All Stories

  1. Modeling Phage Therapy

    Article • November 2025, Cold Spring Harbor Laboratory Press

    Professor Rob J de Boer

  2. Variation in DNA enrichment among deuterium labeling studies is largely explained by different background corrections

    Article • Journal of Immunological Methods, November 2025, Elsevier

    Professor Rob J de Boer

  3. How are estimated cellular turnover rates influenced by the dynamics of a source population?

    Article • PLoS Computational Biology, May 2025, PLOS

    Professor Rob J de Boer

  4. Selective decline of intact HIV reservoirs during the first decade of ART followed by stabilization in memory T cell subsets

    Article • AIDS, February 2025, Wolters Kluwer Health

    Professor Rob J de Boer

  5. The TCR assigns naive T cells to a preferred lymph node

    Article • Science Advances, July 2024, American Association for the Advancement of Science

    Professor Rob J de Boer

  6. Is the exquisite specificity of lymphocytes generated by thymic selection or due to evolution?

    Article • Frontiers in Immunology, March 2024, Frontiers

    Professor Rob J de Boer

  7. Better safe than sorry: Naive T-cell dynamics in healthy ageing

    Article • Seminars in Immunology, November 2023, Elsevier

    Professor Rob J de Boer

  8. Challenges in cybersecurity: Lessons from biological defense systems

    Article • Mathematical Biosciences, August 2023, Elsevier

    Prof. Mohit Tiwari, Professor Rob J de Boer

  9. What explains the poor contraction of the viral load during paediatric HIV infection?

    Article • Journal of Theoretical Biology, August 2023, Elsevier

    Professor Rob J de Boer

  10. On the feasibility of using TCR sequencing to follow a vaccination response – lessons learned

    Article • Frontiers in Immunology, July 2023, Frontiers

    Professor Rob J de Boer

  11. Age-Dependent Normalization Functions for T Lymphocytes in Healthy Individuals

    Article • The Journal of Immunology, April 2023, Oxford University Press (OUP)

    Professor Rob J de Boer

  12. Modeling T Cell Fate

    Article • Annual Review of Immunology, April 2023, Annual Reviews

    Professor Rob J de Boer

  13. Towards a robust comparison of diversity between sampled TCR repertoires

    Article • February 2023, Cold Spring Harbor Laboratory Press

    Professor Rob J de Boer

  14. Compartmentalization and persistence of dominant (regulatory) T cell clones indicates antigen skewing in juvenile idiopathic arthritis

    Article • eLife, January 2023, eLife

    Professor Rob J de Boer

  15. Effect of cellular aging on memory T-cell homeostasis

    Article • Frontiers in Immunology, August 2022, Frontiers

    Professor Rob J de Boer

  16. Author Correction: Replicative history marks transcriptional and functional disparity in the CD8+ T cell memory pool

    Article • Nature Immunology, May 2022, Springer Science + Business Media

    Professor Rob J de Boer

  17. Quantification of CD4 Recovery in Early-Treated Infants Living With HIV

    Article • JAIDS Journal of Acquired Immune Deficiency Syndromes, April 2022, Wolters Kluwer Health

    Professor Rob J de Boer

  18. Replicative history marks transcriptional and functional disparity in the CD8+ T cell memory pool

    Article • Nature Immunology, April 2022, Springer Science + Business Media

    Professor Rob J de Boer

  19. Compartmentalization and persistence of dominant (regulatory) T cell clones indicates antigen skewing in juvenile idiopathic arthritis

    Article • February 2022, Cold Spring Harbor Laboratory Press

    Professor Rob J de Boer

  20. 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

    Article • The Journal of Immunology, February 2022, Oxford University Press (OUP)

    Professor Rob J de Boer

  21. Quantification of T-cell dynamics during latent cytomegalovirus infection in humans

    Article • PLoS Pathogens, December 2021, PLOS

    Professor Rob J de Boer

  22. Age-dependent normalisation functions for T-lymphocytes in healthy individuals

    Article • December 2021, Cold Spring Harbor Laboratory Press

    Professor Rob J de Boer

  23. Hematopoiesis in numbers

    Article • Trends in Immunology, December 2021, Elsevier

    Professor Rob J de Boer

  24. The limitations, dangers, and benefits of simple methods for testing identifiability

    Article • PLoS Computational Biology, October 2021, PLOS

    Professor Rob J de Boer

  25. TCRβ rearrangements without a D segment are common, abundant, and public

    Article • Proceedings of the National Academy of Sciences, September 2021, Proceedings of the National Academy of Sciences

