Theoretical Biology & Bioinformatics

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Rob J. de Boer

Rob J. de Boer

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Niculescu I., Textor J. & De Boer R.J. (2015).
Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration.
PLoS Comput. Biol., 11: e1004280. DOI. PubMed.

Ahmed R., Westera L., Drylewicz J., Elemans M., Zhang Y., Kelly E., Reljic R., Tesselaar K., De Boer R.J., Macallan D.C., Borghans J.A. & Asquith B. (2015).
Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments.
PLoS Comput. Biol., 11: e1004355. DOI. PubMed.

Gadhamsetty S., Beltman J.B. & De Boer R.J. (2015).
What Do Mathematical Models Tell Us about Killing Rates DuringHIV-1 infection?
Immunol Lett., 0: O. DOI. PubMed.

Vrisekoop N., Drylewicz J., Van Gent R., Mugwagwa T., Van Lelyveld S., Veel E., Otto S.A., Ackermans M.T., Vermeulen J.N., Huidekoper H.H., Prins J.M., Miedema F., De Boer R.J., Tesselaar K. & Borghans J.A. (2015).
Quantification of naive and memory T-cell turnover during HIV-1 infection.
AIDS, 0: O. DOI. PubMed.

Carrillo-Bustamante P., Kesmir C. & De Boer R.J. ( 2015a).
The evolution of natural killer cell receptors.
Immunogenetics., 0: O. DOI. PubMed.

Carrillo-Bustamante P., Kesmir C. & De Boer R.J. ( 2015b).
Can Selective MHC Downregulation Explain the Specificity and Genetic Diversity of NK Cell Receptors?
Front. Immunol., 6: 311. DOI. PubMed.

Carrillo-Bustamante P., Kesmir C. & De Boer R.J. ( 2015c).
A Coevolutionary Arms Race between Hosts and Viruses Drives Polymorphism and Polygenicity of NK Cell Receptors.
Mol. Biol. Evol., 32: 2149-2160. DOI. PubMed.

Westera L., Van Hoeven V., Drylewicz J., Spierenburg G., Van Velzen J.F., De Boer R.J., Tesselaar K. & Borghans J.A. (2015).
Lymphocyte maintenance during healthy aging requires no substantial alterations in cellular turnover.
Aging Cell, 14: 219-227. DOI. PubMed.

Saeki K., Doekes H.M. & Boer R.J.D. (2015).
Optimal t cell cross-reactivity and the role of regulatory t cells.
Journal of Theoretical Biology, 375: 4 - 12.
Theories and Modeling of Autoimmunity. DOI.

Van Dorp C.H., Van Boven M. & De Boer R.J. (2014).
Immuno-epidemiological Modeling of HIV-1 Predicts High Heritability of the Set-Point Virus Load, while Selection for CTL Escape Dominates Virulence Evolution.
PLoS Comput. Biol., 10: e1003899. DOI. PubMed.

Textor J., Henrickson S.E., Mandl J.N., Von Andrian U.H., Westermann J., De Boer R.J. & Beltman J.B. (2014).
Random migration and signal integration promote rapid and robust T cell recruitment.
PLoS. Comput. Biol., 10: e1003752. DOI. PubMed.

Pandit A. & De Boer R.J. (2014).
Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants.
Retrovirology., 11: 56. DOI.

Ikeda H., De Boer R.J., Sato K., Morita S., Misawa N., Koyanagi Y., Aihara K. & Iwami S. (2014).
Improving the estimation of the death rate of infected cells from time course data during the acute phase of virus infections: application to acute HIV-1 infection in a humanized mouse model.
Theor. Biol. Med. Model., 11: 22. DOI. PubMed.

Gadhamsetty S., Maree A.F., Beltman J.B. & De Boer R.J. (2014).
A general functional response of cytotoxic T lymphocyte-mediated killing of target cells.
Biophys. J., 106: 1780-1791. DOI.

Perie L., Hodgkin P.D., Naik S.H., Schumacher T.N., De Boer R.J. & Duffy K.R. (2014).
Determining lineage pathways from cellular barcoding experiments.
Cell Rep., 6: 617-624. DOI.

Carrillo-Bustamante P., Kesmir C. & De Boer R.J. (2014).
Quantifying the Protection of Activating and Inhibiting NK Cell Receptors during Infection with a CMV-Like Virus.
Front. Immunol., 5: 20. DOI.

Rao X., De Boer R.J., Van Baarle D., Maiers M. & Kesmir C. (2013).
Complementarity of binding motifs is a general property of HLA-A and HLA-B molecules and does not seem to affect HLA haplotype composition.
Front. Immunol., 4: 374. DOI. PubMed.

