matsuda, Yoichi Takenaka,
Missing value imputation for gene expression data with deep learning,
The Sexteenth Asia Pacific Bioinformatics Conference (APBC 2018), No.A9, Keio University, Yokohama (January 15-17, 2018).

Meya Cho, Shigeto Seno, Hideo Matsuda, Yoichi Takenaka,
Functional analysis of metagenome using composition-based method,
The Sexteenth Asia Pacific Bioinformatics Conference (APBC 2018), No.A18, Keio University, Yokohama (January 15-17, 2018).

Mitsuhiro Eto, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Clustering of cells for single cell analysis using latent Dirichlet allocation,
International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB 2017), No.B-071, Prague Congress Centre, Prague, Czech (July 21-25, 2017).

Hideo Matsuda, Hironori Shigeta, Shigeto Seno, Junichi Kikuta, Masaru Ishii,
Analyzing cell migration dynamics from intravital imaging by deformable image matching,
International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB 2017), No.B-383, Prague Congress Centre, Prague, Czech (July 21-25, 2017).

Shigeto Seno, Masayuki Furuya, Junichi Kikuta, Masaru Ishii, Hideo Matsuda,
A method of bioimage analysis for spatial pattern of cellular interaction and intercalation,
International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB 2017), No.B-384, Prague Congress Centre, Prague, Czech (July 21-25, 2017).

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,
International Conference on Pattern Recognition (ICPR 2016), No.TuPT5.3, Cancun Center, Cancun, Mexico (December 4-8, 2016).

Fuki Iwasaki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
An accurate estimation method for expression profiles of novel transcripts from RNA-Seq data,
International Conference on Intelligent Systems for Molecular Biology (ISMB2016), No.N24, Swan and Dolphin Hotel, Orlando, Florida, USA (July 8-12, 2016).

Hideo Matsuda, Junko Tsuda, Shigeto Seno, Yoichi Takenaka,
A method for reducing false positives of target genes of microRNAs by combining two prediction tools,
International Conference on Intelligent Systems for Molecular Biology (ISMB2016), No.O49, Swan and Dolphin Hotel, Orlando, Florida, USA (July 8-12, 2016).

Yoichi Takenaka, Shigeto Seno, Hideo Matsuda,
Dynamic analysis of gene regulations using leaving-one-out expression profile,
International Conference on Research in Computational Molecular Biology (RECOMB 2016), No.48, UCLA, Los Angeles, California, USA (April 17-21, 2016).

Kazumasa Saito, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Bayesian network inference from gene expression profiles with a small number of samples,
International Conference on Research in Computational Molecular Biology (RECOMB 2016), No.50, UCLA, Los Angeles, California, USA (April 17-21, 2016).

Kojiro Fukuda, Shigeto Seno, Tomohiro Mashita, Yoichi Takenaka, Masaru Ishii, Hideo Matsuda,
An automatic event detection method using semi-supervised learning for time-lapse imaging data,
Bioimage Informatics 2014, No.P22, Provinciehuis Vlaams-Brabant, Leuven, Belgium (October 8-10, 2014).

Kohei Kurashige, Shigeto Seno, Tomohiro Mashita, Junichi Kikuta, Yoichi Takenaka, Masaru Ishii, Hideo Matsuda,
Improvement approach of cell tracking accuracy by using inter-frame information,
Bioimage Informatics 2014, No.P38, Provinciehuis Vlaams-Brabant, Leuven, Belgium (October 8-10, 2014).

Yoichi Takenaka, Shigeto Seno, Hideo Matsuda,
Chronological analysis of regulatory strength on gene regulatory networks,
13th European Conference on Computational Biology (ECCB'14), No.B04, Strasbourg, France (September 7-10, 2014).

Kazunori Waki, Hideo Matsuda,
Causal discovery from omics information using Bayesian network,
International Conference on Genome Informatics (GIW2013), No.41, Biopolis, Singapore (December 16-18, 2013).

Tomoshige Ohno, Shigeto Seno, Hiromi Daiyasu, Yoichi Takenaka, Hideo Matsuda,
Integrative prediction of miRNA-mRNA interactions from high-throughput sequencing data,
RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges 2013, Toronto Reference Library, Toronto, Canada (November 8-12, 2013).

