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An experimental and bioinformatic toolbox for functional epigenomics and its application to epigenetically making and breaking a cancer cell

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Publications

DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma

Author(s): Nathan C Sheffield, Gaelle Pierron, Johanna Klughammer, Paul Datlinger, Andreas Schönegger, Michael Schuster, Johanna Hadler, Didier Surdez, Delphine Guillemot, Eve Lapouble, Paul Freneaux, Jacqueline Champigneulle, Raymonde Bouvier, Diana Walder, Ingeborg M Ambros, Caroline Hutter, Eva Sorz, Ana T Amaral, Enrique de Álava, Katharina Schallmoser, Dirk Strunk, Beate Rinner, Bernadette Liegl-Atzwa
Published in: Nature Medicine, Issue 23/3, 2017, Page(s) 386-395, ISSN 1078-8956
DOI: 10.1038/nm.4273

An ERK-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion

Author(s): Christian Baumgartner, Stefanie Toifl, Matthias Farlik, Florian Halbritter, Ruth Scheicher, Irmgard Fischer, Veronika Sexl, Christoph Bock, Manuela Baccarini
Published in: Cell Stem Cell, Issue 22/6, 2018, Page(s) 879-892.e6, ISSN 1934-5909
DOI: 10.1016/j.stem.2018.05.003

Pooled CRISPR screening with single-cell transcriptome readout

Author(s): Paul Datlinger, André F Rendeiro, Christian Schmidl, Thomas Krausgruber, Peter Traxler, Johanna Klughammer, Linda C Schuster, Amelie Kuchler, Donat Alpar, Christoph Bock
Published in: Nature Methods, Issue 14/3, 2017, Page(s) 297-301, ISSN 1548-7091
DOI: 10.1038/nmeth.4177

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features

Author(s): Boris Simovski, Chakravarthi Kanduri, Sveinung Gundersen, Dmytro Titov, Diana Domanska, Christoph Bock, Lara Bossini-Castillo, Maria Chikina, Alexander Favorov, Ryan M Layer, Andrey A Mironov, Aaron R Quinlan, Nathan C Sheffield, Gosia Trynka, Geir K Sandve
Published in: Nucleic Acids Research, Issue 46/W1, 2018, Page(s) W186-W193, ISSN 0305-1048
DOI: 10.1093/nar/gky474

VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data

Author(s): Heiko Müller, Raul Jimenez-Heredia, Ana Krolo, Tatjana Hirschmugl, Jasmin Dmytrus, Kaan Boztug, Christoph Bock
Published in: Nucleic Acids Research, Issue 45/W1, 2017, Page(s) W567-W572, ISSN 0305-1048
DOI: 10.1093/nar/gkx425

Assessment of established techniques to determine developmental and malignant potential of human pluripotent stem cells

Author(s): Thomas F. Allison1,2, Peter W. Andrews 1, Yishai Avior3, Ivana Barbaric1, Nissim Benvenisty3, Christoph Bock 4,5,6, Jennifer Brehm7, Oliver Brüstle8, Ivan Damjanov 9, Andrew Elefanty10,11, Daniel Felkner7, Paul J. Gokhale1, Florian Halbritter 4, Lyn E. Healy12,13, Tim X. Hu 14, Barbara B. Knowles15,16, Jeanne F. Loring 17, Tenneille E. Ludwig7, Robyn Mayberry10,11, Suzanne Micallef10,11, Jameelah
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
DOI: 10.1038/s41467-018-04011-3

Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium

Author(s): Kenneth Aldape, Samirkumar B Amin, David M Ashley, Jill S Barnholtz-Sloan, Amanda J Bates, Rameen Beroukhim, Christoph Bock, Daniel J Brat, Elizabeth B Claus, Joseph F Costello, John F de Groot, Gaetano Finocchiaro, Pim J French, Hui K Gan, Brent Griffith, Christel C Herold-Mende, Craig Horbinski, Antonio Iavarone, Steven N Kalkanis, Konstantina Karabatsou, Hoon Kim, Mathilde C M Kouwenhoven, Kerr
Published in: Neuro-Oncology, Issue 20/7, 2018, Page(s) 873-884, ISSN 1522-8517
DOI: 10.1093/neuonc/noy020

The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space

Author(s): Johanna Klughammer1,37, Barbara Kiesel2,3,37, Thomas Roetzer3,4, Nikolaus Fortelny1, Amelie Nemc1, Karl-Heinz Nenning5, Julia Furtner3,6, Nathan C. Sheffield7, Paul Datlinger1, Nadine Peter3,4, Martha Nowosielski8,9, Marco Augustin10, Mario Mischkulnig2,3, Thomas Ströbel3,4, Donat Alpar1, Bekir Ergüner1, Martin Senekowitsch1, Patrizia Moser11, Christian F. Freyschlag12, Johannes Kerschbaumer12,
Published in: Nature Medicine, Issue in press, 2018, ISSN 1078-8956
DOI: 10.1038/s41591-018-0156-x

