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Items: 36

1.

Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation.

Brinkman AB, Nik-Zainal S, Simmer F, Rodríguez-González FG, Smid M, Alexandrov LB, Butler A, Martin S, Davies H, Glodzik D, Zou X, Ramakrishna M, Staaf J, Ringnér M, Sieuwerts A, Ferrari A, Morganella S, Fleischer T, Kristensen V, Gut M, van de Vijver MJ, Børresen-Dale AL, Richardson AL, Thomas G, Gut IG, Martens JWM, Foekens JA, Stratton MR, Stunnenberg HG.

Nat Commun. 2019 Apr 15;10(1):1749. doi: 10.1038/s41467-019-09828-0.

2.

Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GKJ, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, Van't Veer L, Tutt A, Knappskog S, Tan BKT, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR.

Nature. 2019 Feb;566(7742):E1. doi: 10.1038/s41586-019-0883-2.

PMID:
30659290
3.

Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency.

van Mierlo G, Dirks RAM, De Clerck L, Brinkman AB, Huth M, Kloet SL, Saksouk N, Kroeze LI, Willems S, Farlik M, Bock C, Jansen JH, Deforce D, Vermeulen M, Déjardin J, Dhaenens M, Marks H.

Cell Stem Cell. 2019 Jan 3;24(1):123-137.e8. doi: 10.1016/j.stem.2018.10.017. Epub 2018 Nov 21.

PMID:
30472157
4.

Corrigendum: A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.

Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S.

Nat Genet. 2017 Oct 27;49(11):1661. doi: 10.1038/ng1117-1661a.

PMID:
29074948
5.

A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.

Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S.

Nat Genet. 2017 Mar;49(3):341-348. doi: 10.1038/ng.3771. Epub 2017 Jan 23. Erratum in: Nat Genet. 2017 Oct 27;49(11):1661.

6.

Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.

Smid M, Rodríguez-González FG, Sieuwerts AM, Salgado R, Prager-Van der Smissen WJ, Vlugt-Daane MV, van Galen A, Nik-Zainal S, Staaf J, Brinkman AB, van de Vijver MJ, Richardson AL, Fatima A, Berentsen K, Butler A, Martin S, Davies HR, Debets R, Gelder ME, van Deurzen CH, MacGrogan G, Van den Eynden GG, Purdie C, Thompson AM, Caldas C, Span PN, Simpson PT, Lakhani SR, Van Laere S, Desmedt C, Ringnér M, Tommasi S, Eyford J, Broeks A, Vincent-Salomon A, Futreal PA, Knappskog S, King T, Thomas G, Viari A, Langerød A, Børresen-Dale AL, Birney E, Stunnenberg HG, Stratton M, Foekens JA, Martens JW.

Nat Commun. 2016 Sep 26;7:12910. doi: 10.1038/ncomms12910.

7.

The topography of mutational processes in breast cancer genomes.

Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M, Butler A, Kim HY, Borg Å, Sotiriou C, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Sale J, Rada C, Stratton MR, Birney E, Nik-Zainal S.

Nat Commun. 2016 May 2;7:11383. doi: 10.1038/ncomms11383.

8.

Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GK, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van't Veer L, Tutt A, Knappskog S, Tan BK, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR.

Nature. 2016 Jun 2;534(7605):47-54. doi: 10.1038/nature17676. Epub 2016 May 2. Erratum in: Nature. 2019 Feb;566(7742):E1.

9.

Regulation of DNA methylation patterns by CK2-mediated phosphorylation of Dnmt3a.

Deplus R, Blanchon L, Rajavelu A, Boukaba A, Defrance M, Luciani J, Rothé F, Dedeurwaerder S, Denis H, Brinkman AB, Simmer F, Müller F, Bertin B, Berdasco M, Putmans P, Calonne E, Litchfield DW, de Launoit Y, Jurkowski TP, Stunnenberg HG, Bock C, Sotiriou C, Fraga MF, Esteller M, Jeltsch A, Fuks F.

Cell Rep. 2014 Aug 7;8(3):743-53. doi: 10.1016/j.celrep.2014.06.048. Epub 2014 Jul 24.

10.

Genome-wide binding of MBD2 reveals strong preference for highly methylated loci.

Menafra R, Brinkman AB, Matarese F, Franci G, Bartels SJ, Nguyen L, Shimbo T, Wade PA, Hubner NC, Stunnenberg HG.