Naoki Matsushita, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Multiplication of Motif Occurrence Profiles for Metagenome Fragment Classification,
35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'13), Short Papers No.3055, Osaka International Convention Center, Osaka (July 3-7, 2013).

Yuta Okuma, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Gene Set Enrichment Analysis for Time-Series Gene Expression Profile,
35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'13), Short Papers No.3225, Osaka International Convention Center, Osaka (July 3-7, 2013).

Tomoyoshi Nakayama, Yoshiyuki Kido, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Estimate Dynamic Gene Regulatory Networks in Adipocyte Differentiation for Detecting Changes of Gene Regulations by Splitting Time Course Data,
23rd International Conference on Genome Informatics (GIW2012), National Cheng Kung University, Tainan, Taiwan (December 13, 2012).

Shigeto Seno, Sakae Maeda, Tomohiro Mashita, Yoichi Takenaka, Masaru Ishii, Hideo Matsuda,
Automatic cell tracking for time-lapse fluorescent images of cell cycle,
International Symposium "Towards Comprehensive Understanding of Immune Dynamism" (TCUID2012), Osaka University, Suita (October 29, 2012).

Shigeto Seno, Tomohiro Mashita, Yoichi Takenaka, Masaru Ishii, Hideo Matsuda,
A cell-tracking method for time-lapse multicolor fluorescent images,
Bioimage Informatics 2012, p.57, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany (September 16-19, 2012).

Yoichi Takenaka, Shigeto Seno, Hideo Matsuda,
All the 1+3n one-mismatch sequences of n-mer DNA are involved in 22.2+0.00879n strings of Perfect Linear Code words on DNA,
International Conference on Intelligent Systems for Molecular Biology (ISMB2012), U44, Long Beach Convention and Entertainment Center, Long Beach (July 17, 2012).

Yoshimi Kawakami, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A random forest approach to the detection of a rare disease in the case control studies,
International Conference on Genome Informatics (GIW2011), P-030, Haeundae Grand Hotel, Busan, Korea (December 5, 2011).

Yoichi Takenaka, Tomoshige Ohno, Kayo Okuda, Shigeto Seno, Hideo Matsuda,
Sequence determination and expression estimation of alleles from RNA-Seq data,
InCoB/ISCB-Asia Joint Conference 2011, 61, Renaissance Hotel, Kuala Lumpur, Malaysia (November 30, 2011).

Yoichi Takenaka, Shigeto Seno, Hideo Matsuda,
Perfect hamming code with Burrow-Wheeler translation for genome mapping,
InCoB/ISCB-Asia Joint Conference 2011, 70, Renaissance Hotel, Kuala Lumpur, Malaysia (December 1, 2011).

Ryo Araki, Yoichi Takenaka, Tomoshige Ohno, Yukito Watanabe, Shigeto Seno, Hideo Matsuda,
Direct unique gene regulatory networks along dendrogram of cell differentiation,
InCoB/ISCB-Asia Joint Conference 2011, 83, Renaissance Hotel, Kuala Lumpur, Malaysia (November 30, 2011).

Tatsuya Kitaguchi, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Network analysis for time-series expression profile using nested effects models,
2011 Joint Conference of CBI and JSBi (CBI/JSBi2011), JSBi-49, Kobe International Conference Center, Kobe (November 8, 2011)

Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Method for Inference of Gene Regulatory Network based on Bayesian Network with Uniting of Partial Problems,
19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2011), N13, Austria Center Vienna, Vienna (July 18, 2011).

Tomoshige Ohno, Kiyoshi Yoshizawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Directed Graphical Gaussian Model for Inferring Gene Regulatory Networks,
19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2011), X16, Austria Center Vienna, Vienna (July 19, 2011).

Masakazu Sugiyama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A method for risk predicition of a serious disease using rule-based analysis,
19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2011), M12, Austria Center Vienna, Vienna (July 19, 2011).

Sho Ohsuga,Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Feature selection for specifying experimental conditions that activate gene transcriptions,
19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2011), N12, Austria Center Vienna, Vienna (July 19, 2011).

Yoichi Takenaka, Shigeto Seno, Hideo Matsuda,
Perfect hamming code as hash key for fast genome mapping,
19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2011), U22, Austria Center Vienna, Vienna (July 19, 2011).

