Joost Beltman
Associate professor
- Name
- Dr. J.B. Beltman
- Telephone
- +31 71 527 4323
- j.b.beltman@lacdr.leidenuniv.nl
- ORCID iD
- 0000-0001-9215-3087
Joost Beltman is assistant professor at the Division of Drug Discovery & Safety.
More information about Joost Beltman
PhD Candidates
News
Former PhD Candidates
Biography
My PhD project (2000-2004) was performed in the Theoretical Biology group of the Institute of Biology (IBL) at Leiden University, supervised by Patsy Haccou, Hans Metz and Carel ten Cate. During this period, I worked on mathematical modeling of the impact of learning processes on evolutionary processes. From 2005-2011, I worked as a postdoc in the Theoretical Biology and Bioinformatics group headed by Rob de Boer at Utrecht University (from 2008-2011 on a prestigious NWO Veni grant). I investigated the dynamic nature of cell migration and cell-cell interactions as can nowadays be observed by in vivo imaging approaches. We developed novel approaches for the quantitative analysis of such dynamic imaging data as well as incorporating experimental data into computational cell migration models. Our questions were related to the functioning of our immune system, e.g., T cell migration, T cell-dendritic cell interactions, recruitment of T cells into the immune response, B cells migrating within germinal centers and the killing of target cells by cytotoxic T lymphocytes. From 2012-2014, I was a senior postdoc/research associate in the group of Ton Schumacher in the Immunology division of the Netherlands Cancer Institute (NKI). Apart from continuing my work on the modelling of T cell migration, I also worked on the analysis of cellular barcoding data in which cells have a unique DNA barcode that allows to follow how much offspring they generate.
In 2013, I was awarded a prestigious NWO Vidi grant to study the role of the immune system in cancer. This allowed me to start my own independent research group as an Assistant Professor at Leiden University (within the Division of Drug Discovery and Safety at the LACDR). In 2020, I was promoted to Associate Professor. My general research interest is to apply computational models and quantitative analysis to primarily dynamic imaging data (although we also exploit other data types such as gene expression measurements and cellular barcoding data). For more information on the topics we currently work on see the research project descriptions and the link to the ‘Image-based Computational Biology’ group on the right.
Associate professor
- Science
- Leiden Academic Centre for Drug Research
- LACDR/Toxicology
- Di Tillio F. & Beltman J.B. (2024), Developing quantitative adverse outcome pathways: an ordinary differential equation-based computational framework, Computational Toxicology 32: 100330.
- Heldring M.M., Duijndam B., Kyriakidou A., Meer O.M. van der, Tedeschi M., Laan J.W. van der, Water B. van de & Beltman J.B. (2024), Interdependency of estradiol-mediated ERα activation and subsequent PR and GREB1 induction to control cell cycle progression, Heliyon 10(21): e38406.
- Di Tillio F. & Beltman J.B. (2024), Developing quantitative adverse outcome pathways: an ordinary differential equation-based computational framework, Computational Toxicology 32: 100330.
- Urbanus J., Cosgrove J., Beltman J.B., Elhanati Y., Moral R.A., Conrad C., Heijst J.W. van, Tubeuf E., Velds A., Kok L., Merle C., Magnusson J.P., Guyonnet L., Frisén J., Fre S., Walczak A.M., Mora T., Jacobs H., Schumacher T.N. & Perié L. (2023), DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age, Nature Communications 14(1): 2184.
- Beck R.J., Sloot S., Matsushita H., Kakimi K. & Beltman J.B. (2023), Mathematical modeling identifies LAG3 and HAVCR2 as biomarkers of T cell exhaustion in melanoma, iScience 26(5): 106666.
- Lems C.M., Burger G.A. & Beltman J.B. (2023), Tumor-mediated immunosuppression and cytokine spreading affects the relation between EMT and PD-L1 status, Frontiers in Immunology 14: 1219669.
