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Prof. dr. R.J. (Rob) de Boer

Emeritus 
Bètawetenschappen
Biologie
Biodynamics and Biocomplexity
Theoretical Biology
Theoretical Biology
Hugo R. Kruytgebouw
Padualaan 8
Kamer N.601
3584 CH Utrecht

Prof. dr. R.J. (Rob) de Boer

Emeritus
Theoretical Biology
r.j.deboer@uu.nl
Profiel Publicaties Activiteiten Onderwijs Nevenwerkzaamheden Contact
Profiel Publicaties Activiteiten Onderwijs Nevenwerkzaamheden Contact
Expertises
Onderzoeksthema's

Publicaties

2022

Wetenschappelijke publicaties

Baliu-Piqué, 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. Journal of Immunology, 208(4), 799-806. https://doi.org/10.4049/jimmunol.2100883
https://dspace.library.uu.nl/bitstream/handle/1874/424076/ji2100883.pdf?sequence=1
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. Nature Immunology, 23(5), 791-801. https://doi.org/10.1038/s41590-022-01171-9
EPIICAL consortium (2022). Quantification of CD4 Recovery in Early-Treated Infants Living With HIV. Journal of acquired immune deficiency syndromes (1999), 89(5), 546-557. https://doi.org/10.1097/QAI.0000000000002905
Swain, A. C., Borghans, J. A. M., & de Boer, R. J. (2022). Effect of cellular aging on memory T-cell homeostasis. Frontiers in Immunology, 13, [947242]. https://doi.org/10.3389/fimmu.2022.947242

2021

Wetenschappelijke publicaties

Cosgrove, J., Hustin, L. S. P., de Boer, R. J., & Perié, L. (2021). Hematopoiesis in numbers. Trends in Immunology, 42(12), 1100-1112. https://doi.org/10.1016/j.it.2021.10.006
https://dspace.library.uu.nl/bitstream/handle/1874/424108/1_s2.0_S1471490621002118_main.pdf?sequence=1
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 Pathogens, 17(12), 1-27. [e1010152]. https://doi.org/10.1371/journal.ppat.1010152
Pandit, A., & Boer, R. J. D. (2021). Delayed Differentiation Makes Many Models Compatible with Data for CD8+ T Cell Differentiation. In C. Molina-París, & G. Lythe (Eds.), Mathematical, Computational and Experimental T Cell Immunology (pp. 121-132). Springer. https://doi.org/10.1007/978-3-030-57204-4_8
https://dspace.library.uu.nl/bitstream/handle/1874/428240/978_3_030_57204_4_8.pdf?sequence=1
de Greef, P. C., & de Boer, R. J. (2021). TCRβ rearrangements without a D segment are common, abundant, and public. Proceedings of the National Academy of Sciences of the United States of America, 118(39), 1-7. [e2104367118]. https://doi.org/10.1073/pnas.2104367118
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. M., & Tesselaar, K. (2021). Cell-density independent increased lymphocyte production and loss rates post-autologous HSCT. eLife, 10, 1-22. [e59775]. https://doi.org/10.7554/eLife.59775
Castro, M., & de Boer, R. J. (2021). The limitations, dangers, and benefits of simple methods for testing identifiability. PLoS Computational Biology, 17(10), 1-2. [e1009425]. https://doi.org/10.1371/journal.pcbi.1009425
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. Nature Communications, 12(1), 1-12. [5217]. https://doi.org/10.1038/s41467-021-25282-3
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. Biophysical Journal, 120(13), 2609-2622. https://doi.org/10.1016/j.bpj.2021.04.036
https://dspace.library.uu.nl/bitstream/handle/1874/413375/1_s2.0_S0006349521004240_main.pdf?sequence=1

