Browsing by Author "Vermeulen, M."

Now showing items 1-50 of 79

Miniaturised interaction proteomics on a microfluidic platform with ultra-low input requirements
Furlan, C.; Dirks, R.A.M.; Thomas, Peter C.; Jones, Robert C.; Wang, Jing; Lynch, Mark; Marks, Hendrik ; Vermeulen, Michiel
2019, Article / Letter to editor (Nature Communications, vol. 10, (2019), article 1525)
CBFβ-MYH11 interferes with megakaryocyte differentiation via modulating a gene program that includes GATA2 and KLF1
Yi, G.; Mandoli, A.; Jussen, L.; Tijchon, E.; Bergen, M.G.J.M. van; Cordonnier, G.; Hansen, M.; Kim, B.; Nguyen, L.N.; Jansen, P. W.; Vermeulen, M. ; Reijden, B.A. van der ; Akker, E. van den; Bond, J.; Martens, J.H.A. et al. sine al.
2019, Article / Letter to editor (Blood Cancer Journal, vol. 9, iss. 3, (2019), pp. 33)
BRD9 binds cell type-specific chromatin regions regulating leukemic cell survival via STAT5 inhibition
Gaudio, Nunzio Del; Costanzo, Antonella Di; Liu, Ning Qing; Conte, Lidio; Migliaccio, Antimo; Vermeulen, Michiel ; Martens, J.H.A. ; Stunnenberg, H.G. ; Altucci, Lucia
2019, Article / Letter to editor (Cell Death and Disease, vol. 10, (2019), pp. 1-14, article 338)
The interactome of a family of potential methyltransferases in HeLa cells
Ignatova, Valentina V.; Jansen, P. W.; Baltissen, M.P.; Vermeulen, Michiel ; Schneider, Robert
2019, Article / Letter to editor (Scientific Reports, vol. 9, (2019), pp. 1-9, article 6584)
The Tudor protein Veneno assembles the ping-pong amplification complex that produces viral piRNAs in Aedes mosquitoes
Joosten, J.; Miesen, P.; Taskopru, E.; Pennings, B. ; Jansen, P.W.T.C.; Huynen, M.A. ; Vermeulen, M. ; Rij, R.P. van
2019, Article / Letter to editor (Nucleic Acids Research, vol. 47, iss. 5, (2019), pp. 2546-2559)
The Nucleosome Remodelling and Deacetylation complex suppresses transcriptional noise during lineage commitment
Burgold, Thomas; Barber, Michael; Kloet, S.L.; Cramard, J.; Gharbi, Sarah; Floyd, Robin; Vermeulen, Michiel ; Dietmann, Sabine; Hendrich, B.
2019, Article / Letter to editor (EMBO Journal, vol. 38, iss. 12, (2019), pp. 1-18, article e100788)
Induction and Suppression of NF-kappa B Signalling by a DNA Virus of Drosophila
Palmer, William H.; Joosten, J.; Overheul, G.J.; Jansen, P. W.; Vermeulen, Michiel ; Obbard, Darren J.; Rij, R.P. van
2019, Article / Letter to editor (Journal of Virology, vol. 93, iss. 3, (2019), pp. 1-20, article e01443-18)
EZH1/2 function mostly within canonical PRC2 and exhibit proliferation-dependent redundancy that shapes mutational signatures in cancer
Wassef, Michel; Luscan, Armelle; Aflaki, Setareh; Zielinski, Dina; Jansen, P.W.T.C.; Baymaz, H.I.; Vermeulen, Michiel ; Pasmant, Eric; Margueron, R.
2019, Article / Letter to editor (Proceedings of the National Academy of Science USA, vol. 116, iss. 13, (2019), pp. 6075-6080)
Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency
Mierlo, G. van; Dirks, R.A.M.; Clerck, Laura De; Brinkman, A.B. ; Huth, Michelle; Kloet, S.L.; Kroeze, L.; Jansen, J.H. ; Vermeulen, Michiel ; Dhaenens, Maarten; Marks, Hendrik et al. sine al.
