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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

Selective Mediator dependence of cell-type-specifying transcription

Author(s): Martin G. Jaeger, Björn Schwalb, Sebastian D. Mackowiak, Taras Velychko, Alexander Hanzl, Hana Imrichova, Matthias Brand, Benedikt Agerer, Someth Chorn, Behnam Nabet, Fleur M. Ferguson, André C. Müller, Andreas Bergthaler, Nathanael S. Gray, James E. Bradner, Christoph Bock, Denes Hnisz, Patrick Cramer, Georg E. Winter
Published in: Nature Genetics, 52/7, 2020, Page(s) 719-727, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-020-0635-0

Disturbed mitochondrial dynamics in CD8+ TILs reinforce T cell exhaustion

Author(s): Yi-Ru Yu, Hana Imrichova, Haiping Wang, Tung Chao, Zhengtao Xiao, Min Gao, Marcela Rincon-Restrepo, Fabien Franco, Raphael Genolet, Wan-Chen Cheng, Camilla Jandus, George Coukos, Yi-Fan Jiang, Jason W. Locasale, Alfred Zippelius, Pu-Ste Liu, Li Tang, Christoph Bock, Nicola Vannini, Ping-Chih Ho
Published in: Nature Immunology, 21/12, 2020, Page(s) 1540-1551, ISSN 1529-2908
Publisher: Nature Publishing Group
DOI: 10.1038/s41590-020-0793-3

Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets

Author(s): Brenda Marquina-Sanchez, Nikolaus Fortelny, Matthias Farlik, Andhira Vieira, Patrick Collombat, Christoph Bock, Stefan Kubicek
Published in: Genome Biology, 21/1, 2020, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-020-02006-2

SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8 + T cell responses

Author(s): Benedikt Agerer, Maximilian Koblischke, Venugopal Gudipati, Luis Fernando Montaño-Gutierrez, Mark Smyth, Alexandra Popa, Jakob-Wendelin Genger, Lukas Endler, David M. Florian, Vanessa Mühlgrabner, Marianne Graninger, Stephan W. Aberle, Anna-Maria Husa, Lisa Ellen Shaw, Alexander Lercher, Pia Gattinger, Ricard Torralba-Gombau, Doris Trapin, Thomas Penz, Daniele Barreca, Ingrid Fae, Sabine Wenda,
Published in: Science Immunology, 6/57, 2021, Page(s) eabg6461, ISSN 2470-9468
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciimmunol.abg6461

Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2

Author(s): Alexandra Popa, Jakob-Wendelin Genger, Michael D. Nicholson, Thomas Penz, Daniela Schmid, Stephan W. Aberle, Benedikt Agerer, Alexander Lercher, Lukas Endler, Henrique Colaço, Mark Smyth, Michael Schuster, Miguel L. Grau, Francisco Martínez-Jiménez, Oriol Pich, Wegene Borena, Erich Pawelka, Zsofia Keszei, Martin Senekowitsch, Jan Laine, Judith H. Aberle, Monika Redlberger-Fritz, Mario Karolyi,
Published in: Science Translational Medicine, 12/573, 2020, Page(s) eabe2555, ISSN 1946-6234
Publisher: American Association for the Advancement of Science
DOI: 10.1126/scitranslmed.abe2555

High-content CRISPR screening

Author(s): Bock C, Datlinger P, Chardon F, Coelho MA, Dong MB, Lawson KA, Lu T, Maroc1 L, Norman TM, Song B, Stanley G, Chen S, Garnett M, Li1 W, Moffat J, Qi LS, Shapiro RS, Shendure J, Weissman JS, Zhuang X
Published in: Nature Reviews Methods Primers, 2022, ISSN 2662-8449
Publisher: Nature Publishing Group
DOI: 10.1038/s43586-021-00093-4

Single-cell transcriptomics combined with interstitial fluid proteomics defines cell type–specific immune regulation in atopic dermatitis

Author(s): Thomas B. Rojahn, Vera Vorstandlechner, Thomas Krausgruber, Wolfgang M. Bauer, Natalia Alkon, Christine Bangert, Felix M. Thaler, Farzaneh Sadeghyar, Nikolaus Fortelny, Victoria Gernedl, Katharina Rindler, Adelheid Elbe-Bürger, Christoph Bock, Michael Mildner, Patrick M. Brunner
Published in: Journal of Allergy and Clinical Immunology, 146/5, 2020, Page(s) 1056-1069, ISSN 0091-6749
Publisher: Mosby Inc.
DOI: 10.1016/j.jaci.2020.03.041

Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing

Author(s): Paul Datlinger, André F. Rendeiro, Thorina Boenke, Martin Senekowitsch, Thomas Krausgruber, Daniele Barreca, Christoph Bock
Published in: Nature Methods, 18/6, 2021, Page(s) 635-642, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01153-z

