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Theoretical Biology & Bioinformatics

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PhD theses

Papers sorted by the year of publication:

2009

2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | Papers before 1999

Althaus C.L., De Vos A.S. & De Boer R.J. (2009).: Reassessing the human immunodeficiency virus type 1 life cycle through age-structured modeling: life span of infected cells, viral generation time, and basic reproductive number, R0.
J. Virol., 83: 7659-7667. DOI. MEDLINE. DownLoad PDF.
Beltman J.B., Henrickson S.E., Von Andrian U.H., De Boer R.J. & Maree A.F. (2009a).: Towards estimating the true duration of dendritic cell interactions with T cells.
J. Immunol. Methods, 347: 54-69. DOI. MEDLINE. DownLoad PDF.
Beltman J.B., Maree A.F. & De Boer R.J. (2009b).: Analysing immune cell migration.
Nat. Rev. Immunol., 9: 789-798. DOI. MEDLINE. DownLoad PDF.
Bernus O., Holden A.V. & Panfilov A.V. (2009).: Nonlinear waves in excitable media: Approaches to cardiac arrhythmias.
Physica D, 238: v-viii. DOI. DownLoad PDF.
Boersema P.J., Foong L.Y., Ding V.M., Lemeer S., Van Breukelen B., Philp R., Boekhorst J., Snel B., Den Hertog J., Choo A.B. & Heck A.J. ( 2009).: In depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immuno-affinity purification and stable isotope dimethyl labeling.
Mol Cell Proteomics., 0: O. DOI. MEDLINE. DownLoad PDF.
Cordero O.X. & Hogeweg P. (2009a).: The consequences of base pair composition biases for regulatory network organization in prokaryotes.
Mol. Biol. Evol., 26: 2171-2173. DOI. MEDLINE. DownLoad PDF.
Cordero O.X. & Hogeweg P. (2009b).: The impact of long-distance horizontal gene transfer on prokaryotic genome size.
Proc. Natl. Acad. Sci. U.S.A., 0: e0907584106. DOI. MEDLINE. DownLoad PDF.
Cordero O.X. & Hogeweg P. (2009c).: Regulome size in Prokaryotes: universality and lineage-specific variations.
Trends Genet., 25: 285-286. DOI. MEDLINE. DownLoad PDF.
Costa A.I., Rao X., Lechenadec E., Van Baarle D. & Kesmir C. ( 2009).: HLA-B molecules target more conserved regions of the HIV-1 proteome.
AIDS, 0: O. DOI. MEDLINE.
Crombach A. & Hogeweg P. (2009).: Evolution of resource cycling in ecosystems and individuals.
BMC. Evol. Biol., 9: 122. DOI. MEDLINE. DownLoad PDF.
Fokkens L. & Snel B. (2009).: Cohesive versus flexible evolution of functional modules in eukaryotes.
PLoS. Comput. Biol., 5: e1000276. DOI. MEDLINE. DownLoad PDF.
Grieneisen V.A. & Scheres B. (2009).: Back to the future: evolution of computational models in plant morphogenesis.
Curr Opin Plant Biol., 0: O. DOI. MEDLINE. DownLoad PDF.
Kamikawa R., Sanchez-Perez G.F., Sako Y., Roger A.J. & Inagaki Y. ( 2009).: Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes.
Mol. Phylogenet. Evol., 53: 565-570. DOI. MEDLINE. DownLoad PDF.
Keldermann R.H., Nash M.P. & Panfilov A.V. (2009a).: Modeling cardiac mechano-electrical feedback using reaction-diffusion-mechanics systems.
Physica D, 238: 1000-1007. DOI. DownLoad PDF.
Keldermann R.H., Ten Tusscher K.H., Nash M.P., Bradley C.P., Hren R., Taggart P. & Panfilov A.V. (2009b).: A computational study of mother rotor VF in the human ventricles.
Am. J. Physiol. Heart. Circ. Physiol., 296: H370-H379. DOI. MEDLINE. DownLoad PDF.
Marmottant P., Mgharbel A., Kafer J., Audren B., Rieu J.P., Vial J.C., Van der Sanden B., Maree A.F., Graner F. & Delanoe-Ayari H. (2009).: The role of fluctuations and stress on the effective viscosity of cell aggregates.
Proc. Natl. Acad. Sci. U.S.A., 106: 17271-17275. DOI. MEDLINE. DownLoad PDF.
Panfilov A. (2009).: Theory of reentry.
In: Zipes Ed D.P. & Jalife J., eds., Cardiac Electrophysiology: From Cell to Bedside, pp. 329-337. Elsevier, 5th edn.
Rao X., Costa A.I., Van Baarle D. & Kesmir C. (2009).: A comparative study of HLA binding affinity and ligand diversity: implications for generating immunodominant CD8 T cell responses.
J. Immunol., 182: 1526-1532. MEDLINE. DownLoad PDF.
Schmid B.V., Kesmir C. & De Boer R.J. (2009).: The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes.
BMC. Evol. Biol., 9: 184. DOI. MEDLINE. DownLoad PDF.
Takeuchi N. & Hogeweg P. (2009).: Multilevel selection in models of prebiotic evolution II: a direct comparison of compartmentalization and spatial self-organization.
PLoS. Comput. Biol., 5: e1000542. DOI. MEDLINE. DownLoad PDF.
Ten Tusscher K.H. & Hogeweg P. (2009).: The role of genome and gene regulatory network canalization in the evolution of multi-trait polymorphisms and sympatric speciation.
BMC. Evol. Biol., 9: 159. DOI. MEDLINE. DownLoad PDF.
Ten Tusscher K.H., Mourad A., Nash M.P., Clayton R.H., Bradley C.P., Paterson D.J., Hren R., Hayward M., Panfilov A.V. & Taggart P. ( 2009).: Organization of ventricular fibrillation in the human heart: experiments and models.
Exp. Physiol., 94: 553-562. DOI. MEDLINE.
Van Dam T.J., Rehmann H., Bos J.L. & Snel B. (2009).: Phylogeny of the CDC25 homology domain reveals rapid differentiation of Ras pathways between early animals and fungi.
Cell Signal., 21: 1579-1585. DOI. MEDLINE. DownLoad PDF.
Van den Ham H.J., De Jager W., Bijlsma J.W., Prakken B.J. & De Boer R.J. (2009).: Differential cytokine profiles in juvenile idiopathic arthritis subtypes revealed by cluster analysis.
Rheumatology. (Oxford)., 48: 899-905. DOI. MEDLINE. DownLoad PDF.
Van der Post D.J. & Hogeweg P. (2009).: Cultural inheritance and diversification of diet in variable environments.
Animal Behaviour, 78: 155-166. DOI. DownLoad PDF.
Van der Post D.J., Ursem B. & Hogeweg P. (2009).: Resource distributions affect social learning on multiple timescales.
Behav. Ecol. Sociobiol., 63: 1643-1658. DOI. MEDLINE. DownLoad PDF.
Van Hoek M.J. & Hogeweg P. (2009).: Metabolic Adaptation after Whole Genome Duplication.
Mol Biol Evol., 0: O. DOI. MEDLINE. DownLoad PDF.
Wels M., Bongers R.S., Boekhorst J., Molenaar D., Sturme M., De Vos W.M., Siezen R.J. & Kleerebezem M. (2009).: Large intergenic cruciform-like supermotifs in the Lactobacillus plantarum genome.
J. Bacteriol., 191: 3420-3423. DOI. MEDLINE. DownLoad PDF.