2019, Article / Letter to editor (Cell Stem Cell, vol. 24, iss. 1, (2019), pp. 123-137, e1-e8)
Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids
Artegiani, Benedetta; Voorthuijsen, L. van; Lindeboom, R.G.H.; Seinstra, Danielle; Heo, Inha; Tapia, Pablo; Peters, P.J. ; Vermeulen, Michiel ; Clevers, Hans
2019, Article / Letter to editor (Cell Stem Cell, vol. 24, iss. 6, (2019), pp. 927-943, e1-e6)
TRiC controls transcription resumption after UV damage by regulating Cockayne syndrome protein A
Pines, Alex; Dijk, Madelon; Makowski, M.M.; Meulenbroek, Elisabeth M.; Vrouwe, Mischa G.; Weegen, Yana van der; Vermeulen, Michiel ; Pannu, Navraj S.; Attikum, Haico van
2018, Article / Letter to editor (Nature Communications, vol. 9, (2018), pp. 1-14, article 1040)
Integrative multi-omics analysis of intestinal organoid differentiation
Lindeboom, R.G.H.; Voorthuijsen, L. van; Oost, Koen C.; Rodriguez-Colman, Maria J.; Luna-Velez, Maria V.; Furlan, C.; Snippert, Hugo J.G.; Vermeulen, Michiel
2018, Article / Letter to editor (Molecular Systems Biology, vol. 14, iss. 6, (2018), pp. 1-16, article e8227)
The HDAC inhibitor SAHA regulates CBX2 stability via a SUMO-triggered ubiquitin-mediated pathway in leukemia
Costanzo, Antonella Di; Gaudio, Nunzio Del; Conte, Lidio; Dell'Aversana, Carmela; Vermeulen, Michiel ; The, Hugues de; Nebbioso, Angela; Altucci, Lucia
2018, Article / Letter to editor (Oncogene, vol. 37, iss. 19, (2018), pp. 2559-2572)
Global profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry
Makowski, M.M.; Gräwe, C.; Foster, Benjamin M.; Nguyen, Nhuong V.; Bartke, Till; Vermeulen, Michiel
2018, Article / Letter to editor (Nature Communications, vol. 9, (2018), pp. 1-10, article 1653)
Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells
Buggenum, A.G.L. van ; Gerlach, J.P.; Tanis, S.E.J.; Hogeweg, M.; Jansen, P.W.T.C.; Middelwijk, Jesse; Vermeulen, M. ; Stunnenberg, H.G. ; Albers, C.A. ; Mulder, K.W.
2018, Article / Letter to editor (Nature Communications, vol. 9, (2018), article 2384)
NuRD-interacting protein ZFP296 regulates genome-wide NuRD localization and differentiation of mouse embryonic stem cells
Kloet, S.L.; Karemaker, I.D.; Voorthuijsen, L. van; Lindeboom, R.G.H.; Baltissen, Marijke P.; Edupuganti, Raghu R.; Jansen, P.W.T.C.; Vermeulen, Michiel
2018, Article / Letter to editor (Nature Communications, vol. 9, (2018), pp. 1-11, article 4588)
Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
Brien, Gerard L.; Remillard, David; Shi, Junwei; Hemming, Matthew L.; Chabon, Jonathon; Wynne, Kieran; Mierlo, G. van; Vermeulen, Michiel ; Vakoc, Christopher R.; Armstrong, Scott A.
2018, Article / Letter to editor (Elife, vol. 7, (2018), pp. 1-26, article e41305)
Proteome-wide identification of ubiquitin interactions using UbIA-MS
Zhang, X.; Smits, A.H.; Tilburg, Gabrielle B.A. van; Ovaa, H.; Huber, Wolfgang; Vermeulen, Michiel
2018, Article / Letter to editor (Nature Protocols, vol. 13, iss. 3, (2018), pp. 530-550)
Splicing and Chromatin Factors Jointly Regulate Epidermal Differentiation
Tanis, S.E.J.; Jansen, P. W.; Zhou, H. ; Heeringen, S.J. van ; Vermeulen, Michiel ; Kretz, Markus; Mulder, Klaas W.
2018, Article / Letter to editor (Cell Reports, vol. 25, iss. 5, (2018), pp. 1292-1303.e5)
Specific Labeling of Stem Cell Activity in Human Colorectal Organoids Using an ASCL2-Responsive Minigene
Oost, Koen C.; Voorthuijsen, L. van; Fumagalli, Arianna; Lindeboom, R.G.H.; Sprangers, Joep; Omerzu, Manja; Vermeulen, Michiel ; Snippert, Hugo J.G.
