Jacobson H. D., Pan S., Fisher J. and Secrier M.
Genome Medicine, 2;15(1):90, 2023Howell 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,Ìý2020Hall 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