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Borgoni, S., Sofyali, E., Soleimani, M., Wilhelm, H., Müller-Decker, K., Will, R., Noronha, A., Beumers, L., Verschure, P. J., Yarden, Y., Magnani, L., van Kampen, A. H. C., Moerland, P. D., & Wiemann, S. (2020). Time-Resolved Profiling Reveals ATF3 as a Novel Mediator of Endocrine Resistance in Breast Cancer. Cancers, 12(10), Article 2918. https://doi.org/10.3390/cancers12102918[details]
Gjaltema, R. A. F., Goubert, D., Huisman, C., Del Pilar García Tobilla, C., Koncz, M., Jellema, P. G., Wu, D., Brouwer, U., Kiss, A., Verschure, P. J., Bank, R. A., & Rots, M. G. (2020). KRAB-Induced Heterochromatin Effectively Silences PLOD2 Gene Expression in Somatic Cells and is Resilient to TGFβ1 Activation. International Journal of Molecular Sciences, 21(10), Article 3634. https://doi.org/10.3390/ijms21103634[details]
Mandemaker, I. K., Zhou, D., Bruens, S. T., Dekkers, D. H., Verschure, P. J., Edupuganti, R. R., Meshorer, E., Demmers, J. A. A., & Marteijn, J. A. (2020). Histone H1 eviction by the histone chaperone SET reduces cell survival following DNA damage. Journal of Cell Science, 133, Article jcs235473. Advance online publication. https://doi.org/10.1242/jcs.235473[details]
Soleimani Dodaran, M., Borgoni, S., Sofyali, E., Verschure, P. J., Wiemann, S., Moerland, P. D., & van Kampen, A. H. C. (2020). Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2-breast cancer. BMC Cancer, 20, Article 676. https://doi.org/10.1186/s12885-020-07100-z[details]
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 3 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673818
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 14 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673806
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 2 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673815
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 10 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673794
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 8 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673833
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 13 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673803
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 1 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673812
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 4 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673821
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 7 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673830
Soleimani Dodaran, M., Borgoni, S., Sofyall, E., Verschure, P. J., Wiemann, S., Moerland, P. D. & Van Kampen, A. H. C. (2020). Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Springer Nature. https://doi.org/10.6084/m9.figshare.c.5067306.v1
2018
Beckman, W., Vuist, I. M., Kempe, H., & Verschure, P. J. (2018). Cell-to-Cell Transcription Variability as Measured by Single-Molecule RNA FISH to Detect Epigenetic State Switching. In A. Jeltsch, & M. G. Rots (Eds.), Epigenome Editing: Methods and Protocols (pp. 385-393). (Methods in Molecular Biology). Humana Press. https://doi.org/10.1007/978-1-4939-7774-1_21[details]
Naue, J., Hoefsloot, H. C. J., Kloosterman, A. D., & Verschure, P. J. (2018). Forensic DNA methylation profiling from minimal traces: How low can we go? Forensic Science International. Genetics, 33, 17-23. https://doi.org/10.1016/j.fsigen.2017.11.004[details]
Naue, J., Sänger, T., Hoefsloot, H. C. J., Lutz-Bonengel, S., Kloosterman, A. D., & Verschure, P. J. (2018). Proof of concept study of age-dependent DNA methylation markers across different tissues by massive parallel sequencing. Forensic Science International. Genetics, 36, 152-159. https://doi.org/10.1016/j.fsigen.2018.07.007[details]
2017
Goubert, D., Beckman, W. F., Verschure, P. J., & Rots, M. G. (2017). Epigenetic editing: towards realization of the curable genome concept. Convergent Science Physical Oncology, 3(1), Article 013006. https://doi.org/10.1088/2057-1739/aa5cc0[details]
Magnani, L., Frigè, G., Gadaleta, R. M., Corleone, G., Fabris, S., Kempe, H., Verschure, P. J., Barozzi, I., Vircillo, V., Hong, S. P., Perone, Y., Saini, M., Trumpp, A., Viale, G., Neri, A., Ali, S., Colleoni, M. A., Pruneri, G., & Minucci, S. (2017). Acquired CYP19A1 amplification is an early specific mechanism of aromatase inhibitor resistance in ERα metastatic breast cancer. Nature genetics, 49(3), 444-450. https://doi.org/10.1038/ng.3773[details]
Naue, J., Hoefsloot, H. C. J., Mook, O. R. F., Rijlaarsdam-Hoekstra, L., van der Zwalm, M. C. H., Henneman, P., Kloosterman, A. D., & Verschure, P. J. (2017). Chronological age prediction based on DNA methylation: Massive parallel sequencing and random forest regression. Forensic Science International. Genetics, 31, 19-28. https://doi.org/10.1016/j.fsigen.2017.07.015[details]
van Hagen, M., Piebes, D. G. E., de Leeuw, W. C., Vuist, I. M., van Roon-Mom, W. M. C., Moerland, P. D., & Verschure, P. J. (2017). The dynamics of early-state transcriptional changes and aggregate formation in a Huntington's disease cell model. BMC Genomics, 18(373), Article 373. https://doi.org/10.1186/s12864-017-3745-z[details]
Hoeijmakers, L., Kempe, H., & Verschure, P. J. (2016). Epigenetic imprinting during assisted reproductive technologies: The effect of temporal and cumulative fluctuations in methionine cycling on the DNA methylation state. Molecular Reproduction and Development, 83(2), 94-107. Advance online publication. https://doi.org/10.1002/mrd.22605[details]
