List of publications

  1. Markov-modulated infinite-server queues: approximations by time-scaling,
    Ton Hellings, Michel Mandjes and Joke Blom
    CWI Report MAC-1101
  2. Traffic generated by a semi-Markov additive process,
    Joke Blom and Michel Mandjes
    Probability in the Engineering and Informational Sciences, 25.1 (2011)
    Revised version of CWI Report PNA-E0913
  3. Gene Circuit Analysis of the Terminal Gap Gene huckebein,
    Maksat Ashyraliyev, Ken Siggens, Hilde Janssens, Joke Blom, Michael Akam, Johannes Jaeger
    PLOS Computational Biology, doi/10.1371/journal.pcbi.1000548 (October 2009)
  4. Systems biology: parameter estimation for biochemical models,
    Maksat Ashyraliyev, Yves Fomekong-Nanfack, Jaap A. Kaandorp, Joke G. Blom
    FEBS Journal, 276:886-902 (2009)
  5. On Parameter Estimation and Determinability for Drosophila Gap Gene Circuits,
    Maksat Ashyraliyev, Johannes Jaeger and Joke G. Blom
    BMC Systems Biology, 2:83 (2008)
  6. Modelling genetic regulation of growth and form in a branching sponge,
    Jaap A. Kaandorp, Joke G. Blom, Jozef Verhoef, Max Filatov, M. Postma and Werner E.G. Mueller
    Proceedings of the Royal Society B, 275:1651:2569-2575 (2008)
  7. On parameter estimation and determinability for the model of pattern formation in Drosophila melanogaster,
    M. Ashyraliyev, J.G. Blom
    CWI Report MAS-E0802
  8. On the Numerical Solution of Diffusion-Reaction Equations with Singular Source Terms,
    M. Ashyraliyev, J.G. Blom, J.G. Verwer,
    J. Comp. Appl. Math, 216:1:20-38 (2008).
    Extended version of CWI Report MAS-E0512
  9. Efficient parameter estimation for spatio-temporal models of pattern formation: Case study of Drosophila melanogaster,
    Yves Fomekong-Nanfack, Jaap Kaandorp, and Joke Blom
    Bioinformatics, 23:24:3356--3363 (2007).
  10. Computational methods for diffusion-influenced biochemical reactions,
    Maciej Dobrzyński, Jordi Vidal Rodríguez, Jaap A. Kaandorp, and Joke G. Blom
    Bioinformatics, 23:15:1969--1977 (2007).
  11. Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli,
    Jordi Vidal Rodríguez, Jaap A. Kaandorp, Maciej Dobrzyński, and Joke G. Blom
    Bioinformatics, 22:15:1895--1901 (2006).
  12. On the Numerical Solution of Diffusion-Reaction Equations with Singular Source Terms,
    M. Ashyraliyev, J.G. Blom, J.G. Verwer,
    CWI Report MAS-E0512,
  13. Modelling Developmental Regulatory Networks,
    T. Krul, J.A. Kaandorp, and J.G. Blom,
    in: Computational Science - ICCS 2003, Pt IV, Proceedings.
    Lect. Notes. Comput. Sc. Vol. 2660: pp. 688-697, Springer, Berlin (2003). [ps | pdf]
  14. A continuum model of lipid bilayers,
    J.G. Blom and M.A. Peletier,
    European Jnl of Applied Mathematics, 15:4:487--508 (2004).
    CWI Report MAS-R0229.
  15. The importance of being cigar-shaped,
    J.G. Blom and M.A. Peletier,
    Report MAS-R0228, CWI, Amsterdam (2002).
  16. Why the Phosphotransferase System of Escherichia Coli Escapes the Diffusion Limitation of Signal Transduction, Transport and Metabolism that Confronts Mammalian Cells,
    Christof Francke, Pieter W. Postma, Hans V. Westerhoff, Joke G. Blom and Mark A. Peletier,
    Biophys. J. 85: 612-622 (2003). Revised version of CWI Report MAS-R0218
  17. Flux control of the bacterial phosphoenolpyruvate:glucose phosphotransferase system and the effect of diffusion.
    Christof Francke, Hans V. Westerhoff, Joke G. Blom and Mark A. Peletier,
    Mol. Biol. Rep. 29: 21-26 (2002).