2008

2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | Papers before 1999

Alonso S. & Panfilov A.V. (2008).: Negative filament tension at high excitability in a model of cardiac tissue.
Phys. Rev. Lett., 100: 218101. MEDLINE. DownLoad PDF.
Althaus C.L. & De Boer R.J. (2008).: Dynamics of immune escape during HIV/SIV infection.
PLoS. Comput. Biol., 4: e1000103. DOI. MEDLINE. DownLoad PDF.
Boekhorst J., Van Breukelen B., Heck A.J. & Snel B. (2008).: Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes.
Genome Biol., 9: R144. DOI. MEDLINE. DownLoad PDF.
Clayton R.H. & Panfilov A.V. (2008).: A guide to modelling cardiac electrical activity in anatomically detailed ventricles.
Prog. Biophys. Mol. Biol., 96: 19-43. DOI. MEDLINE. DownLoad PDF.
Cordero O.X., Snel B. & Hogeweg P. (2008).: Coevolution of gene families in prokaryotes.
Genome Res., 18: 462-468. MEDLINE. DownLoad PDF.
Crombach A. & Hogeweg P. (2008).: Evolution of evolvability in gene regulatory networks.
PLoS. Comput. Biol., 4: e1000112. MEDLINE. DownLoad PDF.
Dutilh B.E., Snel B., Ettema T.J. & Huynen M.A. (2008).: Signature genes as a phylogenomic tool.
Mol. Biol. Evol., 25: 1659-1667. MEDLINE. DownLoad PDF.
Frankild S., De Boer R.J., Lund O., Nielsen M. & Kesmir C. (2008).: Amino acid similarity accounts for T cell cross-reactivity and for "holes" in the T cell repertoire.
PLoS. ONE., 3: e1831. DOI. MEDLINE. DownLoad PDF.
Ganusov V.V. & De Boer R.J. (2008a).: Estimating in vivo death rates of targets due to CD8 T-cell-mediated killing.
J. Virol., 82: 11749-11757. DOI. MEDLINE. DownLoad PDF.
Ganusov V.V. & De Boer R.J. (2008b).: Tissue distribution of lymphocytes and plasma cells and the role of the gut: response to Pabst et al.
Trends Immunol., 29: 209-210. DownLoad PDF.
Groenenboom M.A. & Hogeweg P. (2008a).: The dynamics and efficacy of antiviral RNA silencing: A model study.
BMC. Syst. Biol., 2: 28. MEDLINE. DownLoad PDF.
Groenenboom M.A. & Hogeweg P. (2008b).: RNA silencing can explain chlorotic infection patterns on plant leaves.
BMC. Syst. Biol., 2: 105. DOI. MEDLINE. DownLoad PDF.
Hoof I., Kesmir C., Lund O. & Nielsen M. (2008).: Humans with chimpanzee-like major histocompatibility complex-specificities control HIV-1 infection.
AIDS, 22: 1299-1303. MEDLINE. DownLoad PDF.
Keldermann R.H., Ten Tusscher K.H., Nash M.P., Bradley C.P., Hren R., Taggart P. & Panfilov A.V. (2008a).: A Computational Study of Mother Rotor VF in the Human Ventricles.
Am J Physiol Heart Circ Physiol., 0: O. DOI. MEDLINE. DownLoad PDF.
Keldermann R.H., Ten Tusscher K.H., Nash M.P., Hren R., Taggart P. & Panfilov A.V. (2008b).: Effect of heterogeneous APD restitution on VF organization in a model of the human ventricles.
Am. J. Physiol. Heart. Circ. Physiol., 294: H764-H774. DOI. MEDLINE. DownLoad PDF.
Laskowski M., Grieneisen V.A., Hofhuis H., Hove C.A., Hogeweg P., Maree A.F. & Scheres B. (2008).: Root system architecture from coupling cell shape to auxin transport.
PLoS. Biol., 6: e307. DOI. MEDLINE. DownLoad PDF.
Makkes van der Deijl G.B. & Panfilov A.V. (2008).: Formation of fast spirals on heterogeneities of an excitable medium.
Phys. Rev. E, 78: 012901. MEDLINE. DownLoad PDF.
Maree A.F., Komba M., Finegood D.T. & Edelstein-Keshet L. (2008).: A quantitative comparison of rates of phagocytosis and digestion of apoptotic cells by macrophages from normal (BALB/c) and diabetes-prone (NOD) mice.
J. Appl. Physiol., 104: 157-169. MEDLINE.
Ribeiro R.M. & De Boer R.J. (2008).: The contribution of the thymus to the recovery of peripheral naive T-cell numbers during antiretroviral treatment for HIV infection.
J. Acquir. Immune Defic. Syndr., 49: 1-8. DOI. MEDLINE. DownLoad PDF.
Schellens I.M., Kesmir C., Miedema F., Van Baarle D. & Borghans J.A. (2008).: An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases: the contribution of prediction programs.
AIDS, 22: 33-37. MEDLINE. DownLoad PDF.
Schmid B., Kesmir C. & De Boer R.J. (2008).: The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.
PLoS. ONE., 3: e3525. DOI. MEDLINE. DownLoad PDF.
Severins M., Borghans J.A.M. & De Boer R.J. (2008).: The role of Th1/Th2 phenotypes in T cell vaccination: insights from a mathematical model.
In: Zhang J. & Cohen R.R., eds., T-Cell Vaccination, pp. 139-158. Nova Science Publishers, New York. DownLoad PDF.
Siezen R.J., Starrenburg M.J., Boekhorst J., Renckens B., Molenaar D. & Van Hylckama Vlieg J.E. (2008).: Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche.
Appl. Environ. Microbiol., 74: 424-436. DOI. MEDLINE. DownLoad PDF.
Szklarczyk R., Huynen M.A. & Snel B. (2008).: Complex fate of paralogs.
BMC. Evol. Biol., 8: 337. DOI. MEDLINE. DownLoad PDF.
Takeuchi N. & Hogeweg P. (2008).: Evolution of complexity in RNA-like replicator systems.
Biol. Direct., 3: 11. MEDLINE. DownLoad PDF.
Takeuchi N., Salazar L., Poole A.M. & Hogeweg P. (2008).: The evolution of strand preference in simulated RNA replicators with strand displacement: implications for the origin of transcription.
Biol. Direct., 3: 33. MEDLINE. DownLoad PDF.
Thomas-Vaslin V., Altes H.K., De Boer R.J. & Klatzmann D. (2008).: Comprehensive assessment and mathematical modeling of T cell population dynamics and homeostasis.
J. Immunol., 180: 2240-2250. MEDLINE. DownLoad PDF.
Tusscher K.H. & Panfilov A.V. (2008).: Modelling of the ventricular conduction system.
Prog. Biophys. Mol. Biol., 96: 152-170. DOI. MEDLINE. DownLoad PDF.
Van Dam T.J. & Snel B. (2008).: Protein complex evolution does not involve extensive network rewiring.
PLoS. Comput. Biol., 4: e1000132. MEDLINE. DownLoad PDF.
Van den Ham H.J. & De Boer R.J. (2008).: From the two-dimensional Th1 and Th2 phenotypes to high-dimensional models for gene regulation.
Int. Immunol., 20: 1269-1277. DOI. MEDLINE. DownLoad PDF.
Van Der Post D.J. & Hogeweg P. (2008).: Diet traditions and cumulative cultural processes as side-effects of grouping.
Anim. Behav., 75: 133-144. DownLoad PDF.
Vrisekoop N., Den Braber I., De Boer A.B., Ruiter A.F., Ackermans M.T., Van der Crabben S.N., Schrijver E.H., Spierenburg G., Sauerwein H.P., Hazenberg M.D., De Boer R.J., Miedema F., Borghans J.A. & Tesselaar K. (2008).: Sparse production but preferential incorporation of recently produced naive T cells in the human peripheral pool.
Proc. Natl. Acad. Sci. U.S.A., 105: 6115-6120. DOI. MEDLINE. DownLoad PDF.
Zhou M., Boekhorst J., Francke C. & Siezen R.J. (2008).: Locatep: genome-scale subcellular-location predictor for bacterial proteins.
BMC. Bioinformatics, 9: 173. DOI. MEDLINE. DownLoad PDF.