2020

Wetenschappelijke publicaties

Dorp, C. H. V., Boven, M. V., & Boer, R. J. D. (2020). Modeling the immunological pre-adaptation of HIV-1. (pp. 1-39). bioRxiv. https://doi.org/10.1101/2020.01.08.897983
Wortel, I. M. N., Keşmir, C., de Boer, R. J., Mandl, J. N., & Textor, J. (2020). Is T Cell Negative Selection a Learning Algorithm? Cells, 9(3), [690]. https://doi.org/10.3390/cells9030690
Castro, M., & de Boer, R. J. (2020). Testing structural identifiability by a simple scaling method. PLoS Computational Biology, 16(11), [e1008248]. https://doi.org/10.1371/journal.pcbi.1008248
Schröter, 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. Journal of Acquired Immune Deficiency Syndromes, 83(5), 522-529. https://doi.org/10.1097/QAI.0000000000002291
https://dspace.library.uu.nl/bitstream/handle/1874/409829/Time_to_Viral_Suppression_in_Perinatally.11.pdf?sequence=1
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, 1-24. [e49900]. https://doi.org/10.7554/eLife.49900
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. Journal of acquired immune deficiency syndromes (1999), 85(2), 209-218. https://doi.org/10.1097/QAI.0000000000002425
https://dspace.library.uu.nl/bitstream/handle/1874/409827/Quantifying_the_Dynamics_of_HIV_Decline_in.12.pdf?sequence=1
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. Frontiers in Immunology, 11, 1-17. [2149]. https://doi.org/10.3389/fimmu.2020.02149

2019

Wetenschappelijke publicaties

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. (2019). Characterization of the ferret TRB locus guided by V, D, J, and C gene expression analysis. Immunogenetics. https://doi.org/10.1007/s00251-019-01142-9
Pandit, A., & De Boer, R. J. (2019). Stochastic inheritance of division and death times determines the size and phenotype of CD8+ T cell families. Frontiers in Immunology, 10, [436]. https://doi.org/10.3389/fimmu.2019.00436
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. Journal of Immunology, 202(11), 3318-3325. https://doi.org/10.4049/jimmunol.1801016
Doekes, H. M., De Boer, R. J., & Hermsen, R. (2019). Toxin production spontaneously becomes regulated by local cell density in evolving bacterial populations. PLoS Computational Biology, 15(8), [e1007333]. https://doi.org/10.1371/journal.pcbi.1007333

2018

Wetenschappelijke publicaties

Dorp, C. H. V., Woolthuis, R. G., Yu, J. H. C., Boer, R. J. D., & Boven, M. V. (2018). Estimation of age-specific susceptibility to influenza in the Netherlands and its relation to loss of CD8+ T-cell memory. bioRxiv. https://doi.org/10.1101/259614
behalf of the EPIICAL Consortium (2018). Early and highly suppressive antiretroviral therapy are main factors associated with low viral reservoir in European perinatally HIV-infected children. Journal of Acquired Immune Deficiency Syndromes, 79(2), 269-276. https://doi.org/10.1097/QAI.0000000000001789
https://dspace.library.uu.nl/bitstream/handle/1874/388444/application_pdf.pdf?sequence=1
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. Immunological Reviews, 285(1), 233-248. https://doi.org/10.1111/imr.12693
https://dspace.library.uu.nl/bitstream/handle/1874/373404/borghans.pdf?sequence=1
Baliu-Piqué, 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. Frontiers in Immunology, 9, [2054]. https://doi.org/10.3389/fimmu.2018.02054
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(2), 87-97. https://doi.org/10.1007/s00251-017-1019-1
Müller, V., de Boer, R. J., Bonhoeffer, S., & Szathmáry, E. (2018). An evolutionary perspective on the systems of adaptive immunity. Biological Reviews, 93(1), 505-528. https://doi.org/10.1111/brv.12355

