The Story of Pino. - Hiroaki Kitano; Fuminori Yamasaki; Tatsuya Matsui; Ken Endo; Yukiko Matsuoka; Hiroshi Kaminaga; Yuichiro Kato (Int. J. Humanoid Robotics, 2004)

CellDesigner: a modeling tool for biochemical networks. - Akira Funahashi; Yukiko Matsuoka; Akiya Jouraku; Hiroaki Kitano; Norihiro Kikuchi (WSC, 2006)

Integration of CellDesigner and SABIO-RK. - Akira Funahashi; Akiya Jouraku; Yukiko Matsuoka; Hiroaki Kitano (Silico Biol., 2007)

Connecting Text Mining and Pathways using the PathText Resource. - Rune Sætre; Brian Kemper; Kanae Oda; Naoaki Okazaki; Yukiko Matsuoka; Norihiro Kikuchi; Hiroaki Kitano; Yoshimasa Tsuruoka; Sophia Ananiadou; Jun'ichi Tsujii (LREC, 2008)

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. - Akira Funahashi; Yukiko Matsuoka; Akiya Jouraku; Mineo Morohashi; Norihiro Kikuchi; Hiroaki Kitano (Proc. IEEE, 2008)

PathText: a text mining integrator for biological pathway visualizations. - Brian Kemper; Takuya Matsuzaki; Yukiko Matsuoka; Yoshimasa Tsuruoka; Hiroaki Kitano; Sophia Ananiadou; Jun'ichi Tsujii (Bioinform., 2010)

Payao: a community platform for SBML pathway model curation. - Yukiko Matsuoka; Samik Ghosh; Norihiro Kikuchi; Hiroaki Kitano (Bioinform., 2010)

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. - Tiago J. S. Lopes; Martin H. Schaefer 001; Jason E. Shoemaker; Yukiko Matsuoka; Jean-Fred Fontaine; Gabriele Neumann; Miguel A. Andrade-Navarro; Yoshihiro Kawaoka; Hiroaki Kitano (Bioinform., 2011)

BioPAX support in CellDesigner. - Huaiyu Mi; Anushya Muruganujan; Emek Demir; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Paul D. Thomas (Bioinform., 2011)

Software support for SBGN maps: SBGN-ML and LibSBGN. - Martijn P. van Iersel; Alice Villéger; Tobias Czauderna; Sarah E. Boyd; Frank T. Bergmann; Augustin Luna; Emek Demir; Anatoly A. Sorokin; Ugur Dogrusöz; Yukiko Matsuoka; Akira Funahashi; Mirit I. Aladjem; et al. (Bioinform., 2012)

AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease. - Satoshi Mizuno; Risa Iijima; Soichi Ogishima; Masataka Kikuchi; Yukiko Matsuoka; Samik Ghosh; Tadashi Miyamoto; Akinori Miyashita; Ryozo Kuwano; Hiroshi Tanaka (BMC Syst. Biol., 2012)

Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs. - Jason E. Shoemaker; Satoshi Fukuyama; Amie J. Eisfeld; Yukiko Muramoto; Shinji Watanabe 007; Tokiko Watanabe; Yukiko Matsuoka; Hiroaki Kitano; Yoshihiro Kawaoka (BMC Syst. Biol., 2012)

A versatile platform for multilevel modeling of physiological systems: Template/instance framework for large-scale modeling and simulation. - Yoshiyuki Asai; Takeshi Abe; Hideki Oka; Masao Okita; Tomohiro Okuyama; Kenichi Hagihara; Samik Ghosh; Yukiko Matsuoka; Yoshihisa Kurachi; Hiroaki Kitano (EMBC, 2013)

A comprehensive map of the influenza A virus replication cycle. - Yukiko Matsuoka; Hiromi Matsumae; Manami Katoh; Amie J. Eisfeld; Gabriele Neumann; Takeshi Hase; Samik Ghosh; Jason E. Shoemaker; Tiago J. S. Lopes; Tokiko Watanabe; Shinji Watanabe 007; Satoshi Fukuyama; et al. (BMC Syst. Biol., 2013)

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions. - Martin H. Schaefer 001; Tiago J. S. Lopes; Nancy Mah; Jason E. Shoemaker; Yukiko Matsuoka; Jean-Fred Fontaine; Caroline Louis-Jeune; Amie J. Eisfeld; Gabriele Neumann; Carol Perez-Iratxeta; Yoshihiro Kawaoka; Hiroaki Kitano; et al. (PLoS Comput. Biol., 2013)

systemsDock: a web server for network pharmacology-based prediction and analysis. - Kun-Yi Hsin; Yukiko Matsuoka; Yoshiyuki Asai; Kyota Kamiyoshi; Tokiko Watanabe; Yoshihiro Kawaoka; Hiroaki Kitano (Nucleic Acids Res., 2016)