    Paper presented at the 10-th BTK meeting, 7-10 september 2002, Bordeaux.
  18. Time Integration of the Shallow Water Equations in Spherical Geometry,
    D. Lanser, J.G. Blom and J.G. Verwer,
    J. Comp. Phys., V171, pp. 1-21 (2001).
    CWI Report MAS-R0021.
  19. Diffusive gradients in the PTS system,
    J.G. Blom and Mark A. Peletier,
    Report MAS-R0020, CWI, Amsterdam (2000).
  20. Spatial Discretization of the Shallow Water Equations in Spherical Geometry using Osher's Scheme,
    D. Lanser, J.G. Blom and J.G. Verwer,
    J. Comp. Phys., V165, #2, pp. 542-565 (2000).
    CWI Report MAS-R9918.
  21. A Comparison of Integration Methods for Atmospheric Transport-Chemistry Problems,
    J.G. Blom and J.G. Verwer,
    J. Comp. Appl. Math., V126, #1-2, pp. 381-396 (2000).
    CWI Report MAS-R9910.
  22. Numerical Time Integration for Air Pollution Models,
    J.G. Verwer, W. Hundsdorfer and J.G. Blom,
    Surveys on Mathematics for Industry, Vol. 10 nr. 2, (2002), 107-174.
    CWI Report MAS-R9825.
  23. HPCN and Air Quality Modeling,
    J.G. Blom, W.M. Lioen, J.G. Verwer,
    in: High Performance Computing and Networking. Proceedings of the International Conference and Exhibition. Amsterdam, the Netherlands, April 1998. Eds. Peter Sloot, Marian Bubak, Bob Hertzberger. LNCS 1401, Springer, Berlin, pp. 141-150 (1998).
    CWI Report MAS-R9801.
  24. A Second Order Rosenbrock Method Applied to Photochemical Dispersion Problems,
    J.G. Verwer, E.J. Spee, J.G. Blom, W. Hundsdorfer,
    SIAM J. Sci. Comput., Vol. 20, pp.1456-1480 (1999).
    CWI Report MAS-R9717.
  25. A Numerical Study for Global Atmospheric Transport-Chemistry Problems,
    E.J. Spee, J.G. Verwer, P.M. de Zeeuw, J.G. Blom, W. Hundsdorfer,
    Mathematics and Computers in Simulation, Vol. 48, pp. 177-204 (1998).
    CWI Report MAS-R9702.
  26. Description of the 3D LOTOS model. Part I: Dynamics,
    J.G. Blom, M.G.M. Roemer,
    Report MAS-N9701, CWI, Amsterdam (1997).
  27. Vectorization and Parallelization of a Numerical Scheme for 3D Global Atmospher ic Transport-Chemistry Problems,
    E.J. Spee, P.M. de Zeeuw, J.G. Verwer, J.G. Blom, W. Hundsdorfer,
    Report NM-R9620, CWI, Amsterdam (1996).
  28. Benchmarking Stiff ODE Solvers for Atmospheric Chemistry Problems II: Rosenbrock Solvers,
    A. Sandu, J.G. Verwer, J.G. Blom, E.J. Spee, and G.R. Carmichael
    Atmospheric Environment, Vol. 31, pp. 3459-3472 (1997).
    CWI Report NM-R9614.
  29. An Evaluation of the Cray T3D Programming Paradigms in Atmospheric Chemistry/Transport Models,
    J.G. Blom, Ch. Kessler and J.G. Verwer,
    Report NM-R9604, CWI, Amsterdam (1996).
  30. Experiences with Sparse Matrix Solvers in Parallel ODE Software,
    J.J.B. de Swart and J.G. Blom,
    Computers Math. Applic., Vol. 31, No. 9, pp. 43-55 (1996).
    CWI Report NM-R9520.
