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1.� Shin Kawano, Tsutomu Watanabe, Sohei Mizuguchi, Norie Araki, Toshiaki Katayama and Atsuko Yamaguchi, TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model, RNucl. Acids Res. (2014) doi: 10.1093/nar/gku403[first published online May 14, 2014

2.� Yamagishi, J., Natori, A., Tolba, M.E.M., Mongan, A.E., Sugimoto, C., Katayama, T., Kawashima, S.,

Page 4: 123456åŠ lmn&mo˝ ]˚˛ - ROIS · ¸BioHackathon RDFsummit z“”D]˚˛Q˚ ... (2015).Published online 2014 Dec 9. doi: 10.1093/bioinformatics/btu743 12. Yuichi Kodama,

Makalowski, W., Maeda, R., Eshita, Y., Tuda, J., Suzuki, Y.: Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum. Genome Res. 1433–1444 (2014). doi/10.1101/gr.158980.113. Accepted May 20, 2014.

3.� Kenichi Tanaka, Kiyoko Aoki-Kinoshita, Masaaki Kotera, Hiromichi Sawaki, Shinichiro Tsuchiya, Noriaki Fujita, Toshihide Shikanai, Masaki Kato, Shin Kawano, Issaku Yamada, and Hisashi Narimatsu, WURCS: The Web3 Unique Representation of Carbohydrate Structures. Journal of Chemical Information and Modeling, 54 (6), 1558-1566 (2014). DOI: 10.1021/ci400571e Publication Date (Web): June 4, 2014

4.� Yutaka Takebe, Yuki Naito, Jayna Raghwani, Esther Fearnhill, Takako Sano, Shigeru Kusagawa, Jean L. Mbisa, Hongyi Zhang, Tetsuro Matano, Andrew J. Leigh Brown, Oliver G. Pybus, David Dunn, and Makiko Kondo, on behalf of the UK Collaborative Group on HIV Drug Resistance: Inter-continental dispersal of HIV-1 subtype B associated with transmission among men who have sex with men in Japan. J. Virol. 88, 9864-9876 (2014). doi: 10.1128/JVI.01354-14 Epub 2014 Jun 18.

5.� Hongyan Wu, Toyofumi Fujiwara, Yasunori Yamamoto, Jerven Bolleman and Atsuko Yamaguchi, BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological dat, (Journal of Biomedical Semantics (2014) doi: 10.1186/2041-1480-5-32))Published:10 July 2014

6.� Hongyan Wu and Atsuko Yamaguchi, Semantic Web Technologies for the Big Data in Life Sciences, BioScience Trends, 2014, 8:4, 192-201. doi:10.5582/bst.2014.01048 Released 20140912

7.� Ayako Suzuki, Hiroyuki Wakaguri, Riu Yamashita, Shin Kawano, Katsuya Tsuchihara, Sumio Sugano, Yutaka Suzuki, and Kenta Nakai, DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. Nucleic Acid Research, Database Issue, 43 (D1), D87-D91 (2015). doi: 10.1093/nar/gku1080 Accepted October 16, 2014.

8.� Rene Ranzinger, Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, Shin Kawano, Thomas Lutteke, Shujiro Okuda, Daisuke Shinmachi, Toshihide Shikanai, Hiromichi Sawaki, Philip Toukach, Masaaki Matsubara, Issaku Yamada, and Hisashi Narimatsu, GlycoRDF: An ontology to standardize Glycomics data in RDF. Bioinformatics, 31 (6), 919-925 (2015). doi: 10.1093/bioinformatics/btu732 Accepted October 28, 2014.

