Professor James Bown

Professor of Systems Biology

School School of Design and Informatics

Department Division of Games Technology and Mathematics

Contact info

+44 (0)1382 30 8471

Biography

Innovation and Professional Development; School of Arts, Media and Computer Games: Taught to the MProf in Computer Games Development this module requires students to develop an innovative solution to an identifiable problem that sits beyond their current expertise. The student cohort is a mix of disciplines, including technology, art, design and sound production. Students must work in the face of an uncertain programme of research and development. Students are required to reflect on their development and how it has contributed to their professional practice.

Research Methods; Graduate School: Research Methods is a University-wide module delivered to all our post-graduate taught students. The module develops literature review skills, proposal writing and statistics at Masters level. The module draws on experts from across Abertay to provide insight into the nature of research at Masters level and to guide the production of a research proposal. For statistics teaching, the approach used is problem-led and the module instils in students how to select the right statistics in a given context.

Advanced Systems Biology in Biomedicine; School of Science, Engineering and Technology: Taught to Honours students on the BSc (Hons) Biomedical Science and BSc (Hons) Applied Biomedical Science, this module provides an integrative perspective on the role of systems biology and underpinning experimental systems in understanding and managing diseases, with a particular focus on cancer. Systems biology offers both a conceptual and a technical framework for integrating diverse, multi-scale, multi-stream data in bioscience generally.

My research explores the role of systems biology in understanding cancer. Cancer is a disease characterised by functional dysregulations within and surrounding affected cells, tissues and organs. These dysregulations confer cancerous cells with the ability to, among other features, proliferate at an increased rate, evade death and spread through the body. Cell behaviour is governed by a complex network of signalling regulatory pathways that ultimately dictate the development, maintenance and progression of the cancer as well as its histological and anatomical presentation and organisation. Anti-cancer drugs typically target key elements of this pathway in order to control these dysregulations, by either restoring normal functioning or blocking aberrant behaviour.

A major challenge in cancer therapy is drug resistance, which has at least two root causes. First, evolutionary mutations in cells can mean that the signalling network changes its function and the drugs lose efficacy. Second, the inherent heterogeneity of cells within a tumour combined with the specificity of the anti-cancer drugs means that a given therapy is likely to only target a sub-population of the cells in a tumour. Clearly to address this, we need to understand cellular signalling, tumour morphology and how each drives the other.

My research in cancer systems biology seeks to link cellular signalling and tumour morphology, and this requires a mix of complex systems modelling and agent-based modelling (EPSRC funded CoSMoS project), theoretical ecology in plant and fungal ecosystems, emergent behaviour in multi-agent robotic communities (EPSRC funded Artificial Cultures project) and interactive and dynamic visualisation of complex data. These areas of expertise combine to provide a unique approach to studying cancer based on the following research strands:

Bottom-up – Modelling the single cell. We have developed models of the cellular signalling pathways and their mechanistic responses to drug action. This allows us to explore the effects of cellular mutations on anti-cancer drug resistance (e.g. pdf), to unravel the regulatory mechanisms governing complex signalling dynamics (e.g. pdf) and to design combination therapies (e.g. pdf). Coupled to an innovative technology for dynamic and interactive visualisation of cell signalling dynamics we have developed an in silico drug discovery platform.

Top-down – Modelling the tumour. Tumour morphology may be studied in two dimensions, through imaging to show cross-sectional morphology or stained 2D-sections to revealing inner structures, or three dimensions to study whole tumour (surface) morphology. We have applied statistics developed in soil science to the study of 3D tumours. We have studied quantitatively the morphological response of tumours to therapeutic intervention (pdf).

Linking scales – Multi-cell modelling. In emerging work, we are developing a computational framework where individual cells, with potentially unique intra-cellular signalling networks, are able to interact in physical space. This framework will enable us to study heterogeneous populations of cells and how they interact to form emergent (tissue) structures.