  31. Porting a 3D-model for the Transport of Reactive Air Pollutants to the Parallel Machine T3D,
    Ch. Kessler, J.G. Blom and J.G. Verwer,
    Report NM-R9519, CWI, Amsterdam (1995).
  32. On the Coupled Solution of Diffusion and Chemistry in Air Pollution Models,
    J.G. Verwer and J.G. Blom,
    in: Proceedings of the Third International Congress on Industrial and Applied Mathematics (ICIAM/GAMM 95), ZAMM, Issue 4: Applied Sciences, especially Mechanics (Minisymposia), eds. Edwin Kreuzer / Oskar Mahrenholtz, Akademie Verlag, pp. 454-457 (1996).
    CWI Report NM-R9509.
  33. A Comparison of Stiff ODE Solvers for Atmospheric Chemistry Problems,
    J.G. Verwer, J.G. Blom, M. van Loon and E.J. Spee,
    Atmospheric Environment, Vol. 30, pp. 49-58 (1996).
    CWI Report NM-R9505.
  34. An Implicit-Explicit Approach for Atmospheric Transport-Chemistry Problems,
    J.G. Verwer, J.G. Blom and W. Hundsdorfer,
    Applied Numerical Mathematics, Vol. 20, pp. 191-209 (1996).
    CWI Report NM-R9501.
  35. Vectorization Aspects of a Spherical Advection Scheme on a Reduced Grid,
    J.G. Blom, W. Hundsdorfer and J.G. Verwer,
    Report NM-R9418, CWI, Amsterdam (1994).
  36. Algorithm 758: VLUGR2: A Vectorizable Adaptive Grid Solver for PDEs in 2D,
    J.G. Blom, R.A. Trompert and J.G. Verwer,
    ACM Trans. Math. Softw., Vol. 22, pp. 302-328 (1996).
    CWI Report NM-R9403.
  37. VLUGR3: A Vectorizable Adaptive Grid Solver for PDEs in 3D. I. Algorithmic Aspects and Applications,
    J.G. Blom and J.G. Verwer,
    Appl. Numer. Math., Vol. 16, pp. 129-156 (1994).
    CWI Report NM-R9404.
  38. Algorithm 759: VLUGR3: A Vectorizable Adaptive Grid Solver for PDEs in 3D. II. Code Description,
    J.G. Blom and J.G. Verwer,
    ACM Trans. Math. Softw., Vol. 22, pp. 329-347 (1996).
    CWI Report NM-R9405.
  39. A Vectorizable Adaptive Grid Solver for PDEs in 3D,
    J.G. Blom, J.G. Verwer,
    Report NM-R9319, CWI, Amsterdam (1993).
  40. VLUGR2: A Vectorized Local Uniform Grid Refinement Code for PDEs in 2D,
    J.G. Blom, J.G. Verwer,
    Report NM-R9306, CWI, Amsterdam (1993).
  41. Vectorizing Matrix Operations arising from PDE Discretization on 9-Point Stencils,
    J.G. Blom, J.G. Verwer,
    The J. of Supercomputing, Vol. 8, pp.29-51 (1994).
    CWI Report NM-R9221.
  42. A comparison between direct and iterative methods to solve the linear systems arising from a time-dependent 2D groundwater flow model,
    J.G. Blom, J.G. Verwer, R.A. Trompert,
    Int. J. Comp. Fluid Dynamics, Vol. 1, pp.95-113 (1993).
    CWI Report NM-R9205.
  43. Computing brine transport in porous media with an adaptive-grid method,
    R.A. Trompert, J.G. Verwer, J.G. Blom,
    Int. J. Numer. Meth. in Fluids, Vol. 16. pp.43-63 (1993).
    CWI Report NM-R9201.
  44. A note on the grid movement induced by MFE,
    P.A. Zegeling, J.G. Blom,
    Int. J. for Numer. Meth. in Eng., Vol. 35, pp.623-636 (1992).
    CWI Report NM-R9019.
  45. An evaluation of the Gradient-Weighted Moving-Finite-Element Method in One Space Dimension,
    P.A. Zegeling, J.G. Blom,
    J. Comput. Physics, Vol. 103, pp.422-441 (1992).
    CWI Report NM-R9006.
