- Wilkinson A., Kawata V.K.S., Schütte J., Gao X., Antoniou S., Baumann C., Woodhouse S., Hannah R., Tanaka Y., Swiers G., Moignard V., Fisher J., Hidetoshi S., Tijssen M.R., de Bruijn M.F.T.R., Liu P., and Göttgens B., Single cell analyses of regulatory network perturbations using enhancer targeting TAL Effectors suggest novel roles for PU.1 during haematopoietic specification, in Development, in press, The Company of Biologists, August 2014
- Fisher J., Piterman N., and Rastislav Bodik, Towards Synthesizing Executable Models in Biology, in review, ., August 2014
- Hall B., Jackson E., Hajnal A., and Fisher J., Logic Programming to Predict Cell Fate Patterns and Retrodict Genotypes during Organogenesis, in Royal Society Interface 11: 0140245, Royal Society Publishing, June 2014
- Moignard V., Woodhouse S., Haghverdi L., Lilly J., Tanaka Y., Wilkinson A., Buettner F., Nishikawa S.I., Piterman N., Kouskoff V., Theis F., Fisher J., and Gottgens B., Decoding the Transcriptional Program for Blood Development from Whole Tissue Single Cell Gene Expression Measurements, in review, 2014
- Hall B., Juniwal G., Dahl C., and Fisher J., Automated Refinement of Executable Biological Models, in review, 2014
- Moignarg V, Woodhouse S, Fisher J, and Gottgens B, Transcriptional Hierarchies Regulating Early Blood Cell Development, in Blood Cells, Molecules, and Diseases, Elsevier, September 2013
- Ilsley G, Fisher J, Apweiler R, DePace A, and Luscombe N, Cellular resolution models of cis-regulatory input function in the entire Drosophila embryo, in eLife 2:e00522, August 2013
- Snoek B, van der Velde K, Arends D, Li Y, Beyer A, Elvin M, Fisher J, Hajnal A, Hengartner M, Poulin G, Rodriguez M, Schmid T, Schrimpf S, Xue F, Jansen R, Kammenga J, and Swertz M, WormQTL – Public archive and analysis web portal for natural variation data in Caenorhabditis spp, in Nucleic Acids Research 40(21): 1-6, Oxford University Press, November 2012
- Nusser-Stein S, Beyer A, Rimann I, Adamczyk M, Piterman N, Hajnal A, and Fisher J, Cell-Cycle Regulation of NOTCH Signaling during C. elegans Vulval Development, in Molecular Systems Biology, Featured Article 8:618, Nature Publishing Group, October 2012
- Feiglin A, Hacohen A, Sarusi A, Fisher J, Unger R, and Ofran Y, Static Network Structure Can Be Used to Model the Phenotypic Effects of Perturbations in Regulatory Networks, in Bioinformatics, 28(21): 2811–2818, Oxford University Press, October 2012
- Bonzanni N, Zhang N, Oliver S.G, and Fisher J, The role of proteosome-mediated proteolysis in modulating potentially harmful transcription factor activity in S. cerevisiae, in Bioinformatics, Vol. 27, pages i283–i287, 2011
- Fisher J, Harel D, and Henzinger T.A, Biology as Reactivity, in Communication of the ACM 54 (10): 72-82, 2011
- Beyer A, Thomason P, Li X, Scott J, and Fisher J, Mechanistic Insights into Metabolic Disturbance during Type-II Diabetes and Obesity using Qualitative Networks , in Transactions on Computational Systems Biology, LNBI 5945, pp. 146–162 , January 2010
- Fisher J and Piterman N, The Executable Pathway to Biological Networks, in Briefings in Functional Genomics and Proteomics 9(1): 79-92., Oxford University Press, January 2010
- Wang D, Cardelli L, Phillips A, Piterman N, and Fisher J, Computational Modeling of the EGFR Network Elucidates Control Mechanisms Regulating Signal Dynamics, in BMC Systems Biology 3:118, 22 December 2009
- Kam N, Kugler H, Marelly R, Appleby L, Fisher J, A. Pnueli, D. Harel, M.J. Stern, and E.J.A. Hubbard, A scenario-based approach to modeling development: A prototype model of C. elegans vulval fate specification , in Developmental Biology, vol. 323, no. 1, pp. 1-5, Elsevier , August 2008
- Fisher J and Henzinger T.A, Dichotomies between computational and mathematical models (Correspondence), in Nature Biotechnology , vol. 26, no. 7, pp. 737-8;738-9, 2008
- Sadot A, Fisher J, Barak D, Admanit Y, Stern M.J, Hubbard E.J.A, and Harel D, Towards Verified Biological Models, in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, pp. 1-12, January 2008
- Fisher J and Henzinger T.A, Executable Cell Biology, in Nature Biotechnology, vol. 25, no. 11, pp. 1239-1249, November 2007
- 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.
