Publications: Theoretical Biology / Bioinformatics Group, Utrecht University 2003

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Publications: 2003

Theoretical Biology / Bioinformatics Group, Utrecht University

Bernus O., Verschelde H. & Panfilov A.V. (2003a).: Reentry in an anatomical model of the human ventricles.
Int. J. of Bifurcation and Chaos, 13: 3693-3702.
Bernus O., Verschelde H. & Panfilov A.V. (2003b).: Spiral wave stability in cardiac tissue with biphasic restitution.
Phys Rev E Stat Nonlin Soft Matter Phys., 68: 021917. MEDLINE. DownLoad PDF.
Borghans J.A.M., Noest A.J. & De Boer R.J. (2003).: Thymic selection does not limit the individual MHC diversity.
Eur. J. Immunol., 33: 3353-3358. MEDLINE. DownLoad PDF.
Buus S., Lauemoller S.L., Worning P., Kesmir C., Frimurer T., Corbet S., Fomsgaard A., Hilden J., Holm A. & Brunak S. (2003).: Sensitive quantitative predictions of peptide-mhc binding by a 'query by committee' artificial neural network approach.
Tissue Antigens., 62: 378-384. MEDLINE. DownLoad PDF.
Carcelain G., Saint-Mezard P., Altes H.K., Tubiana R., Grenot P., Rabian C., De Boer R., Costagliola D., Katlama C., Debre P. & Autran B. ( 2003).: IL-2 therapy and thymic production of naive CD4 T cells in HIV-infected patients with severe CD4 lymphopenia.
AIDS, 17: 841-850. MEDLINE. DownLoad PDF.
De Boer R.J., Homann D. & Perelson A.S. (2003a).: Different dynamics of CD4(+) and CD8(+) T cell responses during and after acute lymphocytic choriomeningitis virus infection.
J. Immunol., 171: 3928-3935. MEDLINE. DownLoad PDF.
De Boer R.J., Mohri H., Ho D.D. & Perelson A.S. ( 2003b).: Estimating average cellular turnover from BrdU measurements.
Proc. R. Soc. Lond., B, Biol. Sci., 270: 849-858. MEDLINE. DownLoad PDF.
De Boer R.J., Mohri H., Ho D.D. & Perelson A.S. ( 2003c).: Turnover rates of B cells, T cells, and NK cells in simian immunodeficiency virus-infected and uninfected rhesus macaques.
J. Immunol., 170: 2479-2487. MEDLINE. DownLoad PDF.
Dutilh B. & De Boer R.J. (2003).: Decline in excision circles is no evidence for homeostatic renewal of naive T cells.
J. theor. Biol., 224: 351-358. MEDLINE. DownLoad PDF.
Hazenberg M.D., Borghans J.A., De Boer R.J. & Miedema F. ( 2003a).: Thymic output: a bad TREC record.
Nat. Immunol., 4: 97-99. MEDLINE. DownLoad PDF.
Hazenberg M.D., Otto S.A., Hamann D., Roos M.T., Schuitemaker H., De Boer R.J. & Miedema F. (2003b).: Depletion of naive CD4 T cells by CXCR4-using HIV-1 variants occurs mainly through increased T-cell death and activation.
AIDS, 17: 1419-1424. MEDLINE. DownLoad PDF.
Hogeweg P. (2003).: Computing an organism: on the interface between informatic and dynamic processes.
In: Kumar S. & Bentley J., eds., On Growth, Form and Computers, p. 444. Elsevier.
Hogeweg P. & Takeuchi N. (2003).: Multilevel selection in models of prebiotic evolution: compartments and spatial self-organization.
Orig Life Evol Biosph., 33: 375-403. MEDLINE. DownLoad PDF.
Kesmir C. & De Boer R.J. (2003a).: Clonal exhaustion as a result of immune deviation.
Bull. Math. Biol., 65: 359-374. MEDLINE. DownLoad PDF.
Kesmir C. & De Boer R.J. (2003b).: A spatial model of germinal center reactions: cellular adhesion based sorting of b cells results in efficient affinity maturation.
J. theor. Biol., 222: 9-22. MEDLINE. DownLoad PDF.
Kesmir C., Van Noort V., De Boer R.J. & Hogeweg P. (2003).: Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome.
Immunogenetics., 55: 437-449. MEDLINE. DownLoad PDF.
Korthals Altes H.K., Ribeiro R.M. & De Boer R.J. (2003).: The race between initial T helper expansion and virus growth upon HIV infection influences polyclonality of the response and viral setpoint.
Proc. R. Soc. Lond., B, Biol. Sci., 270: 1349-1358. MEDLINE. DownLoad PDF.
Medvinskii A.B., Rusakov A.V., Moskalenko A.V., Fedorov M.V. & Panfilov A.V. (2003).: The study of autowave mechanisms of electrocardiogram variability during high frequency arrhythmias: mathematical modeling data.
Biofizika, 48: 314-323. MEDLINE.
Saxova P., Buus S., Brunak S. & Kesmir C. (2003).: Predicting proteasomal cleavage sites: a comparison of available methods.
Int Immunol., 15: 781-787. MEDLINE. DownLoad PDF.
Ten Tusscher K.H. & Panfilov A.V. (2003a).: Influence of nonexcitable cells on spiral breakup in two-dimensional and three-dimensional excitable media.
Phys Rev E Stat Nonlin Soft Matter Phys., 68: 062902. MEDLINE. DownLoad PDF.
Ten Tusscher K.H. & Panfilov A.V. (2003b).: Reentry in heterogeneous cardiac tissue described by the luo-rudy ventricular action potential model.
Am.J.Physiol., 284: H542-H548. MEDLINE. DownLoad PDF.