Some recent papers


Agent-based modelling of biological systems


1.                How ants use geometry to find their way home, NATURE, VOL 432, 16 DECEMBER 2004


2.                How wounds in skin heal. Royal Society Interface Journal, (2007) 4, 1077–1092


3.                A detailed model of the NFkappa-B pathway in the mammalian immune system. Biosystems, Volume 85, Issue 1, July 2006


4.                The role of actin filaments in the NFkappa-B pathway PLOSOne 3(6): e2367 (2008)


5.                A survey of agent-based modelling using FLAME - Scientiae Mathematicae Japonicae Online, e-2006, 765–778


6.                        How ants use a negative signal to choose which way to go. NATURE, Vol 438, 24 November 2005


7.                Spatial and temporal variation in pheromone composition of ant foraging trails  BEHAVIORAL ECOLOGY 18 (2): 444-450 MAR-APR 2007


8.                An integrated agent-mathematical model of the effect of intercellular signalling via the epidermal growth factor receptor on cell proliferation  JOURNAL OF THEORETICAL BIOLOGY 242 (3): 774-789 OCT 7 2006


9.                        Longevity and detection of persistent foraging trails in Pharaoh's ants, Monomorium pharaonis (L.) ANIMAL BEHAVIOUR 71: 351-359 Part 2 FEB 2006


10.             Framework definition – EPITHELIOME project. This describes how to build biological models using the FLAME framework


11.             Validation and discovery from computational models – BioSystems Volume 93, Issues 1-2, July-August 2008, Pages 141-150


12.                    Agent Based Modelling Helps in Understanding the Rules by Which Fibroblasts Support Keratinocyte Colony

Formation,Tao Sun. Phil McMinn, Mike Holcombe, Rod Smallwood, Sheila MacNeil. PLOS-0ne    

13.            Introducing Spatial Information into Predictive NF-κB Modelling:An Agent-Based Approach Mark Pogson, Mike Holcombe, Rod Smallwood, Eva Qwarnstrom

14.            Development of a Three Dimensional Multiscale Computational Model of the Human Epidermis, Salem Adra, Tao Sun, Sheila MacNeil, Mike Holcombe, Rod Smallwood PLoS ONE

15.            NIK and IKK<beta>interdependence in NF-<kappa>B signalling - Flux analysis of regulation through metabolites, Hong-Bum Kim, Iona Evans, Rod Smallwood, Mike Holcombe and Eva E. Qwarnstrom, BioSystems, 99, February 2010, Pages 140-149

16.            Exploring Hypotheses of the Actions of TGF-β1 in Epidermal Wound Healing Using a 3D Computational Multiscale Model of the Human Epidermis, Salem Adra, Tao Sun, Sheila MacNeil, Mike Holcombe, Rod Smallwood, PLoS ONE 4(12): e8515. doi:10.1371/journal.pone.0008515

17.            Maleki-Dizaji S, Holcombe M, Rolfe MD, Fisher P, Green J, Poole RK, Graham AI, A Systematic Approach to Understanding Escherichia coli Responses to Oxygen: From Microarray Raw Data to Pathways and Published Abstracts, Online J Bioinformatics, (1):51-59, 2009.



Agent-based modelling of economic systems


1.                        Framework definition – EURACE project. This describes how to build economics models using the FLAME framework.


Software testing

1.          Automated Discovery of State Transitions and their Functions in Source Code,   Software Testing, Verification and Reliability (to appear vol. 18(2), 2008)


2.                        Reverse Engineering State Machines by Interactive Grammar Inference, 14th IEEE Working Conference on Reverse Engineering (WCRE'07)


3.                        Identifying State Transitions and their Functions in Source Code, 1st IEEE Testing Academia & Industrial Conference (TAIC PART'06), Windsor, August 2006

4.            X-machine testing. Formal Aspects of Computing (2006) 18: 3–30


5.                        Hybridizing evolutionary testing with the chaining approach. LECT NOTES COMPUT SC 3103: 1363-1374 2004


Empirical software engineering and agile development.


1.                        The Impact of an Agile Methodology on the Well Being of Development Teams. Empirical Software Engineering, 11(1), 143-167.


2.                        A Formal Experiment Comparing Extreme Programming with Traditional Software Construction. In the Proceedings of the Fourth Mexican International Conference on Computer Science (ENC 2003). Tlaxcala, Mιxico, 73-80. Sep. 8-12, 2003.


3.                         20 Years of Teaching and 7 Years of Research: Research When You Teach, SEEFM 07.


4.                        A Design Change Metric Derived From Extreme X-Machines, SEEFM 07



5.             Empirical investigation towards the effectiveness of Test First programming, Liang Huang *, Mike Holcombe, Information and Software Technology 51 (2009)



6.            A study into the effects of personality type and methodology on cohesion in

software engineering teams, J. S. Karn; S. Syed-Abdullah; A. J. Cowling; M. Holcombe, Behaviour & Information Technology,26:2,99 — 111