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Toxin production spontaneously becomes regulated by local cell density in evolving bacterial populations.

Doekes HM, de Boer RJ, Hermsen R.

PLoS Comput Biol. 2019 Aug 30;15(8):e1007333. doi: 10.1371/journal.pcbi.1007333. eCollection 2019 Aug.


Amino Acid Loss during Continuous Venovenous Hemofiltration in Critically Ill Patients.

Stapel SN, de Boer RJ, Thoral PJ, Vervloet MG, Girbes ARJ, Oudemans-van Straaten HM.

Blood Purif. 2019 Jul 10:1-9. doi: 10.1159/000500998. [Epub ahead of print]


Local Attachment Explains Small World-like Properties of Fibroblastic Reticular Cell Networks in Lymph Nodes.

Soekarjo KMW, Textor J, de Boer RJ.

J Immunol. 2019 Jun 1;202(11):3318-3325. doi: 10.4049/jimmunol.1801016. Epub 2019 Apr 17.


Stochastic Inheritance of Division and Death Times Determines the Size and Phenotype of CD8+ T Cell Families.

Pandit A, De Boer RJ.

Front Immunol. 2019 Mar 14;10:436. doi: 10.3389/fimmu.2019.00436. eCollection 2019.


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.

Baliu-Piqué M, Verheij MW, Drylewicz J, Ravesloot L, de Boer RJ, Koets A, Tesselaar K, Borghans JAM.

Front Immunol. 2018 Sep 11;9:2054. doi: 10.3389/fimmu.2018.02054. eCollection 2018.


Current best estimates for the average lifespans of mouse and human leukocytes: reviewing two decades of deuterium-labeling experiments.

Borghans JAM, Tesselaar K, de Boer RJ.

Immunol Rev. 2018 Sep;285(1):233-248. doi: 10.1111/imr.12693. Review.


How Germinal Centers Evolve Broadly Neutralizing Antibodies: the Breadth of the Follicular Helper T Cell Response.

De Boer RJ, Perelson AS.

J Virol. 2017 Oct 27;91(22). pii: e00983-17. doi: 10.1128/JVI.00983-17. Print 2017 Nov 15.


Dynamics of Recent Thymic Emigrants in Young Adult Mice.

van Hoeven V, Drylewicz J, Westera L, den Braber I, Mugwagwa T, Tesselaar K, Borghans JAM, de Boer RJ.

Front Immunol. 2017 Aug 7;8:933. doi: 10.3389/fimmu.2017.00933. eCollection 2017.


An evolutionary perspective on the systems of adaptive immunity.

Müller V, de Boer RJ, Bonhoeffer S, Szathmáry E.

Biol Rev Camb Philos Soc. 2018 Feb;93(1):505-528. doi: 10.1111/brv.12355. Epub 2017 Jul 26. Review.


Circulatory and maturation kinetics of human monocyte subsets in vivo.

Tak T, Drylewicz J, Conemans L, de Boer RJ, Koenderman L, Borghans JAM, Tesselaar K.

Blood. 2017 Sep 21;130(12):1474-1477. doi: 10.1182/blood-2017-03-771261. Epub 2017 Jul 25. No abstract available.


Specificity of inhibitory KIRs enables NK cells to detect changes in an altered peptide environment.

Carrillo-Bustamante P, de Boer RJ, Keşmir C.

Immunogenetics. 2018 Feb;70(2):87-97. doi: 10.1007/s00251-017-1019-1. Epub 2017 Jul 10.


A Sigmoid Functional Response Emerges When Cytotoxic T Lymphocytes Start Killing Fresh Target Cells.

Gadhamsetty S, Marée AFM, Beltman JB, de Boer RJ.

Biophys J. 2017 Mar 28;112(6):1221-1235. doi: 10.1016/j.bpj.2017.02.008.


Tissue Dimensionality Influences the Functional Response of Cytotoxic T Lymphocyte-Mediated Killing of Targets.

Gadhamsetty S, Marée AF, de Boer RJ, Beltman JB.

Front Immunol. 2017 Jan 11;7:668. doi: 10.3389/fimmu.2016.00668. eCollection 2016.


How lymphocytes add up.

Asquith B, de Boer RJ.

Nat Immunol. 2016 Dec 16;18(1):12-13. doi: 10.1038/ni.3636. No abstract available.


The Reticular Cell Network: A Robust Backbone for Immune Responses.

Textor J, Mandl JN, de Boer RJ.

PLoS Biol. 2016 Oct 11;14(10):e2000827. doi: 10.1371/journal.pbio.2000827. eCollection 2016 Oct.


Long-term adaptation of the influenza A virus by escaping cytotoxic T-cell recognition.

Woolthuis RG, van Dorp CH, Keşmir C, de Boer RJ, van Boven M.

Sci Rep. 2016 Sep 15;6:33334. doi: 10.1038/srep33334.


RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data.

Gerritsen B, Pandit A, Andeweg AC, de Boer RJ.

Bioinformatics. 2016 Oct 15;32(20):3098-3106. Epub 2016 Jun 20.


