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Rob J. de Boer |
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Publications
De Greef P.C., Njeru S.N., Benz C., Fillatreau S., Malissen B., Agenès
F., De Boer R.J. & Kirberg J. (2024).
The TCR assigns naive T cells to a preferred lymph node.
Sci. Adv., 10: eadl0796.
DOI.
PubMed.
De Boer R.J., Kesmir C., Perelson A.S. & Borghans J.A.M. (2024).
Is the exquisite specificity of lymphocytes generated by thymic
selection or due to evolution?
Front. Immunol., 15: 1266349.
DOI.
PubMed.
De Greef P.C., Lanfermeijer J., Hendriks M., Cevirgel A., Vos M., Borghans
J.A.M., Van Baarle D. & De Boer R.J. (2023).
On the feasibility of using TCR sequencing to follow a vaccination
response - lessons learned.
Front. Immunol., 14: 1210168.
DOI.
PubMed.
Schrom E., Kinzig A., Forrest S., Graham A.L., Levin S.A., Bergstrom C.T.,
Castillo-Chavez C., Collins J.P., De Boer R.J., Doupé A., Ensafi R., Feldman
S., Grenfell B.T., Halderman J.A., Huijben S., Maley C., Moses M., Perelson
A.S., Perrings C., Plotkin J., Rexford J. & Tiwari M. (2023).
Challenges in cybersecurity: Lessons from biological defense
systems.
Math. Biosci., 362: 109024.
DOI.
PubMed.
De Boer R.J. & Yates A.J. (2023).
Modeling T Cell Fate.
Annu. Rev. Immunol., 41: 513–532.
DOI.
PubMed.
De Boer R.J., Tesselaar K. & Borghans J.A.M. (2023).
Better safe than sorry: Naive T-cell dynamics in healthy ageing.
Semin. Immunol., 70: 101839.
DOI.
PubMed.
Schroeter J. & De Boer R.J. (2023).
What explains the poor contraction of the viral load during
paediatric HIV infection?
J. theor. Biol., 570: 111521.
DOI.
PubMed.
Schroeter J., Borghans J.A.M., Bitter W.M., Van Dongen J.J.M. & De Boer
R.J. (2023).
Age-Dependent Normalization Functions for T Lymphocytes in
Healthy Individuals.
J. Immunol., 210: 1882–1888.
DOI.
PubMed.
Mijnheer G., Servaas N.H., Leong J.Y., Boltjes A., Spierings E., Chen P.,
Lai L., Petrelli A., Vastert S., De Boer R.J., Albani S., Pandit A. &
Van Wijk F. (2023).
Compartmentalization and persistence of dominant (regulatory) T
cell clones indicates antigen skewing in juvenile idiopathic arthritis.
Elife, 12.
DOI.
PubMed.
Swain A.C., Borghans J.A.M. & De Boer R.J. (2022).
Effect of cellular aging on memory T-cell homeostasis.
Front. Immunol., 13: 947242.
DOI.
PubMed.
Bresser K., Kok L., Swain A.C., King L.A., Jacobs L., Weber T.S., Perié
L., Duffy K.R., De Boer R.J., Scheeren F.A. & Schumacher T.N. (2022).
Replicative history marks transcriptional and functional disparity in
the CD8+ T cell memory pool.
Nat. Immunol., 23: 791–801.
DOI.
PubMed.
Schroeter J., Anelone A.J.N. & De Boer R.J. (2022).
Quantification of CD4 Recovery in Early-Treated Infants
Living With HIV.
J. Acquir. Immune Defic. Syndr., 89: 546–557.
DOI.
PubMed.
Baliu-Pique M., Drylewicz J., Zheng X., Borkner L., Swain A.C., Otto S.A.,
De Boer R.J., Tesselaar K., Cicin-Sain L. & Borghans J.A.M. (2022).
Turnover of Murine Cytomegalovirus-Expanded CD8
T
Cells Is Similar to That of Memory Phenotype T Cells and
Independent of the Magnitude of the Response.
J. Immunol., 208: 799–806.
DOI.
PubMed.
Van den Berg S.P.H., Derksen L.Y., Drylewicz J., Nanlohy N.M., Beckers L.,
Lanfermeijer J., Gessel S.N., Vos M., Otto S.A., De Boer R.J., Tesselaar K.,
Borghans J.A.M. & Van Baarle D. (2021).