Kiyoshi Yoshizawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Revealing regulatory relationships of crosstalk with multiple time-series gene expression profiles,
2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010), P017, Centennial Hall, Kyushu University School of Medicine, Fukuoka (December 13, 2010).

Tomoyoshi Nakayama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A bootstrapping method of S-system model for estimating timeline gene regulatory networks,
2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010), P027, Centennial Hall, Kyushu University School of Medicine, Fukuoka (December 13, 2010).

Yoshiyuki Kido, Takanori Fukumoto, Taishin Nomura, Yoshihisa Kurachi, Hideo Matsuda,
A study of discovery of Web service and modeling data for multi-scale simulation,
7th Korea-Japan e-Science Symposium, (July, 2010).

Takuya Hashimoto, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A method for predicting compound-protein interactions using canonical correlational analysis,
18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2010), M015, Hynes Convention Center, Boston (July 11, 2010).

Daisuke Ueta, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A method for detecting structural variants from massive paired end genome sequences by mapping signatures,
18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2010), U041, Hynes Convention Center, Boston (July 11, 2010).

Tomoyoshi Nakayama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
An estimation method of S-system model of gene regulatory networks using immune algorithm,
18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2010), X060, Hynes Convention Center, Boston (July 12, 2010).

Ly Nguyen, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
An algorithm for fast exact search of chemical compounds by clustered data beforehand,
21st International Workshop on Combinatorial Algorithms, (July, 2010).

Kiyoshi Yoshizawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Method of Estimation of Crosstalk Genes with Multiple Time-Series Gene Expression Profiles,
International Conference on Genome Informatics (GIW2009), P057, Pacifico Yokohama, Yokohama (December 14, 2009).

Yuya Shuto, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Method for the Inference of Gene Regulatory Networks based on Dynamic Bayesian Net-work with Clustering of Time-Series Subsequences,
International Conference on Genome Informatics (GIW2009), P080, Pacifico Yokohama, Yokohama (December 15, 2009).

Takahiro Kishimoto, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Method for Extraction of the Active Compound Groups which Have Strong Relationship be-tween Structure and Activity,
International Conference on Genome Informatics (GIW2009), P133, Pacifico Yokohama, Yokohama (December 14, 2009).

Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Method for Analyzing Gene Expression Profiles based on the Underlying Structures,
17th Annual International Conference on Intelligent Systems for Molecular Biology and 8th European Conference on Computational Biology (ISMB/ECCB2009), M21, Stockholm, Sweden (June 29, 2009).

Yuya Shuto, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Method for Inference of Gene Regulatory Networks based on Bayesian Network with Clustering of Time-Series Subsequences,
17th Annual International Conference on Intelligent Systems for Molecular Biology and 8th European Conference on Computational Biology (ISMB/ECCB2009), X67, Stockholm, Sweden (June 29, 2009).

Yoshiyuki Kido, Yoshiyuki Asai, Taishin Nomura, Yoshihisa Kurachi, Hideo Matsuda,
Discovery of Relation between Modeling Data using in-silico Modeling Ontology and Meta-Ontology,
36th Congress of the International Union of Physiological Sciences (IUPS2009), P2PM-19-19, Kyoto (July 29, 2009).

Mitsuru Jikeya, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Method for Analysis of Tissue-Specific Transcriptional Control Using Distributions of Transcription Starting Sites,
2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008), P044, Senri-Chuo (December 15, 2008).

Reiji Ohsugi, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
The Validity Evaluation of Gene Regulatory Network Motifs Based on Differential Equation Model,
2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008), P045, Senri-Chuo (December 16, 2008).

Junya Seo, Yoshiyuki Kido, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
An Efficient Data Transfer on Workflows for Genome-wide Analysis,
2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008), P075, Senri-Chuo (December 16, 2008).

Yoshiyuki Kido, Yoshiyuki Asai, Taishin Nomura, Yoshihisa Kurachi, Hideo Matsuda,
An Architecture of Modeling Data Search using Ontology and Meta-Ontology,
3rd MEI International Symposium, San Francisco (December 2, 2008).

Junya Seo, Yoshiyuki Kido, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
Architecture of an Efficient Data Transfer System and Manager for Genome-wide Analysis Workflows,
3rd MEI International Symposium, San Francisco (December 2, 2008).