- Sharma R.P., Burgers E.J. & Beltman J.B. (2023), Development of a physiologically based pharmacokinetic model for nitrofurantoin in rabbits, rats, and humans, Pharmaceutics 15(9): 2199.
- Burgers E.J., Sharma R.P., Schildknecht S., Danilyuk T.Y., Wijaya L.S., Hincapie S., Ramirez Zickgraf F.M., Water B. van de & Beltman J.B. (2023), P06-09: Computational modelling of integrated stress response and oxidative stress response for cellular adversity predictions, Toxicology Letters 384: s108.
- Stel W. van der, Yang H., Le Dévédec S.E., Water B. van de, Beltman J.B. & Danen E.H.J. (2023), High-content high-throughput imaging reveals distinct connections between mitochondrial morphology and functionality for oxphos complex I, III, and V inhibitors, Cell Biology and Toxicology 39: 415-433.
- Bajard L., Adamovsky O., Audoze K., Baken K., Barouki R., Beltman J.B., Beronius A., Bonefeld-Jorgensen E.C., Cano-Sancho G., Baat M.L. de, Tillio F. di, Fernandez M.F., FitzGerald R.E., Gundacker C., Hernandez A.F., Hilscherova K., Karakitsios S., Kuchovska E., Long M., Luijten M., Majid S., Marx-Stoelting P., Mustieles V., Negi C.H., Saigiannis D., Scholtz S., Sovadinova I., Stierum R., Tanabe S., Tollefsen K.E., Brand A.D. van den, Vogs C., Wielsoe M., Wittwehr C. & Blaha L. (2023), Application of AOPs to assist regulatory assessment of chemical risks: case studies, needs and recommendations, Environmental Research 217: 114650.
- Stel W. van der, Yang H., Vrijenhoek N.G., Schimming J.P., Callegaro G., Carta G., Darici S., Delp J., Forsby A., White A., Le Dévédec S.E., Leist M., Jennings P., Beltman J.B., Water B. van de & Danen E.H.J. (2022), Mapping the cellular response to electron transport chain inhibitors reveals selective signaling networks triggered by mitochondrial perturbation, Archives of Toxicology 96: 259-285.
- Burger G.A., Water B. van de, Le Dévédec S.E. & Beltman J.B. (2022), Density-dependent migration characteristics of cancer cells driven by pseudopod interaction, Frontiers in Cell and Developmental Biology 10: 854721.
- Hiemstra S.W., Fehling-Kaschek M., Kuijper I.A., Bischoff L.J.M., Wijaya L.S., Rosenblatt M., Esselink J.J., Egmond A. van, Mos J., Beltman J.B., Timmer J., Water B. van de & Kaschek D. (2022), Dynamic modeling of Nrf2 pathway activation in liver cells after toxicant exposure, Scientific Reports 12(1): 7336.
- Bruns I.B. & Beltman J.B. (2022), Quantifying the contribution of transcription factor activity, mutations and microRNAs to CD274 expression in cancer patients, Scientific Reports 12(1): 4374.
- Heldring M.M., Wijaya L.S., Niemeijer M.C., Yang H., Lakhal T., Le Dévédec S.E., Water B. van de & Beltman J.B. (2022), Model-based translation of DNA damage signaling dynamics across cell types, PLoS Computational Biology 18(7): e1010264.
- Heldring M.M., Shaw A.H. & Beltman J.B. (2022), Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury, npj Systems Biology and Applications 8(1): 27.
- Burger G.A., Nesenberend D.N., Lems C.M., Hille S.C. & Beltman J.B. (2022), Bidirectional crosstalk between epithelial-mesenchymal plasticity and IFN gamma-induced PD-L1 expression promotes tumour progression, Royal Society Open Science 9(11): 220186.
- Sharma R.P., Wolters L., Braak B.T., Niemeijer M., Sparham C., Nicol B., White A., Water B. van de, Middleton A.M. & Beltman J.B. (2022), Deciphering the quantitative relationship between chemical kinetics and Nrf2 pathway dynamics, Toxicology Letters 368(Supplement 1): S288.