Quantification of T-cell dynamics during latent cytomegalovirus
infection in humans.
PLOS Pathog., 17: e1010152.
DOI.
PubMed.
Cosgrove J., Hustin L.S.P., De Boer R.J. & Perié L. (2021).
Hematopoiesis in numbers.
Trends Immunol., 42: 1100–1112.
DOI.
PubMed.
Castro M. & De Boer R.J. (2021).
The limitations, dangers, and benefits of simple methods for testing
identifiability.
PLOS Comput. Biol., 17: e1009425.
DOI.
PubMed.
De Greef P.C. & De Boer R.J. (2021).
TCR
rearrangements without a D segment are common,
abundant, and public.
Proc. Natl. Acad. Sci. U.S.A., 118: e1009425.
DOI.
PubMed.
Weigelin B., Den Boer A.T., Wagena E., Broen K., Dolstra H., De Boer R.J.,
Figdor C.G., Textor J. & Friedl P. (2021).
Cytotoxic T cells are able to efficiently eliminate cancer cells by
additive cytotoxicity.
Nat. Commun., 12: 5217.
DOI.
PubMed.
Wortel I.M.N., Niculescu I., Kolijn P.M., Gov N.S., De Boer R.J. & Textor
J. (2021).
Local actin dynamics couple speed and persistence in a cellular
Potts model of cell migration.
Biophys. J., 120: 2609–2622.
DOI.
PubMed.
Baliu-Piqué M., Van Hoeven V., Drylewicz J., Van der Wagen L.E., Janssen
A., Otto S.A., Van Zelm M.C., De Boer R.J., Kuball J., Borghans J.A. &
Tesselaar K. (2021).
Cell-density independent increased lymphocyte production and loss
rates post-autologous HSCT.
Elife, 10: e1010152.
DOI.
PubMed.
Pandit A. & De Boer R.J. (2021).
Delayed Differentiation Makes Many Models Compatible with Data
for CD8+ T Cell Differentiation, pp. 121–132.
Springer International Publishing, Cham.
DOI.
Castro M. & De Boer R.J. (2020).
Testing structural identifiability by a simple scaling method.
PLOS Comput. Biol., 16: e1008248.
DOI.
PubMed.
Silva-Cardoso S.C., Tao W., Angiolilli C., Lopes A.P., Bekker C.P.J.,
Devaprasad A., Giovannone B., Van Laar J., Cossu M., Marut W., Hack E.,
De Boer R.J., Boes M., Radstake T.R.D.J. & Pandit A. (2020).
CXCL4 Links Inflammation and Fibrosis by Reprogramming
Monocyte-Derived Dendritic Cells in vitro.
Front. Immunol., 11: 2149.
DOI.
PubMed.
Morris S.E., Dziobek-Garrett L., Strehlau R., Schröter J., Shiau S.,
Anelone A.J.N., Paximadis M., De Boer R.J., Abrams E.J., Tiemessen C.T., Kuhn
L. & Yates A.J. (2020).
Quantifying the dynamics of HIV decline in perinatally-infected
neonates on antiretroviral therapy.
J Acquir Immune Defic Syndr., 0: O.
DOI.
PubMed.
De Greef P.C., Oakes T., Gerritsen B., Ismail M., Heather J.M., Hermsen
R., Chain B. & De Boer R.J. (2020).
The naive T-cell receptor repertoire has an extremely broad
distribution of clone sizes.
Elife, 9.
DOI.
Schroter J., Anelone A.J.N., Yates A.J. & De Boer R.J. (2020).
Time to Viral Suppression in Perinatally HIV-Infected
Infants Depends on the Viral Load and CD4 T-Cell Percentage
at the Start of Treatment.
J. Acquir. Immune Defic. Syndr., 83: 522–529.
DOI.
PubMed.
Wortel I.M.N., Kesmir C., De Boer R.J., Mandl J.N. & Textor J. ( 2020).
Is T Cell Negative Selection a Learning Algorithm?
Cells, 9: 690.
DOI.
PubMed.
