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• Jacobson H. D., Pan S., Fisher J. and Secrier M.
  
  Genome Medicine, 2;15(1):90, 2023

• Howell R., Davies J., Clarke M.A.,ÌýAppios A., Mesquita I., Jayal Y., Ringham-Terry B., Boned Del Rio I., Fisher J.* and Bennett C.
  
  Science Advances, 9:15, 2023

• Teichmann S.A., Haniffa M. & Fisher J.
  Nature Communications:Ìý13: 4068, 2022
  Ìý
• Howell R., Clarke M.A.,ÌýReuschl A.K., Chen T., Abbott-Imboden S., Singer M., Lowe D.M., Bennett C.L., Chain B., Jolly C. and Fisher J.Ìý
  
  npj Digital Medicine, 5:18, 2022
  Ìý
• Talarmain L., Clarke M.A.,ÌýShorthouseÌýD., Fisher J. and Hall B.A.
  
  Nature Communications:Ìý13: 5829, 2022
  Ìý

• Clarke M.A.Ìý& Fisher J.Ìý
  
  Nature Reviews Cancer 20: 343-354,Ìý2020

• Hall B. & Fisher J.
  
  Current Protocols in Bioinformatics, 69, e95,Ìý2020

• Schneider P., Walters P, Plowright T., Sieroka N., Listgarten J., Goodnow R., Fisher J., Jansen J., Duca J., Rush T., Zentgraf M., Hill J., Krutoholow E., Kohler M., Blaney J., Funatsu K. & Schneider G.
  
  Nature Reviews Drug Discovery 19: 353-364,Ìý2020
  Ìý
• Clarke M.A.Ìý& Fisher J.
  
  Nature Biomedical Engineering, 3:847-849, 2019
  Ìý
• Kreuzaler P., Clarke M.A.,ÌýBrown E., Wilson C.H., Piterman N., Littlewood T., Evan G.I. & Fisher J.
  
  PNAS, 116(44): 22399-22408, 2019
  Ìý
• Koksal A., Beck K., McKenna A., Srivastava S., Bodik R., Wolf-Yadlin A., Fraenkel E., Fisher J., & Gitter A.
  
  Cell Reports, 24:3607–3618, 2018
  Ìý
• Yu M.K, Ma J., Fisher J., Kreisberg J.F., Raphael B.J. & Ideker T.
  
  Cell 173: 1562-1565, 2018
  Ìý
• Paterson Y., Shorthouse D., Pleijzier M., Piterman N., Bendtsen C., Hall B.Ìý & Fisher J.
  
  Integrative Biology 10:370-382, 2018
  Ìý
• Woodhouse S., Piterman N., Wintersteiger C., Gottgens B., & Fisher J.
  
  BMC Sys Biol 12:59, 2018
  Ìý
• Fisher J. & Woodhouse S.
  
  Current Opinion in Systems Biology, 4:64–70, 2017
  Ìý
• Silverbush D., Grosskurth S., Wang D., Powell F., Gottgens B., Dry J.R. & Fisher J.
  
  Cancer Research, 77(4), February 2017
  Ìý
• Lim C.Y., Wang H., Woodhouse S., Piterman N., Wernisch L., Fisher J., & Gottgens B.
  
  BMC Bioinformatics 17:355, September 2016
  Ìý
• Woodhouse S.J., Moignard V., Gottgens B., & Fisher J.
  
  Immunology and Cell Biology, pp 1-10, November 2015
  Ìý
• Hall B., Piterman N., Hajnal A., & Fisher J.
  
  Biophysical Journal, 109:428-438, 2015
  Ìý
• Moignard V., Woodhouse S., Haghverdi L., Lilly J, Tanaka Y, Wilkinson A.C, Buettner F., Nishikawa S.I., Piterman N., Kouskoff V., Theis F.J., Fisher J., & Göttgens B.
  
  Nature Biotechnology, 33, 269–276, 2015
  Ìý
• Chuang R., Benque D., Cook B., Hall B.A., Ishtiaq S., Piterman N., Taylor A., Vardi M., Koschmieder S., Gottgens B. & Fisher J.
  
