systems-biology

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	SBI Publications

SBI Publications

Comparative studies of suppression of malignant cancer cell phenotype by

Hiroi, N.; Funahashi, A.; Kitano, H.;
Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA
Cancer Gene Therapy advance online publication 05 August 2005

Using process diagrams for the graphical representation of biological networks

Kitano, H.; Funahashi, A.; Matsuoka, Y.; Oda, K.;
Using process diagrams for the graphical representation of biological networks
Nature Biotechnology 23(8), 961 - 966 (2005)

A comprehensive pathway map of epidermal growth factor receptor signaling

Oda, K.; Matsuoka, Y.; Funahashi, A.; Kitano, H.;
A comprehensive pathway map of epidermal growth factor receptor signaling
Molecular Systems Biology

*Download the structured data (supplementary SBML file) to view the PubMed reference using the new function of CellDesigner 2.2 - Database connection.

The PANTHER database of protein families, subfamilies, functions and pathways.

Huaiyu Mi, Betty Lazareva-Ulitsky, Rozina Loo, Anish Kejariwal, Jody Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J. Campbell, Hiroaki Kitano and Paul D. Thomas. 2005.
The PANTHER database of protein families, subfamilies, functions and pathways.
Nucl. Acids. Res., 31:334-341.

The PANTHER database of protein families, subfamilies, functions and pathways

Metabolic Syndrome and Robustness Tradeoffs

Kitano, H., Oda, K., Kimura, T., Matsuoka, Y., Csete, M., Doyle, J., Muramatsu, M.. Metabolic Syndrome and Robustness Tradeoffs, Diabetes 53, S6-S15, 2004
PFD file

Biological Robustness

Kitano, H.. Biological Robustness. Nature Review Genetics. 5, 826-837, 2004
PDF file

Molecular Interaction Map of Macrophage

Oda, K.; Kimura, T, Matsuoka, Y.; Funahashi, A.; Muramatsu, M.; Kitano, H. Molecular Interaction Map of Macrophage. AfCS Report. 2004.
PDF file

Evolving a lingua franca and associated software infrastructure for computational systems biology: theSystemsBiologyMarkupLanguage(SBML) project

M. Hucka; A. Finney; B.J. Bornstein; S.M. Keating; B.E. Shapiro; J. Matthews; B.L. Kovitz; M.J. Schilstra; A. Funahashi; J.C. Doyle; and H. Kitano Evolving a lingua franca and associated software infrastructure for computational systems biology: theSystemsBiologyMarkupLanguage(SBML) project.
IEE Systems Biology. 1:41-53, 2004

Cancer as a robust system

Kitano, H. Cancer as a robust system: implications for anticancer therapy. Nature Reviews Cancer 4:227-235, 2004.
Abstract..

Cancer as a robust system: implications for anticancer therapy

Kitano, H. Cancer as a robust system: implications for anticancer therapy. Nature Reviews Cancer 4:227-235, 2004.
Abstract..

Systems Biology: A Brief Overview.

Kitano, H.
Systems Biology: A Brief Overview.
Science. 295, 1662-1664, 2002.
Abstract...

Computational Systems Biology.

Kitano, H.
Computational Systems Biology.
Nature. 420, 206-210, 2002.
Abstract...

Standards for modeling

Kitano, H.
Standards for modeling.
Nat. Biotech. 20, 337, 2002.
Abstract...

The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology.

Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J., and Kitano,H.
The ERATO Systems Biology Workbench: enabling interaction and exchange
between software tools for computational biology.
Proc. Pac Symp Biocomput. 2002, 450-61, 2002.
Abstract...

Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology

Kitano, H.
Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology.
Curr Genet. 41, 1-10, 2002.
Abstract...

Robustness as a measure of plausibility in models of biochemical networks.

Morohashi, M., Winn, A. E., Borisuk, M. T., Bolouri, H., Doyle, J.,
and Kitano, H.
Robustness as a measure of plausibility in models of biochemical networks.
J. Theor. Biol. 216, 19-30, 2002.
Abstract...

A gene network inference method from continuous-value gene expression data of wild-type and mutants

Kyoda, K. M., Morohashi, M., Onami, S., and Kitano, H.
A gene network inference method from continuous-value gene expression data of wild-type and mutants.
Genome Informatics. 11, 196-204, 2000.
Abstract...