Search Results - "Brinkman, Arie B"

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives by Spruijt, Cornelia G., Gnerlich, Felix, Smits, Arne H., Pfaffeneder, Toni, Jansen, Pascal W.T.C., Bauer, Christina, Münzel, Martin, Wagner, Mirko, Müller, Markus, Khan, Fariha, Eberl, H. Christian, Mensinga, Anneloes, Brinkman, Arie B., Lephikov, Konstantin, Müller, Udo, Walter, Jörn, Boelens, Rolf, van Ingen, Hugo, Leonhardt, Heinrich, Carell, Thomas, Vermeulen, Michiel

“…Tet proteins oxidize 5-methylcytosine (mC) to generate 5-hydroxymethyl (hmC), 5-formyl (fC), and 5-carboxylcytosine (caC). The exact function of these…”
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Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells by Habibi, Ehsan, Brinkman, Arie B., Arand, Julia, Kroeze, Leonie I., Kerstens, Hindrik H.D., Matarese, Filomena, Lepikhov, Konstantin, Gut, Marta, Brun-Heath, Isabelle, Hubner, Nina C., Benedetti, Rosaria, Altucci, Lucia, Jansen, Joop H., Walter, Jörn, Gut, Ivo G., Marks, Hendrik, Stunnenberg, Hendrik G.

“…The use of two kinase inhibitors (2i) enables derivation of mouse embryonic stem cells (ESCs) in the pluripotent ground state. Using whole-genome bisulfite…”
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Quantitative comparison of genome-wide DNA methylation mapping technologies by Brinkman, Arie B, Meissner, Alexander, Gu, Hongcang, Müller, Fabian, Bock, Christoph, Jäger, Natalie, Tomazou, Eleni M, Stunnenberg, Hendrik G, Gnirke, Andreas, Simmer, Femke

“…Comparison of the methylation patterns of cells in different developmental or disease states can help to elucidate both normal and pathological regulatory…”
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Dynamic binding of RBPJ is determined by Notch signaling status by Castel, David, Mourikis, Philippos, Bartels, Stefanie J J, Brinkman, Arie B, Tajbakhsh, Shahragim, Stunnenberg, Hendrik G

“…Notch signaling plays crucial roles in mediating cell fate choices in all metazoans largely by specifying the transcriptional output of one cell in response to…”
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Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk by Brinkman, Arie B, Gu, Hongcang, Bartels, Stefanie J J, Zhang, Yingying, Matarese, Filomena, Simmer, Femke, Marks, Hendrik, Bock, Christoph, Gnirke, Andreas, Meissner, Alexander, Stunnenberg, Hendrik G

“…Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using…”
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Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency by van Mierlo, Guido, Dirks, René A.M., De Clerck, Laura, Brinkman, Arie B., Huth, Michelle, Kloet, Susan L., Saksouk, Nehmé, Kroeze, Leonie I., Willems, Sander, Farlik, Matthias, Bock, Christoph, Jansen, Joop H., Deforce, Dieter, Vermeulen, Michiel, Déjardin, Jérôme, Dhaenens, Maarten, Marks, Hendrik

“…The pluripotent ground state is defined as a basal state free of epigenetic restrictions, which influence lineage specification. While naive embryonic stem…”
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Whole-genome DNA methylation profiling using MethylCap-seq by Brinkman, Arie B., Simmer, Femke, Ma, Kelong, Kaan, Anita, Zhu, Jingde, Stunnenberg, Hendrik G.

“…MethylCap-seq is a robust procedure for genome-wide profiling of DNA methylation. The approach consists of the capture of methylated DNA using the MBD domain…”
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Comprehensive evaluation of methods to assess overall and cell-specific immune infiltrates in breast cancer by Nederlof, Iris, De Bortoli, Davide, Bareche, Yacine, Nguyen, Bastien, de Maaker, Michiel, Hooijer, Gerrit K J, Buisseret, Laurence, Kok, Marleen, Smid, Marcel, Van den Eynden, Gert G G M, Brinkman, Arie B, Hudecek, Jan, Koster, Jan, Sotiriou, Christos, Larsimont, Denis, Martens, John W M, van de Vijver, Marc J, Horlings, Hugo M, Salgado, Roberto, Biganzoli, Elia, Desmedt, Christine

“…Breast cancer (BC) immune infiltrates play a critical role in tumor progression and response to treatment. Besides stromal tumor infiltrating lymphocytes…”
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Regulation of DNA Methylation Patterns by CK2-Mediated Phosphorylation of Dnmt3a by Deplus, Rachel, Blanchon, Loïc, Rajavelu, Arumugam, Boukaba, Abdelhalim, Defrance, Matthieu, Luciani, Judith, Rothé, Françoise, Dedeurwaerder, Sarah, Denis, Hélène, Brinkman, Arie B., Simmer, Femke, Müller, Fabian, Bertin, Benjamin, Berdasco, Maria, Putmans, Pascale, Calonne, Emilie, Litchfield, David W., de Launoit, Yvan, Jurkowski, Tomasz P., Stunnenberg, Hendrik G., Bock, Christoph, Sotiriou, Christos, Fraga, Mario F., Esteller, Manel, Jeltsch, Albert, Fuks, François

“…DNA methylation is a central epigenetic modification that is established by de novo DNA methyltransferases. The mechanisms underlying the generation of genomic…”
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MBD2/NuRD and MBD3/NuRD, Two Distinct Complexes with Different Biochemical and Functional Properties by Le Guezennec, Xavier, Vermeulen, Michiel, Brinkman, Arie B., Hoeijmakers, Wieteke A. M., Cohen, Adrian, Lasonder, Edwin, Stunnenberg, Hendrik G.

