Bibliography

Schmid B., Kesmir C. & de Boer R. (2010).
Quantifying how mhc polymorphism prevents pathogens from adapting to the antigen presentation pathway.
Epidemics, In Press, Corrected Proof: -. DOI.

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, 0: O. DOI.

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. MEDLINE.

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 2H2O reveals a human neutrophil lifespan of 5.4 days.
Blood, 116: 625-627. DOI. MEDLINE.

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-1dim cells in the lungs.
PLoS ONE, 5: e10469. DOI.

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. DOI.

Ganusov V.V., Borghans J.A.M. & 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.

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

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.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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

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. DownLoad PDF. 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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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.

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. DownLoad PDF. MEDLINE.

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

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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

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

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. DownLoad PDF. MEDLINE.

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.

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. DownLoad PDF. MEDLINE.

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

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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

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. 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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. 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. DownLoad PDF.

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

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

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad 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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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

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

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. DownLoad 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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. 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. DownLoad 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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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

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

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.

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.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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

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

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

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. DownLoad PDF. MEDLINE.

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. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. MEDLINE.

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

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. MEDLINE.

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. DownLoad PDF. MEDLINE.

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

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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

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. DownLoad PDF. MEDLINE.

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. MEDLINE.

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. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. MEDLINE.

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. MEDLINE.

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

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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. DownLoad PDF. MEDLINE.

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

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. MEDLINE.

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

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

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

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. MEDLINE.

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. MEDLINE.

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

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. MEDLINE.

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

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

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

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. MEDLINE.

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. MEDLINE.

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. MEDLINE.

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. MEDLINE.

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. MEDLINE.

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. MEDLINE.

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

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.