Carrillo-Bustamante P., Kesmir C. & De Boer R.J. (2013).
Virus encoded MHC-like decoys diversify the inhibitory KIR repertoire.
PLoS. Comput. Biol., 9: e1003264. DOI.

Miedema F., Hazenberg M.D., Tesselaar K., Van Baarle D., De Boer R.J. & Borghans J.A. (2013).
Immune Activation and Collateral Damage in AIDS Pathogenesis.
Front. Immunol., 4: 298. DOI. PubMed.

Schittler D., Allgöwer F. & De Boer R.J. (2013).
A new model to simulate and analyze proliferating cell populations in BrdU labeling experiments.
BMC Syst. Biol. (Suppl), 7(Suppl 1):S4. DOI.

Westera L., Drylewicz J., Den Braber I., Mugwagwa T., Van der Maas I., Kwast L., Volman T., Van de Weg-Schrijver E.H., Bartha I., Spierenburg G., Gaiser K., Ackermans M.T., Asquith B., De Boer R.J., Tesselaar K. & Borghans J.A. (2013).
Closing the gap between T-cell life span estimates from stable isotope-labeling studies in mice and humans.
Blood, 122: 2205-2212. DOI. PubMed.

Van Deutekom H.W., Wijnker G. & De Boer R.J. (2013).
The Rate of Immune Escape Vanishes When Multiple Immune Responses Control an HIV Infection.
J. Immunol., 191: 3277-3286. DOI. PubMed.

Van den Ham H.J., Andeweg A.C. & De Boer R.J. ( 2013a).
Induction of appropriate Th cell phenotypes: Cellular decision-making in heterogeneous environments.
Parasite Immunol., 0: O. DOI. PubMed.

Textor J., Sinn M. & De Boer R.J. (2013).
Analytical results on the Beauchemin model of lymphocyte migration.
BMC Bioinformatics, 14: S10. DOI. PubMed.

Naik S.H., Perie L., Swart E., Gerlach C., Van Rooij N., De Boer R.J. & Schumacher T.N. (2013).
Diverse and heritable lineage imprinting of early haematopoietic progenitors.
Nature, 496: 229-232. DOI. PubMed.

Gerlach C., Rohr J.C., Perie L., Van Rooij N., Van Heijst J.W., Velds A., Urbanus J., Naik S.H., Jacobs H., Beltman J.B., De Boer R.J. & Schumacher T.N. (2013).
Heterogeneous differentiation patterns of individual CD8$^+$ T cells.
Science, 340: 635-639. DOI. PubMed.

Van den Ham H.J., De Waal L., Zaaraoui-Boutahar F., Bijl M., Van Ijcken W.F., Osterhaus A.D., De Boer R.J. & Andeweg A.C. ( 2013b).
Early divergence of Th1 and Th2 transcriptomes involves a small core response and sets of transiently expressed genes.
Eur. J. Immunol., 43: 1074-1084. DOI. PubMed.

De Boer R.J. & Perelson A.S. (2013a).
Quantifying T lymphocyte turnover.
J. theor. Biol., 327: 45-87. DOI. PubMed.

Van Berkel K., De Boer R.J., Scheres B. & Ten Tusscher K. (2013).
Polar auxin transport: models and mechanisms.
Development, 140: 2253-2268. DOI. PubMed.

De Boer R.J. & Perelson A.S. (2013b).
Antigen-stimulated CD4 T cell expansion can be limited by their grazing of peptide-MHC complexes.
J. Immunol., 190: 5454-5458. DOI. PubMed.

Ganusov V.V. & De Boer R.J. (2013).
A mechanistic model for bromodeoxyuridine dilution naturally explains labelling data of self-renewing T cell populations.
J R Soc Interface, 10: 20120617. DOI. PDF. PubMed.

Ariotti S., Beltman J.B., Chodaczek G., Hoekstra M.E., Van Beek A.E., Gomez-Eerland R., Ritsma L., Van Rheenen J., Maree A.F., Zal T., De Boer R.J., Haanen J.B. & Schumacher T.N. (2012).
Tissue-resident memory CD8$^+$ T cells continuously patrol skin epithelia to quickly recognize local antigen.
Proc. Natl. Acad. Sci. U.S.A., 109: 19739-19744. DOI. PubMed.

Vroomans R.M., Maree A.F., De Boer R.J. & Beltman J.B. (2012).
Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens.
PLoS. Comput. Biol., 8: e1002763. DOI. PubMed.