Gerritsen B., Pandit A., Zaaraoui-Boutahar F., Van den Hout M.C.G.N.,
Van IJcken W.F.J., De Boer R.J. & Andeweg A.C. (2020).
Characterization of the ferret TRB locus guided by V, D, J,
and C gene expression analysis.
Immunogenetics., 72: 101–108.
DOI.
PubMed.
Doekes H.M., De Boer R.J. & Hermsen R. (2019).
Toxin production spontaneously becomes regulated by local cell
density in evolving bacterial populations.
PLOS Comput. Biol., 15: e1007333.
Pandit A. & De Boer R.J. (2019).
Stochastic Inheritance of Division and Death Times
Determines the Size and Phenotype of CD8 T Cell Families.
Front. Immunol., 10: 436.
PubMed.
Soekarjo K.M.W., Textor J. & De Boer R.J. (2019).
Local Attachment Explains Small World-like Properties of
Fibroblastic Reticular Cell Networks in Lymph Nodes.
J. Immunol., 202: 3318–3325.
PubMed.
Baliu-Pique M., Verheij M.W., Drylewicz J., Ravesloot L., De Boer R.J.,
Koets A., Tesselaar K. & Borghans J.A.M. (2018).
Short Lifespans of Memory T-cells in Bone Marrow, Blood,
and Lymph Nodes Suggest That T-cell Memory Is Maintained by
Continuous Self-Renewal of Recirculating Cells.
Front. Immunol., 9: 2054.
DOI.
PubMed.
Borghans J.A.M., Tesselaar K. & De Boer R.J. (2018).
Current best estimates for the average lifespans of mouse and human
leukocytes: reviewing two decades of deuterium-labeling experiments.
Immunol. Rev., 285: 233–248.
DOI.
PubMed.
Muller V., De Boer R.J., Bonhoeffer S. & Szathmary E. (2018).
An evolutionary perspective on the systems of adaptive immunity.
Biol. Rev. Camb. Philos. Soc., 93: 505–528.
PubMed.
Carrillo-Bustamante P., De Boer R.J. & Kesmir C. (2018).
Specificity of inhibitory KIRs enables NK cells to detect changes
in an altered peptide environment.
Immunogenetics., 70: 87–97.
PubMed.
De Boer R.J. & Perelson A.S. (2017).
How germinal centers evolve broadly neutralizing antibodies: the
breadth of the follicular helper T cell response.
J Virol., 91: e00983–17.
DOI.
Van Hoeven V., Drylewicz J., Westera L., Den Braber I., Mugwagwa T.,
Tesselaar K., Borghans J.A.M. & De Boer R.J. (2017).
Dynamics of Recent Thymic Emigrants in Young Adult Mice.
Front. Immunol., 8: 933.
DOI.
PubMed.
Tak T., Drylewicz J., Conemans L., De Boer R.J., Koenderman L., Borghans
J.A.M. & Tesselaar K. (2017).
Circulatory and maturation kinetics of human monocyte subsets in
vivo.
Blood, 130: 1474–1477.
DOI.
PubMed.
De Visser L., H de Boer J., T Rijkers G., Wiertz K., Van den Ham H.J.,
De Boer R., M van Loon A., Rothova A. & De Groot-Mijnes J.D. (2017).
Cytokines and Chemokines Involved in Acute Retinal
Necrosis.
Invest. Ophthalmol. Vis. Sci., 58: 2139–2151.
DOI.
PubMed.
Gadhamsetty S., Maree A.F.M., Beltman J.B. & De Boer R.J. ( 2017a).
A Sigmoid Functional Response Emerges When Cytotoxic T
Lymphocytes Start Killing Fresh Target Cells.
Biophys. J., 112: 1221–1235.
DOI.
PubMed.
Gadhamsetty S., Maree A.F., De Boer R.J. & Beltman J.B. ( 2017b).
Tissue Dimensionality Influences the Functional Response of
Cytotoxic T Lymphocyte-Mediated Killing of Targets.
Front. Immunol., 7: 668.
DOI.
PubMed.
Asquith B. & De Boer R.J. (2016).
How lymphocytes add up.
Nat. Immunol., 18: 12–13.
DOI.
PubMed.
Textor J., Mandl J.N. & De Boer R.J. (2016).
The Reticular Cell Network: A Robust Backbone for
Immune Responses.
