References

This project builds upon the following track record.

  1. R Breitling, D Gilbert, M Heiner, R Orton:
    A structured approach for the engineering of biochemical network models, illustrated for signalling pathways;
    Brief. in Bioinformatics 9: 404-421 (2008). [ doi ]
  2. R Breitling, R Donaldson, D Gilbert, M Heiner:
    BioModel Engineering - From Structure to Behavior;
    Trans. on Computational Systems Biology XII, Special Issue on Modeling Methodologies, Springer LNCS/LNBI, Vol. 5945, 1-12 (2010). [ doi ]
  3. R Donaldson, D Gilbert:
    A model checking approach to the parameter estimation of biochemical pathways;
    Proc. CMSB, Springer LNCS/LNBI, Vol. 5307, 269–287 (2008).
  4. D Gilbert, D Westhead, N Nagano, J Thornton:
    Motif-based searching in TOPS protein topology databases;
    Bioinformatics 15(4) 317-326 (1999).
  5. D Gilbert, H Fuß, X, R Orton, S Robinson, V Vyshemirsky, M Kurth, C Downes, W Dubitzky:
    Computational Method- ologies for Modelling, Analysis and Simulation of Signalling Networks;
    Briefings in Bioinformatics 7(4):339-353 (2006).
  6. D Gilbert, M Heiner:
    From Petri Nets to Differential Equations - an Integrative Approach for Biochemical Network Analysis;
    Proc. ICATPN, Springer LNCS, Vol. 4024, 181-200 (2006). [ link ]
  7. D Gilbert, M Heiner, S Lehrack:
    A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets;
    Proc. CMSB, Springer LNCS/LNBI, Vol. 4695, 200-216 (2007). [ link ]
  8. D Gilbert, M Heiner, S Rosser, R Fulton, X Gu, M Trybilo:
    A Case Study in Model-driven Synthetic Biology;
    Proc. IFIP WCC/BICC, Springer Boston, IFIP, Vol. 268, 163-175 (2008). [ link ]
  9. D Gilbert, R Breitling, M Heiner, R Donaldson:
    An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways;
    Proc. WMC 2008, Springer LNCS, Vol. 5391, 13-28 (2009).
  10. D Gilbert, M Heiner, R Breitling, R Orton:
    Computational modelling of kinase signalling cascades;
    in R Seger (Ed.): MAP Kinase Signaling Protocols, 2nd Edition; Methods in Molecular Biology, Vol. 661, Part 4, Chapter 22, 369-384 (2010).
  11. M Heiner:
    Petri Net Based Software Validation - Prospects and Limitations;
    ICSI Berkeley, TR-92-022 (1992).
  12. M Heiner, G Ventre, D Wikarski:
    A Petri Net Based Methodology to Integrate Qualitative and Quantitative Analysis;
    J. Information and Software Technology 36(7), 435-441 (1994).
  13. M Heiner, P Deussen, S Spranger:
    A Case Study in Design and Verification of Manufacturing Systems with Hierarchical Petri Nets;
    J. Advanced Manufacturing Technology, 15, 139-152 (1999).
  14. M Heiner, I Koch, K Voss:
    Analysis and Simulation of Steady States in Metabolic Pathways with Petri Nets;
    Proc. CPN Workshop, Univ. of Aarhus, 15-34 (2001).
  15. M Heiner, I Koch:
    Petri Net Based System Validation in Systems Biology;
    Proc. ICATPN, Springer LNCS, Vol. 3099, 216-237 (2004). [ link ]
  16. M. Heiner, D. Gilbert, R. Donaldson:
    Petri Nets for Systems and Synthetic Biology;
    Schools on Formal Methods (SFM), Springer LNCS, Vol. 5016, 215-264 (2008). [ link ]
  17. M Heiner:
    Understanding Network Behaviour by Structured Representations of Transition Invariants - A Petri Net Perspective on Systems and Synthetic Biology;
    Algorithmic Bioprocesses; Springer, Natural Computing Series, 367-389 [ link ]
  18. M. Heiner, S. Lehrack, D. Gilbert, W. Marwan:
    Extended Stochastic Petri Nets for Model-based Design of Wetlab Experiments;
    Trans. on Computational Systems Biology XI, Springer LNCS/LNBI, Vol. 5750, 138-163 (2009). [ link ]
  19. M Heiner, M Schwarick, A Tovchigrechko:
    DSSZ-MC - A Tool for Symbolic Analysis of Extended Petri Nets;
    Proc. PETRI NETS 2009, Springer LNCS, Vol. 5606, 323-332 (2009). [ link ]