2017

Wetenschappelijke publicaties

Tak, T., Drylewicz, J., Conemans, L., de Boer, R. J., Koenderman, L., & Tesselaar, K. (2017). Circulatory and maturation kinetics of human monocyte subsets in vivo. Blood, 130(12), 1474-1477. https://doi.org/10.1182/blood-2017-03-771261
https://dspace.library.uu.nl/bitstream/handle/1874/356190/Circulatory.pdf?sequence=1
van Hoeven, V., Drylewicz, J., Westera, L., den Braber, I., Mugwagwa, T., Tesselaar, K., & de Boer, R. J. (2017). Dynamics of Recent Thymic Emigrants in Young Adult Mice. Frontiers in Immunology, 8, [933]. https://doi.org/10.3389/fimmu.2017.00933
De Boer, R. J., & Perelson, A. S. (2017). How germinal centers evolve broadly neutralizing antibodies: the breadth of the follicular helper T cell response. Journal of Virology, 91(22), [ e00983-17]. https://doi.org/10.1128/JVI.00983-17
Gadhamsetty, S., Marée, A. F. M., de Boer, R. J., & Beltman, J. B. (2017). Tissue Dimensionality Influences the Functional Response of Cytotoxic T Lymphocyte-Mediated Killing of Targets. Frontiers in Immunology, 7, 1-12. [688]. https://doi.org/10.3389/fimmu.2016.00668
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. F. (2017). Cytokines and Chemokines Involved in Acute Retinal Necrosis. Investigative ophthalmology & visual science, 58(4), 2139-2151. https://doi.org/10.1167/iovs.16-20799
Gadhamsetty, S., Marée, A. F. M., Beltman, J. B., & de Boer, R. J. (2017). A Sigmoid Functional Response Emerges When Cytotoxic T Lymphocytes Start Killing Fresh Target Cells. Biophysical Journal, 112(6), 1221-1235. https://doi.org/10.1016/j.bpj.2017.02.008

2016

Wetenschappelijke publicaties

Olde Rikkert, M. G. M., Dakos, V., Buchman, T. G., Boer, R. D., Glass, L., Cramer, A. O. J., 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. Critical Care Medicine, 44(3), 601-606. https://doi.org/10.1097/CCM.0000000000001564
https://dspace.library.uu.nl/bitstream/handle/1874/343708/Slowing.html?sequence=1
Asquith, B., & de Boer, R. J. (2016). How lymphocytes add up. Nature Immunology, 18(1), 12-13. https://doi.org/10.1038/ni.3636
https://dspace.library.uu.nl/bitstream/handle/1874/344463/lymphocytes.pdf?sequence=1
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(20), 3098-3106. https://doi.org/10.1093/bioinformatics/btw339
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. Scientific Reports, 6, [33334]. https://doi.org/10.1038/srep33334
Textor, J., Mandl, J. N., & de Boer, R. J. (2016). The Reticular Cell Network: A Robust Backbone for Immune Responses. PLoS Biology, 14(10), [e2000827]. https://doi.org/10.1371/journal.pbio.2000827
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. M. (2016). Reconciling Longitudinal Naive T-Cell and TREC Dynamics during HIV-1 Infection. PLoS One, 11(3), [e0152513]. https://doi.org/10.1371/journal.pone.0152513
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. https://doi.org/10.1186/s12977-016-0252-2
Gadhamsetty, S., Coorens, T., & de Boer, R. J. (2016). Notwithstanding circumstantial alibis, cytotoxic T cells can be major killers of HIV-1 infected cells. Journal of Virology, 90(16), 7066-7083. https://doi.org/10.1128/JVI.00306-16
Carrillo-Bustamante, P., Kesmir, C., & de Boer, R. J. (2016). The evolution of natural killer cell receptors. Immunogenetics, 68(1), 3-18. https://doi.org/10.1007/s00251-015-0869-7