  46. On the Use of the Arclength and Curvature Monitor in a Moving-Grid Method which is Based on the Method of Lines,
    J.G. Blom, J.G. Verwer,
    Report NM-N8902, CWI, Amsterdam (1989).
  47. Algorithm 731: A Moving-Grid Interface for Systems of One-Dimensional Time-Dependent Partial, Differential Equations
    J.G. Blom, P.A. Zegeling,
    ACM Trans. Math. Softw., Vol. 20, No. 2, (1994), pp. 194-214.
    CWI Report NM-R8904.
  48. A Moving-Grid Method for One-Dimensional PDEs based on the Method of Lines,
    J.G. Verwer, J.G. Blom, R.M. Furzeland, P.A. Zegeling,
    in: Adaptive Methods for Partial Differential Equations, eds. J.E. Flaherty, P.J. Paslow, M.S. Shephard and J.D. Vasilakis, SIAM, Philadelphia (1989), 160-175.
    CWI Report NM-R8818.
  49. An Adaptive Moving Grid Method for One-Dimensional Systems of Partial Differential Equations,
    J.G. Verwer, J.G. Blom, J.M. Sanz-Serna,
    J. Comput. Physics, Vol. 82, No. 2 (1989)
    CWI Report NM-R8804.
  50. A Lagrangian Moving Grid scheme for One-Dimensional Evolutionary Partial Differential Equations,
    J.G. Blom, J.M. Sanz-Serna, J.G. Verwer,
    in: Proceedings of the 12-th IMACS World Congress '88 on Scientific Computation, Paris, July 1988, Numerical and Applied Mathematics, ed. W.F. Ames, Vol. 1.1, IMACS (1989), pg. 247-255.
    CWI Report NM-R8713.
  51. On Simple Moving Grid Methods for One-Dimensional Evolutionary Partial Differential Equations,
    J.G. Blom, J.M. Sanz-Serna and J.G. Verwer,
    J. Comp. Phys., V74, #1, pp. 191-213 (1988).
    CWI Report NM-R8620.
  52. Algorithm 689, Discretized collocation and iterated collocation for nonlinear Volterra integral equations of the second kind,
    J.G. Blom and H. Brunner,
    ACM Trans. Math. Softw., V17, #2, pp. 167-177 (1991).
    CWI Report NM-R8618.
  53. The numerical solution of nonlinear Volterra integral equations of the second kind by collocation and iterated collocation methods,
    J.G. Blom and H. Brunner,
    SIAM J. Sci. Statist. Comput., V8, #5, pp. 806-830 (1987).
    CWI Report NM-R8522.
  54. Stability results for discrete Volterra equations: Numerical experiments,
    P.J. van der Houwen and J.G. Blom,
    in Constructive Methods for the Practical Treatment of Integral Equations, Edited by G. Ha\:mmerlin and K.-H. Hoffmann, ISNM73, Birkhau\:ser Verlag (1985), 166-178
    CWI Report NM-R8409.
  55. A class of Runge-Kutta-Rosenbrock method for solving stiff differential equations,
    J.G. Verwer, S. Scholz, J.G. Blom and M. Louter-Nool,
    ZAMM, Vol. 63, 13-20 (1983).
    MC Report NW 125/82.
  56. Order conditions for a class of Runge-Kutta-Rosenbrock methods,
    J.G. Blom,
    MC Report NN 25/82.
  57. Forced Prey-Predator oscillations,
    J.G. Blom, R. de Bruin, J. Grasman and J.G. Verwer,
    J. Math. Biology, Vol. 12, 141-152 (1981).
    MC Report TW 201/80.
  58. An ALGOL 68 implementation of Urabe's method for nonlinear periodic differential systems,
    J.G. Blom and J.G. Verwer,
    MC Report NN 20/79.
  59. On the numerical solution of Volterra integral equations of the second kind. II. Runge-Kutta methods,
    P.J. van der Houwen and J.G. Blom,
    MC Report NW 61/78.
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