Vermeulen, Michiel

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives

Spruijt, C. G., Gnerlich, F., Smits, A. H., Pfaffeneder, T., Jansen, P. W. T. C., Bauer, C., Münzel, M., Wagner, M., Müller, M., Khan, F., et al. (2013) · Cell

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 973

Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers

Vermeulen, M., Eberl, H. C., Matarese, F., Marks, H., Denissov, S., Butter, F., Lee, K. K., Olsen, J. V., Hyman, A. A., Stunnenberg, H. G., et al. (2010) · Cell

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 806

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

Bartke, T., Vermeulen, M., Xhemalce, B., Robson, S. C., Mann, M., & Kouzarides, T. (2010) · Cell

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 611

MBD2/NuRD and MBD3/NuRD, Two Distinct Complexes with Different Biochemical and Functional Properties

Le Guezennec, X., Vermeulen, M., Brinkman, A. B., Hoeijmakers, W. A. M., Cohen, A., Lasonder, E., & Stunnenberg, H. G. (2006) · Molecular and Cellular Biology

Epigenetics and DNA MethylationCancer-related gene regulation

Cited by 340

The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy

Lindeboom, R. G. H., Vermeulen, M., Lehner, B., & Supek, F. (2019) · Nature Genetics

RNA Research and SplicingRNA regulation and disease

Cited by 327

Stoichiometry of chromatin-associated protein complexes revealed by label-free quantitative mass spectrometry-based proteomics

Smits, A. H., Jansen, P. W. T. C., Poser, I., Hyman, A. A., & Vermeulen, M. (2013) · Nucleic Acids Research

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 258

Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids

Artegiani, B., van Voorthuijsen, L., Lindeboom, R. G. H., Seinstra, D., Heo, I., Tapia, P., López-Iglesias, C., Postrach, D., Dayton, T., Oka, R., et al. (2019) · Cell Stem Cell

Cholangiocarcinoma and Gallbladder Cancer StudiesChromatin Remodeling and Cancer

Cited by 218

A map of general and specialized chromatin readers in mouse tissues generated by label-free interaction proteomics

Eberl, H. C., Spruijt, C. G., Kelstrup, C. D., Vermeulen, M., & Mann, M. (2013) · Molecular Cell

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 189

Single-cell DNA methylation profiling: technologies and biological applications

Karemaker, I. D., & Vermeulen, M. (2018) · Trends in Biotechnology

Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics

Cited by 170

Towards elucidating the stability, dynamics and architecture of the nucleosome remodeling and deacetylase complex by using quantitative interaction proteomics

Kloet, S. L., Baymaz, H. I., Makowski, M., Groenewold, V., Jansen, P. W. T. C., Berendsen, M., Niazi, H., Kops, G. J., & Vermeulen, M. (2015) · The FEBS Journal

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 107

Proteome-Wide Analysis of Disease-Associated SNPs That Show Allele-Specific Transcription Factor Binding

Butter, F., Davison, L., Viturawong, T., Scheibe, M., Vermeulen, M., Todd, J. A., & Mann, M. (2012) · PLoS Genetics

Genetic Associations and EpidemiologyDiabetes and associated disorders

Cited by 91

Insight into the Architecture of the NuRD Complex

Alqarni, S. S. M., Murthy, A., Zhang, W., Przewloka, M. R., Silva, A. P. G., Watson, A. A., Lejon, S., Pei, X. Y., Smits, A. H., Kloet, S. L., et al. (2014) · Journal of Biological Chemistry

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 84

Inactivation of yeast Isw2 chromatin remodeling enzyme mimics longevity effect of calorie restriction via induction of genotoxic stress response

Dang, W., Sutphin, G. L., Dorsey, J. A., Otte, G. L., Cao, K., Perry, R. M., Wanat, J. J., Saviolaki, D., Murakami, C. J., Tsuchiyama, S., et al. (2014) · Cell Metabolism

