The Systems Biology Graphical Notation (2009)
Le Novère, Nicolas, Hucka, Michael, Mi, Huaiyu, Moodie, Stuart, Schreiber, Falk, Sorokin, Anatoly, ...
Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software...
Kanae Oda, Tomomi Kimura, Yukiko Matsuoka, Akira Funahashi, Masaaki Muramatsu
KO and TK equally contributed to this paper. Identifying intracellular molecular interactions is the first step toward understanding complex dynamics and mechanisms of the cell. We have created a...
ABSTRACT CELLDESIGNER: A MODELING TOOL FOR BIOCHEMICAL NETWORKS (2008)
L. F. Perrone, F. P. Wiel, J. Liu, B. G. Lawson, D. M. Nicol, R. M. Fujimoto, ...
Understanding of logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed CellDesigner, a modeling...
Akira Funahashi, Toshihiro Hanawa, Hideharu Amano
this paper, a fault recovery mechanism is attached to these two networks, and proposed Fault tolerant TBSF (F-TBSF) and Fault tolerant PBSF (FPBSF) respectively. Then, the performance degradation...
Routing Algorithms Based on 2D Turn Model for Irregular Networks (2002)
Akiya Jouraku, Michihiro Koibuchi, Hideharu Amano, Akira Funahashi
In order to solve traffic unbalancing caused by up*/down * routing for irregular networks, two-dimensional direction is introduced into a spanning tree, and novel routing algorithms based on...
A comprehensive pathway map of epidermal growth factor receptor signaling
Oda, Kanae, Matsuoka, Yukiko, Funahashi, Akira, Kitano, Hiroaki
The epidermal growth factor receptor (EGFR) signaling pathway is one of the most important pathways that regulate growth, survival, proliferation, and differentiation in mammalian cells. Reflecting...