9.� Masaaki Kotera, Yosuke Nishimura, Zen-Ichi Nakagawa, Ai Muto, Yuki Moriya, Shinobu Okamoto, Shuichi Kawashima, Toshiaki Katayama, Toshiaki Tokimatsu, Minoru Kanehisa, and Susumu Goto, PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list. J. Bioinform. Comput. Biol. 12, 1442001 (2014). DOI: 10.1142/S0219720014420013 Published: 10 November 2014

10.� Steffen Möller, Enis Afgan, Michael Banck, Raoul JP Bonnal, Timothy Booth, John Chilton, Peter JA Cock, Markus Gumbel, Nomi Harris, Richard Holland, Matúš Kalaš, László Kaján, Eri Kibukawa, David R Powel, Pjotr Prins, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi, Torsten Seemann, Clare Sloggett, Stian Soiland-Reyes, William Spooner, Sascha Steinbiss, Andreas Tille, Anthony J Travis, Roman Valls Guimera, Toshiaki Katayama, Brad A Chapman.: Community-driven development for computational biology at Sprints, Hackathons and Codefests. BMC Bioinformatics. 15 Suppl 1, S7 (2014). Published online 2014 November 27. doi: 10.1186/1471-2105-15-S14-S7

11.� Yuki Naito, Kimihiro Hino, Hidemasa Bono, and Kumiko Ui-Tei: CRISPRdirect: software for

Page 5: 123456åŠ lmn&mo˝ ]˚˛ - ROIS · ¸BioHackathon RDFsummit z“”D]˚˛Q˚ ... (2015).Published online 2014 Dec 9. doi: 10.1093/bioinformatics/btu743 12. Yuichi Kodama,

designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics, 31, 1120-1123 (2015).Published online 2014 Dec 9. doi: 10.1093/bioinformatics/btu743

12.� Yuichi Kodama, Jun Mashima, Takehide Kosuge, Toshiaki Katayama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi and Yasukazu Nakamura, The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data, (Nucleic Acid Research Web Server Issue, 42 (W1), W442-W448 (2014). doi: 10.1093/nar/gku1120) first published online December 3, 2014

13.� Yasunori Yamamoto. A SPARQL Endpoint Profiler for an Efficient Question Answering System, Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences, Berlin, Germany, December 9-11, 2014.

14.� Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda, Fumi Hori, Sachi Ishikawa-Kato, Christopher J Mungall, Erik Arner, J Kenneth Baillie, Nicolas Bertin, Hidemasa Bono, Michiel de Hoon, Alexander D Diehl, Emmanuel Dimont, Tom C Freeman, Kaori Fujieda, Winston Hide, Rajaram Kaliyaperuma, Toshiaki Katayama, Timo Lassmann, Terrence F Meehan, Koro Nishikata, Hiromasa Ono, Michael Rehli, Albin Sandelin, Erik A Schultes, Peter AC ‘t Hoen, Zuotian Tatum, Mark Thompson, Tetsuro Toyoda, Derek W Wright, Carsten O Daub, Masayoshi Itoh, Piero Carninci, Yoshihide Hayashizaki, Alistair RR Forrest*, Hideya Kawaji* and the FANTOM consortium, Gateways to the FANTOM5 promoter level mammalian expression atlas, (Genome Biology 2015, 16:22 doi:10.1186/s13059-014-0560-6) Published:5 January 2015

15.� Kiyoko F Aoki-Kinoshita, Akira R Kinjo, Mizuki Morita, Yoshinobu Igarashi, Yi-an Chen, Yasumasa Shigemoto, Takatomo Fujisawa, Yukie Akune, Takeo Katoda, Anna Kokubu, Takaaki Mori, Mitsuteru Nakao, Shuichi Kawashima, Shinobu Okamoto, Toshiaki Katayama and Soichi Ogishima, : Implementation of linked data in the life sciences at BioHackathon 2011. J. Biomed. Semantics. 6, 1–13 (2015). doi:10.1186/2041-1480-6-3 Published:7 January 2015

16.� Sarala M Wimalaratne, Jerven Bolleman, Nick Juty, Toshiaki Katayama, Michel Dumontier, Nicole Redaschi, Nicolas Le Novère, Henning Hermjakob and Camille Laibe, SPARQL-enabled identifier conversion with Identifiers. org. Bioinformatics. 3–4 (2015). first published online: January 31, 2015 doi: 10.1093/bioinformatics/btv064

17.� Tanaka, S., Tanaka, J., Miwa, Y., Horikawa, D.D., Katayama, T., Arakawa, K., Toyoda, A., Kubo, T., Kunieda, T.: Novel Mitochondria-Targeted Heat-Soluble Proteins Identified in the Anhydrobiotic Tardigrade Improve Osmotic Tolerance of Human Cells. PLoS One. 10, e0118272 (2015). Published: February 12, 2015 DOI: 10.1371/journal.pone.0118272