PLoS One. 2014 Jun 13;9(6):e99603. doi: 10.1371/journal.pone.0099603. eCollection 2014.

11.

Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells.

Habibi E, Brinkman AB, Arand J, Kroeze LI, Kerstens HH, Matarese F, Lepikhov K, Gut M, Brun-Heath I, Hubner NC, Benedetti R, Altucci L, Jansen JH, Walter J, Gut IG, Marks H, Stunnenberg HG.

Cell Stem Cell. 2013 Sep 5;13(3):360-9. doi: 10.1016/j.stem.2013.06.002. Epub 2013 Jul 11.

12.

Dynamic binding of RBPJ is determined by Notch signaling status.

Castel D, Mourikis P, Bartels SJ, Brinkman AB, Tajbakhsh S, Stunnenberg HG.

Genes Dev. 2013 May 1;27(9):1059-71. doi: 10.1101/gad.211912.112. Erratum in: Genes Dev. 2013 Jun 1;27(11):1313.

13.

Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives.

Spruijt CG, Gnerlich F, Smits AH, Pfaffeneder T, Jansen PW, Bauer C, Münzel M, Wagner M, Müller M, Khan F, Eberl HC, Mensinga A, Brinkman AB, Lephikov K, Müller U, Walter J, Boelens R, van Ingen H, Leonhardt H, Carell T, Vermeulen M.

Cell. 2013 Feb 28;152(5):1146-59. doi: 10.1016/j.cell.2013.02.004. Epub 2013 Feb 21.

14.

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues.

Simmer F, Brinkman AB, Assenov Y, Matarese F, Kaan A, Sabatino L, Villanueva A, Huertas D, Esteller M, Lengauer T, Bock C, Colantuoni V, Altucci L, Stunnenberg HG.

Epigenetics. 2012 Dec 1;7(12):1355-67. doi: 10.4161/epi.22562. Epub 2012 Oct 18.

15.

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.

Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG.

Genome Res. 2012 Jun;22(6):1128-38. doi: 10.1101/gr.133728.111. Epub 2012 Mar 30.

16.

A SILAC-based screen for Methyl-CpG binding proteins identifies RBP-J as a DNA methylation and sequence-specific binding protein.

Bartels SJ, Spruijt CG, Brinkman AB, Jansen PW, Vermeulen M, Stunnenberg HG.

PLoS One. 2011;6(10):e25884. doi: 10.1371/journal.pone.0025884. Epub 2011 Oct 3.

17.

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis.

Bogdanovic O, Long SW, van Heeringen SJ, Brinkman AB, Gómez-Skarmeta JL, Stunnenberg HG, Jones PL, Veenstra GJ.

Genome Res. 2011 Aug;21(8):1313-27. doi: 10.1101/gr.114843.110. Epub 2011 Jun 2.

18.

Quantitative comparison of genome-wide DNA methylation mapping technologies.

Bock C, Tomazou EM, Brinkman AB, Müller F, Simmer F, Gu H, Jäger N, Gnirke A, Stunnenberg HG, Meissner A.

Nat Biotechnol. 2010 Oct;28(10):1106-14. doi: 10.1038/nbt.1681. Epub 2010 Sep 19.

19.

Whole-genome DNA methylation profiling using MethylCap-seq.

Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG.

Methods. 2010 Nov;52(3):232-6. doi: 10.1016/j.ymeth.2010.06.012. Epub 2010 Jun 11.

PMID:
20542119
20.

CDK2AP1/DOC-1 is a bona fide subunit of the Mi-2/NuRD complex.

Spruijt CG, Bartels SJ, Brinkman AB, Tjeertes JV, Poser I, Stunnenberg HG, Vermeulen M.

Mol Biosyst. 2010 Sep;6(9):1700-6. doi: 10.1039/c004108d. Epub 2010 Jun 4.

PMID:
20523938
21.

PML-RARalpha/RXR Alters the Epigenetic Landscape in Acute Promyelocytic Leukemia.

Martens JH, Brinkman AB, Simmer F, Francoijs KJ, Nebbioso A, Ferrara F, Altucci L, Stunnenberg HG.

Cancer Cell. 2010 Feb 17;17(2):173-85. doi: 10.1016/j.ccr.2009.12.042.

22.

DNA methylation immediately adjacent to active histone marking does not silence transcription.

Brinkman AB, Pennings SW, Braliou GG, Rietveld LE, Stunnenberg HG.