 

2018

Identifying prognostic structural features in tissue sections of colon cancer patients using point pattern analysis

Jones-Todd, C. M., Caie, P., Illian, J. B., Stevenson, B. C., Savage, A., Harrison, D. J. & Bown, J. L. (2018) Identifying prognostic structural features in tissue sections of colon cancer patients using point pattern analysis. . . p. 1421-1441. .
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Engineering simulations as scientific instruments

Stepney, S., Polack, F. A., Alden, K., Andrews, P. S., Bown, J. L., Droop, A., Greaves, R. B. ., Read, M., Sampson, A. T., Timmis, J. & Winfield, A. F. . (2018) Engineering simulations as scientific instruments. . . Cham: Springer.
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Unsupervised machine learning of integrated health and social care data from the Macmillan Improving the Cancer Journey service in Glasgow

Kang, K. L., Greer, M., Bown, J. L., Preston, J., Mabelis, J., Hepburn, L., Fisher, M., Falconer, R. E., McDermott, S. & Deed, S. (2018) Unsupervised machine learning of integrated health and social care data from the Macmillan Improving the Cancer Journey service in Glasgow. . . .
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Narratives for drug design

Bown, J. L. & Goltsov, A. (2018) Narratives for drug design. In: Narrating complexity. Walsh, R. (ed.), Stepney, S. (ed.). p. 253-268. . Springer.
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2017

NRF2 regulates HER1 signaling pathway to modulate the sensitivity of ovarian cancer cells to lapatinib and erlotinib

Hamza Kankia, I., Khalil, H. S., Langdon, S. P., Moult, P. R., Bown, J. L. & Deeni, Y. Y. (2017) NRF2 regulates HER1 signaling pathway to modulate the sensitivity of ovarian cancer cells to lapatinib and erlotinib. . . .
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2016

Validation of a novel assay for cardiology drug screening using hESC-derived cardiomyocyte spheroids - “mini-hearts”

Zhelev, N., Kaske, R. & Bown, J. L. (2016) Validation of a novel assay for cardiology drug screening using hESC-derived cardiomyocyte spheroids - “mini-hearts”. . . p. S108. .
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Cancer systems biology

Bown, J. L. (2016) Cancer systems biology. . . p. S4. .
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Kinetic modelling of in vitro data of PI3K, mTOR1, PTEN enzymes and on-target inhibitors Rapamycin, BEZ235, and LY294002

Goltsov, A., Tashkandi, G., Langdon, S. P., Harrison, D. J. & Bown, J. L. (2016) Kinetic modelling of in vitro data of PI3K, mTOR1, PTEN enzymes and on-target inhibitors Rapamycin, BEZ235, and LY294002. . . p. 170–181. .
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A novel mechanism of action of HER2 targeted immunotherapy is explained by inhibition of NRF2 function in ovarian cancer cells

Khalil, H. S., Langdon, S. P., Goltsov, A., Soininen, T., Harrison, D. J., Bown, J. L. & Deeni, Y. Y. (2016) A novel mechanism of action of HER2 targeted immunotherapy is explained by inhibition of NRF2 function in ovarian cancer cells. . . p. 75874-75901. .
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A signaling visualization toolkit to support rational design of combination therapies and biomarker discovery

Bown, J. L., Shovman, M., Robertson, P., Boiko, A., Goltsov, A., Mullen, P. & Harrison, D. J. (2016) A signaling visualization toolkit to support rational design of combination therapies and biomarker discovery. . . p. 29657-29667. .
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2015

Morphological analysis of cancer spheroids

Bown, J. L., Savage, A., Houston, A. N., Wilson, S., Khalil, H. S., Goltsov, A. & Deeni, Y. Y. (2015) Morphological analysis of cancer spheroids. . . p. S6. .
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The targeting of epidermal growth factor family receptors (ERBBs) in ovarian cancer therapy

Deeni, Y. Y., Khalil, H. S., Goltsov, A., Soininen, T., Langdon, S. P., Harrison, D. J. & Bown, J. L. (2015) The targeting of epidermal growth factor family receptors (ERBBs) in ovarian cancer therapy. . . p. S6-S7. .
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Understanding resistance mechanisms to PI3K/mTOR inhibitors in ovarian cancer model systems

Tashkandi, G., Goltsov, A., Mullen, P., Bown, J., Harrison, D. & Langdon, S. (2015) Understanding resistance mechanisms to PI3K/mTOR inhibitors in ovarian cancer model systems. . . p. B33. .
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NRF2 regulates HER2 and HER3 signaling pathway to modulate sensitivity to targeted immunotherapies

Khalil, H. S., Langdon, S. P., Kankia, I. H., Bown, J. L. & Deeni, Y. Y. (2015) NRF2 regulates HER2 and HER3 signaling pathway to modulate sensitivity to targeted immunotherapies. . . .
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Twist and learn

Shovman, M., Szymkowiak, A., Bown, J. L. & Scott-Brown, K. C. (2015) Twist and learn. In: Proceedings of the 33rd Annual ACM Conference on Human Factors in Computing Systems. . p. 313-316. New York: Association for Computing Machinery (ACM).
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2014