- Wijaya L.S., Trairatphisan P., Gabor A., Niemeijer M.C., Keet J., Alcalà Morera A., Snijders K.E., Wink S., Yang H., Schildknecht S., Stevens J.L., Bouwman R.J.P., Kamp H., Hengstler J., Beltman J.B., Leist M., Le Dévédec S.E., Saez-Rodriguez J. & Water B. van de (2021), Integration of temporal single cell cellular stress response activity with logic-ODE modeling reveals activation of ATF4-CHOP axis as a critical predictor of drug-induced liver injury, Biochemical Pharmacology 190: 114591.
- Beck R.J., Weigelin B. & Beltman J.B. (2021), Mathematical modelling based on in vivo imaging suggests CD137-stimulated cytotoxic T lymphocytes exert superior tumour control due to an enhanced antimitotic effect on tumour cells, Cancers 13(11): 2567.
- Wijaya L.S., Rau C., Braun T.S., Marangoz S., Spegg V., Vlasveld M., Albrecht W., Brecklinghaus T., Kamp H., Beltman J.B., Hengstler J.G., Water B. van de, Leist M. & Schildknecht S. (2021), Stimulation of de novo glutathione synthesis by nitrofurantoin for enhanced resilience of hepatocytes, Cell Biology and Toxicology : .
- Yang H., Stel W. van der, Lee R., Bauch C., Bevan S., Walker P., Water B. van de, Danen E.H.J. & Beltman J.B. (2021), Dynamic modeling of mitochondrial membrane potential upon exposure to mitochondrial inhibitors, Frontiers in Pharmacology 12: 679407.
- Yang H., Niemeijer M.C., Water B. van de & Beltman J.B. (2020), ATF6 Is a Critical Determinant of CHOP Dynamics during the Unfolded Protein Response, iScience 23(2): 100860.
- Zenke S., Palm M.M., Braun J., Gavrilov A., Meiser P., Bottcher J.P., Beyersdorf N., Ehl S., Gerard A., Lammermann T., Schumacher T.N., Beltman J.B. & Rohr J.C. (2020), Quorum Regulation via Nested Antagonistic Feedback Circuits Mediated by the Receptors CD28 and CTLA-4 Confers Robustness to T Cell Population Dynamics, Immunity 52(2): 313-327.
- Kok L. Dijkgraaf F.E. Urbanus J. Bresser K. Vredevoogd D.W. Cardoso R.F. Perié L. Beltman J.B. Schumacher T.N. (2020), A committed tissue-resident memory T cell precursor within the circulating CD8+ effector T cell pool, The Journal of Experimental Medicine 217(10): e20191711.
- Beck R.J. Bijker D.I. Beltman J.B. (2020), Heterogeneous, delayed-onset killing by multiple-hitting T cells: Stochastic simulations to assess methods for analysis of imaging data, PLoS Computational Biology 16(7): e1007972.
- Cazaux M., Grandjean C.L., Lemaitre Fabrice, Garcia Z., Beck R.J., Milo I., Postat J., Beltman J.B., Cheadle E.J. & Bousso P. (2019), Single-cell imaging of CAR T cell activity in vivo reveals extensive functional and anatomical heterogeneity, The Journal of Experimental Medicine 216(5): 1038-1049.
- Beck R.J., Slagter M. & Beltman J.B. (2019), Contact-dependent killing by cytotoxic T lymphocytes is insufficient for EL4 tumor regression in vivo, Cancer Research 79(13): 3406-3416.
- Dijkgraaf F.E., Matos T.R., Hoogenboezem M., Toebes M., Vredevoogd D.W., Mertz M., Broek B. van den, Song J-Y., Teunissen M.B.M., Luiten R.M., Beltman J.B. & Schumacher T.N. (2019), Tissue patrol by resident memory CD8+ T cells in human skin, Nature Immunology 20: 756-764.