  Nature Scientific Reports, 5:8190, 2015
  Ìý
• Taylor A., Fisher J., Cook B., Ishtiaq S., & Piterman N.
  Modelling biology – working through (in-)stabilities and frictions
  Computational Culture, 2014
  Ìý
• Fisher J., Piterman N., & Rastislav Bodik.
  Towards Synthesizing Executable Models in Biology
  Frontiers in Bioengineering and Biotechnology, section Bioinformatics and Computational Biology. December 2014.
  Ìý
• 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., & Göttgens B.
  Single cell analyses of regulatory network perturbations using enhancer targeting TAL Effectors suggest novel roles for PU.1 during haematopoietic specification
  Development, 141: 1-13, 2014
  Ìý
• Hall B., Jackson E., Hajnal A., & Fisher J.
  Logic Programming to Predict Cell Fate Patterns and Retrodict Genotypes during Organogenesis
  Royal Society Interface, 11: 0140245, 2014
  Ìý
• Moignard V., Woodhouse S., Fisher J., & Gottgens B.
  Transcriptional Hierarchies Regulating Early Blood Cell Development
  Blood Cells, Molecules, and Diseases, 2013
  Ìý
• Ilsley G., Fisher J., Apweiler R., DePace A. & Luscombe N.
  Cellular resolution models of cis-regulatory input function in the entire Drosophila embryo
  eLife, 2:e0052, 2013
  Ìý
• 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., & Swertz M.
  WormQTL – Public archive and analysis web portal for natural variation data in Caenorhabditis
  Nucleic Acid Research, 40(21): 1-6, 2012
  Ìý
• Nusser-Stein S., Beyer A., Adamczyk M., Rimann I., Piterman N., Hajnal A., & Fisher J.
  Cell-Cycle Regulation of Notch Signalling During C. elegans Vulval Development
  Molecular Systems Biology, Featured Article 8:618, 2012
  Ìý
• Feiglin A., Hacohen A., Sarusi A., Fisher J., Unger R., & Ofran Y.
  Static network structure can be used to model the phenotypic effects of perturbations in regulatory networks
  Bioinformatics, 28(21): 2811–2818, 2012
  Ìý
• Fisher J., Harel D., & Henzinger T.A.
  Biology as Reactivity
  Communications of ACM 54 (10): 72-82, 2011
  Ìý
• Bonzanni N., Zhang N., Oliver S., & Fisher J.
  The role of proteosome-mediated proteolysis in modulating the activity of potentially harmful transcription factor activity in Saccharomyces cerevisiae
  Bioinformatics, 27: i283–i287, 2011
  Ìý
• Fisher J. & Nir Piterman.
  The Executable Pathway to Biological Networks
  Briefings in Functional Genomics & Proteomics, 9(1): 79-92, 2010
  Ìý
• Beyer A., Thomson P., Scott J., & Fisher J.
  Computational Modelling of Metabolic Disturbance in Fat Tissue during Type-2 Diabetes and Obesity
  Transactions in Computational Systems Biology, LNBI 5945, pp. 146–162, 2010
  Ìý
• Wang D., Cardelli L., Piterman N., & Fisher J.
  Computational modelling of the EGFR network elucidates control mechanisms regulating signal dynamics
  BMC Systems Biology 3:118, 2009
  Ìý
• Kugler H., Kam N., Marelly R., Appleby L., Fisher J., Pnueli A., Harel D., Hubbard E.J.A., & Stern M.J.
  A scenario-based approach to modeling development (II): A Prototype Model of C. elegans Vulval Cell Fate Specification
  Developmental Biology, 323:1–5, 2008
  Ìý
• Sadot A., Fisher J., Barak D., Admanit Y., Stern M., Hubbard J., & Harel D.
  Towards verified biological models
  Transactions on Computational Biology and Bioinformatics, 5(2):1-12, 2008
  Ìý
• Fisher J. & Henzinger T.A.
  Executable Cell Biology
  Nature Biotechnology, 25(11):1239-1249, 2007
  * See also Correspondence in Nature Biotechnology 26(7): 738-739, 2008
  Ìý
• 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
  Ìý
• Schaub M., Henzinger T.A., & Fisher J.
  Qualitative networks: A symbolic approach to analyze biological signaling networks
  BMC Systems Biology 1:4, 2007
  Ìý
• Fisher J., Piterman N., Hubbard J., Stern M., & Harel D.
  Computational insights into C. elegans vulval development
  PNAS. 102 (6): 1951-1956, 2005
  * See also Nature Reviews Genetics 6 (4): 255, 2005.
  Ìý
• 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
  Ìý
• 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
  Ìý
• 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
  Ìý
• 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

Book Chapters & Books

• Clarke M., Woodhouse S., Piterman N., Hall B. and Fisher J.
  Using State Space Exploration to Determine How Gene Regulatory Networks Constrain Mutation Order in Cancer Evolution
  Automated Reasoning for Systems Biology and Medicine, Springer, 2019
  Ìý
• Fisher J. & Piterman N.
  Model Checking for Biology
  System Theoretic and Computational Perspectives in Systems and Synthetic Biology, Springer-Verlag, 2014
  Ìý
• Beyer A., Eberhard R., Piterman N., Hengartner M.O., Hajnal A., and Fisher J.
  A Dynamic Physical Model of Cell Migration, Differentiation and Apoptosis in Caenorhabditis elegans
  Advances in Systems Biology, Springer, 2012
  Ìý
• Fisher J. & Harel D.
  On Statecharts for Biology
  Symbolic Systems Biology: Theory and Methods, Jones and Bartlett Publishers, 2010
  Ìý
• Fisher J. (Ed.).
  Formal Methods in Systems Biology
  Springer, 2008