2007

2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | Papers before 1999

Alonso S. & Panfilov A.V. (2007).: Negative filament tension in the Luo-Rudy model of cardiac tissue.
Chaos., 17: 015102. MEDLINE.
Althaus C.L., Ganusov V.V. & De Boer R.J. (2007).: Dynamics of CD8+ T cell responses during acute and chronic lymphocytic choriomeningitis virus infection.
J. Immunol., 179: 2944-2951. MEDLINE. DownLoad PDF.
Beltman J.B., Maree A.F. & De Boer R.J. (2007a).: Spatial modelling of brief and long interactions between T cells and dendritic cells.
Immunol. Cell Biol., 85: 306-314. MEDLINE. DownLoad PDF.
Beltman J.B., Maree A.F., Lynch J.N., Miller M.J. & De Boer R.J. ( 2007b).: Lymph node topology dictates T cell migration behavior.
J. Exp. Med., 204: 771-780. MEDLINE. DownLoad PDF.
Boekhorst J. & Snel B. (2007).: Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties.
BMC. Bioinformatics, 8: 356. MEDLINE. DownLoad PDF.
Borghans J.A.M. & De Boer R.J. (2007).: Quantification of T-cell dynamics: From telomeres to DNA labelling.
Immunol. Reviews, 216: 35-47. DownLoad PDF.
Borghans J.A.M., Kesmir C. & De Boer R.J. ( 2007a).: MHC diversity in individuals and populations.
In: Flower D. & Timmis J., eds., In Silico Immunology, pp. 177-196. Springer, New York.
Borghans J.A.M., Mølgaard A., De Boer R.J. & Kesmir C. ( 2007b).: HLA alleles associated with slow progression to AIDS truly prefer to present HIV-1 p24.
PLoS ONE, 2: e920. MEDLINE. DownLoad PDF.
Borghans J.A.M., Mølgaard A., De Boer R.J. & Kesmir C. ( 2007c).: HLA molecules that preferentially target the HIV-1 p24 protein are associated with slow progression to AIDS.
submitted.
Clayton R.H. & Panfilov A.V. (2007).: A guide to modelling cardiac electrical activity in anatomically detailed ventricles.
Prog Biophys Mol Biol., 0: O. MEDLINE. DownLoad PDF.
Cordero O.X. & Hogeweg P. (2007).: Large changes in regulome size herald the main prokaryotic lineages.
Trends Genet., 23: 488-493. MEDLINE. DownLoad PDF.
Crombach A. & Hogeweg P. (2007).: Chromosome rearrangements and the evolution of genome structuring and adaptability.
Mol. Biol. Evol., 24: 1130-1139. MEDLINE. DownLoad PDF.
De Boer R.J. (2007a).: Time scales of CD4+ T cell depletion in HIV infection.
PLoS. Med., 4: e193. MEDLINE. DownLoad PDF.
De Boer R.J. (2007b).: Understanding the failure of CD8+ T-cell vaccination against simian/human immunodeficiency virus.
J. Virol., 81: 2838-2848. MEDLINE. DownLoad PDF.
Dutilh B.E., Van Noort V., Van der Heijden R.T., Boekhout T., Snel B. & Huynen M.A. (2007).: Assessment of phylogenomic and orthology approaches for phylogenetic inference.
Bioinformatics, 23: 815-824. MEDLINE. DownLoad PDF.
Frahm N., Kaufmann D.E., Yusim K., Muldoon M., Kesmir C., Linde C.H., Fischer W., Allen T.M., Li B., McMahon B.H., Faircloth K.L., Hewitt H.S., Mackey E.W., Miura T., Khatri A., Wolinsky S., McMichael A., Funkhouser R.K., Walker B.D., Brander C. & Korber B.T. (2007).: Increased sequence diversity coverage improves detection of HIV-specific T cell responses.
J. Immunol., 179: 6638-6650. MEDLINE. DownLoad PDF.
Ganusov V.V. (2007).: Discriminating between different pathways of memory CD8+ T cell differentiation.
J. Immunol., 179: 5006-5013. MEDLINE. DownLoad PDF.
Ganusov V.V. & De Boer R.J. (2007).: Do most lymphocytes in humans really reside in the gut?
Trends Immunol., 28: 514-518. MEDLINE. DownLoad PDF.
Ganusov V.V., Milutinovic D. & De Boer R.J. (2007).: IL-2 regulates expansion of CD4+ T cell populations by affecting cell death: insights from modeling CFSE data.
J. Immunol., 179: 950-957. MEDLINE. DownLoad PDF.
Grieneisen V.A., Xu J., Maree A.F., Hogeweg P. & Scheres B. ( 2007).: Auxin transport is sufficient to generate a maximum and gradient guiding root growth.
Nature, 449: 1008-1013. MEDLINE. DownLoad PDF.
Hogeweg P. (2007).: From population dynamics to ecoinformatics: Ecosystems as multilevel information processing systems.
Ecological Informatics, 2: 103-111. DownLoad PDF.
Jilkine A., Maree A.F. & Edelstein-Keshet L. (2007).: Mathematical model for spatial segregation of the Rho-family GTPases based on inhibitory crosstalk.
Bull. Math. Biol., 69: 1943-1978. MEDLINE. DownLoad PDF.
Kafer J., Hayashi T., Maree A.F., Carthew R.W. & Graner F. (2007).: Cell adhesion and cortex contractility determine cell patterning in the Drosophila retina.
Proc. Natl. Acad. Sci. U.S.A., 104: 18549-18554. MEDLINE. DownLoad PDF.
Keldermann R.H., Nash M.P. & Panfilov A.V. (2007a).: Pacemakers in a reaction-diffusion mechanics system.
Journal of Statistical Physics, 128: 375-392. DownLoad PDF.
