Publications

Jacobson H. D., Pan S., Fisher J. and Secrier M.
Multi-scale characterisation of homologous recombination deficiency in breast cancer
Genome Medicine, 2;15(1):90, 2023
Howell R., Davies J., Clarke M.A., Appios A., Mesquita I., Jayal Y., Ringham-Terry B., Boned Del Rio I., Fisher J.* and Bennett C.
Localized immune surveillance of primary melanoma in the skin deciphered through executable modellingScience Advances, 9:15, 2023
Teichmann S.A., Haniffa M. & Fisher J. Policy proposals to promote inclusion in academia through the lens of women in science
Nature Communications: 13: 4068, 2022
Howell R., Clarke M.A., Reuschl A.K., Chen T., Abbott-Imboden S., Singer M., Lowe D.M., Bennett C.L., Chain B., Jolly C. and Fisher J.
Executable Network of SARS-CoV-2-Host Interaction Predicts Drug Combination Treatments.
npj Digital Medicine, 5:18, 2022
Talarmain L., Clarke M.A., Shorthouse D., Fisher J. and Hall B.A.
HOXA9 has the hallmarks of a biological switch with implications in blood cancers
Nature Communications: 13: 5829, 2022
Clarke M.A. & Fisher J.
Executable Cancer Models: Successes and Challenges
Nature Reviews Cancer 20: 343-354, 2020
Hall B. & Fisher J.
Constructing and Analysing Computational Models of Cell Signalling with BioModelAnalyzer
Current Protocols in Bioinformatics, 69, e95, 2020
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.
Rethinking Drug Design in the Artificial Intelligence Era
Nature Reviews Drug Discovery 19: 353-364, 2020
Clarke M.A. & Fisher J.
Prognostic Hallmarks in AML
Nature Biomedical Engineering, 3:847-849, 2019
Kreuzaler P., Clarke M.A., Brown E., Wilson C.H., Piterman N., Littlewood T., Evan G.I. & Fisher J.
Heterogeneity of Myc Expression in Breast Cancer Reveals New Susceptibilities through Executable Mechanistic Modelling
PNAS, 116(44): 22399-22408, 2019
Koksal A., Beck K., McKenna A., Srivastava S., Bodik R., Wolf-Yadlin A., Fraenkel E., Fisher J., & Gitter A.
Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data
Cell Reports, 24:3607–3618, 2018
Yu M.K, Ma J., Fisher J., Kreisberg J.F., Raphael B.J. & Ideker T.
Visible Machine Learning for Biomedicine
Cell 173: 1562-1565, 2018
Paterson Y., Shorthouse D., Pleijzier M., Piterman N., Bendtsen C., Hall B. & Fisher J.
A Toolbox for Discrete Modelling of Cell Signalling Dynamics
Integrative Biology 10:370-382, 2018
Woodhouse S., Piterman N., Wintersteiger C., Gottgens B., & Fisher J.
SCNS: a graphical tool for reconstructing executable networks
BMC Sys Biol 12:59, 2018
Fisher J. & Woodhouse S.
Program Synthesis Meets Deep Learning for Decoding Regulatory Networks
Current Opinion in Systems Biology, 4:64–70, 2017
Silverbush D., Grosskurth S., Wang D., Powell F., Gottgens B., Dry J.R. & Fisher J.
Cell-Specific Computational Modeling of the PIM pathway in Acute Myeloid Leukemia
Cancer Research, 77(4), February 2017
Lim C.Y., Wang H., Woodhouse S., Piterman N., Wernisch L., Fisher J., & Gottgens B.
BoolTraineR: training asynchronous Boolean models using single-cell expression data
BMC Bioinformatics 17:355, September 2016
Woodhouse S.J., Moignard V., Gottgens B., & Fisher J.
Processing, visualising and reconstructing network models from single cell data
Immunology and Cell Biology, pp 1-10, November 2015
Hall B., Piterman N., Hajnal A., & Fisher J.
Emergent Stem Cell Homeostasis in The C. elegans Germline Revealed by Hybrid Modelling
Biophysical Journal, 109:428-438, 2015
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.
Decoding the regulatory network of early blood development from single-cell gene expression measurments
Nature Biotechnology, 33, 269–276, 2015
Chuang R., Benque D., Cook B., Hall B.A., Ishtiaq S., Piterman N., Taylor A., Vardi M., Koschmieder S., Gottgens B. & Fisher J.
Drug Target Optimization in Chronic Myeloid Leukemia Using an Innovative Computational Platform
Nature Scientific Reports, 5:8190, 2015
Taylor A., Fisher J., Cook B., Ishtiaq S., & Piterman N.
Modelling biology – working through (in-)stabilities and frictions
Computational Culture, 2014
Fisher J., Piterman N., & Rastislav Bodik.
Towards Synthesizing Executable Models in Biology
Frontiers in Bioengineering and Biotechnology, section Bioinformatics and Computational Biology. December 2014.
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
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
Moignard V., Woodhouse S., Fisher J., & Gottgens B.
Transcriptional Hierarchies Regulating Early Blood Cell Development
Blood Cells, Molecules, and Diseases, 2013
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
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
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
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
Fisher J., Harel D., & Henzinger T.A.
Biology as Reactivity
Communications of ACM 54 (10): 72-82, 2011
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
Fisher J. & Nir Piterman.
The Executable Pathway to Biological Networks
Briefings in Functional Genomics & Proteomics, 9(1): 79-92, 2010
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
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
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
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
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
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., 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
* See also Nature Reviews Genetics 6 (4): 255, 2005.
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

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
Fisher J. & Piterman N.
Model Checking for Biology
System Theoretic and Computational Perspectives in Systems and Synthetic Biology, Springer-Verlag, 2014
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
Fisher J. & Harel D.
On Statecharts for Biology
Symbolic Systems Biology: Theory and Methods, Jones and Bartlett Publishers, 2010
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
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
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
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
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
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, 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 Analyzing Biological Networks
CAV 2012, LNCS 7358, pp. 686–692, Springer Verlag, 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
9th International Conference on Information Processing in Cells and Tissues (IPCAT), LNCS 7223, pp. 99–104, Springer Verlag, 2012
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
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
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
Church L., Apagyi K., & Fisher J.
Supporting Life Scientists via End User Programming
Proceedings of the 2008 Microsoft eScience Workshop
Church L., Apagyi K., & Fisher J.
Languages for biological models: Importance, implications and challenges
Proceedings of the Psychology of Programming Interest Group, 2008
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
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
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
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