Baltcheva I., Veel E., Volman T., Koning D., Brouwer A., Le Boudec J.Y., Tesselaar K., De Boer R.J. & Borghans J.A. (2012).
A Generalized Mathematical Model To Estimate T- and B-Cell Receptor Diversities Using AmpliCot.
Biophys. J., 103: 999-1010. DOI. PDF. PubMed.

Iwami S., Sato K., De Boer R.J., Aihara K., Miura T. & Koyanagi Y. ( 2012).
Identifying viral parameters from in vitro cell cultures.
Front. Microbiol., 3: 319. DOI. PubMed.

De Boer R.J. (2012).
Which of our modeling predictions are robust?
PLoS. Comput. Biol., 8: e1002593. DOI. PubMed.

De Boer R.J., Perelson A.S. & Ribeiro R.M. (2012).
Modelling deuterium labelling of lymphocytes with temporal and/or kinetic heterogeneity.
J. R. Soc. Interface, 9: 2191-2200. DOI. PDF. PubMed.

Van den Ham H.J. & De Boer R.J. (2012).
Cell division curtails helper phenotype plasticity and expedites helper T-cell differentiation.
Immunol Cell Biol., 90: 860-868. DOI. PDF. PubMed.

Althaus C.L. & De Boer R.J. (2012).
Impaired immune evasion in HIV through intracellular delays and multiple infection of cells.
Proc. Biol. Sci., 279: 3003-3010. DOI. PDF. PubMed.

Den Braber I., Mugwagwa T., Vrisekoop N., Westera L., Mogling R., De Boer A.B., Willems N., Schrijver E.H., Spierenburg G., Gaiser K., Mul E., Otto S.A., Ruiter A.F., Ackermans M.T., Miedema F., Borghans J.A., De Boer R.J. & Tesselaar K. (2012).
Maintenance of peripheral naive T cells is sustained by thymus output in mice but not humans.
Immunity, 36: 288-297. DOI. PDF. PubMed.

Calis J.J., De Boer R.J. & Kesmir C. (2012).
Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire.
PLoS. Comput. Biol., 8: e1002412. DOI. PDF. PubMed.

Beltman J.B., Allen C.D., Cyster J.G. & De Boer R.J. (2011).
B cells within germinal centers migrate preferentially from dark to light zone.
Proc. Natl. Acad. Sci. U.S.A., 108: 8755-8760. DOI. PDF. PubMed.

Althaus C.L. & De Boer R.J. (2011).
Implications of CTL-mediated killing of HIV-infected cells during the non-productive stage of infection.
PLoS. One., 6: e16468. DOI. PDF. PubMed.

Ganusov V.V., Barber D.L. & De Boer R.J. (2011).
Killing of targets by CD8 T cells in the mouse spleen follows the law of mass action.
PLoS. One., 6: e15959. DOI. PDF. PubMed.

De Boer R.J., Ribeiro R.M. & Perelson A.S. (2010).
Current estimates for HIV-1 production imply rapid viral clearance in lymphoid tissues.
PLoS. Comput. Biol., 6: e1000906. DOI. PDF. PubMed.

Schmid B.V., Kesmir C. & De Boer R.J. (2010).
Quantifying how MHC polymorphism prevents pathogens from adapting to the antigen presentation pathway.
Epidemics., 2: 99-108. DOI. PDF. PubMed.

Van den Ham H.J., De Waal L., Andeweg A.C. & De Boer R.J. (2010).
Identification of helper T cell master regulator candidates using the polar score method.
J. Immunol. Methods., 361: 98-109. DOI. PDF. PubMed.

Engram J.C., Cervasi B., Borghans J.A., Klatt N.R., Gordon S.N., Chahroudi A., Else J.G., Mittler R.S., Sodora D.L., De Boer R.J., Brenchley J.M., Silvestri G. & Paiardini M. (2010).
Lineage-specific T-cell reconstitution following in vivo CD4$^+$ and CD8$^+$ lymphocyte depletion in nonhuman primates.
Blood, 116: 748-758. DOI. PDF. PubMed.

Pillay J., Den Braber I., Vrisekoop N., Kwast L.M., De Boer R.J., Borghans J.A., Tesselaar K. & Koenderman L. (2010).
In vivo labeling with $^2$H$_2$O reveals a human neutrophil lifespan of 5.4 days.
Blood, 116: 625-627. DOI. PDF. PubMed.

Lyadova I.V., Tsiganov E.N., Kapina M.A., Shepelkova G.S., Sosunov V.V., Radaeva T.V., Majorov K.B., Shmitova N.S., Van den Ham H.J., Ganusov V.V., De Boer R.J., Racine R. & Winslow G.M. (2010).
In mice, tuberculosis progression is associated with intensive inflammatory response and the accumulation of gr-1 cells in the lungs.
PLoS ONE, 5: e10469. DOI. PDF. PubMed.

