OKUDA Shujiro

J-GLOBAL         Last updated: Dec 5, 2018 at 08:54
 
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Name
OKUDA Shujiro
Affiliation
Niigata University
Section
Graduate School of Medical and Dental Sciences
Other affiliation
Ritsumeikan UniversityRitsumeikan University
Research funding number
00512310
ORCID ID
0000-0002-7704-8104

Research Areas

 
 

Academic & Professional Experience

 
 
   
 
Assistant Professor, Ritsumeikan University College of Llife Science, Department of Bioinformatics, Institute of Science and Engineering College of Life Sciences Department of Bioinformatics
 

Education

 
 
 - 
2003
"Graduate School, Division of Natural Science", Kyoto University
 
 
 - 
2006
"Graduate School, Division of Natural Science", Kyoto University
 
 
 - 
2001
Faculty of Science and Engineering, Ritsumeikan University
 

Published Papers

 
Tamura R, Nakaoka H, Yoshihara K, Mori Y, Yachida N, Nishikawa N, Motoyama T, Okuda S, Inoue I, Enomoto T
Genes, chromosomes & cancer   57(11) 557-563   Nov 2018   [Refereed]
Takata K, Saito K, Maruyama S, Miyata-Takata T, Iioka H, Okuda S, Ling Y, Karube K, Miki Y, Maeda Y, Yoshino T, Steidl C, Kondo E
Cancer science      Nov 2018   [Refereed]
Ling Y, Okuda S
EBioMedicine      Nov 2018   [Refereed]
Nagahashi M, Sato S, Yuza K, Shimada Y, Ichikawa H, Watanabe S, Takada K, Okamoto T, Okuda S, Lyle S, Takabe K, Tsuchida M, Wakai T
The Journal of surgical research   230 181-185   Oct 2018   [Refereed]
Moriya Y, Kawano S, Okuda S, Watanabe Y, Matsumoto M, Takami T, Kobayashi D, Yamanouchi Y, Araki N, Yoshizawa AC, Tabata T, Iwasaki M, Sugiyama N, Tanaka S, Goto S, Ishihama Y
Nucleic acids research      Oct 2018   [Refereed]
Nagahashi M, Shimada Y, Ichikawa H, Kameyama H, Takabe K, Okuda S, Wakai T
Cancer science      Oct 2018   [Refereed]
Sugiyama Y, Nara M, Sakanaka M, Kitakata A, Okuda S, Kurihara S
Bioscience, biotechnology, and biochemistry   82(9) 1606-1614   Sep 2018   [Refereed]
Gotoh A, Katoh T, Sakanaka M, Ling Y, Yamada C, Asakuma S, Urashima T, Tomabechi Y, Katayama-Ikegami A, Kurihara S, Yamamoto K, Harata G, He F, Hirose J, Kitaoka M, Okuda S, Katayama T
Scientific reports   8(1) 13958   Sep 2018   [Refereed]
Shigemizu D, Miya F, Akiyama S, Okuda S, Boroevich KA, Fujimoto A, Nakagawa H, Ozaki K, Niida S, Kanemura Y, Okamoto N, Saitoh S, Kato M, Yamasaki M, Matsunaga T, Mutai H, Kosaki K, Tsunoda T
Scientific reports   8(1) 10367   Jul 2018   [Refereed]
Okamoto T, Takada K, Sato S, Toyokawa G, Tagawa T, Shoji F, Nakanishi R, Oki E, Koike T, Nagahashi M, Ichikawa H, Shimada Y, Watanabe S, Kikuchi T, Akazawa K, Lyle S, Takabe K, Okuda S, Sugio K, Wakai T, Tsuchida M, Maehara Y
Annals of surgical oncology   25(6) 1564-1571   Jun 2018   [Refereed]
Kawasaki A, Okada M, Tamada A, Okuda S, Nozumi M, Ito Y, Kobayashi D, Yamasaki T, Yokoyama R, Shibata T, Nishina H, Yoshida Y, Fujii Y, Takeuchi K, Igarashi M
iScience   4 190-203   Jun 2018   [Refereed]
Kawai Y, Matsumoto S, Ling Y, Okuda S, Tsuneda S
Microbiology and immunology   62(5) 299-309   May 2018   [Refereed]
Shigemizu D, Miya F, Akiyama S, Okuda S, Boroevich KA, Fujimoto A, Nakagawa H, Ozaki K, Niida S, Kanemura Y, Okamoto N, Saitoh S, Kato M, Yamasaki M, Matsunaga T, Mutai H, Kosaki K, Tsunoda T
Scientific reports   8(1) 5608   Apr 2018   [Refereed]
Matsumoto S, Kawai Y, Miyagawa S, Iwamoto Y, Okuda S, Sánchez-Gorostiaga A, Vicente M, Tsuneda S
Journal of bioscience and bioengineering   125(1) 15-22   Jan 2018   [Refereed]
Sato S, Nagahashi M, Koike T, Ichikawa H, Shimada Y, Watanabe S, Kikuchi T, Takada K, Nakanishi R, Oki E, Okamoto T, Akazawa K, Lyle S, Ling Y, Takabe K, Okuda S, Wakai T, Tsuchida M
Scientific reports   8(1) 1005   Jan 2018   [Refereed]
Tamura R, Yoshihara K, Saito T, Ishimura R, Martínez-Ledesma JE, Xin H, Ishiguro T, Mori Y, Yamawaki K, Suda K, Sato S, Itamochi H, Motoyama T, Aoki Y, Okuda S, Casingal CR, Nakaoka H, Inoue I, Verhaak RGW, Komatsu M, Enomoto T
Oncogenesis   7(1) 4   Jan 2018   [Refereed]