    Professor Rob J de Boer

  26. Cytotoxic T cells are able to efficiently eliminate cancer cells by additive cytotoxicity

    Article • Nature Communications, September 2021, Springer Science + Business Media

    Professor Rob J de Boer

  27. Local actin dynamics couple speed and persistence in a cellular Potts model of cell migration

    Article • Biophysical Journal, July 2021, Elsevier

    Professor Rob J de Boer

  28. TCRβrearrangements without D-segment are common, abundant and public

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Professor Rob J de Boer

  29. Cell-density independent increased lymphocyte production and loss rates post-autologous HSCT

    Article • eLife, February 2021, eLife

    Professor Rob J de Boer

  30. Delayed Differentiation Makes Many Models Compatible with Data for CD8+ T Cell Differentiation

    Article • January 2021, Springer Science + Business Media

    Professor Rob J de Boer

  31. Testing structural identifiability by a simple scaling method

    Article • PLoS Computational Biology, November 2020, PLOS

    Professor Rob J de Boer

  32. Quantifying the Dynamics of HIV Decline in Perinatally Infected Neonates on Antiretroviral Therapy

    Article • JAIDS Journal of Acquired Immune Deficiency Syndromes, October 2020, Wolters Kluwer Health

    Professor Rob J de Boer

  33. CXCL4 Links Inflammation and Fibrosis by Reprogramming Monocyte-Derived Dendritic Cells in vitro

    Article • Frontiers in Immunology, September 2020, Frontiers

    Professor Rob J de Boer

  34. Cancer cell elimination by cytotoxic T cell cooperation and additive damage

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Professor Rob J de Boer

  35. Time to Viral Suppression in Perinatally HIV-Infected Infants Depends on the Viral Load and CD4 T-Cell Percentage at the Start of Treatment

    Article • JAIDS Journal of Acquired Immune Deficiency Syndromes, April 2020, Wolters Kluwer Health

    Professor Rob J de Boer

  36. The naive T-cell receptor repertoire has an extremely broad distribution of clone sizes

    Article • eLife, March 2020, eLife

    Professor Rob J de Boer

  37. Is T Cell Negative Selection a Learning Algorithm?

    Article • Cells, March 2020, MDPI AG

    Professor Rob J de Boer

  38. Testing structural identifiability by a simple scaling method

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Professor Rob J de Boer

  39. Modeling the immunological pre-adaptation of HIV-1

    Article • January 2020, Cold Spring Harbor Laboratory Press

    Professor Rob J de Boer

  40. Characterization of the ferret TRB locus guided by V, D, J, and C gene expression analysis

    Article • Immunogenetics, December 2019, Springer Science + Business Media

    Dr ir Wilfred van IJcken, Professor Rob J de Boer

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

    Article • PLoS Computational Biology, August 2019, PLOS

    Professor Rob J de Boer

  42. The naive T-cell receptor repertoire has an extremely broad distribution of clone sizes

    Article • July 2019, Cold Spring Harbor Laboratory Press

    Professor Rob J de Boer

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

    Article • The Journal of Immunology, April 2019, The American Association of Immunologists

    Professor Rob J de Boer

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

    Article • Frontiers in Immunology, March 2019, Frontiers

    Professor Rob J de Boer

  45. Early and Highly Suppressive Antiretroviral Therapy Are Main Factors Associated With Low Viral Reservoir in European Perinatally HIV-Infected Children

    Article • JAIDS Journal of Acquired Immune Deficiency Syndromes, October 2018, Wolters Kluwer Health

    Professor Rob J de Boer

  46. 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

    Article • Frontiers in Immunology, September 2018, Frontiers

    Professor Rob J de Boer

  47. Robust self-nonself discrimination requires negative T cell selection on non-random peptides

    Article • August 2018, Cold Spring Harbor Laboratory Press

    Professor Rob J de Boer

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

    Article • Immunological Reviews, August 2018, Wiley

    Professor Rob J de Boer

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

    Article • July 2018, Cold Spring Harbor Laboratory Press

    Professor Rob J de Boer

  50. Estimation of age-specific susceptibility to influenza in the Netherlands and its relation to loss of CD8+ T-cell memory