Althaus C.L. & De Boer R.J. (2010).
Intracellular transactivation of HIV can account for the decelerating decay of virus load during drug therapy.
Mol. Syst. Biol., 6: 348. DOI. PDF. PubMed.

Ganusov V.V., Borghans J.A. & De Boer R.J. (2010).
Explicit kinetic heterogeneity: mathematical models for interpretation of deuterium labeling of heterogeneous cell populations.
PLoS Comput. Biol., 6: e1000666. DOI. PDF. PubMed.

Beltman J.B., Maree A.F. & De Boer R.J. (2009a).
Analysing immune cell migration.
Nat. Rev. Immunol., 9: 789-798. DOI. PDF. PubMed.

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. PDF. PubMed.

Beltman J.B., Henrickson S.E., Von Andrian U.H., De Boer R.J. & Marée A.F. (2009b).
Towards estimating the true duration of dendritic cell interactions with T cells.
J Immunol Methods, 54: 54-69. DOI. PDF. PubMed.

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. PDF. PubMed.

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. PDF. PubMed.

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. 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. PDF. PubMed.

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. PDF. PubMed.

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. PDF. PubMed.

Althaus C.L. & De Boer R.J. (2008).
Dynamics of immune escape during HIV/SIV infection.
PLoS Comput. Biol., 4: e1000103. DOI. PDF. PubMed.

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. PDF. PubMed.

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. DOI. PDF. PubMed.

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. PDF. PubMed.

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. PDF. PubMed.

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. PDF. PubMed.

Ganusov V.V. & De Boer R.J. (2007).
Do most lymphocytes in humans really reside in the gut?
Trends Immunol., 28: 514-518. DOI. PDF. PubMed.

Borghans J.A., Mølgaard A., De Boer R.J. & Kesmir C. ( 2007a).
HLA alleles associated with slow progression to AIDS truly prefer to present HIV-1 p24.
PLoS ONE, 2: e920. DOI. PDF. PubMed.

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. PDF. PubMed.

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. PDF. PubMed.

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. DOI. PDF. PubMed.

De Boer R.J. (2007a).
Time scales of CD4$^+$ T cell depletion in HIV infection.
PLoS. Med., 4: e193. PDF. PubMed.

Beltman J.B., Marée 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. PDF. PubMed.

Beltman J.B., Marée 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. PDF. PubMed.

Borghans J.A.M. & De Boer R.J. (2007).
Quantification of T-cell dynamics: From telomeres to DNA labelling.
Immunol. Reviews, 216: 35-47. PDF.

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. DOI. PDF. PubMed.

De Boer R.J. (2007b).
Understanding the failure of CD8$^+$ T-cell vaccination against simian/human immunodeficiency virus.
J. Virol., 81: 2838-2848. DOI. PDF. PubMed.

Borghans J.A.M., Kesmir C. & De Boer R.J. ( 2007b).
MHC diversity in individuals and populations.
In: Flower D. & Timmis J., eds., In Silico Immunology, pp. 177-196. Springer, New York.

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. PDF. PubMed.

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. PDF. PubMed.

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. PDF. PubMed.

Ganusov V.V. & De Boer R.J. (2006).
Estimating costs and benefits of CTL escape mutations in SIV/HIV infection.
PLoS Comput. Biol., 2: 182-187. PDF. PubMed.

Muller V. & De Boer R.J. (2006).
The Integration Hypothesis: An Evolutionary Pathway to Benign SIV Infection.
PLoS. Pathog., 2: 149-151. PDF. PubMed.

De Boer R.J. (2006).
Estimating the role of thymic output in HIV infection.
Curr. Opin. HIV AIDS, 1: 16-21. PDF.

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. PDF. PubMed.

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. PDF. PubMed.

De Boer R.J. & Perelson A.S. (2005).
Estimating division and death rates from CFSE data.
J. Comp. Appl. Math., 184: 140-164. 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. PDF. PubMed.

Burroughs N.J., De Boer R.J. & Kesmir C. (2004).
Discriminating self from nonself with short peptides from large proteomes.
Immunogenetics., 56: 311-320. PDF. PubMed.

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. PDF. PubMed.

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. PDF. PubMed.

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. PDF. PubMed.

Borghans J.A.M., Beltman J.B. & De Boer R.J. (2004).
MHC polymorphism under host-pathogen coevolution.
Immunogenetics., 55: 732-739. PDF. PubMed.

