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UCL Cancer Institute

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Publications

  • 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 A.M., 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 A. M. & 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 A.M. & Fisher J.
    Prognostic Hallmarks in AML
    Nature Biomedical Engineering, 3:847-849, 2019
     
  • Kreuzaler P., Clarke M., 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