Notwithstanding Circumstantial Alibis, Cytotoxic T Cells Can Be Major Killers of HIV-1-Infected Cells.

Gadhamsetty S, Coorens T, de Boer RJ.

J Virol. 2016 Jul 27;90(16):7066-7083. doi: 10.1128/JVI.00306-16. Print 2016 Aug 15.


Quantifying the effect of Vpu on the promotion of HIV-1 replication in the humanized mouse model.

Ikeda H, Nakaoka S, de Boer RJ, Morita S, Misawa N, Koyanagi Y, Aihara K, Sato K, Iwami S.

Retrovirology. 2016 Apr 18;13:23. doi: 10.1186/s12977-016-0252-2.


Reconciling Longitudinal Naive T-Cell and TREC Dynamics during HIV-1 Infection.

Drylewicz J, Vrisekoop N, Mugwagwa T, de Boer AB, Otto SA, Hazenberg MD, Tesselaar K, de Boer RJ, Borghans JA.

PLoS One. 2016 Mar 24;11(3):e0152513. doi: 10.1371/journal.pone.0152513. eCollection 2016.


The Branching Point in Erythro-Myeloid Differentiation.

Perié L, Duffy KR, Kok L, de Boer RJ, Schumacher TN.

Cell. 2015 Dec 17;163(7):1655-62. doi: 10.1016/j.cell.2015.11.059.


HIV-1 CCR5 gene therapy will fail unless it is combined with a suicide gene.

Pandit A, de Boer RJ.

Sci Rep. 2015 Dec 17;5:18088. doi: 10.1038/srep18088.


Subtle CXCR3-Dependent Chemotaxis of CTLs within Infected Tissue Allows Efficient Target Localization.

Ariotti S, Beltman JB, Borsje R, Hoekstra ME, Halford WP, Haanen JB, de Boer RJ, Schumacher TN.

J Immunol. 2015 Dec 1;195(11):5285-95. doi: 10.4049/jimmunol.1500853. Epub 2015 Nov 2.


Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration.

Niculescu I, Textor J, de Boer RJ.

PLoS Comput Biol. 2015 Oct 21;11(10):e1004280. doi: 10.1371/journal.pcbi.1004280. eCollection 2015 Oct.


Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments.

Ahmed R, Westera L, Drylewicz J, Elemans M, Zhang Y, Kelly E, Reljic R, Tesselaar K, de Boer RJ, Macallan DC, Borghans JA, Asquith B.

PLoS Comput Biol. 2015 Oct 5;11(10):e1004355. doi: 10.1371/journal.pcbi.1004355. eCollection 2015 Oct.


The evolution of natural killer cell receptors.

Carrillo-Bustamante P, Keşmir C, de Boer RJ.

Immunogenetics. 2016 Jan;68(1):3-18. doi: 10.1007/s00251-015-0869-7. Epub 2015 Sep 21. Review.


What do mathematical models tell us about killing rates during HIV-1 infection?

Gadhamsetty S, Beltman JB, de Boer RJ.

Immunol Lett. 2015 Nov;168(1):1-6. doi: 10.1016/j.imlet.2015.07.009. Epub 2015 Aug 13. Review.


Quantification of naive and memory T-cell turnover during HIV-1 infection.

Vrisekoop N, Drylewicz J, Van Gent R, Mugwagwa T, Van Lelyveld SF, Veel E, Otto SA, Ackermans MT, Vermeulen JN, Huidekoper HH, Prins JM, Miedema F, de Boer RJ, Tesselaar K, Borghans JA.

AIDS. 2015 Oct 23;29(16):2071-80. doi: 10.1097/QAD.0000000000000822.


Can Selective MHC Downregulation Explain the Specificity and Genetic Diversity of NK Cell Receptors?

Carrillo-Bustamante P, Kesmir C, de Boer RJ.

Front Immunol. 2015 Jun 16;6:311. doi: 10.3389/fimmu.2015.00311. eCollection 2015.


A Coevolutionary Arms Race between Hosts and Viruses Drives Polymorphism and Polygenicity of NK Cell Receptors.

Carrillo-Bustamante P, Keşmir C, de Boer RJ.

Mol Biol Evol. 2015 Aug;32(8):2149-60. doi: 10.1093/molbev/msv096. Epub 2015 Apr 23.


Lymphocyte maintenance during healthy aging requires no substantial alterations in cellular turnover.

Westera L, van Hoeven V, Drylewicz J, Spierenburg G, van Velzen JF, de Boer RJ, Tesselaar K, Borghans JA.

Aging Cell. 2015 Apr;14(2):219-27. doi: 10.1111/acel.12311. Epub 2015 Jan 28.


Corrigendum: Quantifying the Protection of Activating and Inhibiting NK Cell Receptors during Infection with a CMV-Like Virus.

Carrillo-Bustamante P, Keşmir C, De Boer RJ.

Front Immunol. 2015 Jan 5;5:663. doi: 10.3389/fimmu.2014.00663. eCollection 2014.


Immuno-epidemiological modeling of HIV-1 predicts high heritability of the set-point virus load, while selection for CTL escape dominates virulence evolution.

van Dorp CH, van Boven M, de Boer RJ.