Process-based vs. data-driven modelling of cancer cell behaviour

Bown, J. L., Idowu, M. A., Khalil, H. S., Goltsov, A., Deeni, Y., Zhelev, N., Langdon, S. P. & Harrison, D. J. (2014) Process-based vs. data-driven modelling of cancer cell behaviour. . . p. S13-S13. .
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Quantitative analysis of NRF2 pathway reveals key elements of the regulatory circuits underlying antioxidant response and proliferation of ovarian cancer cells

Khalil, H. S., Goltsov, A., Langdon, S. P., Harrison, D. J., Bown, J. & Deeni, Y. (2014) Quantitative analysis of NRF2 pathway reveals key elements of the regulatory circuits underlying antioxidant response and proliferation of ovarian cancer cells. . . p. 12-30. .
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Systems analysis of drug-induced receptor tyrosine kinase reprogramming following targeted mono- and combination anti-cancer therapy

Goltsov, A., Deeni, Y. Y., Khalil, H. S., Soininen, T., Kyriakidis, S., Hu, H., Langdon, S. P., Harrison, D. J. & Bown, J. L. (2014) Systems analysis of drug-induced receptor tyrosine kinase reprogramming following targeted mono- and combination anti-cancer therapy. . . p. 563-591. .
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Understanding tissue morphology: model repurposing using the CoSMoS process

Sampson, A. T., Bown, J. L., Khalil, H. S. & Deeni, Y. Y. (2014) Understanding tissue morphology: model repurposing using the CoSMoS process. . . p. 109–128. .
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2013

Reverse engineering of drug induced DNA damage response signalling pathway reveals dual outcomes of ATM kinase inhibition

Idowu, M. A., Khalil, H. S., Bown, J. L. & Zhelev, N. (2013) Reverse engineering of drug induced DNA damage response signalling pathway reveals dual outcomes of ATM kinase inhibition. . . .
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Matrix-based analytical methods for recasting Jacobian models to power-law models

Idowu, M. A. & Bown, J. L. (2013) Matrix-based analytical methods for recasting Jacobian models to power-law models. In: Proceedings of the eighth EUROSIM Congress on Modelling and Simulation, EUROSIM 2013, September 10-13, Cardiff, Wales. Al-Begain, K. (ed.), Al-Dabass, D. (ed.), Orsoni, A. (ed.), Cant, R. (ed.), Zobel, R. (ed.). p. 250-258. Los Alamitos, CA: IEEE Computer Society.
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Customizing the therapeutic response of signaling networks to promote antitumor responses by drug combinations

Goltsov, A., Langdon, S. P., Goltsov, G., Harrison, D. J. & Bown, J. L. (2013) Customizing the therapeutic response of signaling networks to promote antitumor responses by drug combinations. . . .
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2012

The meaning of graphs

Shovman, M., Scott-Brown, K. C., Szymkowiak, A. & Bown, J. L. (2012) The meaning of graphs. . . p. 381-398. .
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Matrix operations for the simulation and immediate reverse-engineering of time series data

Idowu, M. A. & Bown, J. L. (2012) Matrix operations for the simulation and immediate reverse-engineering of time series data. In: Proceedings: 2012 14th International Conference on Modelling and Simulation. Al-Dabass, D. (ed.), Orsoni, A. (ed.), Cant, R. (ed.). p. 101-106. Piscataway, NJ: IEEE .
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Feedforward and feedback regulation of the MAPK and PI3K oscillatory circuit in breast cancer

Hu, H., Goltsov, A., Bown, J. L., Sims, A. H., Langdon, S. P., Harrison, D. J. & Faratian, D. (2012) Feedforward and feedback regulation of the MAPK and PI3K oscillatory circuit in breast cancer. . . p. 26-32. .
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A new method for identifying a data-consistent self-reconfigurable predictive bio-network model of the cell cycle based on time series data and its application in cancer systems biology

Idowu, M. A., Bown, J. & Zhelev, N. (2012) A new method for identifying a data-consistent self-reconfigurable predictive bio-network model of the cell cycle based on time series data and its application in cancer systems biology. . . .
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Characterising the tumour morphological response to therapeutic intervention

Savage, A., Katz, E., Eberst, A., Falconer, R. E., Houston, A. N., Harrison, D. J. & Bown, J. L. (2012) Characterising the tumour morphological response to therapeutic intervention. . . p. 252-260. .
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Features of the reversible sensitivity-resistance transition in PI3K/PTEN/AKT signalling network after HER2 inhibition

