Výsledky vyhledávání - "Kozo Nishida"

Akademický článek

Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks

Autor: Kozo Nishida, Junichi Maruyama, Kazunari Kaizu, Koichi Takahashi, Katsuyuki Yugi

Publikováno v: npj Systems Biology and Applications, Vol 10, Iss 1, Pp 1-9 (2024)

Abstract Biochemical network visualization is one of the essential technologies for mechanistic interpretation of omics data. In particular, recent advances in multi-omics measurement and analysis require the development of visualization methods that

Externí odkaz: https://doaj.org/article/8b8b1e72d9724f8a83b379ede954e7e5

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Akademický článek

An architecture for collaboration in systems biology at the age of the Metaverse

Autor: Eliott Jacopin, Yuki Sakamoto, Kozo Nishida, Kazunari Kaizu, Koichi Takahashi

Publikováno v: npj Systems Biology and Applications, Vol 10, Iss 1, Pp 1-11 (2024)

Abstract As the current state of the Metaverse is largely driven by corporate interests, which may not align with scientific goals and values, academia should play a more active role in its development. Here, we present the challenges and solutions f

Externí odkaz: https://doaj.org/article/64261beace0640258653a87dd5dac9eb

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Akademický článek

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

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Akademický článek

KEGGscape: a Cytoscape app for pathway data integration [v1; ref status: indexed, http://f1000r.es/3qe]

Autor: Kozo Nishida, Keiichiro Ono, Shigehiko Kanaya, Koichi Takahashi

Publikováno v: F1000Research, Vol 3 (2014)

In this paper, we present KEGGscape a pathway data integration and visualization app for Cytoscape (http://apps.cytoscape.org/apps/keggscape). KEGG is a comprehensive public biological database that contains large collection of human curated pathways

Externí odkaz: https://doaj.org/article/69c3e7d3123c47259a055cea63ca61ce

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transomics2cytoscape: An automated software for interpretable 2.5-dimensional visualization of trans-omic networks

Autor: Kozo Nishida, Junichi Maruyama, Kazunari Kaizu, Koichi Takahashi, Katsuyuki Yugi

Biochemical network visualization is one of the essential technologies for mechanistic interpretation of omics data. In particular, recent advances in multi-omics measurement and analysis require the development of visualization methods that encompas

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::e360bbab68d6e21461589a686a249076
https://doi.org/10.1101/2023.03.08.531686

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A Universal Language for Finding Mass Spectrometry Data Patterns

Autor: Alan K. Jarmusch, Allegra T. Aron, Daniel Petras, Vanessa V. Phelan, Wout Bittremieux, Deepa D. Acharya, Mohammed M. A. Ahmed, Anelize Bauermeister, Matthew J. Bertin, Paul D. Boudreau, Ricardo M. Borges, Benjamin P. Bowen, Christopher J. Brown, Fernanda O. Chagas, Kenneth D. Clevenger, Mario S. P. Correia, William J. Crandall, Max Crüsemann, Tito Damiani, Oliver Fiehn, Neha Garg, William H Gerwick, Jeffrey R. Gilbert, Daniel Globisch, Paulo Wender P. Gomes, Steffen Heuckeroth, C. Andrew James, Scott A. Jarmusch, Sarvar A. Kakhkhorov, Kyo Bin Kang, Roland D Kersten, Hyunwoo Kim, Riley D. Kirk, Oliver Kohlbacher, Eftychia E. Kontou, Ken Liu, Itzel Lizama-Chamu, Gordon T. Luu, Tal Luzzatto Knaan, Michael T. Marty, Andrew C. McAvoy, Laura-Isobel McCall, Osama G. Mohamed, Omri Nahor, Timo H.J. Niedermeyer, Trent R. Northen, Kirsten E. Overdahl, Tomáš Pluskal, Johannes Rainer, Raphael Reher, Elys Rodriguez, Timo T. Sachsenberg, Laura M. Sanchez, Robin Schmid, Cole Stevens, Zhenyu Tian, Ashootosh Tripathi, Hiroshi Tsugawa, Kozo Nishida, Yuki Matsuzawa, Justin J.J. van der Hooft, Andrea Vicini, Axel Walter, Tilmann Weber, Quanbo Xiong, Tao Xu, Haoqi Nina Zhao, Pieter C. Dorrestein, Mingxun Wang

Even though raw mass spectrometry data is information rich, the vast majority of the data is underutilized. The ability to interrogate these rich datasets is handicapped by the limited capability and flexibility of existing software. We introduce the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a8f988ad1b439278436871971e6c216c
https://doi.org/10.1101/2022.08.06.503000

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