Keldermann R.H., Ten Tusscher K.H., Nash M.P., Hren R., Taggart P. & Panfilov A.V. (2007b).: Effect of heterogeneous APD restitution on VF organization in a model of the human ventricles.
Am J Physiol Heart Circ Physiol., 0: O. MEDLINE. DownLoad PDF.
Lundegaard C., Lund O., Kesmir C., Brunak S. & Nielsen M. (2007).: Modeling the adaptive immune system: predictions and simulations.
Bioinformatics, 23: 3265-3275. MEDLINE. DownLoad PDF.
Maree A.F., Komba M., Finegood D.T. & Edelstein-Keshet L. ( 2007a).: A quantitative comparison of rates of phagocytosis and digestion of apoptotic cells by macrophages from normal (BALB/c) and diabetes-prone (NOD) mice.
J Appl Physiol., 0: O. MEDLINE.
Maree A.F.M., Grieneisen V.A. & Hogeweg P. (2007b).: The cellular potts model and biophysical properties of cells, tissues and morphogenesis.
In: Anderson A.R.A., Chaplin M.A.J. & Rejniak K.A., eds., Single-Cell-Based Models in Biology and Medicine. Birkhauser Verlag, Basel/Switserland.
Milutinovic D. & De Boer R.J. (2007).: Process noise: an explanation for the fluctuations in the immune response during acute viral infection.
Biophys. J., 92: 3358-3367. MEDLINE. DownLoad PDF.
Navis M., Schellens I., Van Baarle D., Borghans J., Van Swieten P., Miedema F., Kootstra N. & Schuitemaker H. (2007).: Viral replication capacity as a correlate of HLA B57/B5801-associated nonprogressive HIV-1 infection.
J. Immunol., 179: 3133-3143. MEDLINE. DownLoad PDF.
Panfilov A.V., Keldermann R.H. & Nash M.P. (2007).: Drift and breakup of spiral waves in reaction-diffusion-mechanics systems.
Proc. Natl. Acad. Sci. U.S.A., 104: 7922-7926. MEDLINE. DownLoad PDF.
Siezen R.J., Renckens B. & Boekhorst J. (2007).: Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues.
Proteins., 67: 681-694. MEDLINE. DownLoad PDF.
Siezen R.J., Starrenburg M.J., Boekhorst J., Renckens B., Molenaar D. & Van Hylckama Vlieg J.E. (2008).: Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche.
Appl. Environ. Microbiol., 74: 424-436. MEDLINE. DownLoad PDF.
Takeuchi N. & Hogeweg P. (2007a).: Error-threshold exists in fitness landscapes with lethal mutants.
BMC. Evol. Biol., 7: 15. MEDLINE. DownLoad PDF.
Takeuchi N. & Hogeweg P. (2007b).: The Role of Complex Formation and Deleterious Mutations for the Stability of RNA-Like Replicator Systems.
J. Mol. Evol., 65: 668-686. MEDLINE. DownLoad PDF.
Ten Tusscher K.H., Hren R. & Panfilov A.V. (2007).: Organization of ventricular fibrillation in the human heart.
Circ. Res., 100: e87-e101. MEDLINE.
Ten Tusscher K.H. & Panfilov A.V. (2007a).: Influence of diffuse fibrosis on wave propagation in human ventricular tissue.
Europace., 9: vi38-vi45. MEDLINE. DownLoad PDF.
Ten Tusscher K.H. & Panfilov A.V. (2007b).: Modelling of the ventricular conduction system.
Prog Biophys Mol Biol., 0: O. MEDLINE. DownLoad PDF.
Tsegaye A., Ran L., Wolday D., Petros B., Dorigo W., Piriou E., Messele T., Sanders E., Tilahun T., Eshetu D., Schuitemaker H., Coutinho R.A., Miedema F., Borghans J. & Van Baarle D. (2007a).: HIV-1 Subtype C gag-specific T-cell responses in relation to human leukocyte antigens in a diverse population of HIV-infected Ethiopians.
J. Acquir. Immune Defic. Syndr., 45: 389-400. MEDLINE. DownLoad PDF.
Tsegaye A., Ran L., Wolday D., Petros B., Nanlohy N.M., Meles H., Girma M., Hailu E., Borghans J., Miedema F. & Van Baarle D. ( 2007b).: Stable pattern of HIV-1 subtype C Gag-specific T-cell responses coincides with slow rate of CD4 T-cell decline in HIV-infected Ethiopians.
AIDS, 21: 369-372. MEDLINE.
Van der Heijden R.T., Snel B., Van Noort V. & Huynen M.A. (2007).: Orthology prediction at scalable resolution by phylogenetic tree analysis.
BMC. Bioinformatics, 8: 83. MEDLINE. DownLoad PDF.
Van Hoek M. & Hogeweg P. (2007a).: The effect of stochasticity on the lac operon: an evolutionary perspective.
PLoS. Comput. Biol., 3: e111. MEDLINE. DownLoad PDF.
Van Hoek M.J. & Hogeweg P. (2007b).: The role of mutational dynamics in genome shrinkage.
Mol. Biol. Evol., 24: 2485-2494. MEDLINE. DownLoad PDF.
Van Noort V., Snel B. & Huynen M.A. (2007).: Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.
Genome Biol., 8: R197. MEDLINE. DownLoad PDF.
Von Mering C., Jensen L.J., Kuhn M., Chaffron S., Doerks T., Kruger B., Snel B. & Bork P. (2007).: STRING 7-recent developments in the integration and prediction of protein interactions.
Nucleic. Acids. Res., 35: D358-D362. MEDLINE. DownLoad PDF.
Wucherpfennig K.W., Allen P.M., Celada F., Cohen I.R., De Boer R., Garcia K.C., Goldstein B., Greenspan R., Hafler D., Hodgkin P., Huseby E.S., Krakauer D.C., Nemazee D., Perelson A.S., Pinilla C., Strong R.K. & Sercarz E.E. (2007).: Polyspecificity of T cell and B cell receptor recognition.
Semin. Immunol., 19: 216-224. MEDLINE. DownLoad PDF.