Goltsov, A., Faratian, D., Langdon, S. P., Mullen, P., Harrison, D. J. & Bown, J. L. (2012) Features of the reversible sensitivity-resistance transition in PI3K/PTEN/AKT signalling network after HER2 inhibition. . . p. 493-504. .
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Engineering simulations for cancer systems biology

Bown, J. L., Andrews, P. S., Deeni, Y. Y., Goltsov, A., Idowu, M. A., Polac, F. A., Sampson, A. T., Shovman, M. & Stepney, S. (2012) Engineering simulations for cancer systems biology. . . p. 1560-1574. .
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2011

Linking individual behaviour to community scale patterns in fungi

Falconer, R. E., Bown, J. L., White, N. A. & Crawford, J. W. (2011) Linking individual behaviour to community scale patterns in fungi. . . p. 76-82. .
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Compensatory effects in the PI3K/PTEN/AKT signaling network following receptor tyrosine kinase inhibition

Goltsov, A., Faratian, D., Langdon, S. P., Bown, J. L., Goryanin, I. & Harrison, D. J. (2011) Compensatory effects in the PI3K/PTEN/AKT signaling network following receptor tyrosine kinase inhibition. . . p. 407-416. .
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Towards an exact reconstruction of a time-invariant model from time series data

Idowu, M. A. & Bown, J. L. (2011) Towards an exact reconstruction of a time-invariant model from time series data. . . .
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Modelling of Healthcare Associated Infections: a study on the dynamics of pathogen transmission by using an individual-based approach

Milazzoa, L., Bown, J. L., Eberst, A., Phillips, G. & Crawford, J. W. (2011) Modelling of Healthcare Associated Infections: a study on the dynamics of pathogen transmission by using an individual-based approach. . . p. 260-265. .
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2010

Is visual search a high-level phenomenon? Evidence from structure perception in 3-D scatterplots

Shovman, M., Szymkowiak, A., Bown, J. L. & Scott-Brown, K. C. (2010) Is visual search a high-level phenomenon? Evidence from structure perception in 3-D scatterplots. . . p. 1149-1150. .
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Symbiotic cognitive networks

Rasheed, T., Hart, E., Bown, J. L. & Falconer, R. E. (2010) Symbiotic cognitive networks. In: Artificial Immune Systems: 9th International Conference, ICARIS 2010, Edinburgh, UK, July 26-29, 2010: proceedings. Hart, E. (ed.), McEwan, C. (ed.), Timmis, J. (ed.), Hone, A. (ed.). p. 326-328. Berlin: Springer-Verlag.
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Modelling fungal colonies and communities

Falconer, R. E., Bown, J. L., McAdam, E. V., Perez-Reche, P., Sampson, A. T., van den Bulcke, J., White, N. A. & Perez-Reche, F. J. (2010) Modelling fungal colonies and communities. . . p. 155-159. .
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Information visualization and the arts-science-social science interface

Bown, J. L., Fee, K., Sampson, A. T., Shovman, M., Falconer, R. E., Goltsov, A., Issacs, J. P., Robertson, P., Scott-Brown, K. C. & Szymkowiak, A. (2010) Information visualization and the arts-science-social science interface. In: Proceeding of the First International Conference on Intelligent Interactive Technologies and Multimedia: IITM 10. . p. 9-17. . Association for Computing Machinery (ACM).
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2009

Changing the view

Shovman, M., Szymkowiak, A., Bown, J. L. & Scott-Brown, K. C. (2009) Changing the view. In: Proceedings: Information Visualisation IV 2009. Banissi, E. (ed.), Stuart, L. (ed.), Wyeld, T. (ed.), Jern, M. (ed.), Andrienko, G. (ed.), Memon, N. (ed.), Alhajj, R. (ed.), Burkhard, R. (ed.), Grinstein, G. (ed.), Groth, D. (ed.), Ursyn, A. (ed.), Johansson, J. (ed.), Forsell, C. (ed.), Cvek, U. (ed.), Trutschl, M. (ed.), Marchese, F. (ed.), Maple, C. (ed.), Cowell, A. (ed.), Moere, A. (ed.). p. 135-138. Los Alamitos, CA: IEEE .
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A novel ataxia-telangiectasia mutated autoregulatory feedback mechanism in murine embryonic stem cells

Clyde, R. G., Craig, A. L., Breed, L. d., Bown, J. L., Forrester, L., Vojtesek, B., Smith, G., Hupp, T. R. & Crawford, J. W. (2009) A novel ataxia-telangiectasia mutated autoregulatory feedback mechanism in murine embryonic stem cells. . . p. 1167-1177. .
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2008