    Article • February 2018, Cold Spring Harbor Laboratory Press

    Professor Rob J de Boer

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

    Article • Journal of Virology, September 2017, ASM Journals

    Professor Rob J de Boer

  52. Dynamics of Recent Thymic Emigrants in Young Adult Mice

    Article • Frontiers in Immunology, August 2017, Frontiers

    Professor Rob J de Boer

  53. An evolutionary perspective on the systems of adaptive immunity

    Article • Biological Reviews, July 2017, Wiley

    Viktor Müller, Professor Rob J de Boer

  54. Circulatory and maturation kinetics of human monocyte subsets in vivo

    Article • Blood, July 2017, American Society of Hematology

    Professor Rob J de Boer

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

    Article • Immunogenetics, July 2017, Springer Science + Business Media

    Professor Rob J de Boer

  56. Cytokines and Chemokines Involved in Acute Retinal Necrosis

    Article • Investigative Ophthalmology & Visual Science, May 2017, Association for Research in Vision and Ophthalmology (ARVO)

    Professor Rob J de Boer, Prof Ger T Rijkers

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

    Article • Biophysical Journal, March 2017, Elsevier

    Professor Rob J de Boer

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

    Article • Frontiers in Immunology, January 2017, Frontiers

    Professor Rob J de Boer

  59. How lymphocytes add up

    Article • Nature Immunology, December 2016, Nature

    Professor Rob J de Boer

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

    Article • PLoS Biology, October 2016, PLOS

    Professor Rob J de Boer

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

    Article • Scientific Reports, September 2016, Springer Science + Business Media

    Professor Rob J de Boer

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

    Article • Bioinformatics, June 2016, Oxford University Press (OUP)

    Professor Rob J de Boer

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

    Article • Journal of Virology, May 2016, ASM Journals

    Professor Rob J de Boer

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

    Article • Retrovirology, April 2016, Springer Science + Business Media

    Professor Rob J de Boer

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

    Article • PLOS One, March 2016, PLOS

    Professor Rob J de Boer

  66. Slowing Down of Recovery as Generic Risk Marker for Acute Severity Transitions in Chronic Diseases

    Article • Critical Care Medicine, March 2016, Wolters Kluwer Health

    Professor Rob J de Boer

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

    Article • Scientific Reports, December 2015, Nature

    Professor Rob J de Boer

  68. The Branching Point in Erythro-Myeloid Differentiation

    Article • Cell, December 2015, Elsevier

    Professor Rob J de Boer

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

    Article • The Journal of Immunology, November 2015, The American Association of Immunologists

    Professor Rob J de Boer

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

    Article • Immunology Letters, November 2015, Elsevier

    Professor Rob J de Boer

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

    Article • PLoS Computational Biology, October 2015, PLOS

    Professor Rob J de Boer

  72. Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments

    Article • PLoS Computational Biology, October 2015, PLOS

    Professor Rob J de Boer

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

    Article • AIDS, October 2015, Wolters Kluwer Health

    Professor Rob J de Boer

  74. The evolution of natural killer cell receptors

    Article • Immunogenetics, September 2015, Springer Science + Business Media

    Professor Rob J de Boer

  75. Common myeloid progenitors are made up of distinct subpopulations that either yield erythrocytes or myeloid cells

    Article • Experimental Hematology, September 2015, Elsevier

    Professor Rob J de Boer

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

    Article • Frontiers in Immunology, June 2015, Frontiers

    Professor Rob J de Boer

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

    Article • Journal of Theoretical Biology, June 2015, Elsevier

    Professor Rob J de Boer

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

    Article • Molecular Biology and Evolution, April 2015, Oxford University Press (OUP)

    Professor Rob J de Boer

  79. HIV Molecular Immunology 2014

    Article • February 2015, Office of Scientific and Technical Information (OSTI)

    Professor Rob J de Boer

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

    Article • Aging Cell, January 2015, Wiley

    Professor Rob J de Boer

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

    Article • Frontiers in Immunology, January 2015, Frontiers

    Professor Rob J de Boer

  82. Immune system modeling and analysis

    Article • January 2015

    Professor Rob J de Boer

  83. Immuno-epidemiological Modeling of HIV-1 Predicts High Heritability of the Set-Point Virus Load, while Selection for CTL Escape Dominates Virulence Evolution