Wijchers, P. J., Krijger, P. H. L., Geeven, G., Zhu, Y., Denker, A., Verstegen, M. J. A. M., Valdes-Quezada, C., Vermeulen, C., Janssen, M., Teunissen, H., Anink-Groenen, L. C. M., Verschure, P. J., & de Laat, W. (2016). Cause and Consequence of Tethering a SubTAD to Different Nuclear Compartments. Molecular Cell, 61(3), 461-473. https://doi.org/10.1016/j.molcel.2016.01.001[details]
Kempe, H., Schwabe, A., Crémazy, F., Verschure, P. J., & Bruggeman, F. J. (2015). The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise. Molecular Biology of the Cell, 26(4), 797-804. https://doi.org/10.1091/mbc.E14-08-1296[details]
Anink-Groenen, L. C. M., Maarleveld, T. R., Verschure, P. J., & Bruggeman, F. J. (2014). Mechanistic stochastic model of histone modification pattern formation. Epigenetics & Chromatin, 7, 30. https://doi.org/10.1186/1756-8935-7-30[details]
Brink, M. C., Piebes, D. G. E., de Groote, M. L., Luijsterburg, M. S., Casas-Delucchi, C. S., van Driel, R., Rots, M. G., Cardoso, M. C., & Verschure, P. J. (2013). A role for MeCP2 in switching gene activity via chromatin unfolding and HP1γ displacement. PLoS ONE, 8(7), e69347. https://doi.org/10.1371/journal.pone.0069347[details]
Muraro, M. J., Kempe, H., & Verschure, P. J. (2013). Concise Review: The Dynamics of Induced Pluripotency and Its Behavior Captured in Gene Network Motifs. Stem Cells, 31(5), 838-848. Advance online publication. https://doi.org/10.1002/stem.1340[details]
de Groote, M. L., Verschure, P. J., & Rots, M. G. (2012). Epigenetic Editing: targeted rewriting of epigenetic marks to modulate expression of selected target genes. Nucleic Acids Research, 40(21), 10596-10613. https://doi.org/10.1093/nar/gks863[details]
Schwabe, A., Dobrzynski, M., Rybakova, E., Verschure, P. J., & Bruggeman, F. J. (2011). Origins of stochastic intracellular processes and consequences for cell-to-cell variability and cellular survival strategies. Methods in Enzymology, 500, 597-625. https://doi.org/10.1016/B978-0-12-385118-5.00028-1[details]
2010
Scassellati, C., Albi, E., Cmarko, D., Tiberi, C., Cmarkova, J., Bouchet‑Marquis, C., Verschure, P. J., van Driel, R., Viola Magni, M., & Fakan, S. (2010). Intranuclear sphingomyelin is associated with transcriptionally active chromatin and plays a role in nuclear integrity. Biology of the Cell, 102(6), 361-375. https://doi.org/10.1042/BC20090139[details]
2009
Luijsterburg, M. S., Dinant, C., Lans, H., Stap, J., Wiernasz, E. S., Lagerwerf, S., Warmerdam, D. O., Lindh, M., Brink, M. C., Dobrucki, J. W., Aten, J. A., Fousteri, M. I., Jansen, G., Dantuma, N. P., Vermeulen, W., Mullenders, L. H. F., Houtsmuller, A. B., Verschure, P. J., & van Driel, R. (2009). Heterochromatin protein 1 is recruited to various types of DNA damage. Journal of Cell Biology, 185(4), 577-586. https://doi.org/10.1083/jcb.200810035[details]
Mateos-Langerak, J., Bohn, M., de Leeuw, W., Giromus, O., Manders, E. M. M., Verschure, P. J., Indemans, M. H. G., Gierman, H. J., Heermann, D. W., van Driel, R., & Goetze, S. (2009). Spatially confined folding of chromatin in the interphase nucleus. Proceedings of the National Academy of Sciences of the United States of America, 106(10), 3812-3817. https://doi.org/10.1073/pnas.0809501106[details]
2002
Sanchez-Montanes, M. A., Konig, P., & Verschure, P. J. (2002). Learning sensory maps with real-world stimuli in real time using a biophysically realistic learning rule. IEEE Transactions on Neural Networks, 13(3), 619-32. https://doi.org/10.1109/TNN.2002.1000128
Verschure, P. J. (speaker) (14-4-2011). Wie ben ik, wat onderzoek ik, waarom is wetenschappelijk onderzoek zo interessant, Girlsday VHTO, Amsterdam, the Netherlands.
2017
Kempe, H. (2017). Understanding gene expression variability in its biological context using theoretical and experimental analyses of single cells. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
Soleimani Dodaran, M., Borgoni, S., Sofyall, E., Verschure, P. J., Wiemann, S., Moerland, P. D. & Van Kampen, A. H. C. (2020). Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Springer Nature. https://doi.org/10.6084/m9.figshare.c.5067306.v1
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 4 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673821
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 7 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673830
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 13 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673803
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 10 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673794
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 2 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673815
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 1 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673812
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 8 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673833
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 3 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673818
Soleimani Dodaran, M., Sofyall, E., Verschure, P. J., Van Kampen, A. H. C., Borgoni, S., Wiemann, S., Moerland, P. D. & Sofyalı, E. (2020). Additional file 14 of Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. Figshare. https://doi.org/10.6084/m9.figshare.12673806
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