2006

2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | Papers before 1999

Boekhorst J., Helmer Q., Kleerebezem M. & Siezen R.J. ( 2006a).: Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria.
Microbiology., 152: 273-280. MEDLINE. DownLoad PDF.
Boekhorst J., Wels M., Kleerebezem M. & Siezen R.J. ( 2006b).: The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment.
Microbiology., 152: 3175-3183. MEDLINE. DownLoad PDF.
Ciccarelli F.D., Doerks T., Von Mering C., Creevey C.J., Snel B. & Bork P. (2006).: Toward automatic reconstruction of a highly resolved tree of life.
Science, 311: 1283-1287. MEDLINE. DownLoad PDF.
Clayton R.H., Zhuchkova E.A. & Panfilov A.V. (2006).: Phase singularities and filaments: simplifying complexity in computational models of ventricular fibrillation.
Prog. Biophys. Mol. Biol., 90: 378-398. MEDLINE. DownLoad PDF.
Cordero O.X. & Hogeweg P. (2006).: Feed-forward loop circuits as a side effect of genome evolution.
Mol. Biol. Evol., 23: 1931-1936. MEDLINE. DownLoad PDF.
De Boer R.J. (2006).: Estimating the role of thymic output in hiv infection.
Curr. Opin. HIV AIDS, 1: 16-21.
De Boer R.J., Ganusov V.V., Milutinovic D., Hodgkin P.D. & Perelson A.S. (2006).: Estimating lymphocyte division and death rates from CFSE data.
Bull. Math. Biol., 68: 1011-1031. MEDLINE. DownLoad PDF.
Dutilh B.E., Huynen M.A. & Snel B. (2006).: A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.
BMC. Genomics., 7: 10. MEDLINE. DownLoad PDF.
Franke L., Bakel H., Fokkens L., De Jong E.D., Egmont-Petersen M. & Wijmenga C. (2006).: Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes.
Am. J. Hum. Genet., 78: 1011-1025. MEDLINE. DownLoad PDF.
Gabaldon T., Snel B., Van Zimmeren F., Hemrika W., Tabak H. & Huynen M.A. (2006).: Origin and evolution of the peroxisomal proteome.
Biol. Direct., 1: 8. MEDLINE. DownLoad PDF.
Ganusov V.V. & Antia R. (2006).: Imperfect vaccines and the evolution of pathogens causing acute infections in vertebrates.
Evolution. Int. J. Org. Evolution., 60: 957-969. MEDLINE. DownLoad PDF.
Ganusov V.V. & De Boer R.J. (2006).: Estimating Costs and Benefits of CTL Escape Mutations in SIV/HIV Infection.
PLoS. Comput. Biol., 2: e24. MEDLINE. DownLoad PDF.
Ganusov V.V., Pilyugin S.S., Ahmed R. & Antia R. (2006).: How does cross-reactive stimulation affect the longevity of CD8+ T cell memory?
PLoS. Comput. Biol., 2: e55. MEDLINE. DownLoad PDF.
Kafer J., Hogeweg P. & Maree A.F. (2006).: Moving forward moving backward: directional sorting of chemotactic cells due to size and adhesion differences.
PLoS. Comput. Biol., 2: e56. MEDLINE. DownLoad PDF.
Korthals Altes H., De Boer R. & Boerlijst M. (2006).: Role of avidity and breadth of the CD4 T cell response in progression to AIDS.
Proc. Biol. Sci., 273: 1697-1704. MEDLINE. DownLoad PDF.
Kuramae E.E., Robert V., Snel B. & Boekhout T. ( 2006a).: Conflicting phylogenetic position of Schizosaccharomyces pombe.
Genomics., 88: 387-393. MEDLINE. DownLoad PDF.
Kuramae E.E., Robert V., Snel B., Weiss M. & Boekhout T. ( 2006b).: Phylogenomics reveal a robust fungal tree of life.
FEMS. Yeast. Res., 6: 1213-1220. MEDLINE.
Maree A.F., Jilkine A., Dawes A., Grieneisen V.A. & Edelstein-Keshet L. (2006a).: Polarization and movement of keratocytes: a multiscale modelling approach.
Bull. Math. Biol., 68: 1169-1211. MEDLINE. DownLoad PDF.
Maree A.F., Kublik R., Finegood D.T. & Edelstein-Keshet L. ( 2006b).: Modelling the onset of Type 1 diabetes: can impaired macrophage phagocytosis make the difference between health and disease?
Philos. Transact. A. Math. Phys. Eng. Sci., 364: 1267-1282. MEDLINE. DownLoad PDF.
Maree A.F., Santamaria P. & Edelstein-Keshet L. ( 2006c).: Modeling competition among autoreactive CD8+ T cells in autoimmune diabetes: implications for antigen-specific therapy.
Int. Immunol., 18: 1067-1077. MEDLINE. DownLoad PDF.
Merks R.M., Hoekstra A.G., Kaandorp J., Sloot P.M.A. & Hogeweg P. ( 2006).: Problem-solving environments for biological morphogenesis.
Computing in Science and Engineering, 8: 61-72.
Muller V. & De Boer R.J. (2006).: The integration hypothesis: an evolutionary pathway to benign SIV infection.
PLoS. Pathog., 2: e15. MEDLINE. DownLoad PDF.
Oti M., Snel B., Huynen M.A. & Brunner H.G. (2006).: Predicting disease genes using protein-protein interactions.
J. Med. Genet., 43: 691-698. MEDLINE. DownLoad PDF.
Panfilov A.V. (2006).: Is heart size a factor in ventricular fibrillation? Or how close are rabbit and human hearts?
Heart. Rhythm., 3: 862-864. MEDLINE. DownLoad PDF.
Rapin N., Kesmir C., Frakild S., Nielsen M., Lundegaard C., Brunak S. & Lund O. (2006).: Modelling the human immune system by combining bioinformatics and systems biology approaches.
J. Biol.Phys., 32: 335-353. DownLoad PDF.
Siezen R., Boekhorst J., Muscariello L., Molenaar D., Renckens B. & Kleerebezem M. (2006).: Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria.
BMC. Genomics., 7: 126. MEDLINE. DownLoad PDF.
Strous M., Pelletier E., Mangenot S., Rattei T., Lehner A., Taylor M.W., Horn M., Daims H., Bartol-Mavel D., Wincker P., Barbe V., Fonknechten N., Vallenet D., Segurens B., Schenowitz-Truong C., Medigue C., Collingro A., Snel B., Dutilh B.E., Op den Camp H.J., Van der Drift C., Cirpus I., Van de Pas-Schoonen K.T., Harhangi H.R., Van Niftrik L., Schmid M., Keltjens J., Van de Vossenberg J., Kartal B., Meier H., Frishman D., Huynen M.A., Mewes H.W., Weissenbach J., Jetten M.S., Wagner M. & Le Paslier D. (2006).: Deciphering the evolution and metabolism of an anammox bacterium from a community genome.
Nature, 440: 790-794. MEDLINE. DownLoad PDF.
Ten Tusscher K.H., Bernus O., Hren R. & Panfilov A.V. (2006).: Comparison of electrophysiological models for human ventricular cells and tissues.
Prog. Biophys. Mol. Biol., 90: 326-345. MEDLINE. DownLoad PDF.
Ten Tusscher K.H. & Panfilov A.V. (2006a).: Alternans and spiral breakup in a human ventricular tissue model.
Am. J. Physiol. Heart. Circ. Physiol., 291: H1088-H1100. MEDLINE. DownLoad PDF.
Ten Tusscher K.H. & Panfilov A.V. (2006b).: Cell model for efficient simulation of wave propagation in human ventricular tissue under normal and pathological conditions.
Phys. Med. Biol., 51: 6141-6156. MEDLINE. DownLoad PDF.
Van den Dool C. & De Boer R.J. (2006).: The effects of age, thymectomy, and HIV Infection on alpha and beta TCR excision circles in naive T cells.
J. Immunol., 177: 4391-4401. MEDLINE. DownLoad PDF.
Van Der Post D.J. & Hogeweg P. (2006).: Resource distributions and diet development by trial-and-error learning.
Behav. Ecol. Sociobiol., 61: 65-80. DownLoad PDF.
Van Hoek M.J. & Hogeweg P. (2006).: In silico evolved lac operons exhibit bistability for artificial inducers, but not for lactose.
Biophys. J., 91: 2833-2843. MEDLINE. DownLoad PDF.