RnBeads 2.0: comprehensive analysis of DNA methylation data

Author(s): Fabian Müller, Michael Scherer, Yassen Assenov, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock
Published in: Genome Biology, Issue 20/1, 2019, ISSN 1474-760X
DOI: 10.1186/s13059-019-1664-9

Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis

Author(s): Florian Halbritter, Matthias Farlik, Raphaela Schwentner, Gunhild Jug, Nikolaus Fortelny, Thomas Schnoller, Hanja Pisa, Linda Christina Schuster, Andrea Reinprecht, Thomas Czech, Johannes Gojo, Wolfgang Holter, Milen Minkov, Wolfgang M Bauer, Ingrid Simonitsch-Klupp, Christoph Bock, Caroline Hutter
Published in: Cancer Discovery, 2019, Page(s) CD-19-0138, ISSN 2159-8274
DOI: 10.1158/2159-8290.cd-19-0138

Combined chemosensitivity and chromatin profiling prioritizes drug combinations in CLL

Author(s): Christian Schmidl, Gregory I. Vladimer, André F. Rendeiro, Susanne Schnabl, Thomas Krausgruber, Christina Taubert, Nikolaus Krall, Tea Pemovska, Mohammad Araghi, Berend Snijder, Rainer Hubmann, Anna Ringler, Kathrin Runggatscher, Dita Demirtas, Oscar Lopez de la Fuente, Martin Hilgarth, Cathrin Skrabs, Edit Porpaczy, Michaela Gruber, Gregor Hoermann, Stefan Kubicek, Philipp B. Staber, Medhat Sheh
Published in: Nature Chemical Biology, Issue 15/3, 2019, Page(s) 232-240, ISSN 1552-4450
DOI: 10.1038/s41589-018-0205-2

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

Author(s): Tahsin Stefan Barakat, Florian Halbritter, Man Zhang, André F. Rendeiro, Elena Perenthaler, Christoph Bock, Ian Chambers
Published in: Cell Stem Cell, Issue 23/2, 2018, Page(s) 276-288.e8, ISSN 1934-5909
DOI: 10.1016/j.stem.2018.06.014

Colocalization analyses of genomic elements: approaches, recommendations and challenges

Author(s): Chakravarthi Kanduri, Christoph Bock, Sveinung Gundersen, Eivind Hovig, Geir Kjetil Sandve
Published in: Bioinformatics, Issue 35/9, 2018, Page(s) 1615-1624, ISSN 1367-4803
DOI: 10.1093/bioinformatics/bty835

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation

Author(s): Matthias Farlik, Florian Halbritter, Fabian Müller, Fizzah A. Choudry, Peter Ebert, Johanna Klughammer, Samantha Farrow, Antonella Santoro, Valerio Ciaurro, Anthony Mathur, Rakesh Uppal, Hendrik G. Stunnenberg, Willem H. Ouwehand, Elisa Laurenti, Thomas Lengauer, Mattia Frontini, Christoph Bock
Published in: Cell Stem Cell, Issue 19/6, 2016, Page(s) 808-822, ISSN 1934-5909
DOI: 10.1016/j.stem.2016.10.019

Systematic characterization of BAF mutations provides insights into intracomplex synthetic lethalities in human cancers

Author(s): Sandra Schick, André F. Rendeiro, Kathrin Runggatscher, Anna Ringler, Bernd Boidol, Melanie Hinkel, Peter Májek, Loan Vulliard, Thomas Penz, Katja Parapatics, Christian Schmidl, Jörg Menche, Guido Boehmelt, Mark Petronczki, André C. Müller, Christoph Bock, Stefan Kubicek
Published in: Nature Genetics, Issue 51/9, 2019, Page(s) 1399-1410, ISSN 1061-4036
DOI: 10.1038/s41588-019-0477-9

Chromatin mapping and single-cell immune profiling define the temporal dynamics of ibrutinib response in CLL

Author(s): André F. Rendeiro, Thomas Krausgruber, Nikolaus Fortelny, Fangwen Zhao, Thomas Penz, Matthias Farlik, Linda C. Schuster, Amelie Nemc, Szabolcs Tasnády, Marienn Réti, Zoltán Mátrai, Donát Alpár, Csaba Bödör, Christian Schmidl, Christoph Bock
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
DOI: 10.1038/s41467-019-14081-6