Yoichi Takenaka, Hideo Matsuda,
Tissue specificity measured by differences in information content between target tissue and whole tissue,
16th International Conference on Intelligent Systems for Molecular Biology (ISMB2008), A21, Toronto (July 21, 2008).

Mitsuru Jikeya, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Clustering Method for Expression Patterns of Transcription Starting Sites,
16th International Conference on Intelligent Systems for Molecular Biology (ISMB2008), J29, Toronto (July 20, 2008).

Junya Seo, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Data Transmission Method for Web Services in Bioinformatics Workflows,
16th International Conference on Intelligent Systems for Molecular Biology (ISMB2008), E36, Toronto (July 21, 2008).

Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A method for analysis of tissue-specific alternative transcripts using CAGE tags,
16th International Conference on Intelligent Systems for Molecular Biology (ISMB2008), J30, Toronto (July 21, 2008).

Takeru Nakazato, Hidemasa Bono, Hideo Matsuda, Toshihisa Takagi,
Functional analysis of groups of genes with MeSH hierarchy,
Systems Biology: Global Regulation of Gene Expression (Cold Spring Harbor Laboratory Meeting), New York, p.101 (March 27-30, 2008).

Junya Seo, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda,
A Method for Retrieving Functionally Similar Bioinformatics Workflows,
2007 Annual Conference of Japanese Society for Bioinformatics, P011, Tokyo (December 17, 2007) .

Hideo Matsuda,
An Information Integration System on Data Grid Environment,
1st DIALOGUE Workshop: Applications-Driven Issues in Data Grids, Columbus, Ohio (August 2, 2005).

Hideo Matsuda, Masato Kitajima, Gen Kawamura, Kentaro Wakatsuki, Takehiro Furudate, Takahiro Kosaka, Susumu Date, Shinji Shimojo,
Information Integration of Heterogeneous Databases through Grid Data Services,
GGF e-Science Workshop, Seoul (March 15, 2005) .

Kohei Taki, Reiji Teramoto, Yoichi Takenaka, Hideo Matsuda,
Inference of Gene Regulatory Network Based on Module Network Model with Gene Functional Classifications,
3rd IEEE Computer Society Bioinformatics Conference (CSB2004), pp.632-633, Palo Alto (August 16-19, 2004)

Shoko Miyake, Yoichi Takenaka, Hideo Matsuda,
A Graph Analysis Method to Detect Metabolic Sub-networks Based on Phylogenetic Profile,
3rd IEEE Computer Society Bioinformatics Conference (CSB2004), pp.634-635, Palo Alto (August 16-19, 2004) .

Masato Kitajima, Takahiro Kosaka, Kazuto Yamazaki, Reiji Teramoto, Gen Kawamura, Susumu Date, Shinji Shimojo, Hideo Matsuda,
Bridging life science databases using grid technology for genome-based drug discovery,
International Conference on Intelligent Systems for Molecular Biology (ISMB2004), Glasgow (August 1st, 2004) .

Vorathaya Tantoolvesm, Yoichi Takenaka, Satoshi Harashima, Hideo Matsuda,
Mapping of Artificial Nucleosome Positioning Sequences to the Saccharomyces cerevisiae Genome,
Genome Informatics, Vol.14, pp.462-463 (December 15-17, 2003) .

Yusuke Saito, Manabu Gomi, Hideo Matsuda, Naohisa Goto, Ken Kurokawa, Teruo Yasunaga,
Real-Time Mapping System of cDNAs and Genomes using Grid Computing,
Genome Informatics, Vol.14, pp.569-570 (December 15-17, 2003) .

Shigeto Seno, Reiji Teramoto, Yoichi Takenaka, Hideo Matsuda,
P-Quasi Complete Linkage Clustering Method for Gene-Expression Profiles based on Distribution Analysis,
11th International Conference on Intelligent Systems for Molecular Biology (ISMB2003), B-59 (July 1, 2003).

Shoko Miyake, Yukako Tohsato, Hideo Matsuda,
An Application of a Pathway Alignment Method to Comparative Analysis between Genome and Pathways,
1st IEEE Computer Society Bioinformatics Conference (CSB2002), p.329, Palo Alto (August 14-16, 2002) .