18.� Koki Tsuyuzaki*, Gota Morota Manabu Ishii, Takeru Nakazato, Satoru Miyazaki and Itoshi Nikaido* MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis, (BMC Bioinformatics 2015, 16:45 doi:10.1186/s12859-015-0453-z) Published:15 February 2015

19.� Yosui Nojima, Katsuhiko Ito, Hiromasa Ono, Takeru Nakazato, Hidemasa Bono, Takeshi Yokoyama, Ryoichi Sato, Yoshitaka Suetsugu, Yuki Nakamura, Kimiko Yamamoto, Jun-ichi Satoh, Hiroko Tabunoki and Hajime Fugo, “Superoxide Dismutases, SOD1 and SOD2, Play a Distinct Role in the Fat Body during Pupation in Silkworm Bombyx mori, (PLOS ONE. 2015 Feb 25;10(2):e0116007. doi: 10.1371/journal.pone.0116007)

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2.� ��¨F��ÍÈ¥Rij[��6ÙöRij[�«N~Ï, CRISPR/Cas � ���<1���¿}��n�� æ6PQ. �þöH 2014Ï 7ª., p.1697-1703, �¢s (2014).

3.� Chemical Compound Complexity in Biological Pathways, Atsuko YamaguchiRij[ and Kiyoko F. Aoki-Kinoshita, in Matthias Dehmer and Frank Emmert-Streib(Editors), Quantitative Graph Theory: Mathematical Foundations and Applications, pp. 471-493, Chapman and Hall/CRC, 2014/10/23.

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�z� 1.� Toshiaki Katayama, BioHackathons: Accelerating cross project collaborations in bioinformatics,

AllBio conference, Florence, Italy, 11 Jun 2014. �z�

1.� �6ÙöU�Øö÷"¾�L����H(ym�m�nã��w5 )U��GHöH´U�� 2014.4.7

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2.� �6ÙöU¨�]��Q� Àj.�골©Ï¾¦]��yz���m52�¯m� NGS D..�íÞ��wm� GGH��_���LUG 2014.4.11

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4.� �6ÙöU¨�]��Q� Àj.�ê³|D�¢�D=.��`H��U� 29° DDBJing 2Pt in * 2014.6.12

5.� GÞ #U��·��v�&�À@Aê³��+��óãÀ8É�¨���k�]��Q� U� 186° ��Tô��t �tU4%�å�k�åts�L�ÓU2014.07.11

6.� W�¹U12��w5 ]��D�t��]��Q� U�÷12����Ht 2014ÏGtU-�U2014.7.17-18

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9.� �6ÙöUlmn&mo� ��D¨�]��Q� D¦��óDSA�UóôGH FG`Hº»������Uóô 2015.1.23

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�z� 1.� Shin Kawano, jPOST: Japan ProteOme STandard repository/database, ProteomeXchange meeting

2014, Frankfurt, Germany, 2014.4.16-17 2.� Jin-Dong Kim and Kevin Bretonnel Cohen, Triple Pattern Variation Operations for Flexible Graph

Search, Proceedings of the 1st international workshop on Natural Language Interfaces for Web of Data (NLIWoD), 2014.10.19

3.� Atsuko Yamaguchi, Kouji Kozaki, Kai Lenz, Hongyan Wu and Norio Kobayashi, An Intelligent SPARQL Query Builder for Exploration of Various Life-science Databases. Intelligent Exploration on Semantic Data (IESD 2014), CEUR Workshop Proceedings vol.1279, 19-20 Oct. 2014

4.� Yasunori Yamamoto. A SPARQL Endpoint Profiler for an Efficient Question Answering System, Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences, Berlin, Germany, December 9-11, 2014.

5.� Tazro Ohta, Hiromasa Ono, Yuki Naito, Takeru Nakazato, *Hidemasa Bono Facilitating the Use of Next-Gen Sequence Data for Data-Driven Biology. International Plant & Animal Genome XXIII (PAG), San Diego, CA, USA 2015.1.10-14

6.� Jin-Dong Kim, Kevin Bretonnel Cohen and Jung-Jae Kim, PubAnnotation-query: a search tool for multi-layer RDF-annotated corpora, Proceedings of the 1st Biomedical Linked Annotation Hackathon Symposium (BLAH), 2015.2.27.