2005

2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | Papers before 1999

Clayton R.H., Zhuchkova E.A. & Panfilov A.V. (2006).: Phase singularities and filaments: Simplifying complexity in computational models of ventricular fibrillation.
Prog. Biophys. Mol. Biol., 90: 378-398. MEDLINE. DownLoad PDF.
De Boer R.J. & Perelson A.S. (2005).: Estimating division and death rates from CFSE data.
J. Comp. Appl. Math., 184: 140-164. DownLoad PDF.
Dowling M.R., Milutinovic D. & Hodgkin P.D. (2005).: Modelling cell lifespan and proliferation: is likelihood to die or to divide independent of age?
J. R. Soc. Interface, 2: 517-526.
Ganusov V.V., Pilyugin S.S., De Boer R.J., Murali-Krishna K., Ahmed R. & Antia R. (2005).: Quantifying cell turnover using CFSE data.
J. Immunol. Methods, 298: 183-200. MEDLINE. DownLoad PDF.
Groenenboom M.A., Maree A.F. & Hogeweg P. (2005).: The RNA silencing pathway: the bits and pieces that matter.
PLoS. Comput. Biol., 1: 155-165. MEDLINE. DownLoad PDF.
Han B., Serra P., Amrani A., Yamanouchi J., Maree A.F., Edelstein-Keshet L. & Santamaria P. (2005).: Prevention of diabetes by manipulation of anti-IGRP autoimmunity: high efficiency of a low-affinity peptide.
Nat. Med., 11: 645-652. MEDLINE. DownLoad PDF.
Hogeweg P. (2005a).: Interlocking of selforganization and evolution.
In: Hemelrijk C.K., ed., Self-organization and evolution of Social Systems, pp. 166-189. Cambridge Univ press.
Hogeweg P. (2005b).: Multilevel particle systems and the study of biological evolution.
Markov processes and related fields, 11: 291-312.
Luciani F., Kesmir C., Mishto M., Or-Guil M. & De Boer R.J. ( 2005).: A mathematical model of protein degradation by the proteasome.
Biophys. J., 88: 2422-2432. MEDLINE. DownLoad PDF.
Lund O., Nielsen M., Lundegaard C., Kesmir C. & Brunak S. (2005).: Immunological bioinformatics.
MIT Press, Cambridge, Mass.
Maree A.F., Komba M., Dyck C., Labecki M., Finegood D.T. & Edelstein-Keshet L. (2005).: Quantifying macrophage defects in type 1 diabetes.
J. theor. Biol., 233: 533-551. MEDLINE. DownLoad PDF.
Nielsen M., Lundegaard C., Lund O. & Kesmir C. (2005).: The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage.
Immunogenetics., 57: 33-41. MEDLINE. DownLoad PDF.
Panfilov A.V., Keldermann R.H. & Nash M.P. (2005).: Self-organized pacemakers in a coupled reaction-diffusion-mechanics system.
Phys. Rev. Lett, 95: 258104/1-258104/4.
Rusakov A., Medvinsky A.B. & Panfilov A.V. (2005).: Scroll waves meandering in a model of an excitable medium.
Phys. Rev. E, 72: 022902. MEDLINE. DownLoad PDF.
Takeuchi N., Poorthuis P.H. & Hogeweg P. (2005).: Phenotypic error threshold; additivity and epistasis in RNA evolution.
BMC. Evol. Biol., 5: 9. MEDLINE. DownLoad PDF.
Ten Tusscher K.H., Bernus O., Hren R. & Panfilov A.V. (2006).: Comparison of electrophysiological models for human ventricular cells and tissues.
Prog. Biophys. Mol. Biol., 90: 326-345. MEDLINE. DownLoad PDF.
Ten Tusscher K.H., Noble D., Noble P.J. & Panfilov A.V. (2005).: Comments on "A model for human ventricular tissue".
Am.J.Physiol, 288: 253-254.
Ten Tusscher K.H. & Panfilov A.V. (2005).: Wave propagation in excitable media with randomly distributed obstacles.
SIAM Journal of Multiscale Modeling & Simulation, 3: 265-282.

2004

2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | Papers before 1999

Borghans J.A.M., Beltman J.B. & De Boer R.J. (2004).: MHC polymorphism under host-pathogen coevolution.
Immunogenetics., 55: 732-739. MEDLINE. DownLoad PDF.
Burroughs N.J., De Boer R.J. & Kesmir C. (2004).: Discriminating self from nonself with short peptides from large proteomes.
Immunogenetics., 56: 311-320. MEDLINE. DownLoad PDF.
De Boer R.J., Borghans J.A., Van Boven M., Kesmir C. & Weissing F.J. (2004).: Heterozygote advantage fails to explain the high degree of polymorphism of the MHC.
Immunogenetics., 55: 725-731. MEDLINE. DownLoad PDF.
Hazenberg M.D., Otto S.A., Van Rossum A.M., Scherpbier H.J., De Groot R., Kuijpers T.W., Lange J.M., Hamann D., De Boer R.J., Borghans J.A. & Miedema F. (2004).: Establishment of the CD4+ T-cell pool in healthy children and untreated children infected with HIV-1.
Blood, 104: 3513-3519. MEDLINE. DownLoad PDF.
Lund O., Nielsen M., Kesmir C., Petersen A.G., Lundegaard C., Worning P., Sylvester-Hvid C., Lamberth K., Roder G., Justesen S., Buus S. & Brunak S. (2004).: Definition of supertypes for HLA molecules using clustering of specificity matrices.
Immunogenetics, 55: 797-810. MEDLINE. DownLoad PDF.
Nash M.P. & Panfilov A.V. (2004).: Electromechanical model of excitable tissue to study reentrant cardiac arrhythmias.
Prog. Biophys. Mol. Biol., 85: 501-522. MEDLINE. DownLoad PDF.
Nobile M., Correa R., Borghans J.A., D'Agostino C., Schneider P., De Boer R.J. & Pantaleo G. (2004).: De novo T-cell generation in patients at different ages and stages of HIV-1 disease.
Blood, 104: 470-477. MEDLINE. DownLoad PDF.
Panfilov A.V. & Kerkhof P.L.M. (2004).: Quantifying ventricular fibrillation: in silico research and clinical implications.
IEEE Trans. Biomed. Eng, 51: 195-196. MEDLINE.
Saxova P., Buus S. & Kesmir C. (2004).: Integrating proteasome and MHC predictions for better identification of CTL epitopes.
In: Hansen J.A. & Dupont B., eds., HLA 2004: Immunobiology of the human MHC. Proceedings of the 13th International Histocompatibility Workshop and Congress, pp. 45-51. IHWG Press, Seattle, WA.
Scherer A., Noest A. & De Boer R.J. (2004).: Activation-threshold tuning in an affinity model for the T-cell repertoire.
Proc. R. Soc. Lond. B. Biol. Sci., 271: 609-616. MEDLINE. DownLoad PDF.
Ten Tusscher K.H., Noble D., Noble P.J. & Panfilov A.V. (2004).: A model for human ventricular tissue.
Am.J.Physiol., 286: 1573-1589. MEDLINE. DownLoad PDF.
Ten Tusscher K.H. & Panfilov A.V. (2004).: Eikonal formulation of the minimal principle for scroll wave filaments.
Phys. Rev. Lett, 93: 108106. MEDLINE. DownLoad PDF.
Van der Post D.J. & Hogeweg P. (2004).: Learning what to eat: Studying inter-relations between learning, grouping and evironmental conditions in an artificial world.
LNCS, 3305: 492-501. DownLoad PDF.