2018, Article / Letter to editor (Cell Reports, vol. 22, iss. 6, (2018), pp. 1600-1614)
Erratum to: Proteomic landscape of the primary somatosensory cortex upon sensory deprivation.
Kole, K. ; Lindeboom, R.G.H.; Baltissen, M.P.; Jansen, P. W.; Vermeulen, M. ; Tiesinga, P.H.E.; Celikel, T.
2018, Article / Letter to editor (Gigascience, vol. 7, iss. 7, (2018), pp. 1)
Single-Cell DNA Methylation Profiling: Technologies and Biological Applications
Karemaker, I.D.; Vermeulen, M.
2018, Article / Letter to editor (Trends in Biotechnology, vol. 36, iss. 9, (2018), pp. 952-965)
ZBTB2 reads unmethylated CpG island promoters and regulates embryonic stem cell differentiation
Karemaker, I.D.; Vermeulen, Michiel
2018, Article / Letter to editor (EMBO Reports, vol. 19, iss. 4, (2018), pp. 1-11, article UNSP e44993)
Mass Spectrometry-Based Absolute Quantification of Single Xenopus Embryo Proteomes
Lindeboom, R.G.H.; Smits, A.H. ; Perino, M.; Veenstra, Gert Jan C. ; Vermeulen, M.
2018, Article / Letter to editor (Cold Spring Harbor Protocols, (2018))
MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding
Perino, M.; Mierlo, G. van; Karemaker, I.D.; Genesen, Siebe van ; Vermeulen, Michiel ; Marks, Hendrik ; Heeringen, S.J. van ; Veenstra, Gert Jan C.
2018, Article / Letter to editor (Nature Genetics, vol. 50, iss. 7, (2018), pp. 1002-1016)
Functional characterization of a multi-cancer risk locus on chr5p15.33 reveals regulation of TERT by ZNF148
Fang, J.; Jia, J.; Makowski, M.M.; Xu, M.; Jansen, P. W.; Vermeulen, M. ; Brown, K.M.; Amundadottir, L.T.; al., E.
2017, Article / Letter to editor (Nature Communications, vol. 8, (2017), pp. 1-15, article 15034)
Proteomic landscape of the primary somatosensory cortex upon sensory deprivation
Kole, K. ; Lindeboom, R.G.H.; Baltissen, M.P.A; Vermeulen, M. ; Tiesinga, P.; Celikel, T.
2017, Article / Letter to editor (Gigascience, vol. 6, iss. 10, (2017), pp. 1-10)
An interaction landscape of ubiquitin signaling
Zhang, X.; Smits, A.H.; van Tilburg, G.B.; Jansen, P. W.; Makowski, M.M.; Ovaa, H.; Vermeulen, M.
2017, Article / Letter to editor (Molecular Cell, vol. 65, iss. 5, (2017), pp. 941-955)
Phospho-h1 decorates the inter-chromatid axis and is evicted along with shugoshin by SET during mitosis
Krishnan, S.; Smits, A.H.; Vermeulen, M. ; Reinberg, D.
2017, Article / Letter to editor (Molecular Cell, vol. 67, iss. 4, (2017), pp. 579-593.e6)
A common intronic variant of PARP1 confers melanoma risk and mediates melanocyte growth via regulation of MITF
Choi, J.Y. ; Xu, M.; Makowski, M.M.; Zhang, T.W.; Law, M.H.; Kovacs, M.A.; Granzhan, A.; Kim, W.D.J.; Parikh, H.; Gartside, M.; Trent, J.M.; Teulade-Fichou, M.P.; Iles, M.M.; Newton-Bishop, J.A.; Bishop, D.T.; MacGregor, S.; Hayward, N.K.; Vermeulen, M. ; Brown, K.M. et al. sine al.
2017, Article / Letter to editor (Nature Genetics, vol. 49, iss. 9, (2017), pp. 1326-1339)
SDHD promoter mutations ablate GABP transcription factor binding in melanoma
Zhang, T.; Xu, M.; Makowski, M.M.; Lee, C.; Kovacs, M.; Fang, J.; Willems, E.; Trent, J.M.; Hayward, N.K.; Vermeulen, M. ; Brown, K.M. et al. sine al.