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. 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. PDF. PubMed.

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. PDF. PubMed.

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. 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. PDF.

Kesmir C. & De Boer R.J. (2003a).
Spatial models of affinity maturation in germinal centers.
J. theor. Biol., 222: 9-22. PDF.

Kesmir C. & De Boer R.J. (2003b).
Clonal exhaustion as a result of immune deviation.
Bull. Math. Biol., 65: 359-374. PDF.

Hazenberg M.D., Otto S.A., Hamann D., Roos M.T., Schuitemaker H., De Boer R.J. & Miedema F. (2003a).
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. PDF. PubMed.

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. PDF. PubMed.

De Boer R.J., Mohri H., Ho D.D. & Perelson A.S. ( 2003b).
Turnover rates of B cells, T cells, and NK cells in simian immunodeficiency virus-infected and uninfected rhesus macaques.
J. Immunol., 170: 2479-2487. PDF. PubMed.

De Boer R.J., Mohri H., Ho D.D. & Perelson A.S. ( 2003c).
Estimating average cellular turnover from BrdU measurements.
Proc. R. Soc. Lond., B, Biol. Sci., 270: 849-858. PDF.

Hazenberg M.D., Borghans J.A., De Boer R.J. & Miedema F. ( 2003b).
Thymic output: a bad TREC record.
Nat. Immunol., 4: 97-99. PDF. PubMed.

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. PDF. PubMed.

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. PDF. PubMed.

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

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

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. PDF.

De Boer R.J., Oprea M., Antia R., Murali-Krishna K., Ahmed R. & Perelson A.S. (2001a).
Recruitment times, proliferation, and apoptosis rates during the CD8$^+$ T-cell response to lymphocytic choriomeningitis virus.
J. Virol., 75: 10663-10669. DOI. PDF. PubMed.

De Boer R.J., Freitas A.A. & Perelson A.S. (2001b).
Resource competition determines selection of B cell repertoires.
J. theor. Biol., 212: 333-343. PDF. PubMed.

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. PDF. PubMed.

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. PDF. PubMed.

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. PDF. PubMed.

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. PDF. PubMed.

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. PDF.

Cohen Stuart J.W., Hazenberg 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. PDF. PubMed.

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. PDF. PubMed.

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. (2000a).
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. PDF. PubMed.

Kesmir C., Borghans J.A.M. & De Boer R.J. (2000).
Diversity of human $\alpha$$\beta$ T cell receptors.
Science, 288: 1135a. 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. PDF. PubMed.

Hazenberg M.D., Cohen Stuart J.W., Otto S.A., Borleffs J.C., Boucher C.A., De Boer R.J., Miedema F. & Hamann D. (2000b).
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. PDF. PubMed.

Borghans J.A.M., Taams L.S., Wauben M.H. & De Boer R.J. ( 1999a).
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. PDF. PubMed.

Kesmir C. & De Boer R.J. (1999).
A mathematical model on germinal center kinetics and termination.
J. Immunol., 163: 2463-2469. PDF. PubMed.

Borghans J.A.M., Noest A.J. & De Boer R.J. (1999b).
How specific should immunological memory be?
J. Immunol., 163: 569-575. PDF. PubMed.

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. PubMed.

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. PubMed.

Cohen Stuart J.W., Slieker W.A., Rijkers G.T., Noest A., Boucher C.A., Suur M.H., De Boer R.J., Geelen S.P., Scherpbier H.J., Hartwig N.G., Hooijkaas H., Roos M.T., De Graeff-Meeder B. & De Groot R. (1998).
Early recovery of CD4$^+$ T lymphocytes in children on highly active antiretroviral therapy. Dutch study group for children with HIV infections.
AIDS, 12: 2155-2159. PDF. PubMed.

De Boer R.J., Boucher C.A. & Perelson A.S. (1998).
Target cell availability and the successful suppression of HIV by hydroxyurea and didanosine.
AIDS, 12: 1567-1570. PDF. PubMed.

Kesmir C. & De Boer R.J. (1998).
How does cytopathicity affect the production of neutralizing antibody?
Scand. J. Immunol., 48: 347-349. PubMed.

Borghans J.A.M. & De Boer R.J. (1998a).
Neonatal tolerance revisited by mathematical modelling.
Scand. J. Immunol., 48: 283-285. PubMed.

Borghans J.A.M. & De Boer R.J. (1998b).
Crossreactivity of the T-cell receptor.
Immunol. Today, 19: 428-429. PDF. PubMed.

