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Publications: 2002

Theoretical Biology / Bioinformatics Group, Utrecht University

Beltman J.B., Borghans J.A.M. & De Boer R.J. (2002).
Major histocompatibility complex: Polymorphism from coevolution.
In: Dieckmann U., Metz H., Sabelis M. & Sigmund K., eds., Adaptive Dynamics of Infectious Diseases. In Pursuit of Virulence Management, vol. 2 of Cambridge Studies in Adaptive Dynamics, pp. 185-197. Cambridge University Press, Cambridge, U.K.

Bernus O., Van Eyck B., Verschelde H. & Panfilov A.V. ( 2002a).
Transition from ventricular fibrillation to ventricular tachycardia: a simulation study on the role of Ca(2+)-channel blockers in human ventricular tissue.
Phys. Med. Biol., 47: 4167-4179. MEDLINE.

Bernus O., Verschelde H. & Panfilov A.V. (2002b).
Modified ionic models of cardiac tissue for efficient large scale computations.
Phys. Med. Biol., 47: 1947-1959. MEDLINE.

Bernus O., Wilders R., Zemlin C.W., Verschelde H. & Panfilov A.V. ( 2002c).
A computationally efficient electrophysiological model of human ventricular cells.
Am. J. Physiol. Heart Circ. Physiol., 282: H2296-H2308. MEDLINE. DownLoad PDF.

Bonhoeffer S., Barbour A.D. & De Boer R.J. (2002).
Procedures for reliable estimation of viral fitness from time-series data.
Proc. R. Soc. Lond. B. Biol. Sci., 269: 1887-1893. MEDLINE. DownLoad PDF.

Borghans J.A. & De Boer R.J. (2002).
Memorizing innate instructions requires a sufficiently specific adaptive immune system.
Int. Immunol., 14: 525-532. MEDLINE. DownLoad PDF.

Cohen Stuart J., Hamann D., Borleffs J., Roos M., Miedema F., Boucher C. & De Boer R. (2002).
Reconstitution of naive T cells during antiretroviral treatment of HIV-infected adults is dependent on age.
AIDS, 16: 2263-2266. MEDLINE. DownLoad PDF.

De Boer R.J. (2002).
Mathematical models of human CD4+ T-cell population kinetics.
Neth. J. Med., 60S: 17-26. MEDLINE.

Groenenboom M.A.C. & Hogeweg P. (2002).
Space and the persistence of male-killing endosymbionts in insect populations.
Proc. R. Soc. Lond. B. Biol. Sci., 269: 2509-2518. MEDLINE. DownLoad PDF.

Hogeweg P. (2002a).
Computing an organism: on the interface between informatic and dynamic processes.
Biosystems, 64: 97-109. MEDLINE. DownLoad PDF.

Hogeweg P. (2002b).
Multilevel evolution: The fate of duplicated genes.
Z. Phys. Chem., 216: 77-90. DownLoad PDF.

Hogeweg P. (2002c).
Multilevel processes in evolution and development: computational models and biological insights.
In: Lässig M. & Valleriani A., eds., Biological Evolution and Statistical Physics, Springer lecture notes in physics 585, pp. 217-239. Springer Verlag. DownLoad PDF.

Jensen L.J., Gupta R., Blom N., Devos D., Tamames J., Kesmir C., Nielsen H., Staerfeldt H.H., Rapacki K., Workman C., Andersen C.A., Knudsen S., Krogh A., Valencia A. & Brunak S. (2002).
Prediction of human protein function from post-translational modifications and localization features.
J Mol Biol., 319: 1257-1265. MEDLINE. DownLoad PDF.

Kesmir C., Nussbaum A.K., Schild H., Detours V. & Brunak S. ( 2002).
Prediction of proteasome cleavage motifs by neural networks.
Protein Eng., 15: 287-296. MEDLINE. DownLoad PDF.

Lund O., Nielsen M., Kesmir C., Christensen J.K., Lundegaard C., Worning P. & Brunak S. (2002).
Web-based Tools for Vaccine Design.
In: Korber B.T., Brander C., Haynes B.F., Koup R., Kuiken C., Moore J.P., Walker B.D. & Watkins D., eds., HIV Molecular Immunology 2002, pp. 45-51. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, LA-UR 03-5816. Weblink. DownLoad PDF.

Marée A.F.M. & Hogeweg P. (2002).
Modelling Dictyostelium discoideum morphogenesis: the culmination.
Bull. Math. Biol., 64: 327-353. MEDLINE. DownLoad PDF.

Panfilov A.V. (2002).
Spiral breakup in an array of coupled cells: The role of the intercellular conductance.
Phys. Rev. Lett., 88: 118101. MEDLINE. DownLoad PDF.

Panfilov A.V. & Zemlin C.W. (2002).
Wave propagation in an excitable medium with a negatively sloped restitution curve.
Chaos, 12: 800-806. MEDLINE.

Rusakov A.V., Aliev A.A., Panfilov A.V. & Medvinskii A.B. (2002).
Instability of a three-dimnsional linear vortex in a simple model of a heterogeneous excitable medium.
Biofizika, 47: 111-115. MEDLINE.

Sørensen H.A., Sperotto M.M., Petersen M., Kesmir C., Radzikowski L., Jacobsen S. & Søndergaard I. (2002).
Variety identification of wheat using mass spectrometry with neural networks and the influence of mass spectra processing prior to neural network analysis.
Rapid. Commun. Mass. Spectrom., 16: 1232-1237. MEDLINE. DownLoad PDF.

Yusim K., Kesmir C., Gaschen B., Addo M.M., Altfeld M., Brunak S., Chigaev A., Detours V. & Korber B.T. (2002).
Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation.
J Virol., 76: 8757-8768. MEDLINE. DownLoad PDF.