    Article • PLoS Computational Biology, December 2014, PLOS

    Professor Rob J de Boer

  84. Random Migration and Signal Integration Promote Rapid and Robust T Cell Recruitment

    Article • PLoS Computational Biology, August 2014, PLOS

    Professor Rob J de Boer

  85. Combining cellular barcoding and mathematical modeling to infer the structure of the hematopoietic pathway

    Article • Experimental Hematology, August 2014, Elsevier

    Professor Rob J de Boer

  86. A General Functional Response of Cytotoxic T Lymphocyte-Mediated Killing of Target Cells

    Article • Biophysical Journal, April 2014, Elsevier

    Professor Rob J de Boer

  87. Determining Lineage Pathways from Cellular Barcoding Experiments

    Article • Cell Reports, February 2014, Elsevier

    Professor Rob J de Boer, Shalin Naik

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

    Article • Frontiers in Immunology, January 2014, Frontiers

    Professor Rob J de Boer

  89. Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants

    Article • Retrovirology, January 2014, Springer Science + Business Media

    Professor Rob J de Boer

  90. 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

    Article • Theoretical Biology and Medical Modelling, January 2014, Springer Science + Business Media

    Professor Rob J de Boer

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

    Article • Parasite Immunology, October 2013, Wiley

    Professor Rob J de Boer

  92. Virus Encoded MHC-Like Decoys Diversify the Inhibitory KIR Repertoire

    Article • PLoS Computational Biology, October 2013, PLOS

    Professor Rob J de Boer

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

    Article • Blood, September 2013, American Society of Hematology

    Professor Rob J de Boer

  94. Diverse and heritable lineage imprinting of early hematopoietic progenitors

    Article • Experimental Hematology, August 2013, Elsevier

    Professor Rob J de Boer, Shalin Naik

  95. Quantifying T lymphocyte turnover

    Article • Journal of Theoretical Biology, June 2013, Elsevier

    Professor Rob J de Boer

  96. Diverse and heritable lineage imprinting of early haematopoietic progenitors

    Article • Nature, April 2013, Nature

    Professor Rob J de Boer, Shalin Naik

  97. Early divergence of Th1 and Th2 transcriptomes involves a small core response and sets of transiently expressed genes

    Article • European Journal of Immunology, March 2013, Wiley

    Professor Rob J de Boer, Dr ir Wilfred van IJcken

  98. Immune Activation and Collateral Damage in AIDS Pathogenesis

    Article • Frontiers in Immunology, January 2013, Frontiers

    Professor Rob J de Boer

  99. Analytical results on the Beauchemin model of lymphocyte migration

    Article • BMC Bioinformatics, January 2013, Springer Science + Business Media

    Professor Rob J de Boer

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

    Article • BMC Systems Biology, January 2013, Springer Science + Business Media

    Professor Rob J de Boer

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

    Article • Frontiers in Immunology, January 2013, Frontiers

    Professor Rob J de Boer

  102. Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens

    Article • PLoS Computational Biology, November 2012, PLOS

    Professor Rob J de Boer

  103. A Generalized Mathematical Model To Estimate T- and B-Cell Receptor Diversities Using AmpliCot

    Article • Biophysical Journal, September 2012, Elsevier

    Professor Rob J de Boer

  104. Which of Our Modeling Predictions Are Robust?

    Article • PLoS Computational Biology, July 2012, PLOS

    Professor Rob J de Boer

  105. Cell division curtails helper phenotype plasticity and expedites helper T-cell differentiation

    Article • Immunology and Cell Biology, May 2012, Nature

    Professor Rob J de Boer

  106. Modelling deuterium labelling of lymphocytes with temporal and/or kinetic heterogeneity

    Article • Journal of The Royal Society Interface, April 2012, Royal Society Publishing

    Professor Rob J de Boer

  107. Impaired immune evasion in HIV through intracellular delays and multiple infection of cells

    Article • Proceedings of the Royal Society B Biological Sciences, April 2012, Royal Society Publishing