“…Article Usage Stats Services MCB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis by Bogdanovic, Ozren, Long, Steven W, van Heeringen, Simon J, Brinkman, Arie B, Gómez-Skarmeta, Jose Luis, Stunnenberg, Hendrik G, Jones, Peter L, Veenstra, Gert Jan C

“…DNA methylation is a tightly regulated epigenetic mark associated with transcriptional repression. Next-generation sequencing of purified methylated DNA…”
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A SILAC-based screen for Methyl-CpG binding proteins identifies RBP-J as a DNA methylation and sequence-specific binding protein by Bartels, Stefanie J J, Spruijt, Cornelia G, Brinkman, Arie B, Jansen, Pascal W T C, Vermeulen, Michiel, Stunnenberg, Hendrik G

“…DNA methylation is an epigenetic modification that plays a crucial role in a variety of biological processes. Methylated DNA is specifically bound by…”
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Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues by Simmer, Femke, Brinkman, Arie B., Assenov, Yassen, Matarese, Filomena, Kaan, Anita, Sabatino, Lina, Villanueva, Alberto, Huertas, Dori, Esteller, Manel, Lengauer, Thomas, Bock, Christoph, Colantuoni, Vittorio, Altucci, Lucia, Stunnenberg, Hendrik G.

“…Aberrant DNA methylation often occurs in colorectal cancer (CRC). In our study we applied a genome-wide DNA methylation analysis approach, MethylCap-seq, to…”
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The Lrp family of transcriptional regulators by Brinkman, Arie B., Ettema, Thijs J. G., De Vos, Willem M., Van Der Oost, John

“…Summary Genome analysis has revealed that members of the Lrp family of transcriptional regulators are widely distributed among prokaryotes, both bacteria and…”
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Genome-wide binding of MBD2 reveals strong preference for highly methylated loci by Menafra, Roberta, Brinkman, Arie B, Matarese, Filomena, Franci, Gianluigi, Bartels, Stefanie J J, Nguyen, Luan, Shimbo, Takashi, Wade, Paul A, Hubner, Nina C, Stunnenberg, Hendrik G

“…MBD2 is a subunit of the NuRD complex that is postulated to mediate gene repression via recruitment of the complex to methylated DNA. In this study we adopted…”
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Transcription of the Rod-Shaped Viruses SIRV1 and SIRV2 of the Hyperthermophilic Archaeon Sulfolobus by KESSLER, Alexandra, BRINKMAN, Arie B, VAN DER OOST, John, PRANGISHVILI, David

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Molecular characterization of a conserved archaeal copper resistance (cop) gene cluster and its copper-responsive regulator in Sulfolobus solfataricus P2 by Ettema, Thijs J. G, Brinkman, Arie B, Lamers, Packo P, Kornet, Noor G, de Vos, Willem M, van der Oost, John

“…Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands Correspondence Thijs J.G. Ettema…”
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The Sulfolobus solfataricus Lrp-like Protein LysM Regulates Lysine Biosynthesis in Response to Lysine Availability by Brinkman, Arie B., Bell, Stephen D., Lebbink, Robert Jan, de Vos, Willem M., van der Oost, John

“…Although the archaeal transcription apparatus resembles the eukaryal RNA polymerase II system, many bacterial-like regulators can be found in archaea…”
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A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers by Glodzik, Dominik, Morganella, Sandro, Davies, Helen, Simpson, Peter T, Li, Yilong, Zou, Xueqing, Diez-Perez, Javier, Staaf, Johan, Alexandrov, Ludmil B, Smid, Marcel, Brinkman, Arie B, Rye, Inga Hansine, Russnes, Hege, Raine, Keiran, Purdie, Colin A, Lakhani, Sunil R, Thompson, Alastair M, Birney, Ewan, Stunnenberg, Hendrik G, van de Vijver, Marc J, Martens, John W M, Børresen-Dale, Anne-Lise, Richardson, Andrea L, Kong, Gu, Viari, Alain, Easton, Douglas, Evan, Gerard, Campbell, Peter J, Stratton, Michael R, Nik-Zainal, Serena

“…Serena Nik-Zainal and colleagues present a detailed analysis of somatic rearrangements in 560 breast cancers. They highlight 33 rearrangement hotspots…”
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Clonotypic Features of Rearranged Immunoglobulin Genes Yield Personalized Biomarkers for Minimal Residual Disease Monitoring in Multiple Myeloma by Langerhorst, Pieter, Brinkman, Arie B, VanDuijn, Martijn M, Wessels, Hans J C T, Groenen, Patricia J T A, Joosten, Irma, van Gool, Alain J, Gloerich, Jolein, Scheijen, Blanca, Jacobs, Joannes F M

“…Due to improved treatment, more patients with multiple myeloma (MM) reach a state of minimal residual disease (MRD). Different strategies for MM MRD monitoring…”
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