Sugiyama Y, Nara M, Sakanaka M, Gotoh A, Kitakata A, Okuda S, Kurihara S
The international journal of biochemistry & cell biology   93 52-61   Dec 2017   [Refereed]
Hoya S, Watanabe Y, Hishimoto A, Nunokawa A, Kaneko N, Muratake T, Shinmyo N, Otsuka I, Okuda S, Inoue E, Igeta H, Shibuya M, Egawa J, Orime N, Sora I, Someya T
Psychiatry and clinical neurosciences   71(11) 780-788   Nov 2017   [Refereed]
Shimada Y, Kameyama H, Nagahashi M, Ichikawa H, Muneoka Y, Yagi R, Tajima Y, Okamura T, Nakano M, Sakata J, Kobayashi T, Nogami H, Maruyama S, Takii Y, Hayashida T, Takaishi H, Kitagawa Y, Oki E, Konishi T, Ishida F, Kudo SE, Ring JE, Protopopov A, Lyle S, Ling Y, Okuda S, Ishikawa T, Akazawa K, Takabe K, Wakai T
Oncotarget   8(55) 93567-93579   Nov 2017   [Refereed]
Gotoh A, Nara M, Sugiyama Y, Sakanaka M, Yachi H, Kitakata A, Nakagawa A, Minami H, Okuda S, Katoh T, Katayama T, Kurihara S
Bioscience, biotechnology, and biochemistry   81(10) 2009-2017   Oct 2017   [Refereed]
Ichikawa H, Nagahashi M, Shimada Y, Hanyu T, Ishikawa T, Kameyama H, Kobayashi T, Sakata J, Yabusaki H, Nakagawa S, Sato N, Hirata Y, Kitagawa Y, Tanahashi T, Yoshida K, Nakanishi R, Oki E, Vuzman D, Lyle S, Takabe K, Ling Y, Okuda S, Akazawa K, Wakai T
Genome medicine   9(1) 93   Oct 2017   [Refereed]
Shimada Y, Yagi R, Kameyama H, Nagahashi M, Ichikawa H, Tajima Y, Okamura T, Nakano M, Nakano M, Sato Y, Matsuzawa T, Sakata J, Kobayashi T, Nogami H, Maruyama S, Takii Y, Kawasaki T, Homma KI, Izutsu H, Kodama K, Ring JE, Protopopov A, Lyle S, Okuda S, Akazawa K, Wakai T
Human pathology   66 1-9   Aug 2017   [Refereed]
Yamada C, Gotoh A, Sakanaka M, Hattie M, Stubbs KA, Katayama-Ikegami A, Hirose J, Kurihara S, Arakawa T, Kitaoka M, Okuda S, Katayama T, Fushinobu S
Cell chemical biology   24(4) 515-524.e5   Apr 2017   [Refereed]
Okuda S, Watanabe Y, Moriya Y, Kawano S, Yamamoto T, Matsumoto M, Takami T, Kobayashi D, Araki N, Yoshizawa AC, Tabata T, Sugiyama N, Goto S, Ishihama Y
Nucleic acids research   45(D1) D1107-D1111   Jan 2017   [Refereed]
Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA
Nucleic acids research   45(D1) D1100-D1106   Jan 2017   [Refereed]
Okuda A, Kurokawa S, Takehashi M, Maeda A, Fukuda K, Kubo Y, Nogusa H, Takatani-Nakase T, Okuda S, Ueda K, Tanaka S
BMC neuroscience   18(1) 14   Jan 2017   [Refereed]
Sakai A, Nakato R, Ling Y, Hou X, Hara N, Iijima T, Yanagawa Y, Kuwano R, Okuda S, Shirahige K, Sugiyama S
Frontiers in neuroscience   11 307   2017   [Refereed]
Suda M, Shimizu I, Yoshida Y, Hayashi Y, Ikegami R, Katsuumi G, Wakasugi T, Yoshida Y, Okuda S, Soga T, Minamino T
PloS one   12(8) e0182422   2017   [Refereed]
Kasahara M, Suetsugu N, Urano Y, Yamamoto C, Ohmori M, Takada Y, Okuda S, Nishiyama T, Sakayama H, Kohchi T, Takahashi F
Scientific reports   6 39232   Dec 2016   [Refereed]
Nagahashi M, Wakai T, Shimada Y, Ichikawa H, Kameyama H, Kobayashi T, Sakata J, Yagi R, Sato N, Kitagawa Y, Uetake H, Yoshida K, Oki E, Kudo SE, Izutsu H, Kodama K, Nakada M, Tse J, Russell M, Heyer J, Powers W, Sun R, Ring JE, Takabe K, Protopopov A, Ling Y, Okuda S, Lyle S
Genome medicine   8(1) 136   Dec 2016   [Refereed]
[New Classification for Advanced Colorectal Cancer Using CancerPlex®Genomic Tests].
Kameyama H, Shimada Y, Ichikawa H, Nagahashi M, Sakata J, Kobayashi T, Nogami H, Maruyama S, Takii Y, Okuda S, Ling Y, Izutsu H, Kodama K, Nakada M, Wakai T
Gan to kagaku ryoho. Cancer & chemotherapy   43(11) 1361-1365   Nov 2016   [Refereed]
Shigehara Y, Okuda S, Nemer G, Chedraoui A, Hayashi R, Bitar F, Nakai H, Abbas O, Daou L, Abe R, Sleiman MB, Kibbi AG, Kurban M, Shimomura Y
Human molecular genetics   25(20) 4484-4493   Oct 2016   [Refereed]
Egawa J, Hoya S, Watanabe Y, Nunokawa A, Shibuya M, Ikeda M, Inoue E, Okuda S, Kondo K, Saito T, Kaneko N, Muratake T, Igeta H, Iwata N, Someya T
American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics   171(6) 797-805   Sep 2016   [Refereed]