2017, Article / Letter to editor (Cancer Research, vol. 77, iss. 7, (2017), pp. 1-14)
N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis
Edupuganti, V.S.R.R.; Geiger, S.; Lindeboom, R.G.H.; Shi, H.; Hsu, P.J.; Lu, Z.; Wang, S.; Baltissen, M.P.A.; Jansen, P. W.; Rossa, M.; Muller, M; Stunnenberg, H. ; He, C.; Carell, T.; Vermeulen, M. et al. sine al.
2017, Article / Letter to editor (Nature Structural & Molecular Biology, vol. 24, iss. 10, (2017), pp. 870-878)
The Nucleosome Remodeling and Deacetylase Complex NuRD Is Built from Preformed Catalytically Active Sub-modules
Zhang, W; Aubert, A.; de Segura, J.M.G.; Karuppasamy, M.; Basu, S.; Murthy, A.S.; Diamante, A.; Drury, T.A.; Balmer, J.; Cramard, J.; Watson, A.A.; Lando, D.; Lee, S.F.; Palayret, M.; Kloet, S.L; Smits, A.H.; Deery, M.J.; Vermeulen, M. ; Hendrich, B.; Klenerman, D.; Schaffitzel, C.; Berger, I.; Laue, E.D. et al. sine al.
2016, Article / Letter to editor (Journal of Molecular Biology, vol. 428, iss. 14, (2016), pp. 2931-2942)
ZMYND8 Co-localizes with NuRD on Target Genes and Regulates Poly(ADP-Ribose)-Dependent Recruitment of GATAD2A/NuRD to Sites of DNA Damage
Spruijt, C.G. ; Luijsterburg, M.S.; Menafra, R.; Lindeboom, R.G.H.; Jansen, P. W.; Edupuganti, V.S.R.R.; Baltissen, M.P.; Wiegant, W.W.; Voelker-Albert, M.C.; Matarese, F. ; Mensinga, A.; Poser, I.; Vos, H.R.; Stunnenberg, H. ; van Attikum, H.; Vermeulen, M. et al. sine al.
2016, Article / Letter to editor (Cell Reports, vol. 17, iss. 3, (2016), pp. 783-798)
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, Article / Letter to editor (Development, vol. 143, iss. 17, (2016), pp. 3074-3084)
Characterizing Protein-Protein Interactions Using Mass Spectrometry: Challenges and Opportunities
Smits, A.H.; Vermeulen, M.
2016, Article / Letter to editor (Trends in Biotechnology, vol. 34, iss. 10, (2016), pp. 825-834)
In need of good neighbours: transcription factors require local DNA hypomethylation for target binding
Karemaker, I.D.; Vermeulen, M.
2016, Article / Letter to editor (EMBO Journal, vol. 35, iss. 4, (2016), pp. 374-375)
Active DNA demethylation at enhancers during the vertebrate phylotypic period
Bogdanovic, O.; Smits, A.H.; de la Calle Mustienes, E.; Tena, J.J.; Ford, E.; Williams, R.; Senanayake, U.; Schultz, M.D.; Hontelez, S. ; Kruijsbergen, I. van; Rayon, T.; Gnerlich, F.; Carell, T.; Veenstra, G.J.C. ; Manzanares, M.; Sauka-Spengler, T.; Ecker, J.R.; Vermeulen, M. ; Gomez-Skarmeta, J.L.; Lister, R. et al. sine al.
2016, Article / Letter to editor (Nature Genetics, vol. 48, iss. 4, (2016), pp. 417-426)
Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification
Makowski, M.M.; Willems, E. ; Jansen, P. W.; Vermeulen, M.
2016, Article / Letter to editor (Molecular & Cellular Proteomics, vol. 15, iss. 3, (2016), pp. 854-865)
Recruitment of the Mammalian Histone-modifying EMSY Complex to Target Genes Is Regulated by ZNF131
Varier, R. A.; Carrillo de Santa Pau, E.; van der Groep, P.; Lindeboom, R.G.H.; Matarese, F. ; Mensinga, A.; Smits, A.H. ; Edupuganti, V.S.R.R.; Baltissen, M.P.; Jansen, P. W.; Ter Hoeve, N.; van Weely, D.R.; Poser, I.; van Diest, P.J.; Stunnenberg, H. ; Vermeulen, M. et al. sine al.