2003

2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | Papers before 1999

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.

2002

2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | Papers before 1999

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.

2001

2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | Papers before 1999

Bernus O., Wilders R. ADN Zemlin C.W., Verschelde H. & Panfilov A.V. (2001).: A realistic and efficient model of human ventricular tissue.
Proc. Physiol. Soc. New Zealand, 20,Suppl.1: 18.
Bloch H.A., Petersen M., Sperotto M.M., Kesmir C., Radzikowski L., Jacobsen S. & Sondergaard I. (2001).: Identification of barley and rye varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks.
Rapid. Commun. Mass. Spectrom., 15: 440-445. MEDLINE.
Borghans J.A.M. & De Boer R.J. (2001).: Diversity in the Immune System.
In: Segel L.A. & Cohen I.R., eds., Design Principles for the Immune System and Other Distributed Autonomous Systems, pp. 161-183. Oxford University Press, Oxford, U.K.
De Boer R.J. & Freitas A. A. Perelson A.S. (2001).: Resource competition determines selection of B cell repertoires.
J. theor. Biol., 212: 333-343. MEDLINE. DownLoad PDF.
De Boer R.J., Oprea M., Antia R., Murali-Krishna K., Ahmed R. & Perelson A.S. (2001).: Recruitment Times, Proliferation, and Apoptosis Rates during the CD8+ T-Cell Response to Lymphocytic Choriomeningitis Virus.
J. Virol., 75: 10663-10669. MEDLINE. DownLoad PDF.
De Ronde A., Van Dooren M., Van Der Hoek L., Bouwhuis D., De Rooij E., Van Gemen B., De Boer R.J. & Goudsmit J. (2001).: Establishment of new transmissible and drug-sensitive human immunodeficiency virus type 1 wild types due to transmission of nucleoside analogue-resistant virus.
J. Virol., 75: 595-602. MEDLINE. DownLoad PDF.
Korber B., Gaschen B., Yusim K., Thakallapally R., Kesmir C. & Detours V. (2001).: Evolutionary and immunological implications of contemporary HIV-1 variation.
Br. Med. Bull., 58: 19-42. MEDLINE. DownLoad PDF.
Lukashov V.V., Huismans R., Jebbink M.F., Danner S.A., De Boer R.J. & Goudsmit J. (2001).: Selection by azt and rapid replacement in the absence of drugs of hiv type 1 resistant to multiple nucleoside analogs.
AIDS Res. Hum. Retroviruses., 17: 807-818. MEDLINE. DownLoad PDF.
Marée A.F.M. & Hogeweg P. (2001).: How amoeboids self-organize into a fruiting body: Multicellular coordination in Dictyostelium discoideum.
Proc. Natl. Acad. Sci. USA, 98: 3879-3883. MEDLINE. DownLoad PDF.
Müller V., Marée A.F. & De Boer R.J. (2001).: Small variations in multiple parameters account for wide variations in HIV-1 set-points: a novel modelling approach.
Proc. R. Soc. Lond. B. Biol. Sci., 268: 235-242. MEDLINE. DownLoad PDF.
Müller V., Marée A.F.M. & De Boer R.J. (2001).: Release of virus from lymphoid tissue affects human immunodeficiency virus type 1 and hepatitis C virus kinetics in the blood.
J. Virol., 75: 2597-2603. MEDLINE. DownLoad PDF.
Panfilov A.V. & Pertsov A.M. (2001).: Ventricular fibrillation: evolution of the multiple-wavelet hypothesis.
Phil. Trans. R. Soc. Lond. A, 359: 1315-1325. DownLoad PDF.
van Boxtel J.J.A. & Panfilov A.V. (2001).: Spiral breakup in an array of coupled cells. the role of the gap junctional conductance.
XXXIVth International Congress of Physiological Sciences, Christchurch, New Zealand, abstract 440.
Zemlin C.W., Herzel H., Yen Ho S.Y. & Panfilov A.V. (2001).: A realistoc and efficient model of excitation propagation in the human atria.
In: Virag N., Blank O. & Kappemberger L., eds., Computer simulation and experimental assessment of cardiac electrophysiology, pp. 29-34. Future publishing Company Inc., Armonk N.Y.
Zemlin C.W. & Panfilov A.V. (2001).: Spiral waves in excitable media with negative restitution.
Phys. Rev. E, 63: 041912. MEDLINE. DownLoad PDF.

