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. 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

7.          A. Degasperi, M. Calder.
Process Algebra with Hooks for Models of Pattern Formation.
CS2Bio2010, ENTCS 268, pages 31-47, Elsevier, 2010

8.         R. Donaldson, M. Calder.
Modelling and and Analysis of Biochemical Signalling Pathway Crosstalk.
FBTC 2010, ENTCS 118, pp. 01-15, Elsevier, 2010.

9.         M. Calder, J. Hillston.
Process algebra modelling styles for biomolecular processes.
Transactions on Computational Systems Biology XI, LNBI 5750, pp.1-25, Springer, 2009.

10.      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.

11.      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.

12.      M. Calder, S. Gilmore (Editors)
Computational Methods for Systems Biology

Theoretical Computer Science, volume 408, Elsevier, 2008.

13.      M. Calder, S. Gilmore (Editors)
Computational Methods for Systems Biology
Lecture Notes in Bioinformatics, volume 4695, Springer, 2007.

14.      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.

15.      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.

16.      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.

17.      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.

18.      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.

19.      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.

20.      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.

21.      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.

22.      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.