Borghans J.A.M., De Boer R.J., Sercarz E. & Kumar V. (1998).
T cell vaccination in experimental autoimmune encephalomyelitis: a mathematical model.
J. Immunol., 161: 1087-1093. PDF. PubMed.

Fleury S., De Boer R.J., Rizzardi G.P., Wolthers K.C., Otto S.A., Welbon C.C., Graziosi C., Knabenhans C., Soudeyns H., Bart P.A., Gallant S., Corpataux J.M., Gillet M., Meylan P., Schnyder P., Meuwly J.Y., Spreen W., Glauser M.P., Miedema F. & Pantaleo G. (1998).
Limited CD4$^+$ T-cell renewal in early HIV-1 infection: effect of highly active antiretroviral therapy.
Nat. Med., 4: 794-801. PubMed.

De Boer R.J. & Perelson A.S. (1998).
Target cell limited and immune control models of HIV infection: A comparison.
J. theor. Biol., 190: 201-214. PDF. PubMed.

Pakker N.G., Notermans D.W., De Boer R.J., Roos M.T., De Wolf F., Hill A., Leonard J.M., Danner S.A., Miedema F. & Schellekens P.T. (1998).
Biphasic kinetics of peripheral blood T cells after triple combination therapy in HIV-1 infection: a composite of redistribution and proliferation.
Nat. Med., 4: 208-214. PubMed.

De Boer R.J. & Noest A.J. (1998).
T cell renewal rates, telomerase, and telomere length shortening.
J. Immunol., 160: 5832-5837. PDF. PubMed.

De Jong M.D., De Boer R.J., De Wolf F., Foudraine N.A., Boucher C.A., Goudsmit J. & Lange J.M. (1997).
Overshoot of HIV-1 viraemia after early discontinuation of antiretroviral treatment.
AIDS, 11: F79-F84. PubMed.

Noest A.J., Takumi K. & D Boer R.J. (1997).
Pattern formation in B-cell immune networks: Domains and dots in shape-space.
Physica D, 105: 285-306.

Huisman G. & De Boer R.J. (1997).
A formal derivation of the ``Beddington'' functional response.
J. theor. Biol., 185: 389-400.

Goudsmit J., De Ronde A., De Rooij E. & De Boer R.J. (1997).
Broad spectrum of in vivo fitness of human immunodeficiency virus type 1 subpopulations differing at reverse transcriptase codons 41 and 215.
J. Virol., 71: 4479-4484. PDF. PubMed.

De Boer R.J. & Perelson A.S. (1997).
Competitive control of the self-renewing T cell repertoire.
Int. Immunol., 9: 779-790. PubMed.

Stilianakis N.I., Boucher C.A., De Jong M.D., Van Leeuwen R., Schuurman R. & De Boer R.J. (1997).
Clinical data sets of human immunodeficiency virus type 1 reverse transcriptase-resistant mutants explained by a mathematical model.
J. Virol., 71: 161-168. PDF. PubMed.

De Jong M.D., Veenstra J., Stilianakis N.I., Schuurman R., Lange J.M., De Boer R.J. & Boucher C.A. (1996).
Host-parasite dynamics and outgrowth of virus containing a single K70R amino acid change in reverse transcriptase are responsible for the loss of human immunodeficiency virus type 1 RNA load suppression by zidovudine.
Proc. Natl. Acad. Sci. U.S.A., 93: 5501-5506. PDF. PubMed.

Takumi K. & De Boer R.J. (1996).
Self assertion modeled as a network repertoire of multi-determinant antibodies.
J. theor. Biol., 183: 55-66. PubMed.

De Boer R.J. & Boucher C.A. (1996).
Anti-CD4 therapy for AIDS suggested by mathematical models.
Proc. R. Soc. Lond., B, Biol. Sci., 263: 899-905. PDF. PubMed.

De Boer R.J., Boerlijst M.C., Sulzer B. & Perelson A.S. (1996).
A new bell-shaped function for idiotypic interactions based on cross-linking.
Bull. Math. Biol., 58: 285-312. PubMed.

Sulzer B., De Boer R.J. & Perelson A.S. (1996).
Cross-linking reconsidered: binding and cross-linking fields and the cellular response.
Biophys. J., 70: 1154-1168. PubMed.

Borghans J.A.M., De Boer R.J. & Segel L.A. (1996).
Extending the quasi-steady state approximation by changing variables.
Bull. Math. Biol., 58: 43-63. PDF. PubMed.

Scheffer M. & De Boer R.J. (1995).
Implications of spatial heterogeneity for the paradox of enrichment.
Ecology, 76: 2270-2277.