Saito T, Ichimura Y, Taguchi K, Suzuki T, Mizushima T, Takagi K, Hirose Y, Nagahashi M, Iso T, Fukutomi T, Ohishi M, Endo K, Uemura T, Nishito Y, Okuda S, Obata M, Kouno T, Imamura R, Tada Y, Obata R, Yasuda D, Takahashi K, Fujimura T, Pi J, Lee MS, Ueno T, Ohe T, Mashino T, Wakai T, Kojima H, Okabe T, Nagano T, Motohashi H, Waguri S, Soga T, Yamamoto M, Tanaka K, Komatsu M
Nature communications   7 12030   Jun 2016   [Refereed]
Vieira-Silva S, Falony G, Darzi Y, Lima-Mendez G, Garcia Yunta R, Okuda S, Vandeputte D, Valles-Colomer M, Hildebrand F, Chaffron S, Raes J
Nature microbiology   1(8) 16088   Jun 2016   [Refereed]
Moriya Y, Yamada T, Okuda S, Nakagawa Z, Kotera M, Tokimatsu T, Kanehisa M, Goto S
Journal of chemical information and modeling   56(3) 510-516   Mar 2016   [Refereed]
Aoki-Kinoshita K, Agravat S, Aoki NP, Arpinar S, Cummings RD, Fujita A, Fujita N, Hart GM, Haslam SM, Kawasaki T, Matsubara M, Moreman KW, Okuda S, Pierce M, Ranzinger R, Shikanai T, Shinmachi D, Solovieva E, Suzuki Y, Tsuchiya S, Yamada I, York WS, Zaia J, Narimatsu H
Nucleic acids research   44(D1) D1237-42   Jan 2016   [Refereed]
Tamura R, Yoshihara K, Yamawaki K, Suda K, Ishiguro T, Adachi S, Okuda S, Inoue I, Verhaak RG, Enomoto T
Scientific reports   5 18657   Dec 2015   [Refereed]
Peddie V, Takada K, Okuda S, Ise Y, Morii Y, Yamawaki N, Takatani T, Arakawa O, Okada S, Matsunaga S
Journal of natural products   78(11) 2808-2813   Nov 2015   [Refereed]
Takachi T, Takahashi M, Takahashi-Yoshita M, Higuchi M, Obata M, Mishima Y, Okuda S, Tanaka Y, Matsuoka M, Saitoh A, Green PL, Fujii M
Cancer science   106(4) 461-465   Apr 2015   [Refereed]
Ranzinger R, Aoki-Kinoshita KF, Campbell MP, Kawano S, Lütteke T, Okuda S, Shinmachi D, Shikanai T, Sawaki H, Toukach P, Matsubara M, Yamada I, Narimatsu H
Bioinformatics (Oxford, England)   31(6) 919-925   Mar 2015   [Refereed]
Yoshizaki H, Okuda S
GigaScience   4 21   2015   [Refereed]
Kimura K, Okuda S, Nakayama K, Shikata T, Takahashi F, Yamaguchi H, Skamoto S, Yamaguchi M, Tomaru Y
PloS one   10(11) e0142731   2015   [Refereed]
Inoue E, Watanabe Y, Xing J, Kushima I, Egawa J, Okuda S, Hoya S, Okada T, Uno Y, Ishizuka K, Sugimoto A, Igeta H, Nunokawa A, Sugiyama T, Ozaki N, Someya T
PloS one   10(12) e0144624   2015   [Refereed]
Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T
Journal of biomedical semantics   5(1) 5   Feb 2014   [Refereed]
Takihara H, Ogihara J, Yoshida T, Okuda S, Nakajima M, Iwabuchi N, Sunairi M
Microbes and environments   29(4) 346-352   2014   [Refereed]
Aoki-Kinoshita KF, Bolleman J, Campbell MP, Kawano S, Kim JD, Lütteke T, Matsubara M, Okuda S, Ranzinger R, Sawaki H, Shikanai T, Shinmachi D, Suzuki Y, Toukach P, Yamada I, Packer NH, Narimatsu H
Journal of biomedical semantics   4(1) 39   Nov 2013   [Refereed]
Aoki-Kinoshita KF, Sawaki H, An HJ, Cho JW, Hsu D, Kato M, Kawano S, Kawasaki T, Khoo KH, Kim J, Kim JD, Li X, Lütteke T, Okuda S, Packer NH, Paulson JC, Raman R, Ranzinger R, Shen H, Shikanai T, Yamada I, Yang P, Yamaguchi Y, Ying W, Yoo JS, Zhang Y, Narimatsu H
Glycobiology   23(2) 144-146   Feb 2013   [Refereed]
Nakaya A, Katayama T, Itoh M, Hiranuka K, Kawashima S, Moriya Y, Okuda S, Tanaka M, Tokimatsu T, Yamanishi Y, Yoshizawa AC, Kanehisa M, Goto S
Nucleic acids research   41(Database issue) D353-7   Jan 2013   [Refereed]
Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, Peng Y, Zhang D, Jie Z, Wu W, Qin Y, Xue W, Li J, Han L, Lu D, Wu P, Dai Y, Sun X, Li Z, Tang A, Zhong S, Li X, Chen W, Xu R, Wang M, Feng Q, Gong M, Yu J, Zhang Y, Zhang M, Hansen T, Sanchez G, Raes J, Falony G, Okuda S, Almeida M, LeChatelier E, Renault P, Pons N, Batto JM, Zhang Z, Chen H, Yang R, Zheng W, Li S, Yang H, Wang J, Ehrlich SD, Nielsen R, Pedersen O, Kristiansen K, Wang J
Nature   490(7418) 55-60   Oct 2012   [Refereed]
Okuda S, Tsuchiya Y, Kiriyama C, Itoh M, Morisaki H
Nature communications   3 1203   2012   [Refereed]
Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernández JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T
Journal of biomedical semantics   2 4   Aug 2011   [Refereed]