    Professor Rob J de Boer

  108. Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire

    Article • PLoS Computational Biology, March 2012, PLOS

    Professor Rob J de Boer

  109. Maintenance of Peripheral Naive T Cells Is Sustained by Thymus Output in Mice but Not Humans

    Article • Immunity, February 2012, Elsevier

    Professor Rob J de Boer

  110. Identifying viral parameters from in vitro cell cultures

    Article • Frontiers in Microbiology, January 2012, Frontiers

    Professor Rob J de Boer

  111. Response: The in vivo half-life of human neutrophils

    Article • Blood, June 2011, American Society of Hematology

    Professor Rob J de Boer

  112. Implications of CTL-Mediated Killing of HIV-Infected Cells during the Non-Productive Stage of Infection

    Article • PLOS One, February 2011, PLOS

    Professor Rob J de Boer

  113. Killing of Targets by CD8+ T Cells in the Mouse Spleen Follows the Law of Mass Action

    Article • PLOS One, January 2011, PLOS

    Professor Rob J de Boer, Dr Vitaly V Ganusov

  114. Current Estimates for HIV-1 Production Imply Rapid Viral Clearance in Lymphoid Tissues

    Article • PLoS Computational Biology, September 2010, PLOS

    Professor Rob J de Boer

  115. Identification of helper T cell master regulator candidates using the polar score method

    Article • Journal of Immunological Methods, September 2010, Elsevier

    Professor Rob J de Boer

  116. Quantifying how MHC polymorphism prevents pathogens from adapting to the antigen presentation pathway

    Article • Epidemics, September 2010, Elsevier

    Professor Rob J de Boer

  117. Lineage-specific T-cell reconstitution following in vivo CD4+ and CD8+ lymphocyte depletion in nonhuman primates

    Article • Blood, August 2010, American Society of Hematology

    Professor Rob J de Boer

  118. In Mice, Tuberculosis Progression Is Associated with Intensive Inflammatory Response and the Accumulation of Gr-1dim Cells in the Lungs

    Article • PLOS One, May 2010, PLOS

    Dr Vitaly V Ganusov, Professor Rob J de Boer

  119. Intracellular transactivation of HIV can account for the decelerating decay of virus load during drug therapy

    Article • Molecular Systems Biology, February 2010, EMBO

    Professor Rob J de Boer

  120. Explicit Kinetic Heterogeneity: Mathematical Models for Interpretation of Deuterium Labeling of Heterogeneous Cell Populations

    Article • PLoS Computational Biology, February 2010, PLOS

    Professor Rob J de Boer, Dr Vitaly V Ganusov

  121. Analysing immune cell migration

    Article • Nature Reviews Immunology, October 2009, Springer Science + Business Media

    Professor Rob J de Boer

  122. Towards estimating the true duration of dendritic cell interactions with T cells

    Article • Journal of Immunological Methods, August 2009, Elsevier

    Professor Rob J de Boer

  123. Correction: The Specificity and Polymorphism of the MHC Class I Prevents the Global Adaptation of HIV-1 to the Monomorphic Proteasome and TAP

    Article • PLOS One, January 2009, PLOS

    Professor Rob J de Boer

  124. The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes

    Article • BMC Evolutionary Biology, January 2009, Springer Science + Business Media

    Professor Rob J de Boer

  125. The Specificity and Polymorphism of the MHC Class I Prevents the Global Adaptation of HIV-1 to the Monomorphic Proteasome and TAP

    Article • PLOS One, October 2008, PLOS

    Professor Rob J de Boer

  126. The Contribution of the Thymus to the Recovery of Peripheral Naive T-Cell Numbers During Antiretroviral Treatment for HIV Infection

    Article • JAIDS Journal of Acquired Immune Deficiency Syndromes, September 2008, Wolters Kluwer Health

    Professor Rob J de Boer

  127. Dynamics of Immune Escape during HIV/SIV Infection

    Article • PLoS Computational Biology, July 2008, PLOS

    Professor Rob J de Boer

  128. Tissue distribution of lymphocytes and plasma cells and the role of the gut: response to Pabst et al.

    Article • Trends in Immunology, May 2008, Elsevier

    Professor Rob J de Boer

  129. Sparse production but preferential incorporation of recently produced naïve T cells in the human peripheral pool

    Article • Proceedings of the National Academy of Sciences, April 2008, Proceedings of the National Academy of Sciences

    Professor Rob J de Boer

  130. Amino Acid Similarity Accounts for T Cell Cross-Reactivity and for “Holes” in the T Cell Repertoire

    Article • PLOS One, March 2008, PLOS

    Professor Rob J de Boer

  131. Do most lymphocytes in humans really reside in the gut?

    Article • Trends in Immunology, December 2007, Elsevier

    Professor Rob J de Boer, Dr Vitaly V Ganusov

  132. HLA Alleles Associated with Slow Progression to AIDS Truly Prefer to Present HIV-1 p24

    Article • PLOS One, September 2007, PLOS

    Professor Rob J de Boer

  133. Time Scales of CD4+ T Cell Depletion in HIV Infection

    Article • PLoS Medicine, May 2007, PLOS

    Professor Rob J de Boer

  134. Spatial modelling of brief and long interactions between T cells and dendritic cells

    Article • Immunology and Cell Biology, April 2007, Nature

    Professor Rob J de Boer

  135. Lymph node topology dictates T cell migration behavior

    Article • Journal of Cell Biology, April 2007, Rockefeller University Press

    Professor Rob J de Boer

  136. Lymph node topology dictates T cell migration behavior

    Article • Journal of Experimental Medicine, March 2007, Rockefeller University Press