2015

Wetenschappelijke publicaties

Perié, L., Duffy, K. R., Kok, L., de Boer, R. J., & Schumacher, T. N. (2015). The Branching Point in Erythro-Myeloid Differentiation. Cell, 163(7), 1655-1662. https://doi.org/10.1016/j.cell.2015.11.059
https://dspace.library.uu.nl/bitstream/handle/1874/329675/Branching.pdf?sequence=1
Pandit, A., & de Boer, R. J. (2015). HIV-1 CCR5 gene therapy will fail unless it is combined with a suicide gene. Scientific Reports, 5, [18088]. https://doi.org/10.1038/srep18088
Ariotti, S., Beltman, J. B., Borsje, R., Hoekstra, M. E., Halford, W. P., Haanen, J. B. A. G., de Boer, R. J., & Schumacher, T. N. M. (2015). Subtle CXCR3-Dependent Chemotaxis of CTLs within Infected Tissue Allows Efficient Target Localization. Journal of Immunology, 195(11), 5285-5295. https://doi.org/10.4049/jimmunol.1500853
https://dspace.library.uu.nl/bitstream/handle/1874/329674/5285.full.pdf?sequence=1
Niculescu, I., Textor, J., & de Boer, R. J. (2015). Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration. PLoS Computational Biology, 11(10), [e1004280]. https://doi.org/10.1371/journal.pcbi.1004280
https://dspace.library.uu.nl/bitstream/handle/1874/324908/280.pdf?sequence=1
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. M. (2015). Quantification of naive and memory T-cell turnover during HIV-1 infection. AIDS, 29(16), 2071–2080. https://doi.org/10.1097/QAD.0000000000000822
https://dspace.library.uu.nl/bitstream/handle/1874/329451/6.pdf?sequence=1
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. M., & Asquith, B. (2015). Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments. PLoS Computational Biology, 11(10), e1004355. https://doi.org/10.1371/journal.pcbi.1004355
Westera, L., van Hoeven, V., Drylewicz, J., Spierenburg, G., van Velzen, J. F., de Boer, R. J., Tesselaar, K., & Borghans, J. A. M. (2015). Lymphocyte maintenance during healthy aging requires no substantial alterations in cellular turnover. Aging Cell, 14(2), 219-227. https://doi.org/10.1111/acel.12311
https://dspace.library.uu.nl/bitstream/handle/1874/324906/Cell.pdf?sequence=1
Saeki, K., Doekes, H. M., & De Boer, R. J. (2015). Optimal T cell cross-reactivity and the role of regulatory T cells. Journal of Theoretical Biology, 375, 4-12. https://doi.org/10.1016/j.jtbi.2014.11.007
https://dspace.library.uu.nl/bitstream/handle/1874/329450/50X_main.pdf?sequence=1
Gadham Setty, S., Beltman, J. B., & de Boer, R. J. (2015). What do mathematical models tell us about killing rates during HIV-1 infection? Immunology Letters, 168(1), 1-6. https://doi.org/10.1016/j.imlet.2015.07.009
Carrillo-Bustamante, P., Kesmir, C., & de Boer, R. J. (2015). A Coevolutionary Arms Race between Hosts and Viruses Drives Polymorphism and Polygenicity of NK Cell Receptors. Molecular Biology and Evolution, 32(8), 2149-2160. https://doi.org/10.1093/molbev/msv096
Carrillo-Bustamante, P., Kesmir, C., & de Boer, R. J. (2015). Can Selective MHC Downregulation Explain the Specificity and Genetic Diversity of NK Cell Receptors? Frontiers in Immunology [E], 6, 311. https://doi.org/10.3389/fimmu.2015.00311

2014

Wetenschappelijke publicaties

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 Computational Biology, 10(12), e1003899. https://doi.org/10.1371/journal.pcbi.1003899
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. Theoretical Biology and Medical Modelling, 11, [11:22 ]. https://doi.org/10.1186/1742-4682-11-22
Perié, 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 Reports [E], 6(4), 617-624. https://doi.org/10.1016/j.celrep.2014.01.016
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. Frontiers in Immunology [E], 5, [20]. https://doi.org/10.3389/fimmu.2014.00020
Gadham Setty, S., Marée, A. F. M., Beltman, J. B., & de Boer, R. J. (2014). A general functional response of cytotoxic T lymphocyte-mediated killing of target cells. Biophysical Journal, 106(8), 1780-1791. https://doi.org/10.1016/j.bpj.2014.01.048
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), [11:56]. https://doi.org/10.1186/1742-4690-11-56
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 Computational Biology, 10(8), [e1003752]. https://doi.org/10.1371/journal.pcbi.1003752

