BioHackathon 2015: Semantics of data for life sciences and reproducible research [version 1; peer review: 2 approved]

Autor: Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan Bolton, Raoul J. P. Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin B. Cohen, Eric W. Deutsch, Jesualdo T. Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy Nguyen-Xuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi

Publikováno v: F1000Research, Vol 9 (2020)

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss i

Externí odkaz: https://doaj.org/article/6d102248ecd24affbea7a5223da6573a

Denosumab effect on bone mineral density and urinary-NTX in breast cancer patients receiving aromatase inhibitors

Autor: Masahiro Shibata, Mai Okumura, Shin Kawano, Hirotoshi Noda, Chihiro Toyota, Yutaka Mizuno

Publikováno v: Journal of Bone and Mineral Metabolism.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::5012eea4b16aef143e553502c5aaaa38
https://doi.org/10.1007/s00774-023-01429-8

Proteomics Standards Initiative at twenty years : current activities and future work

Autor: Eric W. Deutsch, Juan Antonio Vizcaíno, Andrew R. Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, Yasset Perez-Riverol, David L. Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D. Mak, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C. E. Tosatto, Sandra E. Orchard

Publikováno v: Journal of proteome research
JOURNAL OF PROTEOME RESEARCH

The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry sin

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0c134d30524765e956ad3db0844e8b11
https://hdl.handle.net/10067/1935320151162165141

Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

Autor: Richard D. LeDuc, Eric W. Deutsch, Pierre-Alain Binz, Ryan T. Fellers, Anthony J. Cesnik, Joshua A. Klein, Tim Van Den Bossche, Ralf Gabriels, Arshika Yalavarthi, Yasset Perez-Riverol, Jeremy Carver, Wout Bittremieux, Shin Kawano, Benjamin Pullman, Nuno Bandeira, Neil L. Kelleher, Paul M. Thomas, Juan Antonio Vizcaíno

Publikováno v: JOURNAL OF PROTEOME RESEARCH

There is the need to represent in a standard manner all the possible variations of a protein or peptide primary sequence, including both artefactual and post-translational modifications of peptides and proteins. With that overall aim, here, the Human

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d0b87cb7688120d502c3cdcb23796615
https://pubmed.ncbi.nlm.nih.gov/35290070

Organelle membrane-specific chemical labeling and dynamic imaging in living cells

Autor: Kohjiro Nagao, Itaru Hamachi, Yasushi Tamura, Yuying Shen, Toshiya Endo, Masaki Tsuchiya, Shin Kawano, Alma Fujisawa, Masato Umeda, Tomonori Tamura

Publikováno v: Nature Chemical Biology. 16:1361-1367

Lipids play crucial roles as structural elements, signaling molecules and material transporters in cells. However, the functions and dynamics of lipids within cells remain unclear because of a lack of methods to selectively label lipids in specific o

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fa880426ef2198357b95b88463664350
https://doi.org/10.1038/s41589-020-00651-z