    Professor Rob J de Boer

  137. MHC diversity in Individuals and Populations

    Article • January 2007, Springer Science + Business Media

    Professor Rob J de Boer

  138. Erratum to “Quantifying cell turnover using CFSE data” [J. Immunol. Methods (298) (2005) 183]

    Article • Journal of Immunological Methods, December 2006, Elsevier

    Professor Rob J de Boer

  139. Estimating Lymphocyte Division and Death Rates from CFSE Data

    Article • The Bulletin of Mathematical Biophysics, May 2006, Springer Science + Business Media

    Professor Rob J de Boer, Dr Vitaly V Ganusov

  140. The Integration Hypothesis: An Evolutionary Pathway to Benign SIV Infection

    Article • PLoS Pathogens, March 2006, PLOS

    Viktor Müller, Professor Rob J de Boer

  141. Estimating the role of thymic output in HIV infection

    Article • Current Opinion in HIV and AIDS, January 2006, Wolters Kluwer Health

    Professor Rob J de Boer

  142. Estimating Costs and Benefits of CTL Escape Mutations in SIV/HIV Infection

    Article • PLoS Computational Biology, January 2006, PLOS

    Professor Rob J de Boer, Dr Vitaly V Ganusov

  143. Estimating division and death rates from CFSE data

    Article • Journal of Computational and Applied Mathematics, December 2005, Elsevier

    Professor Rob J de Boer

  144. A Mathematical Model of Protein Degradation by the Proteasome

    Article • Biophysical Journal, April 2005, Elsevier

    Professor Rob J de Boer

  145. Quantifying cell turnover using CFSE data

    Article • Journal of Immunological Methods, March 2005, Elsevier

    Professor Rob J de Boer, Dr Vitaly V Ganusov

  146. Estimating Costs and Benefits of CTL Escape Mutations in SIV/HIV Infection

    Article • PLoS Computational Biology, January 2005, PLOS

    Professor Rob J de Boer

  147. Discriminating self from nonself with short peptides from large proteomes

    Article • Immunogenetics, July 2004, Springer Science + Business Media

    Professor Rob J de Boer

  148. MHC polymorphism under host-pathogen coevolution

    Article • Immunogenetics, January 2004, Springer Science + Business Media

    Professor Rob J de Boer

  149. Heterozygote advantage fails to explain the high degree of polymorphism of the MHC

    Article • Immunogenetics, January 2004, Springer Science + Business Media

    Professor Rob J de Boer

  150. Thymic selection does not limit the individual MHC diversity

    Article • European Journal of Immunology, December 2003, Wiley

    Professor Rob J de Boer

  151. Decline in excision circles requires homeostatic renewal or homeostatic death of naive T cells

    Article • Journal of Theoretical Biology, October 2003, Elsevier

    Prof. Dr. Bas E. Dutilh, Professor Rob J de Boer

  152. Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome

    Article • Immunogenetics, August 2003, Springer Science + Business Media

    Professor Rob J de Boer

  153. The race between initial T–helper expansion and virus growth upon HIV infection influences polyclonality of the response and viral set–point

    Article • Proceedings of the Royal Society B Biological Sciences, July 2003, Royal Society Publishing

    Professor Rob J de Boer

  154. Depletion of naive CD4 T cells by CXCR4-using HIV-1 variants occurs mainly through increased T-cell death and activation

    Article • AIDS, July 2003, Wolters Kluwer Health

    Professor Rob J de Boer

  155. A spatial model of germinal center reactions: cellular adhesion based sorting of B cells results in efficient affinity maturation