De Boer R.J. & Perelson A.S. (1995).
Towards a general function describing T cell proliferation.
J. theor. Biol., 175: 567-576. PubMed.

De Boer R.J. & Borghans J.A.M. (1995).
Theoretical models for T-cell vaccination.
In: Zhang J. & Raus F., eds., Autoimmune disease and T cell vaccination: perpectives on clonotypic regulation and propects for therapy., pp. 61-82. R.G. Landes company, Austin, Texas.

De Boer R.J. (1995).
The evolution of polymorphic compatibility molecules.
Mol. Biol. Evol., 12: 494-502.

Borghans J.A.M. & De Boer R.J. (1995).
A minimal model for T-cell vaccination.
Proc. R. Soc. Lond., B, Biol. Sci., 259: 173-178. PubMed.

De Boer R.J. & Perelson A.S. (1994).
T cell repertoires and competitive exclusion.
J. theor. Biol., 169: 375-390. PDF. PubMed.

Merrill S., De Boer R.J. & Perelson A.S. (1994).
Development of the T-cell repertoire: clone size distribution.
Rocky Mt. J. Math., 24: 214-231.

De Boer R.J. & Boerlijst M.C. (1994).
Diversity and virulence thresholds in AIDS.
Proc. Natl. Acad. Sci. U.S.A., 91: 544-548. PDF. PubMed.

De Boer R.J. & Perelson A.S. (1993).
How diverse should the immune system be?
Proc. R. Soc. Lond., B, Biol. Sci., 252: 171-175. PDF. PubMed.

De Boer R.J., Perelson A.S. & Kevrekidis I.G. ( 1993a).
Immune network behavior-II. From oscillations to chaos and stationary states.
Bull. Math. Biol., 55: 781-816. PDF. PubMed.

De Boer R.J., Perelson A.S. & Kevrekidis I.G. ( 1993b).
Immune network behavior-I. From stationary states to limit cycle oscillations.
Bull. Math. Biol., 55: 745-780. PDF. PubMed.

Perelson A.S., Kirschner D.E. & De Boer R.J. (1993).
Dynamics of HIV infection of CD4$^+$ T cells.
Math. Biosci., 114: 81-125. PDF. PubMed.

De Boer R.J., Neumann A.U., Perelson A.S., Segel L.A. & Weisbuch G.W. (1993c).
Recent approaches to immune networks.
In: Demongeot J. & Capasso V., eds., Mathematics Applied to Biology and Medicine, pp. 243-261. Wuerz Publishing, Winnipeg, Canada.

De Boer R.J., Van der Laan J.D. & Hogeweg P. (1992a).
Randomness and pattern scale in the immune network.
In: Stein W.D. & Varela F.J., eds., Thinking about Biology, SFI Lectures in Complex Systems, pp. 231-252. Addison-Wesley, Redwood City, CA.

De Boer R.J., Hogeweg P. & Perelson A.S. (1992b).
Growth and recruitment in the immune network.
In: Perelson A.S. & Weisbuch G., eds., Theoretical and Experimental insight into Immunology, vol. H66 of NATO ASI Series, pp. 223-247. Springer-Verlag, Berlin.

De Boer R.J., Segel L.A. & Perelson A.S. (1992c).
Pattern formation in one- and two-dimensional shape-space models of the immune system.
J. theor. Biol., 155: 295-333. PubMed.

De Boer R.J. (1991a).
Recent developments in idiotypic network theory.
Neth. J. Med., 39: 254-262. PubMed.

De Boer R.J. (1991b).
Allelic variations of human TCR V gene products.
Immunol. Today, 12: 169. PubMed.

Perelson A.S. & De Boer R.J. (1991).
Autoimmunity and T cell vaccination in a model idiotypic network.
J. Cell. Biochem., Suppl. 15A: 266.

De Boer R.J. & Perelson A.S. (1991).
Size and connectivity as emergent properties of a developing immune network.
J. theor. Biol., 149: 381-424. PubMed.

De Boer R.J., Kevrekidis I.G. & Perelson A.S. (1990).
A simple idiotypic network model with complex dynamics.
Chemical Eng. Science, 45: 2375-2382.

Weisbuch G., De Boer R.J. & Perelson A.S. (1990).
Localized memories in idiotypic networks.
J. theor. Biol., 146: 483-499. PubMed.

De Boer R.J. (1989a).
Poor repertoire selection in symmetric idiotypic network models.
Immunol. Lett., 22: 101-112. PubMed.

De Boer R.J., Ballieux R.E. & Hogeweg P. (1989).
Theoretical immunology: Proceedings of a one-day symposium held april 1989.
Immunol. Lett., 22: 79-82.