�z�

1.� ÍÇ�{UØ÷XÜ: lmn&mo� z.D%�56]����U2014Ï'q�|ªHtkzGtUÑØU2014.5.12-15

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2014.8.10-12 3.� Ø÷XÜ: RDF �ê³ MeSH �lmn&mo� z.À@Aê³��`H¬¸�ao��÷�¯å¬

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2014UÆ+¸¹½�kU2014Ï 10ª 5� 6.� Ø÷XÜ: SPINÀA.³ SPARQLo�x�m�6D ª\]� ��U� 34°����wæ5v4

I���623���tUóôU2014.11.20 Ë� ��Ì

�z� 1.� Takeru Nakazato, Tazro Ohta, Hidemasa Bono, DBCLS SRA: Functional mining and

characterization of public NGS data, European Conference on Computational Biology (ECCB’14), Strasbourg, France, 2014.9.7-10

2.� Toshiaki Katayama, Integration of TogoStanza and BioJS, EU codefest, European Bioinformatics Institute, Cambridge, UK, 18-19 Sep 2014.

3.� Hiromasa Ono, Hidemasa Bono RefEx: Reference Expression Dataset for cell and tissue transcriptome. Genome Informatics 2014, Churchill College, Cambridge, UK 2014.9.21-24

4.� Naito, Y., Bono, H.: GGRNA and GGGenome: ultrafast search engines for nucleotide sequence database. Genome Informatics 2014, Cambridge, UK. 2014.9.21-24

5.� Shin Kawano, Yasushi Ishihama, Tadashi Yamamoto, Shujiro Okuda, Takeshi Tomonaga, Masaki Matsumoto, Hirofumi Nakagami, Tadashi Kondo, Masaya Ono, Sumio Ohtsuki, and Norie Araki, Concept of Japan Proteome Standard repository/database (jPOST), HUPO 13th Annual World Congress, Madrid, Spain, 2014.10.5-8

6.� Tazro Ohta, Hiromasa Ono, Yuki Naito, Takeru Nakazato, Hidemasa Bono Promoting the use of next-gen sequence data to maintain the research environment for data-driven biology. Biological Data Science, Cold Spring Harbor Laboratory, NY, USA 2014.11.5-8

7.� Norio Kobayashi, Kai Lenz, Hongyan Wu, Kouji Kozaki and Atsuko Yamaguchi,� Prototype implementation of SPARQL Builder for Life-science Databases by intelligent schema analysis on RDF datasets, 7th International SWAT4LS Workshop, 9-11 Dec. 2014.

8.� Jin-Dong Kim, Natural Language Interfaces to SPARQL Endpoints � SWAT4LS (Tutorial), SWAT4LS, Semiraris Campus Hotel, Berlin, Germany, 9-12 Dec 2014.

9.� Toshiaki Katayama � D3SPARQL: JavaScript library for visualization of SPARQL results, SWAT4LS, Semiraris Campus Hotel, Berlin, Germany, 9-12 Dec 2014.

10.� Naito, Y., Hino, K., Ui-Tei, K., Bono, H.: CRISPRdirect: web-based tool for designing CRISPR/Cas guide RNA with reduced off-target sites. CRISPR 2015 OXFORD, Oxford, UK. 2015.3.23

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Kondo, Masaya Ono, Masaki Matsumoto, Tadashi Yamamoto, Shujiro Okuda, Shin Kawano, Toshifusa Toda, Hisashi Hirano, Hisashi Narimatsu, jPOST: Japan ProteOme STandard repository/database, �÷12����Ht 2014ÏGtU-�U2014.7.17-18

3.� Rene RanzingerU�¥�ÏUMatthew P. CampbellUW�¹UThomas LuttekeU¢Þ¥\#U��G>U��TÙU��ùPUPhilip ToukachUÑÇä�UØÞ7!UEÑNUGlycoRDF: ì���623��=�ì�Lq]��D RDF�U� 33°�÷ì�HtÏtUå78U2014.8.10-12

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