Acute BAF perturbation causes immediate changes in chromatin accessibility

Author(s): Sandra Schick, Sarah Grosche, Katharina Eva Kohl, Danica Drpic, Martin G. Jaeger, Nara C. Marella, Hana Imrichova, Jung-Ming G. Lin, Gerald Hofstätter, Michael Schuster, André F. Rendeiro, Anna Koren, Mark Petronczki, Christoph Bock, André C. Müller, Georg E. Winter, Stefan Kubicek
Published in: Nature Genetics, 53/3, 2021, Page(s) 269-278, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-021-00777-3

Single-Cell RNA Sequencing Analysis Reveals a Crucial Role for CTHRC1 (Collagen Triple Helix Repeat Containing 1) Cardiac Fibroblasts After Myocardial Infarction

Author(s): Adrián Ruiz-Villalba, Juan P. Romero, Silvia C. Hernández, Amaia Vilas-Zornoza, Nikolaus Fortelny, Laura Castro-Labrador, Patxi San Martin-Uriz, Erika Lorenzo-Vivas, Paula García-Olloqui, Marcel Palacio, Juan José Gavira, Gorka Bastarrika, Stefan Janssens, Ming Wu, Elena Iglesias, Gloria Abizanda, Xabier Martinez de Morentin, Miren Lasaga, Nuria Planell, Christoph Bock, Diego Alignani, Gema Me
Published in: Circulation, 142/19, 2020, Page(s) 1831-1847, ISSN 0009-7322
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/circulationaha.119.044557

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, 23/3, 2017, Page(s) 386-395, ISSN 1078-8956
Publisher: Nature Publishing Group
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, 22/6, 2018, Page(s) 879-892.e6, ISSN 1934-5909
Publisher: Cell Press
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, 14/3, 2017, Page(s) 297-301, ISSN 1548-7091
Publisher: Nature Publishing Group
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, 46/W1, 2018, Page(s) W186-W193, ISSN 0305-1048
Publisher: Oxford University Press
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, 45/W1, 2017, Page(s) W567-W572, ISSN 0305-1048
Publisher: Oxford University Press
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, 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
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, 20/7, 2018, Page(s) 873-884, ISSN 1522-8517
Publisher: Duke University Press
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, in press, 2018, ISSN 1078-8956
Publisher: Nature Publishing Group
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, 20/1, 2019, ISSN 1474-760X
Publisher: BMC
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
Publisher: American Association for Cancer Research Inc.
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, 15/3, 2019, Page(s) 232-240, ISSN 1552-4450
Publisher: Nature Publishing Group
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, 23/2, 2018, Page(s) 276-288.e8, ISSN 1934-5909
Publisher: Cell Press
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, 35/9, 2018, Page(s) 1615-1624, ISSN 1367-4803
Publisher: Oxford University Press
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, 19/6, 2016, Page(s) 808-822, ISSN 1934-5909
Publisher: Cell Press
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, 51/9, 2019, Page(s) 1399-1410, ISSN 1061-4036
Publisher: Nature Publishing Group
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, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-14081-6

Structural cells are key regulators of organ-specific immune responses

Author(s): Thomas Krausgruber, Nikolaus Fortelny, Victoria Fife-Gernedl, Martin Senekowitsch, Linda C. Schuster, Alexander Lercher, Amelie Nemc, Christian Schmidl, André F. Rendeiro, Andreas Bergthaler, Christoph Bock
Published in: Nature, 583/7815, 2020, Page(s) 296-302, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2424-4

Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden

Author(s): Peter Peneder, Adrian M. Stütz, Didier Surdez, Manuela Krumbholz, Sabine Semper, Mathieu Chicard, Nathan C. Sheffield, Gaelle Pierron, Eve Lapouble, Marcus Tötzl, Bekir Ergüner, Daniele Barreca, André F. Rendeiro, Abbas Agaimy, Heidrun Boztug, Gernot Engstler, Michael Dworzak, Marie Bernkopf, Sabine Taschner-Mandl, Inge M. Ambros, Ola Myklebost, Perrine Marec-Bérard, Susan Ann Burchill, Berna
Published in: Nature Communications, 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-23445-w

Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data

Author(s): Nikolaus Fortelny, Christoph Bock
Published in: Genome Biology, 21/1, 2020, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-020-02100-5

Spontaneously Resolved Atopic Dermatitis Shows Melanocyte and Immune Cell Activation Distinct From Healthy Control Skin

Author(s): Katharina Rindler, Thomas Krausgruber, Felix M. Thaler, Natalia Alkon, Christine Bangert, Harald Kurz, Nikolaus Fortelny, Thomas B. Rojahn, Constanze Jonak, Johannes Griss, Christoph Bock, Patrick M. Brunner
Published in: Frontiers in Immunology, 12, 2021, ISSN 1664-3224
Publisher: Frontiers Media S.A.
DOI: 10.3389/fimmu.2021.630892

The Organoid Cell Atlas

Author(s): Christoph Bock, Michael Boutros, J. Gray Camp, Laura Clarke, Hans Clevers, Juergen A. Knoblich, Prisca Liberali, Aviv Regev, Anne C. Rios, Oliver Stegle, Hendrik G. Stunnenberg, Sarah A. Teichmann, Barbara Treutlein, Robert G. J. Vries
Published in: Nature Biotechnology, 39/1, 2021, Page(s) 13-17, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-020-00762-x