Use of 'pop-out' paradigm to test graph comprehension in a three-dimensional scatter plot

Shovman, M., Scott-Brown, K. C., Szymkowiak, A. & Bown, J. L. (2008) Use of 'pop-out' paradigm to test graph comprehension in a three-dimensional scatter plot. . . p. 79-80. .
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Modelling interactions in fungi

Falconer, R. E., Bown, J. L., White, N. A. & Crawford, J. W. (2008) Modelling interactions in fungi. . . p. 603-615. .
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Dynamic emotional expression choreography

Sloan, R. J. S., Robinson, B., Cook, M. & Bown, J. L. (2008) Dynamic emotional expression choreography. In: Inaugural SAND Academic Peer Reviewed Papers. Capey, M. (ed.), Ip, B. (ed.), Blastland, F. (ed.). Swansea: Swansea Metropolitan University.
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A new paradigm for SpeckNets

Falconer, R. E., Bown, J. L., Hart, E. & Timmis, J. (2008) A new paradigm for SpeckNets. In: Proceedings of the Second IEEE International Conference on Self-Adaptive and Self-Organizing Systems Workshops. Di Marzo Serugendo, G. (ed.), Gleizes, M. (ed.). p. 90-95. Piscataway, NJ: IEEE .
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2007

Biomass recycling

Falconer, R. E., Bown, J. L., White, N. A. & Crawford, J. W. (2007) Biomass recycling. . . p. 1558-1568. .
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Consequences of intraspecific variation for the structure and function of ecological communities

Bown, J. L., Pachepsky, E., Eberst, A., Bausenwein, U., Millard, P., Squire, G. R. & Crawford, J. W. (2007) Consequences of intraspecific variation for the structure and function of ecological communities. . . p. 264-276. .
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Consequences of intraspecific variation for the structure and function of ecological communities Part 2:

Pachepsky, E., Bown, J. L., Eberst, A., Bausenwein, U., Millard, P., Squire, G. R. & Crawford, J. W. (2007) Consequences of intraspecific variation for the structure and function of ecological communities Part 2:. . . p. 277-285. .
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2006

The role of modelling in identifying drug targets for diseases of the cell cycle

Clyde, R. G., Bown, J. L., Hupp, T. R., Zhelev, N. & Crawford, J. W. (2006) The role of modelling in identifying drug targets for diseases of the cell cycle. . . p. 617-627. .
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2005

Biomass recycling and the origin of phenotype in fungal mycelia

Falconer, R. E., Bown, J. L., White, N. A. & Crawford, J. W. (2005) Biomass recycling and the origin of phenotype in fungal mycelia. . . p. 1727-1734. .
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2002

The effects of fungal inoculum arrangement (scale and context) on emergent community development in an agar model system

Sturrock, C. J., Ritz, K., Samson, W. B., Bown, J. L., Staines, H. J., Palfreyman, J. W., Crawford, J. W. & White, N. A. (2002) The effects of fungal inoculum arrangement (scale and context) on emergent community development in an agar model system. . . p. 9-16. .
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2001

Towards a general theory of biodiversity

Pachepsky, E., Crawford, J. W., Bown, J. L. & Squire, G. (2001) Towards a general theory of biodiversity. . . p. 923-926. .
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1999

Evidence for emergent behaviour in the community-scale dynamics of a fungal microcosm

Bown, J. L., Sturrock, C. J., Samson, W. B., Staines, H. J., Palfreyman, J. W., White, N. A., Ritz, K. & Crawford, J. W. (1999) Evidence for emergent behaviour in the community-scale dynamics of a fungal microcosm. . . p. 1947-1952. .
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1998

Interspecific fungal interactions in spatially heterogeneous systems

White, N. A., Sturrock, C. J., Ritz, K., Samson, W. B., Bown, J. L., Staines, H. J., Palfreyman, J. W. & Crawford, J. W. (1998) Interspecific fungal interactions in spatially heterogeneous systems. . . p. 21-32. .
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More Information

Esteem

Esteem

Visiting Fellow, Department of Computer Science, University of York, 2011-

External examiner, Media School, Bournemouth University, 2011-

QAA Scotland Enhancement Theme for Research-Teaching linkages. Institutional Contact, 2007

Meet the rest of the team

Mr Grant Clarke

Mr Grant Clarke

Division of Games Technology and Mathematics | Lecturer

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Dr Kean Lee Kang

Dr Kean Lee Kang

Division of Games Technology and Mathematics | Lecturer

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