Nucleic Acids Res. 2007;35(3):801-11. Epub 2007 Jan 3.

23.

Molecular characterization of a conserved archaeal copper resistance (cop) gene cluster and its copper-responsive regulator in Sulfolobus solfataricus P2.

Ettema TJ, Brinkman AB, Lamers PP, Kornet NG, de Vos WM, van der Oost J.

Microbiology. 2006 Jul;152(Pt 7):1969-79.

PMID:
16804172
24.

Histone modification patterns associated with the human X chromosome.

Brinkman AB, Roelofsen T, Pennings SW, Martens JH, Jenuwein T, Stunnenberg HG.

EMBO Rep. 2006 Jun;7(6):628-34. Epub 2006 Apr 28.

25.

Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family.

Thaw P, Sedelnikova SE, Muranova T, Wiese S, Ayora S, Alonso JC, Brinkman AB, Akerboom J, van der Oost J, Rafferty JB.

Nucleic Acids Res. 2006 Mar 9;34(5):1439-49. Print 2006. Erratum in: Nucleic Acids Res. 2006;34(6):1944.

26.

MBD2/NuRD and MBD3/NuRD, two distinct complexes with different biochemical and functional properties.

Le Guezennec X, Vermeulen M, Brinkman AB, Hoeijmakers WA, Cohen A, Lasonder E, Stunnenberg HG.

Mol Cell Biol. 2006 Feb;26(3):843-51.

27.

Targeted discovery tools: proteomics and chromatin immunoprecipitation-on-chip.

Le Guezennec X, Brinkman AB, Vermeulen M, Denissov SG, Gazziola C, Lohrum ME, Stunnenberg HG.

BJU Int. 2005 Dec;96 Suppl 2:16-22. Review.

28.

Transcription of the rod-shaped viruses SIRV1 and SIRV2 of the hyperthermophilic archaeon sulfolobus.

Kessler A, Brinkman AB, van der Oost J, Prangishvili D.

J Bacteriol. 2004 Nov;186(22):7745-53.

29.

The Lrp family of transcriptional regulators.

Brinkman AB, Ettema TJ, de Vos WM, van der Oost J.

Mol Microbiol. 2003 Apr;48(2):287-94. Review.

30.

A novel ligand-binding domain involved in regulation of amino acid metabolism in prokaryotes.

Ettema TJ, Brinkman AB, Tani TH, Rafferty JB, Van Der Oost J.

J Biol Chem. 2002 Oct 4;277(40):37464-8. Epub 2002 Jul 23.

31.

The Sulfolobus solfataricus Lrp-like protein LysM regulates lysine biosynthesis in response to lysine availability.

Brinkman AB, Bell SD, Lebbink RJ, de Vos WM, van der Oost J.

J Biol Chem. 2002 Aug 16;277(33):29537-49. Epub 2002 May 31.

32.

Crystallization and quaternary structure analysis of an Lrp-like regulatory protein from the hyperthermophile Pyrococcus furiosus.

Sedelnikova SE, Smits SH, Leonard PM, Brinkman AB, van der Oost J, Rafferty JB, Rice DW.

Acta Crystallogr D Biol Crystallogr. 2001 Jun;57(Pt 6):886-8. Epub 2001 May 25.

PMID:
11375518
33.

The archaeal TFIIEalpha homologue facilitates transcription initiation by enhancing TATA-box recognition.

Bell SD, Brinkman AB, van der Oost J, Jackson SP.

EMBO Rep. 2001 Feb;2(2):133-8.

34.

Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus.

Leonard PM, Smits SH, Sedelnikova SE, Brinkman AB, de Vos WM, van der Oost J, Rice DW, Rafferty JB.

EMBO J. 2001 Mar 1;20(5):990-7.

35.

An Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus is negatively autoregulated.

Brinkman AB, Dahlke I, Tuininga JE, Lammers T, Dumay V, de Heus E, Lebbink JH, Thomm M, de Vos WM, van Der Oost J.

J Biol Chem. 2000 Dec 8;275(49):38160-9.

36.

Explaining the bias in the 23S rRNA gene mutations associated with clarithromycin resistance in clinical isolates of Helicobacter pylori.

Debets-Ossenkopp YJ, Brinkman AB, Kuipers EJ, Vandenbroucke-Grauls CM, Kusters JG.

Antimicrob Agents Chemother. 1998 Oct;42(10):2749-51.

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