2016, Article / Letter to editor (Journal of Biological Chemistry, vol. 291, iss. 14, (2016), pp. 7313-7324)
Click-MS: Tagless Protein Enrichment Using Bioorthogonal Chemistry for Quantitative Proteomics
Smits, A.H.; Borrmann, A.; Roosjen, M.; van Hest, J.C.M. ; Vermeulen, M.
2016, Article / Letter to editor (Acs Chemical Biology, vol. 11, iss. 12, (2016), pp. 3245-3250)
The dynamic interactome and genomic targets of polycomb complexes during stem-cell differentiation
Kloet, S.L.; Makowski, M.M.; Baymaz, H.I.; Voorthuijsen, L. van; Karemaker, I.D.; Santanach, A.; Jansen, P. W.; Di Croce, L.; Vermeulen, M.
2016, Article / Letter to editor (Nature Structural & Molecular Biology, vol. 23, iss. 7, (2016), pp. 682-690)
xIP-MS: topological analysis of chromatin-associated protein complexes using single affinity purification
Makowski, M.M.; Willems, E.; Jansen, P. W.; Vermeulen, M.
2015, Article / Letter to editor (Molecular & Cellular Proteomics, (2015))
Perspective on unraveling the versatility of 'co-repressor' complexes
Baymaz, H.I.; Karemaker, I.D.; Vermeulen, M.
2015, Article / Letter to editor (Biochimica et Biophysica Acta, Gene Regulatory Mechanisms, vol. 1849, iss. 8, (2015), pp. 1051-1056)
A Me6Age for pluripotency
Stunnenberg, H.G. ; Vermeulen, M. ; Atlasi, Y.
2015, Article / Letter to editor (Science, vol. 347, iss. 6222, (2015), pp. 614-615)
Analysis of the Histone H3.1 Interactome: A Suitable Chaperone for the Right Event
CAmpos, E.I.; Smits, A.H. ; Kang, Y.-H.; Landry, S.; Escobar, T.M.; Nayak, S.; Ueberheide, B.M.; Durocher, D.; Vermeulen, M. ; Hurwitz, J.; Reinberg, D. et al. sine al.
2015, Article / Letter to editor (Molecular Cell, vol. 60, iss. 4, (2015), pp. 697-709)
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.M.; Groenewold, V.; Jansen, P.; Berendsen, M.; Niazi, H.; Kops, G.J.; Vermeulen, M.
2015, Article / Letter to editor (Febs Journal, vol. 282, iss. 9, (2015), pp. 1774-1785)
Developmental biology. A me6age for pluripotency
Stunnenberg, H.G. ; Vermeulen, M. ; Atlasi, Y.
2015, Article / Letter to editor (Science, vol. 347, iss. 6222, (2015), pp. 614-615)
CBFB-MYH11/RUNX1 together with a compendium of hematopoietic regulators, chromatin modifiers and basal transcription factors occupies self-renewal genes in inv(16) acute myeloid leukemia
Mandoli, A.; Singh, A.A.; Jansen, P. W.; Wierenga, A.T.; Riahi, H.; Franci, G.; Prange, K.; Saeed, S.; Vellenga, E.; Vermeulen, M. ; Stunnenberg, H.G. ; Martens, J.H. et al. sine al.
2014, Article / Letter to editor (Leukemia, (2014))
Cbfb-myh11/runx1 together with a compendium of hematopoietic regulators, chromatin modifiers and basal transcription factors occupies self-renewal genes in inv(16) acute myeloid leukemia
Mandoli, A.; Singh, A.A.; Jansen, P. W.; Wierenga, A.T.; Riahi, H.; Franci, G.; Prange, K.; Saeed, S.; Vellenga, E.; Vermeulen, M. ; Stunnenberg, H.G. ; Martens, J.H. et al. sine al.
2014, Article / Letter to editor (Leukemia, vol. 28, iss. 4, (2014), pp. 770-778)

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