2013

Wetenschappelijke publicaties

van den Ham, H. J., Waal, L., Zaaraoui-Boutahar, F., Bijl, M., van IJcken, W., Osterhaus, A. D., de Boer, R. J., & Andeweg, A. C. (2013). Early divergence of Th1 and Th2 transcriptomes involves a small core response and sets of transiently expressed genes. European Journal of Immunology, 43(4), 1074-84.
Schittler, D., Allgöwer, F., & de Boer, R. J. (2013). A new model to simulate and analyze proliferating cell populations in BrdU labeling experiments. BMC Systems Biology, 7(Suppl. 1), S4.
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 Effect HLA Haplotype Composition. Frontiers in Immunology [E], 4, 374. https://doi.org/10.3389/fimmu.2013.00374
Gerlach, C., Rohr, J. C., Perie, L., van Rooij, N., 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.
Textor, J. C., Sinn, M., & de Boer, R. J. (2013). Analytical results on the Beauchemin model of lymphocyte migration. BMC Bioinformatics, 14, S10.
van den Ham, H. J., Andeweg, A. C., & de Boer, R. J. (2013). Induction of appropriate Th cell phenotypes: cellular decision-making in heterogeneous environments. Parasite Immunology. https://doi.org/10.1111/pim.12053
van Berkel, K., de Boer, R. J., Scheres, B. J. G., & ten Tusscher, K. H. W. J. (2013). Polar auxin transport: models and mechanisms. Development (Rome), 140, 2253-2268.
Miedema, F., Hazenberg, M., Tesselaar, K., van Baarle, D., de Boer, R. J., & Borghans, J. A. M. (2013). Immune activation and collateral damage in aids pathogenesis. Frontiers in Immunology [E], 4, 298. http://www.ncbi.nlm.nih.gov/pubmed/24133492

2012

Wetenschappelijke publicaties

Althaus, C. L., & De Boer, R. J. (2012). Impaired immune evasion in HIV through intracellular delays and multiple infection of cells. Proceedings of the Royal Society B: Biological Sciences, 279(1740), 3003-3010. https://doi.org/10.1098/rspb.2012.0328
van den Ham, H. J., & de Boer, R. J. (2012). Cell division curtails helper phenotype plasticity and expedites helper T-cell differentiation. Immunology and Cell Biology, 90, 860-868.
Baltcheva, I., Veel, E. M., Volman, T. J. H., Koning, D., Brouwer, A. I., Le Boudec, J. Y., Tesselaar, N. A., de Boer, R. J., & Borghans, J. A. M. (2012). A Generalized Mathematical Model To Estimate T- and B-Cell Receptor Diversities Using AmpliCot. Biophysical Journal, 103(5), 999-1010. http://www.cell.com/biophysj/retrieve/pii/S0006349512007928
Calis, J. J. A., 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 Computational Biology, 8(3), e1002412.
Iwami, S., Sato, K., de Boer, R. J., Aihara, K., Miura, T., & Koyanagi, Y. (2012). Identifying viral parameters from in vitro cell cultures. Frontiers of biology, 3, 319-319.
den Braber, A. J., Mugwagwa, T., Vrisekoop, N., Westera, L., Mögling, R., de Boer, A. B., Willems, N., Schrijver, E. H. R., Spierenburg, G. T., Gaiser, J. F., Mul, E., Otto, S. A., Ruiter, A. F., Ackermans, M. T., Miedema, F., Borghans, J. A. M., de Boer, R. J., & Tesselaar, N. A. (2012). Maintenance of peripheral naive T cells is sustained by thymus output in mice but not humans. Immunity, 36(2), 288-297. http://www.cell.com/immunity/retrieve/pii/S1074761312000556

2011

Wetenschappelijke publicaties

Pillay, J., den Braber, A. J., Vrisekoop, N., Kwast, L. M., de Boer, R. J., Borghans, J. A. M., & Tesselaar, N. A. (2011). Response: The in vivo half-life of human neutrophils. Blood, 117(22), 6053-6054. https://doi.org/10.1182/blood-2010-11-317875
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. Proceedings of the National Academy of Sciences of the United States of America, 108, 8755-8760.
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.

