Laboratory for Integrated Cellular Systems

The Laboratory for Cellular Systems Modeling has been carrying out research to identify biological networks and its regulatory principles using computational, theoretical and experimental approaches. Our research interest is to identify and reconstruct biological regulatory circuits from experimentally observable data using computational and theoretical approaches to unveil the complexity of signal transduction networks, which determine cell fate in mammalian cells. By doing this, we are able to identify rules specified in immunological systems.

Research Fields

Engineering / Biology & Biochemistry / Molecular Biology & Genetics / Computer Science

Research Subjects

• Systems Biology of signal-transcription network
• Measurement and modeling of signal transduction pathways
• Modeling of cell fate

Publications

1. Oyama M, Nagashima T, Suzuki T, Kozuka-Hata H, Yumoto N, Shiraishi Y, Ikeda K, Kuroki Y, Gotoh N, Ishida T, Inoue S, Kitano H, Okada-Hatakeyama M.:
   "Integrated quantitative analysis of the phosphoproteome and transcriptome in tamoxifen-resistant breast cancer."
   J Biol Chem. 286(1):818-829(2011)
2. Nakakuki T, Birtwistle MR, Saeki Y, Yumoto N, Ide K, Nagashima T, Brusch L, Ogunnaike BA, Okada-Hatakeyama M, Kholodenko BN.:
   "Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics."
   Cell. 141(5):884-896 (2010)
3. Birtwistle MR, Hatakeyama M, Yumoto N, Ogunnaike BA, Hoek JB, Kholodenko BN.:
   "Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses."
   Mol Syst Biol. 3:144. (2007)
4. Nagashima T, Shimodaira H, Ide K, Nakakuki T, Tani Y, Takahashi K, Yumoto N, Hatakeyama M.:
   "Quantitative transcriptional control of ErbB receptor signaling undergoes graded to biphasic response for cell differentiation."
   J Biol Chem. 282(6):4045-4056. (2007)
5. Hatakeyama M, Kimura S, Naka T, Kawasaki T, Yumoto N, Ichikawa M, Kim JH, Saito K, Saeki M, Shirouzu M, Yokoyama S, Konagaya A.:
   "A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling."
   Biochem J. 373(Pt 2):451-463 (2003)