  20. M Heiner, K Sriram:
    Structural Analysis to Determine the Core of Hypoxia Response Network;
    PLoS ONE 5(1): e8600 (2010). [ doi ]
  21. M Heiner, R Donaldson, D Gilbert:
    Petri Nets for Systems Biology;
    in MS Iyengar (Ed.): Symbolic Systems Biology: Theory and Methods, Jones & Bartlett Learning, Chapter 3, 61-97 (2010). [ link ]
  22. M Heiner, C Mahulea, M Silva:
    On the Importance of the Deadlock Trap Property for Monotonic Liveness;
    Proc. Workshop BioPPN 2010, satellite event of Petri Nets 2010, 39-54 (2010). [ pdf ]
  23. M Heiner, C Rohr, M Schwarick, S Streif:
    A Comparative Study of Stochastic Analysis Techniques;
    Proc. CMSB 2010, ACM digital library, 96-106 (2010). [ doi ]
  24. X Liu, JJiang, O Ajayi, X Gu, D Gilbert:
    BioNessie(G) – a GRID enabled biochemical networks simulation environment;
    Studies in Health Technology and Informatics, 138:147-157 (2008).
  25. F Liu, M Heiner:
    Coloured Petri nets to model and simulate biological systems;
    Proc. Workshop BioPPN 2010, satellite event of Petri Nets 2010, 70-84 (2010). [ pdf ]
  26. W Marwan, C Rohr, M Heiner:
    Petri nets in Snoopy: A unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks;
    in Jv Helden, A Toussaint, D Thieffry (Eds): Methods in Molecular Biology - Bacterial Molecular Networks, Humana Press, Chapter 21. [ link ]
  27. I Michalopoulos, G Torrance, D Gilbert, D Westhead:
    TOPS: an enhanced database of protein structural topology;
    Nucleic Acids Research, 32, D251-D254 (2003).
  28. R Orton, O Sturm, V Vyshemirsky, M Calder, D Gilbert, W Kolch:
    Computational Modelling of the Tyrosine Receptor Kinase Activated MAPK Pathway;
    Biochemical Journal 392 249-261 (2005).
  29. R Orton, M Adriaens, A Gormand, O Sturm, W Kolch, D Gilbert:
    Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway;
    BMC Systems Biology 3(100), 2009.
  30. L Popova-Zeugmann, M Heiner, I Koch:
    Time Petri Nets for Modelling and Analysis of Biochemical Networks;
    Fundamenta Informaticae 67, 149-16 (2005). [ link ]
  31. L Popova, M Heiner:
    Quantitative Evaluation of Time Petri Nets and Applications to Technical and Biochemical Networks;
    Proc. CS&P, vol. 2, 473-484 (2007).
  32. C Rohr, W Marwan, M Heiner:
    Snoopy - a unifying Petri net framework to investigate biomolecular networks;
    Bioinformatics 26(7): 974-975 (2010). [ link ]
  33. M Schwarick, M Heiner:
    CSL Model Checking of Biochemical Networks with Interval Decision Diagrams;
    Proc. CMSB, Springer LNCS/LNBI, Vol. 5688, 296-312 (2009). [ link ]
  34. S Soliman and M Heiner:
    A Unique Transformation from Ordinary Differential Equations to Reaction Networks;
    PLoS ONE, 5(12):e14284, 2010. [ doi ]
  35. J van Helden, A Naim, R Mancuso, M Eldridge, L Wernisch, D Gilbert, S Wodak:
    Representing and analysing molecular and cellular function in the computer;
    J. Biological Chemistry 381(9-10) 921-935 (2000).
  36. J van Helden, L Wernisch, D Gilbert, S Wodak:
    Graph-based analysis of metabolic networks;
    Bioinformatics and Genome Analysis, Ernst Schering Research Foundation Workshop Vol. 38, 245-274 (2002).
  37. K Voss, M Heiner, I Koch:
    Steady State Analysis of Metabolic Pathways Using Petri Nets;
    In Silico Biology 3, 0031 (2003). [ link ]
  38. A Williams, D Gilbert, D Westhead:
    Multiple structural alignment for distantly related all beta structures using TOPS pattern discovery and simulated annealing;
    Protein Engineering 16(12), 913-923 (2003).
  39. Z Wu, Q Gao, D Gilbert:
    Target driven biochemical network reconstruction based on Petri nets and simulated annealing;
    Proc. CMSB 2010, ACM digital library, 33-42 (2010).

latest update: December 12, 2011, at 10:03 AM