De Boer R.J. (1989b).
Extensive percolation in reasonable idiotypic networks.
In: Atlan H. & Cohen I., eds., Theories of Immune Networks. Springer-Verlag, Berlin.

De Boer R.J. (1989c).
Information processing in immune systems: clonal selection versus idiotypic network models.
In: Goldbeter A., ed., Cell to Cell Signalling: From Experiments to Theoretical Models, pp. 285-302. Academic Press, London.

De Boer R.J. (1989d).
Clonal Selection Versus Idiotypic Network Models of the Immune System: A Bioinformatic Approach..
Ph.D. thesis, Theoretical Biology, Utrecht University.

De Boer R.J. & Hogeweg P. (1989a).
Idiotypic networks incorporating T-B cell co-operation. The conditions for percolation.
J. theor. Biol., 139: 17-38. PubMed.

De Boer R.J. & Hogeweg P. (1989b).
Unreasonable implications of reasonable idiotypic network assumptions.
Bull. Math. Biol., 51: 381-408. PubMed.

De Boer R.J. & Hogeweg P. (1989c).
Memory but no suppression in low-dimensional symmetric idiotypic networks.
Bull. Math. Biol., 51: 223-246. PubMed.

De Boer R.J. & Hogeweg P. (1989d).
Stability of symmetric idiotypic networks-a critique of Hoffmann's analysis.
Bull. Math. Biol., 51: 217-222. PubMed.

De Boer R.J. (1988).
Symmetric idiotypic networks: connectance and switching, stability, and suppression.
In: Perelson A., ed., Theoretical Immunology, Part Two, vol. III of SFI Studies in the Science of Complexity, pp. 265-289. Addison-Wesley, Redwood City, CA.

De Boer R.J. (1987).
Self tolerance due to memory accumulation.
In: Matzinger P., Flajnik M., Nemazee D., Rammensee H.G., Rolink T., Stockinger B. & Nicklin L., eds., The Tolerance Workshop 1986, vol. 2, pp. 58-72. Editiones ``Roche'' Basle, Switzerland.

Peters J.P., Rademakers L.H., De Boer R.J. & Van Unnik J.A. ( 1987).
Cellular composition of follicles of follicle centre cell lymphomas in relation to germinal centres of reactive lymph nodes. A morphometrical electromicroscopical study.
J. Pathol., 153: 233-244. PubMed.

De Boer R.J. & Hogeweg P. (1987a).
Self-nonself discrimination due to immunological nonlinearities: the analysis of a series of models by numerical methods.
IMA. J. Math. Appl. Med. Biol., 4: 1-32. PubMed.

De Boer R.J. & Hogeweg P. (1987b).
Immunological discrimination between self and non-self by precursor depletion and memory accumulation.
J. theor. Biol., 124: 343-369. PubMed.

De Boer R.J., Michelson S. & Hogeweg P. (1986).
Concomitant immunization by the fully antigenic counterparts prevents modulated tumor cells from escaping cellular immune elimination.
J. Immunol., 136: 4319-4327. PubMed.

De Boer R.J. & Hogeweg P. (1986a).
Interactions between macrophages and T-lymphocytes: tumor sneaking through intrinsic to helper T cell dynamics.
J. theor. Biol., 120: 331-351. PubMed.

De Boer R.J. & Hogeweg P. (1986b).
Implications of macrophage T-lymphocyte interactions for tumor rejectability.
In: Hoffmann G.W. & Hraba T., eds., Immunology and Epidemiology, vol. 65 of Lecture Notes in Biomathematics, pp. 120-140. Springer-Verlag, Berlin.

De Weger R.A., Dullens H.F.J., De Boer R.J. & Den Otter W. (1985).
Mathematical analysis of the cellular immune reactions against tumor cells.
Immunol. Today, 6: 316-317.

De Boer R.J., Hogeweg P., Dullens H.F., De Weger R.A. & Den Otter W. (1985).
Macrophage T lymphocyte interactions in the anti-tumor immune response: a mathematical model.
J. Immunol., 134: 2748-2758. PubMed.

De Boer R.J. & Hogeweg P. (1985).
Tumor escape from immune elimination: simplified precursor bound cytotoxicity models.
J. theor. Biol., 113: 719-736. PubMed.

Van Schaik C.P., Van Noordwijk M.A., De Boer R. & Den Tonkelaar I. ( 1983).
The effect of group size on time budgets and social behaviour in wild long-tailed macaques (macaca fascicularis).
Behav. Ecol. Sociobiol., 13: 173-181.