PLoS Biol., 14: e2000827.
DOI.
PubMed.
Woolthuis R.G., Van Dorp C.H., Kesmir C., De Boer R.J. & Van Boven M.
(2016).
Long-term adaptation of the influenza A virus by escaping cytotoxic
T-cell recognition.
Sci. Rep., 6: 33334.
DOI.
PubMed.
Gerritsen B., Pandit A., Andeweg A.C. & De Boer R.J. (2016).
RTCR: a pipeline for complete and accurate recovery of T cell
repertoires from high throughput sequencing data.
Bioinformatics, 32: 3098–3106.
DOI.
PubMed.
Gadhamsetty S., Coorens T. & De Boer R.J. (2016).
Notwithstanding circumstantial alibis, cytotoxic T cells can be
major killers of HIV-1-infected cells.
J. Virol., 90: 7066–7083.
DOI.
PubMed.
Ikeda H., Nakaoka S., De Boer R.J., Morita S., Misawa N., Koyanagi Y.,
Aihara K., Sato K. & Iwami S. (2016).
Quantifying the effect of Vpu on the promotion of HIV-1
replication in the humanized mouse model.
Retrovirology., 13: 23.
DOI.
PubMed.
Drylewicz J., Vrisekoop N., Mugwagwa T., De Boer A.B., Otto S.A.,
Hazenberg M.D., Tesselaar K., De Boer R.J. & Borghans J.A. (2016).
Reconciling Longitudinal Naive T-Cell and TREC Dynamics
during HIV-1 Infection.
PLoS One., 11: e0152513.
DOI.
PubMed.
Olde Rikkert M.G., Dakos V., Buchman T.G., Boer R.J., Glass L., Cramer
A.O., Levin S., Van Nes E., Sugihara G., Ferrari M.D., Tolner E.A., Van de
Leemput I., Lagro J., Melis R. & Scheffer M. (2016).
Slowing Down of Recovery as Generic Risk Marker for Acute
Severity Transitions in Chronic Diseases.
Crit. Care. Med., 44: 601–606.
DOI.
PubMed.
Carrillo-Bustamante P., Kesmir C. & De Boer R.J. (2016).
The evolution of natural killer cell receptors.
Immunogenetics., 68: 3–18.
DOI.
PubMed.
Perie L., Duffy K.R., Kok L., De Boer R.J. & Schumacher T.N. ( 2015).
The Branching Point in Erythro-Myeloid Differentiation.
Cell, 163: 1655–1662.
DOI.
PubMed.
Pandit A. & De Boer R.J. (2015).
HIV-1 CCR5 gene therapy will fail unless it is combined with a
suicide gene.
Sci. Rep., 5: 18088.
DOI.
PubMed.
Ariotti S., Beltman J.B., Borsje R., Hoekstra M.E., Halford W.P., Haanen
J.B., De Boer R.J. & Schumacher T.N. (2015).
Subtle CXCR3-Dependent Chemotaxis of CTLs within Infected
Tissue Allows Efficient Target Localization.
J. Immunol., 195: 5285–5295.
DOI.
PubMed.
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 during
HIV-1 infection?
Immunol. Lett., 168: 1–6.
DOI.
PubMed.
Vrisekoop N., Drylewicz J., Van Gent R., Mugwagwa T., Van Lelyveld S.F.,
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, 29: 2071–2080.
DOI.
PubMed.
Carrillo-Bustamante P., Kesmir C. & De Boer R.J. ( 2015a).
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. ( 2015b).
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.
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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.
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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 
H
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.
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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.
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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.
Milutinović 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.
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PubMed.
De Boer R.J. (2007b).
Understanding the failure of CD8 T-cell vaccination against
simian/human immunodeficiency virus.
J. Virol., 81: 2838–2848.
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PubMed.
Borghans J.A.M., Keşmir 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 
and
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.
Keşmir C. & De Boer R.J. (2003a).
Spatial models of affinity maturation in germinal centers.
J. theor. Biol., 222: 9–22.
PDF.
Keşmir 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.
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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.
Keşmir C., Borghans J.A.M. & De Boer R.J. (2000).
Diversity of human 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.
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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.
Keşmir 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.
Keşmir 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.
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.
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.