- Schaub M.A., Henzinger, T.A., & Fisher J. Qualitative Networks: A Symbolic Approach to Analyze Biological Signaling Networks. BMC Systems Biology. 1:4, 2007.
- Fisher J., Piterman N., Hubbard J., Stern M., & Harel D. Computational insights into C. elegans vulval development. PNAS 102(6):1951-1956, 2005. [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.
- 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.
- 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.
- 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.
- Fisher J and Piterman N, Model Checking in Biology, in System Theoretic and Computational Perspectives in Systems and Synthetic Biology, Springer Verlag, 2014
- Beyer A, Eberhard R, Piterman N, Hengartner M, Hajnal A, and Fisher J, A Dynamic Physical Model of Cell Migration, Differentiation and Apoptosis in Caenorhabditis elegans, in Advances in Systems Biology, Springer, 2012
- Fisher J and Harel D, On Statecharts for Biology, in Symbolic Systems Biology: Theory and Methods, Jones and Bartlett Publishers, 2010
Refereed Conference Papers
- Cook B, Fisher J, Hall B, Ishtiaq S, Juniwal G, and Piterman N, Finding Instability in Biological Models, in Computer Aided Verification (CAV), 2014
- Claessen K, Fisher J, Ishtiaq S, Piterman N, and Wang Q, Model-Checking Signal Transduction Networks through Decreasing Reachability Sets, in Computer Aided Verification (CAV), 2013
- Koksal A.S, Pu Y, Srivastava S, Bodik R, Piterman N, and Fisher J, Synthesis of Biological Models from Mutation Experiments, in Principles of Programming Languages (POPL), ACM, 2013
- Taylor A.S, Piterman N, Ishtiaq S, Fisher J, Cook B, Cockerton C, Bourton S, and Benque D, At the Interface of Biology and Computation, in Conference on Human-Computer Interaction (CHI), ACM, 2013
- Benque D, Bourton S, Cockerton C, Cook B, Fisher J, Ishtiaq S, Piterman N, Taylor A, and Vardi M, Bio Model Analyzer: Visual Tool for Modeling and Analysis of Biological Networks, in Computer Aided Verification (CAV) 2012. LNCS 7358, pp. 686–692 , Springer Verlag, July 2012
- Beyer A, Eberhard R, Piterman N, Hengartner M, Hajnal A, and Fisher J, Predictive Modelling of Stem Cell Differentiation and Apoptosis in C. elegans, in 9th International Conference on Information Processing in Cells and Tissues (IPCAT), LNCS 7223, pp. 99–104, Springer Verlag, 2012
- Fisher J, Henzinger T, Nickovic D, Piterman N, Singh A, and Vardi M, Dynamic Reactive Modules, in 22nd International Conference on Concurrency Theory, LNCS 6901, pp. 404–418, Springer Verlag, September 2011
- Fisher J, Piterman N, and Vardi Y.M, The Only Way Is Up: On A Tower of Abstractions for Biology, in 17th International Symposium on Formal Methods, LNCS 6664, pp. 3–11 , Springer Verlag, June 2011
- Cook B, Fisher J, Krepska E, and Piterman N, Proving Stabilization of Biological Systems, in 12th International Conference on Verification, Model Checking, and Abstract Interpretation Conference VMCAI'11. R. Jhala and D. Schmidt (Eds.), LNCS vol. 6538, pp 134-149 , Springer Verlag, January 2011
- J. Fisher, T.A. Henzinger, M. Mateescu, and N. Piterman, Bounded Asynchrony: A biologically-inspired notion of concurrency, in Proceedings of FMSB ’08 Cambridge, UK, Springer, January 2008
- L. Church, K. Apagyi, and J. Fisher, Languages for Biological Models: Importance, Implications and Challenges - A Work In Progress, in Proceedings of the Psychology of Programming Interest Group, January 2008
- Marc Schaub, April Bezdek, Thomas Henzinger, Freddy Radtke, and Jasmin Fisher, Qualitative Crosstalk Analysis of Wnt and Notch Signaling in Mammalian Skin, in RECOMB Systems Biology, ’07 San Diego, CA, Springer, January 2007
- 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.
- 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.