    Article • Journal of Theoretical Biology, May 2003, Elsevier

    Professor Rob J de Boer

  156. IL-2 therapy and thymic production of naive CD4 T cells in HIV-infected patients with severe CD4 lymphopenia

    Article • AIDS, April 2003, Wolters Kluwer Health

    Professor Rob J de Boer

  157. Thymic output: a bad TREC record

    Article • Nature Immunology, February 2003, Nature

    Professor Rob J de Boer

  158. Reconstitution of naive T cells during antiretroviral treatment of HIV-infected adults is dependent on age

    Article • AIDS, November 2002, Wolters Kluwer Health

    Professor Rob J de Boer

  159. Resource Competition Determines Selection of B Cell Repertoires

    Article • Journal of Theoretical Biology, October 2001, Elsevier

    Professor Rob J de Boer

  160. Selection by AZT and Rapid Replacement in the Absence of Drugs of HIV Type 1 Resistant to Multiple Nucleoside Analogs

    Article • AIDS Research and Human Retroviruses, June 2001, Mary Ann Liebert Inc

    Professor Rob J de Boer

  161. The Dominant Source of CD4+ and CD8+ T-Cell Activation in HIV Infection Is Antigenic Stimulation

    Article • JAIDS Journal of Acquired Immune Deficiency Syndromes, November 2000, Wolters Kluwer Health

    Professor Rob J de Boer

  162. The Dominant Source of CD4+ and CD8+ T-Cell Activation in HIV Infection Is Antigenic Stimulation

    Article • JAIDS Journal of Acquired Immune Deficiency Syndromes, November 2000, Wolters Kluwer Health

    Professor Rob J de Boer

  163. Predicting the duration of antiviral treatment needed to suppress plasma HIV-1 RNA

    Article • Journal of Clinical Investigation, March 2000, American Society for Clinical Investigation

    Professor Rob J de Boer

  164. Normal Telomere Lengths in Naive and Memory CD4+ T Cells in HIV Type 1 Infection: A Mathematical Interpretation

    Article • AIDS Research and Human Retroviruses, August 1999, Mary Ann Liebert Inc

    Professor Rob J de Boer

  165. T Cell Dynamics in HIV-1 Infection

    Article • January 1999, Elsevier

    Professor Rob J de Boer

  166. Early recovery of CD4+ T lymphocytes in children on highly active antiretroviral therapy

    Article • AIDS, November 1998, Wolters Kluwer Health

    Professor Rob J de Boer, Prof Ger T Rijkers

  167. Crossreactivity of the T-cell receptor

    Article • Immunology Today, September 1998, Elsevier

    Professor Rob J de Boer

  168. Target cell availability and the successful suppression of HIV by hydroxyurea and didanosine

    Article • AIDS, September 1998, Wolters Kluwer Health

    Professor Rob J de Boer

  169. Biphasic kinetics of peripheral blood T cells after triple combination therapy in HIV-1 infection: A composite of redistribution and proliferation

    Article • Nature Reports Stem Cells, February 1998, Nature

    Professor Rob J de Boer

  170. Overshoot of HIV-1 viraemia after early discontinuation of antiretroviral treatment

    Article • AIDS, September 1997, Wolters Kluwer Health

    Professor Rob J de Boer

  171. T-cell vaccination: Insights and questions raised by a mathematical model

    Article • Immunology Letters, May 1997, Elsevier

    Professor Rob J de Boer

  172. Reduction of memory cytotoxic T cell numbers by heterologous viral infections: A mathematical model

    Article • Immunology Letters, May 1997, Elsevier

    Professor Rob J de Boer

  173. The context of an immune response: Interactions between innate and adaptive immunity

    Article • Immunology Letters, May 1997, Elsevier

    Professor Rob J de Boer

  174. A Formal Derivation of the “Beddington” Functional Response

    Article • Journal of Theoretical Biology, April 1997, Elsevier

    Professor Rob J de Boer

  175. Self Assertion Modeled as a Network Repertoire of Multi-Determinant Antibodies

    Article • Journal of Theoretical Biology, November 1996, Elsevier

    Professor Rob J de Boer

  176. A new bell-shaped function for idiotypic interactions based on cross-linking

    Article • The Bulletin of Mathematical Biophysics, March 1996, Springer Science + Business Media

    Professor Rob J de Boer

  177. Extending the quasi-steady state approximation by changing variables

    Article • The Bulletin of Mathematical Biophysics, January 1996, Springer Science + Business Media