Misc

 
Fujita S., Ohnishi T., Okuda S., Kobayashi R., Fukuno S., Furuta D., Kikuchi T., Yoshikawa T., Fujita N.
J. Mol. Model.      2011
Yamada, T., Letunic, I., Okuda, S., Kanehisa, M., and Bork, P.
Nucleic Acids Res.   39 W412-W415   2011
Okuda, S., Akiyasu C. Yoshizawa.
Nucleic Acids Res.   39 D552-D555   2011
Yamada, H., Takahashi, N., Okuda, S., Tsuchiya, Y., and Morisaki, H.
Appl Environ Microbiol.   76(16) 5409-5414   2010
Hashimoto, K., Tokimatsu, T., Kawano, S., Yoshizawa, C. A., Okuda, S., Goto, S., and Kanehisa, M.
Carbohydr. Res.   344(7) 881-887   2009

Conference Activities & Talks

 
Computational Methods for the Interpretation of Clinical Meta­Omics Data: from a ‘Bag of Genes’ to Ecosystem Networks and Clinical Markers.
International Human microbiome Congress   2011   
iPath: Interactive Pathways Explorer.
ECCB 2010   2010   
From Parts Lists to Ecosystem Networks: Development of a 2nd Generation Toolkit for Meta­Omics Analysis.
Human Microbiome Research Conference   2010   
From Parts Lists to Ecosystem Networks: Development of a 2nd Generation Toolkit for Meta­Omics Analysis.
Human Microbiome Research Conference   2010   
A systems biology approach to elucidating mechanisms underlying smog-induced airway inflammation.
8th Siena Meeting   2008   

Research Grants & Projects

 
Toward understanding interaction between life and the environment