Journal Papers
-
Fisher J. & Henzinger T.A. Executable Cell Biology. Nature
Biotechnology 25(11):1239-1249, 2007. [PDF, 759Kb]
See also correspondence in Nature
Biotechnology 26(7):737-8;738-9,
2008. [PDF, 145Kb]
[PDF, 161Kb]
- Sadot A., Fisher J., Barak D., Admanit Y., Stern M.J.,
Hubbard E.J.A., & Harel D. Towards Verified Biological Models. IEEE/ACM
Trans. Comput. Biology and Bioinformatics. 5(2):1-12, 2008.
[PDF, 2.4Mb]
- Fisher J., Piterman N., Hajnal A., & Henzinger, T.A.
Predictive Modeling of Signaling Crosstalk during C. elegans Vulval
Development. PLoS Computational Biology. 3(5):e92, 2007.
[PLoS]
[PDF,
973Kb] [PDF,
5914Kb]
- Schaub M.A., Henzinger, T.A., & Fisher J. Qualitative
Networks: A Symbolic Approach to Analyze Biological Signaling Networks. BMC
Systems Biology. 1:4, 2007. [PDF,
488Kb].
- Fisher J., Piterman N., Hubbard J., Stern M., & Harel D.
Computational insights into C. elegans vulval development. PNAS
102(6):1951-1956, 2005. [PDF, 491Kb] [Supporting
Information].
See also Nature Reviews Genetics 6(4):255,
2005. [html].
- Schwartz M., Shaked I., Fisher J., Mizrahi T., & Schori
H. Protective autoimmunity against the enemy within: fighting glutamate
toxicity. Trends in Neuroscience 26(6):297-302, 2003.
[PDF,
217Kb].
- Wolf S., Fisher J., Bechman I., Steiner B., Kwidzinski E., & Nitsch R.
Neuroprotection by T-cells depends on their subtype and activation state. Journal of Neuroimmunology 133:72-80, 2002.
[PDF,
410Kb].
- Fisher J., Mizrahi T., Schori H., Yoles E., Levkovich-Verbin H., Haggiag
S., Ravel M., & Schwartz M. Increased post-traumatic survival of neurons
in IL-6 knockout mice on a background of EAE susceptibility. Journal of
Neuroimmunology 119:1-9, 2001. [PDF,
350Kb].
- Fisher J., Levkovitch-Verbin H., Schori H., Yoles E.,
Butovsky O., Kaye J.F., Ben-Nun A., & Schwartz M. Vaccination for
neuroprotection in the mouse optic nerve: Implications for optic neuropathies.
The Journal of Neuroscience 21(1):136-142, 2001.
[PDF,
650Kb].
Book Chapters
- Fisher J. & Harel D. On Statecharts for Biology in
Symbolic Systems Biology: Theory and Methods, Jones and Bartlett
Publishers, 2008. In
press.
Refereed Conference Papers
- Fisher J., Henzinger T. A., Mateescu M., & Piterman N. Bounded Asynchrony:
Concurrency for Modeling Cell-Cell Interactions. Proc. of Formal Methods
in Systems Biology (FMSB '08), Lecture Notes in Bioinformatics, Vol.
5054, pp. 17-32, Springer-Verlag, 2008. [PDF,
601Kb]
- Church L., Apagyi K., & Fisher J. Languages for Biological Models:
Importance, Implications and Challenges - A Work in Progress. Proc. of
the 4th Psychology of Programming, Work in Progress Meeting 2008,
Brighton, UK. [PDF,
142Kb]
- Schaub M., Bezdek A., Henzinger T.A., Radtke F., & Fisher J. Qualitative
Crosstalk Analysis of Wnt and Notch Signaling in Mammalian Skin. RECOMB
Systems Biology, 2007 San Diego, CA. Lecture Notes in Bioinformatics. [PDF,
226Kb]
- Fisher J. & Henzinger T. A. Executable Biology. Proc. of the Winter
Simulation Conference - Track on Modeling and Simulation in Computational
Biology. pp. 1675-1682, 2006. [PDF,
130Kb].
- Fisher J., Harel D., Hubbard J., Piterman N., Stern M., & Swerdlin N.
Combining state-based and scenario-based approaches in modeling biological
systems. Proc. of Computational Methods in Systems Biology (CMSB '04),
Lecture Notes in Bioinformatics, Vol. 3082, pp. 236-241, Springer-Verlag,
2004. [PDF,
31Kb].