    Professor Rob J de Boer

  178. Implications of Spatial Heterogeneity for the Paradox of Enrichment

    Article • Ecology, October 1995, Wiley

    Professor Rob J de Boer

  179. Towards a general function describing t cell proliferation

    Article • Journal of Theoretical Biology, August 1995, Elsevier

    Professor Rob J de Boer

  180. T Cell Repertoires and Competitive Exclusion

    Article • Journal of Theoretical Biology, August 1994, Elsevier

    Professor Rob J de Boer

  181. Immune network behavior—II. From oscillations to chaos and stationary states

    Article • The Bulletin of Mathematical Biophysics, July 1993, Springer Science + Business Media

    Professor Rob J de Boer

  182. Immune network behavior—I. From stationary states to limit cycle oscilations

    Article • The Bulletin of Mathematical Biophysics, July 1993, Springer Science + Business Media

    Professor Rob J de Boer

  183. Dynamics of HIV infection of CD4+ T cells

    Article • Mathematical Biosciences, March 1993, Elsevier

    Professor Rob J de Boer

  184. Pattern formation in one- and two-dimensional shape-space models of the immune system

    Article • Journal of Theoretical Biology, April 1992, Elsevier

    Professor Rob J de Boer

  185. Growth and Recruitment in the Immune Network

    Article • January 1992, Springer Science + Business Media

    Professor Rob J de Boer

  186. Size and connectivity as emergent properties of a developing immune network

    Article • Journal of Theoretical Biology, April 1991, Elsevier

    Professor Rob J de Boer

  187. Allelic variations of human TCR V gene products

    Article • Immunology Today, January 1991, Elsevier

    Professor Rob J de Boer

  188. Localized memories in idiotypic networks

    Article • Journal of Theoretical Biology, October 1990, Elsevier

    Professor Rob J de Boer

  189. Poor repertoire selection in symmetric idiotypic network models

    Article • Immunology Letters, August 1989, Elsevier

    Professor Rob J de Boer

  190. Proceedings of a one-day symposium held in Utrecht, The Netherlands, May 1989

    Article • Immunology Letters, August 1989, Elsevier

    Professor Rob J de Boer

  191. Idiotypic networks incorporating T-B cell co-operation. The conditions for percolation

    Article • Journal of Theoretical Biology, July 1989, Elsevier

    Professor Rob J de Boer

  192. Unreasonable implications of reasonable idiotypic network assumptions

    Article • The Bulletin of Mathematical Biophysics, May 1989, Springer Science + Business Media

    Professor Rob J de Boer

  193. Stability of symmetric idiotypic networks—a critique of Hoffmann's analysis

    Article • The Bulletin of Mathematical Biophysics, March 1989, Springer Science + Business Media

    Professor Rob J de Boer

  194. Memory but no suppression in low-dimensional symmetric idiotypic networks

    Article • The Bulletin of Mathematical Biophysics, March 1989, Springer Science + Business Media

    Professor Rob J de Boer

  195. Information processing in immune systems: Clonal selection versus idiotypic network models

    Article • January 1989, Elsevier

    Professor Rob J de Boer

  196. Immunological discrimination between self and non-self by precursor depletion and memory accumulation

    Article • Journal of Theoretical Biology, February 1987, Elsevier

    Professor Rob J de Boer

  197. Self-Nonself Discrimination due to Immunological Nonlinearities: the Analysis of a Series of Models by Numerical Methods

    Article • Mathematical Medicine and Biology A Journal of the IMA, January 1987, Oxford University Press (OUP)

    Professor Rob J de Boer

  198. Interactions between macrophages and T-lymphocytes: Tumor sneaking through intrinsic to helper T cell dynamics

    Article • Journal of Theoretical Biology, June 1986, Elsevier

    Professor Rob J de Boer

  199. Implications of Macrophage T-Lymphocyte Interactions for Tumor Rejectability

    Article • January 1986, Springer Science + Business Media

    Professor Rob J de Boer

  200. Mathematical analysis of the cellular immune reaction against tumour cells

    Article • Immunology Today, November 1985, Elsevier

    Professor Rob J de Boer

  201. The effect of group size on time budgets and social behaviour in wild long-tailed macaques (Macaca fascicularis)

    Article • Behavioral Ecology and Sociobiology, September 1983, Springer Science + Business Media

    Professor Rob J de Boer

  202. Diversity and virulence thresholds in AIDS

    Article • Cambridge University Press

    Professor Rob J de Boer

  203. Major Histocompatibility Complex: Polymorphism from Coevolution

    Article • Cambridge University Press

    Professor Rob J de Boer