PLoS Comput Biol. 2014 Dec 18;10(12):e1003899. doi: 10.1371/journal.pcbi.1003899. eCollection 2014 Dec.


Optimal T cell cross-reactivity and the role of regulatory T cells.

Saeki K, Doekes HM, De Boer RJ.

J Theor Biol. 2015 Jun 21;375:4-12. doi: 10.1016/j.jtbi.2014.11.007. Epub 2014 Nov 20.


Random migration and signal integration promote rapid and robust T cell recruitment.

Textor J, Henrickson SE, Mandl JN, von Andrian UH, Westermann J, de Boer RJ, Beltman JB.

PLoS Comput Biol. 2014 Aug 7;10(8):e1003752. doi: 10.1371/journal.pcbi.1003752. eCollection 2014 Aug.


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.

Ikeda H, de Boer RJ, Sato K, Morita S, Misawa N, Koyanagi Y, Aihara K, Iwami S.

Theor Biol Med Model. 2014 May 21;11:22. doi: 10.1186/1742-4682-11-22.


A general functional response of cytotoxic T lymphocyte-mediated killing of target cells.

Gadhamsetty S, Marée AF, Beltman JB, de Boer RJ.

Biophys J. 2014 Apr 15;106(8):1780-91. doi: 10.1016/j.bpj.2014.01.048.


Quantifying the Protection of Activating and Inhibiting NK Cell Receptors during Infection with a CMV-Like Virus.

Carrillo-Bustamante P, Keşmir C, de Boer RJ.

Front Immunol. 2014 Jan 30;5:20. doi: 10.3389/fimmu.2014.00020. eCollection 2014. Review. Erratum in: Front Immunol. 2014;5:663.


Determining lineage pathways from cellular barcoding experiments.

Perié L, Hodgkin PD, Naik SH, Schumacher TN, de Boer RJ, Duffy KR.

Cell Rep. 2014 Feb 27;6(4):617-24. doi: 10.1016/j.celrep.2014.01.016. Epub 2014 Feb 6.


A new model to simulate and analyze proliferating cell populations in BrdU labeling experiments.

Schittler D, Allgöwer F, De Boer RJ.

BMC Syst Biol. 2013;7 Suppl 1:S4. doi: 10.1186/1752-0509-7-S1-S4. Epub 2013 Aug 12.


Complementarity of Binding Motifs is a General Property of HLA-A and HLA-B Molecules and Does Not Seem to Effect HLA Haplotype Composition.

Rao X, De Boer RJ, van Baarle D, Maiers M, Kesmir C.

Front Immunol. 2013 Nov 14;4:374. doi: 10.3389/fimmu.2013.00374. eCollection 2013. Review.


Immune activation and collateral damage in AIDS pathogenesis.

Miedema F, Hazenberg MD, Tesselaar K, van Baarle D, de Boer RJ, Borghans JA.

Front Immunol. 2013 Sep 26;4:298. doi: 10.3389/fimmu.2013.00298. Review.


Virus encoded MHC-like decoys diversify the inhibitory KIR repertoire.

Carrillo-Bustamante P, Keşmir C, de Boer RJ.

PLoS Comput Biol. 2013;9(10):e1003264. doi: 10.1371/journal.pcbi.1003264. Epub 2013 Oct 10.


Closing the gap between T-cell life span estimates from stable isotope-labeling studies in mice and humans.

Westera L, Drylewicz J, den Braber I, Mugwagwa T, van der Maas I, Kwast L, Volman T, van de Weg-Schrijver EH, Bartha I, Spierenburg G, Gaiser K, Ackermans MT, Asquith B, de Boer RJ, Tesselaar K, Borghans JA.

Blood. 2013 Sep 26;122(13):2205-12. doi: 10.1182/blood-2013-03-488411. Epub 2013 Aug 14.


The rate of immune escape vanishes when multiple immune responses control an HIV infection.

van Deutekom HW, Wijnker G, de Boer RJ.

J Immunol. 2013 Sep 15;191(6):3277-86. doi: 10.4049/jimmunol.1300962. Epub 2013 Aug 12.


Induction of appropriate Th-cell phenotypes: cellular decision-making in heterogeneous environments.

van den Ham HJ, Andeweg AC, de Boer RJ.

Parasite Immunol. 2013 Nov;35(11):318-30. doi: 10.1111/pim.12053. Review.


Analytical results on the Beauchemin model of lymphocyte migration.

Textor J, Sinn M, de Boer RJ.

BMC Bioinformatics. 2013;14 Suppl 6:S10. doi: 10.1186/1471-2105-14-S6-S10. Epub 2013 Apr 17.


Polar auxin transport: models and mechanisms.

van Berkel K, de Boer RJ, Scheres B, ten Tusscher K.

Development. 2013 Jun;140(11):2253-68. doi: 10.1242/dev.079111.


Antigen-stimulated CD4 T cell expansion can be limited by their grazing of peptide-MHC complexes.

De Boer RJ, Perelson AS.

J Immunol. 2013 Jun 1;190(11):5454-8. doi: 10.4049/jimmunol.1203569. Epub 2013 Apr 19.

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