Shigeto Seno, Reiji Teramoto, Hideo Matsuda,
P-Quasi Complete Linkage Analysis for Gene-Expression Data,
1st IEEE Computer Society Bioinformatics Conference (CSB2002), p.342, Palo Alto (August 14-16, 2002).Best Poster Award

Hideo Matsuda, Christian Schoenbach, Hideya Kawaji, Jun Kawai, Yoshihide Hayashizaki,
A Tool for Annotating Novel Motifs Detected in Mouse Full-Length cDNA Sequences,
Joint Cold Spring Harbor Laboratory / Wellcome Trust Conference on Genome Informatics, (August 8-12, 2001).

Yukako Tohsato, Ryutaro Saijo, Hideo Matsuda, Akihiro Hashimoto,
An Algorithm for Detecting Similar Reaction Patterns between Metabolic Pathways,
9th International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), (July 21-25, 2001) .

Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto,
An Application of a Pathway Alignment Method to the Analysis of Amino Acid Biosynthesis,
Genome Informatics, Vol.11, pp.284-285 (December, 2000).

Hideya Kawaji, Hideo Matsuda, Shinji Kondo, Jun Kawai, Yoshihide Hayashizaki, Akihiro Hashimoto,
Analysis of Functional Motifs in Mouse Full-Length cDNA Sequences,
14th International Mouse Genome Conference (IMGC 2000), C13, p.180 (October, 2000) .

Hideya Kawaji, Hideo Matsuda, Shinji Kondo, Jun Kawai, Yoshihide Hayashizaki, Akihiro Hashimoto,
A Method to Detect Conserved Domains in Mouse Full-Length cDNA Data,
8th International Conference on Intelligent Systems for Molecular Biology (ISMB 2000) (August, 2000) .

Aaron J. Stokes, Hideo Matsuda, Akihiro Hashimoto,
A Structured Genome Document Database System for Making High-level Queries on Diverse Genome Data,
Currents in Computational Molecular Biology (RECOMB2000), pp.91-92 (April, 2000) .

Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto,
A Local Alignment Algorithm for Metabolic Pathway Analysis,
Currents in Computational Molecular Biology (RECOMB2000), pp.171-173 (April, 2000) .

Takashi Abe, Shigehiko Kanaya, Makoto Kinouchi, Yoshihiro Kudo, Hirotada Mori, Hideo Matsuda, Carlos Del Carpio, Toshimichi Ikemura,
Gene Classification Method Based on Batch-Learning SOM,
Genome Informatics, Vol.10, pp.314-315 (December, 1999).

Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto,
Application to Gene Cluster Analysis of Inductive Inference of Languages over Patterns with Conceptual Hierarchy,
Genome Informatics, Vol.10, pp.324-325 (December, 1999) .

Takeshi Ara, Kenji Suzuki, Hideo Matsuda, Hirotada Mori,
Distribution of Species Specific Gene Family in Microorganisms,
Genome Informatics, Vol.10, pp.326-327 (December, 1999).

Wataru Fujibuchi, Hiroyuki Ogata, Hideo Matsuda, Minoru Kanehisa,
Automatic Detection of Gene Clusters by P-Quasi Complete Linkage Grouping,
Genome Informatics, Vol.9, pp.300-301, Universal Academy Press (December, 1998).

Aaron J. Stokes, Hideo Matsuda, Akihiro Hashimoto,
A Query Language for Retrieving Complete Genomes by Viewing Them as Structured Documents,
Genome Informatics, Vol.9, pp.314-315, Universal Academy Press (December, 1998).

Hideo Matsuda,
Classifying Molecular Sequences with Pairwise Similarities by a Graph Covering Method,
International Workshop on Recent Advance in Genome Biology of Micro-organisms, p.28 (October, 1996).

Hideo Matsuda, Fumihiro Taniguchi, Akihiro Hashimoto,
A Notation of Amino Acid Conformations for Exploring Similar Protein Structure,
1st Pacific Symposium on Biocomputing, pp.732-733, World Scientific (January, 1996).

Gary Olsen, Carl Woese, Ray Hagstrom, Hideo Matsuda. Ross Overbeek,
Inference of Phylogenetic Trees Using Maximum Likelihood,
1st Delta Applications Workshop, pp.247-262 (February, 1992).