Country/region
[
change
]
Terms of use
All of IBM
Home
Products
Services & solutions
Support & downloads
My account
IBM Research
Journals Home
Systems Journal
Journal of Research
and Development
Current Issue
Recent Issues
Papers in Progress
Search Journal Archives
Subscribe/Order
Description
Author's Guide
Staff
Contact Us
Related links
IBM Research: Computational Biology and Medical Informatics
IBM Research: Functional Genomics and Systems Biology
IBM Healthcare and Life Sciences
IBM Blue Gene
Systems Biology
Volume 50, Number 6, 2006
Table of contents:
HTML
PDF
This article:
HTML
PDF
Copyright info
Model-based design approaches in drug discovery: A parallel to traditional engineering approaches - References
by B.
Schoeberl
,
U. B.
Nielsen
,
and R.
Paxson
References
S. V. Aksenov, B. Church, A. Dhiman, A. Georgieva, R. Sarangapani, G. Helmlinger, and I. G. Khalil, “An Integrated Approach for Inference and Mechanistic Modeling for Advancing Drug Development,”
FEBS Lett.
579
, No. 8, 1878–1883 (2005).
G. Apic, T. Ignjatovic, S. Boyer, and R. B. Russell, “Illuminating Drug Discovery with Biological Pathways,”
FEBS Lett.
579
, No. 8, 1872–1877 (2005).
U. B. Nielsen and B. Schoeberl, “Using Computational Modeling to Drive the Development of Targeted Therapeutics,”
IDrugs
8
, No. 10, 822–826 (2005).
B. N. Kholodenko, A. Kiyatkin, F. J. Bruggeman, E. Sontag, H. V. Westerhoff, and J. B. Hoek, “Untangling the Wires: A Strategy to Trace Functional Interactions in Signaling and Gene Networks,”
Proc. Natl. Acad. Sci. USA
99
, No. 20, 12841–12846 (2002).
K. Sachs, O. Perez, D. Pe'er, D. A. Lauffenburger, and G. P. Nolan, “Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data,”
Science
308
, No. 5721, 523–529 (2005).
C. J. Needham, J. R. Bradford, A. J. Bulpitt, and D. R. Westhead, “Inference in Bayesian Networks,”
Nature Biotechnol.
24
, No. 1, 51–53 (2006).
A. Hooker and P. Vicini, “Simultaneous Population Optimal Design for Pharmacokinetic–Pharmacodynamic Experiments,”
AAPS J.
7
, No. 4, E759–E785 (2005).
J. M. Gallo, P. Vicini, A. Orlansky, S. Li, F. Zhou, J. Ma, S. Pulfer, M. A. Bookman, and P. Guo, “Pharmacokinetic Model-Predicted Anticancer Drug Concentrations in Human Tumors,”
Clin. Cancer Res.
10
, No. 23, 8048–8058 (2004).
J. A. Papin, J. L. Reed, and B. O. Palsson, “Hierarchical Thinking in Network Biology: The Unbiased Modularization of Biochemical Networks,”
Trends Biochem. Sci.
29
, No. 12, 641–647 (2004).
A. Ma'ayan, R. D. Blitzer, and R. Iyengar, “Toward Predictive Models of Mammalian Cells,”
Annu. Rev. Biophys. Biomolec. Struct.
34
, 319–349 (2005).
O. Wolkenhauer, S. N. Sreenath, P. Wellstead, M. Ullah, and K.-H. Cho, “A Systems- and Signal-Oriented Approach to Intracellular Dynamics,”
Biochem. Soc. Trans.
33
, Pt. 3, 507–515 (2005).
C. G. Moles, P. Mendes, and J. R. Banga, “Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods,”
Genome Res.
13
, No. 11, 2467–2474 (2003).
M. Bentele, I. Lavrik, M. Ulrich, S. Stosser, D. W. Heermann, H. Kalthoff, P. H. Krammer, and R. Eils, “Mathematical Modeling Reveals Threshold Mechanism in CD95-Induced Apoptosis,”
J. Cell Biol.
166
, No. 6, 839–851 (2004).
J. J. Hornberg, B. Binder, F. J. Bruggeman, B. Schoeberl, R. Heinrich, and H. V. Westerhoff, “Control of MAPK Signalling: From Complexity to What Really Matters,”
Oncogene
24
, No. 36, 5533–5542 (2005).
H. Song, P. Smolen, E. Av-Ron, D. A. Baxter, and J. H. Byrne, “Bifurcation and Singularity Analysis of a Molecular Network for the Induction of Long-Term Memory,”
Biophys. J.
(2006); see
http://www.biophysj.org/cgi/content/abstract/90/7/2309
.
A. Hoffmann, A. Levchenko, M. L. Scott, and D. Baltimore, “The IκB–NF–κB Signaling Module: Temporal Control and Selective Gene Activation,”
Science
298
, No. 5596, 1241–1245 (2002).
E. D. Sontag, “Some New Directions in Control Theory Inspired by Systems Biology,”
Syst. Biol.
1
, No. 1, 9–18 (2004).
K. W. Kohn, “Molecular Interaction Maps as Information Organizers and Simulation Guides,”
Chaos
11
, No. 1, 84–97 (2001).
R. Maimon and S. Browning, “Diagrammatic Notation and Computational Structure of Gene Networks,”
Proceedings of the 2nd International Conference on Systems Biology
, 2001; see
http://www.gnsbiotech.com/papers/dac.pdf
.
H. Kitano, A. Funahashi, Y. Matsuoka, and K. Oda, “Using Process Diagrams for the Graphical Representation of Biological Networks,”
Nature Biotechnol.
23
, No. 8, 961–966 (2005).
C. Starbuck and D. A. Lauffenburger, “Mathematical Model for the Effects of Epidermal Growth Factor Receptor Trafficking Dynamics on Fibroblast Proliferation Responses,”
Biotechnol. Progress
8
, No. 2, 132–143 (1992).
C.-Y. F. Huang and J. E. Ferrell, Jr., “Ultrasensitivity in the Mitogen-Activated Protein Kinase Cascade,”
Proc. Natl. Acad. Sci. USA
93
, No. 19, 10078–10083 (1996).
B. N. Kholodenko, O. V. Demin, G. Moehren, and J. B. Hoek, “Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor,”
J. Biol. Chem.
274
, No. 42, 30169–30181 (1999).
B. Schoeberl, C. Eichler-Jonsson, E. D. Gilles, and G. Muller, “Computational Modeling of the Dynamics of the MAP Kinase Cascade Activated by Surface and Internalized EGF Receptors,”
Nature Biotechnol.
20
, No. 4, 370–375 (2002).
About IBM
Privacy
Contact