- Zgheib E., Gao W., Limonciel A., Aladjov G., Yang H., Tebby C., Gayraud G., Jennings P., Sachana M., Beltman J.B. & Bois F.Y. (2019), Application of three approaches for quantitative AOP development to renal toxicity, Computational Toxicology 11(August): 1-13.
- Bischoff L.J.M., Kuijper I.A., Schimming J.P., Wolters L., Braak B. ter, Langenberg J.P., Noort D., Beltman J.B. & Water B. van de (2019), A systematic analysis of Nrf2 pathway activation dynamics during repeated xenobiotic exposure, Archives of Toxicology 93(2): 435-451.
- Palm M.M., Elemans M. & Beltman J.B. (2018), Heritable tumor cell division rate heterogeneity induces clonal dominance, PLoS Computational Biology 14(2): e1005954.
- Kuijper I.A., Yang H., Water B. van de & Beltman J.B. (2017), Unraveling cellular pathways contributing to drug-induced liver injury by dynamical modeling, Expert Opinion on Drug Metabolism & Toxicology 13(1): 5-17.
- Gadhamsetty S., Maree A.F.M., Boer R.J. de & Beltman J.B. (2017), Tissue Dimensionality Influences the Functional Response of Cytotoxic T Lymphocyte-Mediated Killing of Targets, Frontiers in Immunology 7: 668.
- Gadhamsetty S., Maree A.F.M., Beltman J.B. & Boer R.J. de (2017), A Sigmoid Functional Response Emerges When Cytotoxic T Lymphocytes Start Killing Fresh Target Cells, Biophysical Journal 112(6): 1221-1235.
- Burger G.A., Danen E.H.J. & Beltman J.B. (2017), Deciphering Epithelial-Mesenchymal Transition Regulatory Networks in Cancer through Computational Approaches, Frontiers in Oncology 7: 162.
- Leist M., Ghallab A., Graepel R., Marcahn R., Hassan R., Hougaard Bennekou S., Limonciel A., Vinken M., Schildknecht S., Waldmann T., Danen E.H.J., Ravenzway B. van, Kamp H., Gardner I., Godoy P., Bois F.Y., Braeuning A., Reif R., Oesch F., Drasdo D., Hoehme S., Schwarz M., Hartung T., Braunbeck T., Beltman J.B., Vrieling H., Sanza F., Forsby A., Gadaleta D., Fisher C., Kelm J., Fluri D., Ecker G., Zdrqazil B., terron A., Jennings P., Burg B. van der, Dooley S., Meijer A.H., Willighagen E., Martens M., Evelo C., Mombelli E., Taboureau O., Manovani A., Hardy B., Koch B., Escher S., Thriel C. van, Cadenas C., Kroese D., Water B. van de & Hengstler J.G. (2017), Adverse outcome pathways : opportunities, limitations and open questions, Archives of Toxicology 91(11): 3477-3505.
- Palm M.M., Elemans M. & Beltman J.B. (2017), Heritable tumor cell division rate heterogeneity explains in vitro clonal dominance, Cancer Research 77(13): 4535.
- Beltman J.B., Urbanus J., Velds A., Rooij N. van, Rohr J.C., Naik S.H. & Schumacher T.N. (2016), Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells, BMC Bioinformatics 17: 151.
- Swart M., Verbrugge I. & Beltman J.B. (2016), Combination Approaches with Immune-Checkpoint Blockade in Cancer Therapy, Frontiers in Oncology 6: 233.
- Gadhamsetty S., Beltman J.B. & Boer R.J. de (2015), What do mathematical models tell us about killing rates during HIV-1 infection?, Immunology Letters 168(1): 1-6.
- Ariotti S., Beltman J.B., Borsje R., Hoekstra M.E., Halford W.P., Haanen J.B., Boer R.J. de & Schumacher T.N. (2015), Subtle, CXCR3-dependent, chemotaxis of cytotoxic cells within infected tissues allows efficient target localization, Journal of Immunology 195(11): 5285-5295.