Genetics, Aging, and Longevity in Model OrganismsGenomics and Chromatin Dynamics

Cited by 83

Sall4 controls differentiation of pluripotent cells independently of the Nucleosome Remodelling and Deacetylation (NuRD) complex

Miller, A., Ralser, M., Kloet, S. L., Loos, R., Nishinakamura, R., Bertone, P., Vermeulen, M., & Hendrich, B. (2016) · Development

Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation

Cited by 78

A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair

van den Heuvel, D., Spruijt, C. G., González-Prieto, R., Kragten, A., Paulsen, M. T., Zhou, D., Wu, H., Apelt, K., van der Weegen, Y., Yang, K., et al. (2021) · Nature Communications

DNA Repair MechanismsGenomics and Chromatin Dynamics

Cited by 70

A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair

van den Heuvel, D., Spruijt, C. G., González-Prieto, R., Kragten, A., Paulsen, M. T., Zhou, D., Wu, H., Apelt, K., van der Weegen, Y., Yang, K., et al. (2020) · Nature Communications

DNA Repair MechanismsGenomics and Chromatin Dynamics

Cited by 69

Two Chromatin Remodeling Activities Cooperate during Activation of Hormone Responsive Promoters

Vicent, G. P., Zaurin, R., Nacht, A. S., Li, A., Font-Mateu, J., Le Dily, F., Vermeulen, M., Mann, M., & Beato, M. (2009) · PLoS Genetics

Chromatin Remodeling and CancerGenomics and Chromatin Dynamics

Cited by 55

SALL4 controls cell fate in response to DNA base composition

Pantier, R., Chhatbar, K., Quante, T., Skourti-Stathaki, K., Cholewa-Waclaw, J., Alston, G., Alexander-Howden, B., Lee, H. Y., Cook, A. G., Spruijt, C. G., et al. (2021) · Molecular Cell

Genomics and Chromatin DynamicsPluripotent Stem Cells Research

Cited by 45

A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation

Valverde, J. M., Dubra, G., Phillips, M., Haider, A., Elena-Real, C., Fournet, A., Alghoul, E., Chahar, D., Andrés-Sanchez, N., Paloni, M., et al. (2023) · Nature Communications

Microtubule and mitosis dynamicsRNA Research and Splicing

Cited by 33

Multiomics of Colorectal Cancer Organoids Reveals Putative Mediators of Cancer Progression Resulting from SMAD4 Inactivation

Dijkstra, J. J., Neikes, H. K., Rezaeifard, S., Ma, X., Voest, E. E., Tauriello, D. V. F., & Vermeulen, M. (2023) · Journal of Proteome Research

TGF-β signaling in diseasesCancer Cells and Metastasis

Cited by 23

The small CRL4CSA ubiquitin ligase component DDA1 regulates transcription-coupled repair dynamics

Llerena Schiffmacher, D. A., Lee, S.-H., Kliza, K. W., Theil, A. F., Akita, M., Helfricht, A., Bezstarosti, K., Gonzalo-Hansen, C., van Attikum, H., Verlaan-de Vries, M., et al. (2024) · Nature Communications

DNA Repair MechanismsUbiquitin and proteasome pathways

Cited by 19

DDA1, a novel factor in transcription-coupled repair, modulates CRL4CSA dynamics at DNA damage-stalled RNA polymerase II

Pines, A., Schiffmacher, D. L., Lee, S.-H., Kliza, K., Theil, A., Akita, M., Helfricht, A., Bezstarosti, K., Gonzalo-Hansen, C., Attikum, H. V., et al. (2023) · Nature Communications

DNA Repair MechanismsUbiquitin and proteasome pathways

Cited by 19

Exploring Chromatin Readers Using High-Accuracy Quantitative Mass Spectrometry-Based Proteomics

Smits, A. H., & Vermeulen, M. (2014) · Systems Analysis of Chromatin-Related Protein Complexes in Cancer

Advanced Proteomics Techniques and ApplicationsGenomics and Chromatin Dynamics

Cited by 2