Publications related
to Systems Biology
1.
A. Degasperi, M. Calder.
A Process Algebra Framework for Multi-Scale Modelling of Biological Systems.
Theoretical
Computer Science, Elsevier, vol. 488, pp. 15--45, 2013. http://dx.doi.org/10.1016/j.tcs.2013.03.018
2.
M. Calder, R. Donaldson.
Modular modelling of signalling pathways and their crosstalk.
Theoretical
Computer Science, Volume 456, pp. 30-50, October 2012.http://dx.doi.org/10.1016/j.tcs.2012.07.003
3.
O. Andrei, M. Calder.
Trend-based Analysis of a Population Model of the AKAP Scaffold Protein.
Transactions
on Computational Systems Biology XIV, LNBI vol. 7625, pp. 1--25, Springer, 2012.
4.
A. Degasperi, M. Calder.
Multi-Scale Modelling of Biological Systems in Process Algebra with Multi-way
Synchronisation.
Proceedings 9th International CMSB
2011 (International Computational Systems Biology), Paris, France. isbn 978-1-4503-0817-5, 2011.
5.
R. Donaldson, C. Talcott, M. Knapp, M. Calder.
Understanding Signalling Networks as
Collections of Signal Transduction Pathways
Proceedings of 8th International CMSB (Computational Methods in
Systems Biology), ACM, 2010. http://portal.acm.org/citation.cfm?id=1839764\&picked=prox2010
6.
O. Sturm, R. Orton, J Grindlay,
M. Birtwistle V. Vyshemirsky,
D. Gilbert, M. Calder, A. Pitt, B. Kholodenko, W. Kolch
The mammalian MAPK/ERK pathway exhibits properties of a negative feedback
amplifier
Science signaling 3 (153) 2010
7.
O. Andrei
and M. Calder.A Model and Analysis of the AKAP Scaffold
A Model
and Analysis of the AKAP Scaffold.
CS2Bio2010, ENTCS 268, pages 3-15, Elsevier, 2010
8.
A. Degasperi,
M. Calder.
Process
Algebra with Hooks for Models of Pattern Formation.
CS2Bio2010, ENTCS 268, pages 31-47, Elsevier, 2010
9.
R. Donaldson, M. Calder.
Modelling and and Analysis of Biochemical Signalling
Pathway Crosstalk.
FBTC
2010, ENTCS 118, pp. 01-15,
Elsevier, 2010.
10. M. Calder, J. Hillston.
Process algebra modelling styles for biomolecular processes.
Transactions
on Computational Systems Biology XI, LNBI 5750, pp.1-25,
Springer, 2009.
11. M. Calder, S. Gilmore, J. Hillston and V. Vyshemirsky
Formal methods for biochemical signalling pathways
Formal Methods: State of the Art and New Directions, Springer, 2009.
12. F. Ciochetta, A. Degasperi, J. Hillston, M.
Calder.
Some investigations concerning the CTMC and the ODE model derived from
Bio-PEPA
Proceedings of
FBTC 2008, ENTCS vol. 17350,
Elsevier, 2008.
13. M. Calder, S. Gilmore (Editors)
Computational Methods for Systems Biology
Theoretical
Computer Science, volume 408, Elsevier, 2008.
14. M. Calder, S. Gilmore (Editors)
Computational Methods for Systems Biology Lecture Notes in
Bioinformatics, volume 4695, Springer, 2007.
15.
M. Calder, S. Gilmore and
J. Hillston
Modelling the influence of RKIP on the ERK signalling pathway using the
stochastic process algebra PEPA
Transactions
on Computational Systems Biology VII, vol. 4230, pp. 1-23, Springer, 2006.
16. M. Calder, A. Duguid, S. Gilmore and J.
Hillston.
Stronger computational modelling of signalling pathways using both continuous
and discrete-space methods
Computational
Methods in Systems Biology (CMSB 2006), LNBI vol. 421, pp. 63-78, 2006.
17. M. Calder, V. Vyshemirsky, D. Gilbert, and R.
Orton.
Analysis of Signalling Pathways using Continuous Time Markov Chains
Transactions
on Computational Systems Biology VI, vol. 4220, pp. 44-67, Springer, 2006.
18. M. Calder and J. Hillston
What do scaffold proteins really do?
Fifth
Workshop on Process Algebra and Stochastically Timed Activities (PASTA 2006),
Imperial College, 2006.
19. M. Calder, S. Gilmore and J. Hillston.
Automatically deriving ODEs from process algebra models of signalling
pathways
Proceedings
of CMSB 2005 (Computational Methods in Systems Biology), pp 204-215, 2005.
20. M. Calder, V. Vyshemirsky, D. Gilbert and R.
Orton.
Analysis of Signalling Pathways using the Prism Model
Checker
Proceedings of CMSB 2005 (Computational Methods in Systems Biology), pp 179-190, 2005.
21. W. Kolch, M. Calder and D. Gilbert.
When kinases meet mathematics: the systems biology of MAPK signalling
FEBS Letters, vol. 579, pp 1891--1895,
2005.
22. R.
Orton, O. Sturm, V. Vyshemirsky, M. Calder, D. Gilbert and W. Kolch.
Computational Modelling of the Receptor Tyrosine Kinase Activated MAPK
Pathway
Biochemical Journal, vol. 392, pp 249--261,
2005.
23. M. Calder, S. Gilmore and J. Hillston.
Modelling the influence of RKIP on the ERK signalling
pathway using the stochastic process algebra PEPA
Proceedings
of Bio-CONCUR 2004, Electronic Notes in Theoretical Computer Science, 2004.