John M. Wagner

Long-Term Supplemental

Research lab: Watson Research Center

Current Position

Long-Term Supplemental
Functional Genomics and Systems Biology Group
Computational Biology Center
IBM T.J. Watson Research Center

Contact Information

John Wagner
IBM T.J. Watson Research Center
P.O. Box 281
Yorktown Heights, NY 10598
(914) 945-3079
(914) 945-4104 (FAX)
e-mail: wagnerjo@us.ibm.com

Eduction

PhD, Applied Mathematics, University of California, Davis, 1998.
MS, Applied Mathematics, University of California, Davis, 1994.
BS, Mathematics, University of California, Davis, 1990.

Research Interests

Cancer Biology, Modeling, Simulation, Biological Applications for High-Performance Computing, Cellular Signaling and Pathway Models, Cellular Calcium Dynamics

Work Experience

NIH NRSA Postdoctoral Fellow (Supervisor: Dr. Leslie Loew), Department of Physiology, University of Connecticut Health Center Farmington, CT, 2000-2003.

Postdoctoral Fellow (Supervisor: Dr. Leslie Loew), Department of Physiology, University of Connecticut Health Center Farmington, CT, 1999-2003.

Scientific Programmer/Programmer IV (Supervisor: Dr. Joel Keizer), Institute of Theoretical Dynamics, University of California, Davis, Davis, CA, 1998-1999.

Research Assistant (Supervisor: Dr. James Quinn), Information Center for the Environment, University of California, Davis, Davis, CA, 1994-1997.

Teaching Assistant / Associate-in-Teaching (Supervisor: Dr. Angela Cheer), Department of Mathematics, University of California, Davis, Davis, CA, 1994-1995.

Research Assistant (Supervisor: Dr. Joel Keizer), Institute of Theoretical Dynamics, University of California, Davis, Davis, CA, 1992 - 1998.

Site Aide/Postgraduate Researcher (Supervisor: Dr. Joel Keizer), Institute of Theoretical Dynamics, University of California, Davis, Davis, CA, 1989-1992.

Praktikant/Software Developer (Supervisor: Wolfgang Kögler), Product Marketing and Support, Nixdorf Computer AG, Paderborn, Germany, 1988.

Publications

J. Wagner, L. Ma, J.J. Rice, W. Hu, A. Levine and G.A. Stolovitzky. p53–Mdm2 loop is controlled by a balance of its feedback strength and effective dampening using ATM and delayed feedback. IEE Journal of Systems Biology, 152(3):109—118, 2005.

L. Ma, J. Wagner, J.J. Rice, A. Levine, W. Hu and G. Stolovitzky. A plausible model for the digital response of p53 to DNA damage. Proceedings of the National Academy of Sciences, 102(40): 14266—14271, 2005. (PubMed)

C. P. Fall, J. Wagner, L. M. Loew and R. L. Nuccitelli. Cortically restricted production of IP3 leads to propagation of the fertilization Ca2+ wave along the cell surface in a model of the Xenopus egg. Journal of Theoretical Biology, 231(4):487—496, 2004. (PubMed)

J. Wagner, C. P. Fall, F. Hong, C. E. Sims, N. L. Allbritton, R. A. Fontanilla, I. I. Moraru, L. M. Loew, and R. Nuccitelli. A wave of IP3 production accompanies the fertilization Ca2+ wave in the egg of the frog, Xenopus laevis: theoretical and experimental support. Cell Calcium, 35:433—447, 2004. (PubMed)

M. Hucka et al. (43 authors, including J. Wagner). The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 19(4):524—531, 2003. (PubMed)

C. P. Fall, E. S. Marland, J. M. Wagner and J. J. Tyson (Editors). Computational Cell Biology. Springer-Verlag, New York, 2002. (Web Site)

J. C. Schaff, B. M. Slepchenko, Y.-S. Choi, J. Wagner, D. Resasco, L. M. Loew. Analysis of non-linear dynamics on arbitrary geometries with the Virtual Cell. Chaos, 11(1):115—131, 2001. (PubMed)

J. Wagner, Y.-X. Li, J. Pearson and J. Keizer. Simulation of the fertilization Ca2+ wave in Xenopus laevis eggs. Biophysical Journal, 75:2088—2097, 1998. (PubMed)

G. D. Smith, J. Wagner and J. Keizer. Validity of the rapid buffering approximation near a point source of calcium ions. Biophysical Journal, 70:2527—2539, 1996. (PubMed)

J. Wagner and J. Keizer. Effects of rapid buffers on Ca2+ diffusion and Ca2+ oscillations. Biophysical Journal, 67:447—456, 1994. (PubMed)

J. Keizer, R. Fox, and J. Wagner. On the amplification of molecular fluctuations for nonstationary systems: hydrodynamic fluctuations for the Lorenz model. Physics Letters A, 175:17—22, 1993.

Last updated 19 Mar 2006