2000

2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | Papers before 1999

Cohen Stuart J.W., Hazebergh M.D., Hamann D., Otto S.A., Borleffs J.C., Miedema F., Boucher C.A. & De Boer R.J. (2000).: The dominant source of CD4+ and CD8+ T-cell activation in HIV infection is antigenic stimulation.
J. Acquir. Immune Defic. Syndr., 25: 203-211. MEDLINE. DownLoad PDF.
Hazenberg M.D., Cohen Stuart J.W., Otto S.A., Borleffs J.C., Boucher C.A., De Boer R.J., Miedema F. & Hamann D. ( 2000a).: T-cell division in human immunodeficiency virus (HIV)-1 infection is mainly due to immune activation: a longitudinal analysis in patients before and during highly active antiretroviral therapy (HAART).
Blood, 95: 249-255. MEDLINE. DownLoad PDF.
Hazenberg M.D., Otto S.A., Stuart J.W., Verschuren M.C., Borleffs J.C., Boucher C.A., Coutinho R.A., Lange J.M., De Wit T.F., Tsegaye A., Van Dongen J.J., Hamann D., De Boer R.J. & Miedema F. (2000b).: Increased cell division but not thymic dysfunction rapidly affects the T-cell receptor excision circle content of the naive T cell population in HIV-1 infection.
Nat. Med., 6: 1036-1042. MEDLINE. DownLoad PDF.
Hogeweg P. (2000a).: Evolving mechanisms of morphogenesis: on the interplay between differential adhesion and cell differentiation.
J. theor. Biol., 203: 317-333. MEDLINE. DownLoad PDF.
Hogeweg P. (2000b).: Shapes in the shadow: Evolutionary dynamics of morphogenesis.
Artif. Life, 6: 85-101. MEDLINE. DownLoad PDF.
Kesmir C., Borghans J.A.M. & De Boer R.J. ( 2000).: Diversity of human alpha beta T cell receptors.
Science, 288: 1135a. DownLoad PDF.
Lauemøller S., Kesmir C., Corbet S.L., Fomsgaard A., Holm A., Claesson M.H., Brunak S. & Buus S. (2000).: Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project.".
Rev. Immunogenet., 2(4): 477-491. MEDLINE. DownLoad PDF.
Marée A.F.M., Keulen W., Boucher C.A.B. & De Boer R.J. (2000).: Estimating relative fitness in viral competition experiments.
J. Virol., 74: 11067-11072. MEDLINE. DownLoad PDF.
Noest A.J. (2000).: Designing lymphocyte functional structure for optimal signal detection: Voilà, T cells.
J. theor. Biol., 207: 195-216. MEDLINE. DownLoad PDF.
Pagie L.W.P. & Hogeweg P. (2000a).: Individual- and population-based diversity in restriction-modification systems.
Bull. Math. Biol., 62: 759-774. MEDLINE. DownLoad PDF.
Pagie L.W.P. & Hogeweg P. (2000b).: Information integration and red queen dynamics in coevolutionary optimization.
Proceedings CEC 2000, pp. 797-806. DownLoad PDF.
Pagie L.W.P. & Hogeweg P. (2000c).: Optimization as side-effect of evolving allelopathic diversity.
vol. 1917 of Lecture Notes in Computer Science, pp. 797-806. Proceedings PPSN VI. DownLoad PDF.
Panfilov A.V., Müller S.C., Zykov V.Z. & Keener J.P. (2000).: Elimination of spiral waves in cardiac tissue by multiple electrical shocks.
Phys.Rev.E, 61: 4644-4647. MEDLINE. DownLoad PDF.
Rizzardi G.P., De Boer R.J., Hoover S., Tambussi G., Chapuis A., Halkic N., Bart P.A., Miller V., Staszewski S., Notermans D.W., Perrin L., Fox C.H., Lange J.M., Lazzarin A. & Pantaleo G. (2000).: Predicting the duration of antiviral treatment needed to suppress plasma HIV-1 RNA.
J. Clin. Invest., 105: 777-782. MEDLINE. DownLoad PDF.
Zuidema W.H. & Hogeweg P. (2000).: Selective advantages of syntactic language - a model study.
Proceedings of the 22nd Annual Meeting of the Cognitive Science Society. Lawrence Erlbaum Associates, Hillsdale, USA. DownLoad PDF.

1999

2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | Papers before 1999

Borghans J.A., Noest A.J. & De Boer R.J. (1999a).: How specific should immunological memory be?
J. Immunol., 163: 569-575. MEDLINE. DownLoad PDF.
Borghans J.A., Taams L.S., Wauben M.H. & De Boer R.J. ( 1999b).: Competition for antigenic sites during T cell proliferation: a mathematical interpretation of in vitro data.
Proc. Natl. Acad. Sci. U.S.A., 96: 10782-10787. MEDLINE. DownLoad PDF.
Clark D.R., De Boer R.J., Wolthers K.C. & Miedema F. (1999).: T cell dynamics in HIV-1 infection.
Adv. Immunol., 73: 301-327. MEDLINE.
Dandekar T., Schuster S., Snel B., Huynen M. & Bork P. (1999).: Pathway alignment: application to the comparative analysis of glycolytic enzymes.
Biochem. J., 343: 115-124. MEDLINE. DownLoad PDF.
Huynen M.A., Dandekar T. & Bork P. (1999).: Variation and evolution of the citric-acid cycle: a genomic perspective.
Trends Microbiol., 7: 281-291. MEDLINE. DownLoad PDF.
Kesmir C. & De Boer R.J. (1999).: A mathematical model on germinal center kinetics and termination.
J. Immunol., 163: 2463-2469. MEDLINE. DownLoad PDF.
Maree A.F., Panfilov A.V. & Hogeweg P. (1999a).: Migration and thermotaxis of Dictyostelium discoideum slugs, a model study.
J. theor. Biol., 199: 297-309. MEDLINE. DownLoad PDF.
Maree A.F., Panfilov A.V. & Hogeweg P. (1999b).: Phototaxis during the slug stage of Dictyostelium discoideum: a model study.
Proc.R.Soc.Lond., 266: 1351-1360. DownLoad PDF.
Pagie L. & Hogeweg P. (1999).: Colicin diversity: a result of eco-evolutionary dynamics.
J. theor. Biol., 196: 251-261. MEDLINE. DownLoad PDF.
Panfilov A.V. (1999a).: Three-dimensional organization of electrical turbulence in the heart.
Phys. Rev. E, 59: R6251-R6254. MEDLINE. DownLoad PDF.
Panfilov A.V. (1999b).: Three dimensional wave propagation in mathematical models of ventricular fibrillation.
In: Zipes D.P. & Jalife J., eds., Cardiac Electrophysiology. From cell to bedside, pp. 271-276. Sauners Company.
Savill N.J. & Hogeweg P. (1999).: Competition and dispersal in predator-prey waves.
Theor. Popul. Biol., 56: 243-263. MEDLINE. DownLoad PDF.
Snel B., Bork P. & Huynen M.A. (1999).: Genome phylogeny based on gene content.
Nat. Genet., 21: 108-110. MEDLINE. DownLoad PDF.
Van Nimwegen E., Crutchfield J.P. & Huynen M. (1999).: Neutral evolution of mutational robustness.
Proc. Natl. Acad. Sci. U.S.A., 96: 9716-9720. MEDLINE. DownLoad PDF.
Wolthers K.C., Noest A.J., Otto S.A., Miedema F. & De Boer R.J. ( 1999).: Normal telomere lengths in naive and memory CD4+ T cells in HIV type 1 infection: a mathematical interpretation.
AIDS Res. Hum. Retroviruses., 15: 1053-1062. MEDLINE.
Yamamoto T. & Hogeweg P. (1999).: Evolution to complexity: replication, elongation and assembly in an rna world.
In: Floreano D., Nicoud J.D. & Mondada F., eds., Advances in Artificial Life, pp. 422-426. Springer verlag. DownLoad PDF.

2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | Papers before 1999