2010

Wetenschappelijke publicaties

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 Computational Biology, 6(9), e1000906. https://doi.org/10.1371/journal.pcbi.1000906
de Boer, R. J., Ribeiro, R. M., & Perelson, A. S. (2010). Current estimates for HIV-1 production imply rapid viral clearance in lymphoid tissue. PLoS Computational Biology, 6, e1000906.
Engram, J. C., Cervasi, B., Borghans, J. A. M., 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(5), 748-758. https://doi.org/10.1182/blood-2010-01-263814
Pillay, J., den Braber, I., Vrisekoop, N., Kwast, L. M., de Boer, R. J., Borghans, J. A. M., Tesselaar, K., & Koenderman, L. (2010). In vivo labeling with 2H2O reveals a human neutrophil lifespan of 5.4 days. Blood, 116(4), 625-627.
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. Journal of Immunological Methods, 361(1-2), 98-109. https://doi.org/10.1016/j.jim.2010.07.009

2009

Wetenschappelijke publicaties

Beltman, J. B., Henrickson, S. E., von Andrian, U. H., de Boer, R. J., & Maree, A. F. M. (2009). Towards estimating the true duration of dendritic cell interactions with T cells. Journal of Immunological Methods, 347, 54-69.
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 Evolutionary Biology, 9, 184.

2008

Wetenschappelijke publicaties

Althaus, C. L., & de Boer, R. J. (2008). Dynamics of immune escape during HIV/SIV infection. PLoS Computational Biology, 4, e1000103.
Ganusov, V. V., & de Boer, R. J. (2008). Tissue distribution of lymphocytes and plasma cells and the role of the gut: response to Pabst et al. Trends in Immunology, 29, 209-210.
Deutsch, A., Bravo de la Parra, R., de Boer, R. J., Diekmann, O., Jagers, P., Kisdi, E., Kretzschmar, M. E. E., Lansky, P., & Metz, H. (2008). Mathematical Modeling of Biological Systems, Volume II. Birkhaüser.
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. International Immunology, 20, 1269-1277.
Vrisekoop, N., den Braber, I., de Boer, A. B., Ruiter, A. F. C., Ackermans, M. T., van der Crabben, S. N., Schrijver, E. H. R., Spierenburg, G. T., Sauerwein, H. P., Hazenberg, M. D., de Boer, R. J., Miedema, F., Borghans, J. A. M., & Tesselaar, K. (2008). Sparse production but preferential incorporation of recently produced naive T cells in the human peripheral pool. Proceedings of the National Academy of Sciences of the United States of America, 105(16), 6115-6120. https://doi.org/10.1073/pnas.0709713105

2007

Wetenschappelijke publicaties

de Boer, R. J. (2007). Understanding the failure of CD8+ T-cell vaccination against simian/human immunodeficiency virus. Journal of Virology, 81, 2838-2848.
Milutinovic, D., & de Boer, R. J. (2007). Process noise: an explanation for the fluctuations in the immune response during acute viral infection. Biophysical Journal, 92, 3358-3367.
Beltman, J. B., Mare, A. F., Lynch, J. N., Miller, M. J., & de Boer, R. J. (2007). Lymph node topology dictates T cell migration behavior. Journal of Experimental Medicine, 16, 771-780.
Beltman, J. B., Maree, A. F. M., & de Boer, R. J. (2007). Spatial modelling of brief and long interactions between T cells and dendritic cells. Immunology and Cell Biology, 85, 306-314.
Wucherpfennig, K. W., Allen, P. M., Celada, F., Cohen, I. R., de Boer, R. J., Perelson, A. S., & Sercarz, E. E. (2007). Polyspecificity of T cell and B cell receptor recognition. Semin Immunology, 19, 216-224.
https://dspace.library.uu.nl/bitstream/handle/1874/27122/wucherpfennig%2520et%2520al.pdf?sequence=2
Borghans, J. A. M., Kesmir, C., & de Boer, R. J. (2007). MHC diversity in individuals and populations. In In: J. Silico Immunology (pp. 177-196). Springer (Flower, D. & Timmis, J., eds.).