Computer Science Papers

• Ahmed Z., Benque D., Berezin S., Dahl C., Fisher J., Hall B., Ishtiaq S., Nanavati J., Piterman N., Riechert M., Skoblov N.
  Bringing LTL Model Checking to Biologists.
  Verification, Model Checking and Abstract Interpretation (VMCAI), LNCS 10145, pp. 1-13, Springer, 2017
  Ìý
• Woodhouse S., Piterman N., Köksal A. and Fisher J.
  Synthesizing Executable Gene Regulatory Networks from Single-Cell Gene Expression Data
  CAV LNCS 9206, pp. 544-560, Springer-Verlag, 2015
  Ìý
• Cook B., Fisher J., Hall B., Ishtiaq S., Juniwal G., and Piterman N.
  Efficient Verification of Cyclic Instability in Biological Models
  CAV LNCS 8559, pp. 358-372, Springer, 2014
  Ìý
• Claessen K., Fisher J., Ishtiaq S., Piterman N., and Wang Q.
  Model-Checking Signal Transduction Networks through Decreasing Reachability Sets
  CAV LNCS 8044, pp. 85-100, Springer-Verlag, 2013
  Ìý
• Taylor A., Benque D., Bourton S., Cockerton C., Cook B., Fisher J., Ishtiaq S., Piterman N.
  At the Intersection of Biology and Computation
  CHI pp. 493-502 ACM, 2013
  Ìý
• Koksal A., Pu Y., Srivastava S., Bodik R., Fisher J., and Piterman N.
  Synthesis of Biological Models from Mutation Experiments
  POPL pp. 469-482 ACM, 2013Ìý
  Ìý
• 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 Analyzing Biological Networks
  CAV 2012, LNCS 7358, pp. 686–692, Springer Verlag, 2012
  Ìý
• Beyer A., Eberhard R., Piterman N., Hengartner M., Hajnal A., and Fisher J.
  Predictive Modelling of Stem Cell Differentiation and Apoptosis in C. elegans
  9th International Conference on Information Processing in Cells and Tissues (IPCAT), LNCS 7223, pp. 99–104, Springer Verlag, 2012
  Ìý
• Fisher J., Henzinger T.A., Nickovic D., Piterman N., Singh A.V., and Vardi M.Y.
  Dynamic reactive Modules
  Concur 2011, LNCS 6901, pp. 404–418, 2011
  Ìý
• Fisher J., Piterman N., & Vardi M.
  Tower of Abstractions in Biology: The Only Way Is Up
  Formal Methods 2011, Invited Paper. LNCS 6664, pp. 3–11, 2011
  Ìý
• Cook B., Fisher J., Krepska E., & Piterman N.
  Proving stabilization for biological systems
  Proceedings of 12th International Conference on Verification, Model Checking and Abstract Interpretation Conference VMCAI ’11 R. Jhala and D. Schmidt (Eds.), LNCS vol. 6538, pages 134-149, 2011
  Ìý
• Church L., Apagyi K., & Fisher J.
  Supporting Life Scientists via End User Programming
  Proceedings of the 2008 Microsoft eScience Workshop
  Ìý
• Church L., Apagyi K., & Fisher J.
  Languages for biological models: Importance, implications and challenges
  Proceedings of the Psychology of Programming Interest Group, 2008
  Ìý
• Fisher J., Henzinger T.A., Mateescu M., & Piterman N.
  Bounded Asynchrony for Modeling Cell-Cell Interactions
  Proceedings of FMSB ’08 Cambridge, UK. Lecture Notes in Bioinformatics, 5054: pages 17-32, Springer-Verlag, 2008
  Ìý
• 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, ’07 San Diego, CA. Lecture Notes in Bioinformatics
  Ìý
• Fisher J. & Henzinger T.A.
  Executable Biology
  Proceedings of the 2006 Winter Simulation Conference - Track on Modeling and Simulation in Computational Biology pp. 1675-1682, 2006
  Ìý
• Fisher J., Harel D., Hubbard J., Piterman N., Stern M., & Swerdllin N.
  Combining state-based and scenario-based approaches in modeling biological systems
  Proceedings of CMSB ‘04 Paris, France. Lecture Notes in Bioinformatics 3083: 236-241, Springer-Verlag, 2004