- Textor J., Henrickson S.E., Mandl J.N., Von Andrian U.H., Westermann J., Boer R.J. de & Beltman J.B. (2014), Random migration and signal integration promote rapid and robust T cell recruitment, PLoS Computational Biology 10(8): e1003752.
- Gadhamsetty S., Maree Athanasius F.M., Beltman J.B. & Boert R.J. de (2014), A General Functional Response of Cytotoxic T Lymphocyte-Mediated Killing of Target Cells, Biophysical Journal 106(8): 1780-1791.
- Gerlach C., Rohr J.C., Perie L., Rooij N. van, Heijst J.W.J. van, Velds A., Urbanus J., Naik S.H., Jacobs H., Beltman J.B., Boer R.J. de & Schumacher T.N.M. (2013), Heterogeneous Differentiation Patterns of Individual CD8(+) T Cells, Science 340(6132): 635-639.
- Beltman J.B., Hendriks C., Tum M. & Schaap M. (2013), The impact of large scale biomass production on ozone air pollution in Europe, Atmospheric Environment 71: 352-363.
- Vroomans R.M., Marée A.F., Boer R.J. de & Beltman J.B. (2012), Chemotactic migration of T cells towards dendritic cells promotes the detection of rare antigens, PLoS Computational Biology 8(11): e1002763.
- Kvistborg P., Shu C.J., Heemskerk B., Fankhauser M., Thrue C.A., Toebes M., Rooij N. van, Linnemann C., Buuren M.M. van, Urbanus J.H., Beltman J.B., Thor Straten P., Li Y.F., Robbins P.F., Besser M.J., Schachter J., Kenter G.G., Dudley M.E., Rosenberg S.A., Haanen J.B.A.G., Hadrup S.R. & Schumacher T.N.M. (2012), TIL therapy broadens the tumor-reactive CD8(+) T cell compartment in melanoma patients, OncoImmunology 1(4): 409-418.
- Ariotti S., Beltman J.B., Chodaczek G., Hoekstra M.E., Beek A.E. van, Gomez-Eerland R., Ritsma L., Rheenen J. van, Maree A.F.M., Zal T., Boer R.J. de, Haanen J.B.A.G. & Schumacher T.N. (2012), Tissue-resident memory CD8(+) T cells continuously patrol skin epithelia to quickly recognize local antigen, Proceedings of the National Academy of Sciences 109(48): 19739-19744.
- Beltman J.B., Allen C.D.C., Cyster J.G. & Boer R.J. de (2011), B cells within germinal centers migrate preferentially from dark to light zone, Proceedings of the National Academy of Sciences 108(21): 8755-8760.
- Beltman J.B., Maree A.F.M. & Boer R.J. de (2009), Analysing immune cell migration, Nature Reviews Immunology 9(11): 789-798.
- Beltman J.B., Henrickson S.E., Andrian U.H. von der, Boer R.J. de & Maree A.F.M. (2009), Towards estimating the true duration of dendritic cell interactions with T cells, Journal of Immunological Methods 347(1-2): 54-69.
- Beltman J.B., Maree A.F.M., Lynch J.N., Miller M.J. & Boer R.J. de (2007), Lymph node topology dictates T cell migration behavior, The Journal of Experimental Medicine 204(4): 771-780.
- Beltman J.B., Maree A.F.M. & Boer R.J. de (2007), Spatial modelling of brief and long interactions between T cells and dendritic cells, Immunology and Cell Biology 85(4): 306-314.
- Beltman J.B. & Metz J.A.J. (2005), Speciation: more likely through a genetic or through a learned habitat preference?, Proceedings of the Royal Society B: Biological Sciences 272(1571): 1455-1463.
- Beltman J.B. & Haccou P. (2005), Speciation through the learning of habitat features, Theoretical Population Biology 67(3): 189-202.
- Borghans J.A.M., Beltman J.B. & Boer R.J. de (2004), MHC polymorphism under host-pathogen coevolution, Immunogenetics 55(11): 732-739.