2006

Wetenschappelijke publicaties

de Boer, R. J. (2006). Estimating the role of thymic output in HIV infection. Current Opinion in HIV and AIDS, 1, 16-21.
de Boer, R. J., Ganusov, V. V., Milutinovic, D., Hodgkin, P. D., & Perelson, A. S. (2006). Estimating Lymphocyte Division and Death Rates from CFSE Data. Bulletin of Mathematical Biology, 68, 1011-1031.
van den Dool, C., & de Boer, R. J. (2006). The effects of age, thymectomy, and HIV infection on alpha and beta TCR excis ion circles in naive T cells. Journal of Immunology, 177, 4391-4401.
Korthals Altes, H., de Boer, R. J., & Boerlijst, M. (2006). Role of avidity and breadth of the CD4 T cell response in progression to AIDS. Proceedings of the Royal Society B-Biological Sciences, 273, 1697-1704.
Ganusov, V. V., & de Boer, R. J. (2006). Estimating costs and benefits of CTL escape mutations in SIV/HIV infection. PLoS Computational Biology, 2, 182-187.

2005

Wetenschappelijke publicaties

Ganusov, V. V., Pilyugin, S. S., de Boer, R. J., Murali-Krishna, K., Ahmed, R., & Antia, R. (2005). Quantifying cell turnover using CFSE data. Journal of Immunological Methods, 298, 183-200.
Luciani, F., Kesmir, C., Mishto, M., Or-Guil, M., & de Boer, R. J. (2005). A mathematical model of protein degradation by the proteasome. Biophysical Journal, 88, 2422-2432.
de Boer, R. J., & Perelson, A. S. (2005). Estimating division and death rates from CFSE data. Journal of Computational and Applied Mathematics, 184, 140-164.

2004

Wetenschappelijke publicaties

Burroughs, N. J., de Boer, R. J., & Kesmir, C. (2004). Discriminating self from nonself with short peptides from large proteosomes. Immunogenetics, 56, 311-320.
de Boer, R. J., Borghans, J. A. M., 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.
Nobile, M., Correa, R., Borghans, J. A. M., 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.

2003

Wetenschappelijke publicaties

Korthals Altes, H., 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 set-point. Proceedings of the Royal Society B: Biological Sciences, 270(1522), 1349-1358. https://doi.org/10.1098/rspb.2003.2377
Dutilh, B. E., & de Boer, R. J. (2003). Decline in excision circles requires homeostatic renewal or homeostatic death of naive T cells. Journal of Theoretical Biology, 224(3), 351-8.
Hazenberg, M. D., Otto, S. A., Hamann, D., Roos, M. T., Schuitemaker, H., de Boer, R. J., & Miedema, F. (2003). 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.
Kesmir, C., & de Boer, R. J. (2003). Clonal exhaustion as a result of immune deviation. Bulletin of Mathematical Biology, 65, 359-374.
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.
Borghans, J. A. M., Noest, A. J., & de Boer, R. J. (2003). Thymic selection does not limit the individual MHC diversity. European Journal of Immunology, 33, 3353-3358.
Dutilh, B. E., & de Boer, R. J. (2003). Decline in excision circles is no evidence for homeostatic renewal of naive T cells. Journal of Theoretical Biology, 224, 351-358.

2002

Wetenschappelijke publicaties

Bonhoeffer, S., Barbour, A. D., & de Boer, R. J. (2002). Procedures for reliable estimation of viral fitness from time-series data. Proceedings of the Royal Society B-Biological Sciences, 269, 1887-1893.
de Boer, R. J. (2002). Mathematical models of human CD4+ T-cell population kinetics. Netherlands Journal of Medicine, 60S, 17-26.
Cohen Stuart, J. W. T., Hamann, D., Borleffs, J. C. C., Roos, M., Miedema, F., Boucher, C. A. B., & de Boer, R. J. (2002). Reconstitution of naive T-cells during treatment of HIV infected adults is dependent on age. AIDS, 16, 2263-2266.

2001

Wetenschappelijke publicaties

de Boer, R. J., Freitas, A. A., & Perelson, A. S. (2001). Resource competition determines selection of B cell repertoires. Journal of Theoretical Biology, 212, 333-343.
Borghans, J. A. M., & de Boer, R. J. (2001). Diversity in the Immune System. In L. A. Segel, & I. R. Cohen (Eds.), Design Principles for the Immune System and Other Distributed Autonomous Systems (pp. 161-183). Oxford University Press.

2000

Wetenschappelijke publicaties

Kesmir, C., Borghans, J. A. M., & de Boer, R. J. (2000). Diversity of human alpha beta T cell receptors. Science, 288, 1135a-1135a.
Hazenberg, M. D., Cohen Stuart, J. W. T., Otto, S. A., Borleffs, J. C. C., Boucher, C. A. B., de Boer, R. J., Miedema, F., & Hamann, D. (2000). T-cell division in human immunodeficiency virus (HIV)-1 infection is mainly due to immune activation: a longitudinal analaysis in patients before and during highly active antiretroviral therapy (HAART). Blood, 95, 249-255.
Müller, V., Marée, A. F. M., & de Boer, R. J. (2000). Small variations in multiple parameters account for wide variations in HIV-1 set points: a novel modeling approach. Proceedings of the Royal Society B-Biological Sciences, 268(1464).
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. Journal of Clinical Investigation, 105, 777-782.

1998

Wetenschappelijke publicaties

Keşmir, C., De Boer, R. J., & Kesmir, C. (1998). How does cytopathicity affect the production of neutralizing antibody? Scandinavian Journal of Immunology, 48(4), 347-9.
de Boer, R. J., Boucher, C. A. B., & Perelson, A. S. (1998). Target Cell Availability and the Successful Suppression of HIV by Hydroxyurea and Didanosine. AIDS, 12, 1567-1570.

1997

Wetenschappelijke publicaties

Stilianakis, N. I., Boucher, C. A. B., 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. Journal of Virology, 71(1), 161-168.
Stilianakis, N. I., Boucher, C. A. B., de Jong, M. D., Schuurman, R., & de Boer, R. J. (1997). Clinical data sets of human immunodeficiency virus type 1 reverse transcriptase mutants explained by a mathomatical model. Journal of Virology, 71, 161-168.
Stilianakis, N. I., Boucher, C. A. B., de Jong, T. M. C., van Leeuwen, R., Schuurman, R., & de Boer, R. J. (1997). RJ.Clinical data sets of human immunodeficiency virus type 1 reverse transcriptase-resistant mutants explained by a mathematical model. Journal of Virology, 71, 161-168.

1996

Wetenschappelijke publicaties

de Jong, M. D., Veenstra, J., Stilianakis, N. I., Schuurman, R., de Boer, R. J., Lange, J. M. A., & Boucher, C. A. B. (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. Proceedings of the National Academy of Sciences of the United States of America, 93, 5501-5506.

1993

Wetenschappelijke publicaties

Perelson, A. S., Kirschner, D. E., & De Boer, R. (1993). Dynamics of HIV infection of CD4+ T cells. Mathematical Biosciences, 114(1), 81-125. https://doi.org/10.1016/0025-5564(93)90043-A

1985

Wetenschappelijke publicaties

De Weger, R. A., Dullens, H. F. J., De Boer, R. J., & Den Otter, W. (1985). Mathematical analysis of the cellular immune reaction against tumour cells. Immunology Today, 6(11), 316-317. https://doi.org/10.1016/0167-5699(85)90119-7

1983

Wetenschappelijke publicaties

van Schaik, C. P., van Noordwijk, M. A., de Boer, R. J., & den Tonkelaar, I. (1983). The effect of group size on time budgets and social behaviour in wild long-tailed macaques (Macaca fascicularis). Behavioral Ecology and Sociobiology, 13(3), 173-181. https://doi.org/10.1007/BF00299920
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