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

Publications

Selective Mediator dependence of cell-type-specifying transcription

Auteurs: 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
Publié dans: Nature Genetics, Numéro 52/7, 2020, Page(s) 719-727, ISSN 1061-4036
Éditeur: Nature Publishing Group
DOI: 10.1038/s41588-020-0635-0

Disturbed mitochondrial dynamics in CD8+ TILs reinforce T cell exhaustion

Auteurs: 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
Publié dans: Nature Immunology, Numéro 21/12, 2020, Page(s) 1540-1551, ISSN 1529-2908
Éditeur: 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

Auteurs: Brenda Marquina-Sanchez, Nikolaus Fortelny, Matthias Farlik, Andhira Vieira, Patrick Collombat, Christoph Bock, Stefan Kubicek
Publié dans: Genome Biology, Numéro 21/1, 2020, ISSN 1474-760X
Éditeur: BioMed Central
DOI: 10.1186/s13059-020-02006-2

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

Auteurs: 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,
Publié dans: Science Immunology, Numéro 6/57, 2021, Page(s) eabg6461, ISSN 2470-9468
Éditeur: 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

Auteurs: 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,
Publié dans: Science Translational Medicine, Numéro 12/573, 2020, Page(s) eabe2555, ISSN 1946-6234
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/scitranslmed.abe2555

High-content CRISPR screening

Auteurs: 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
Publié dans: Nature Reviews Methods Primers, 2022, ISSN 2662-8449
Éditeur: 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

Auteurs: 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
Publié dans: Journal of Allergy and Clinical Immunology, Numéro 146/5, 2020, Page(s) 1056-1069, ISSN 0091-6749
Éditeur: Mosby Inc.
DOI: 10.1016/j.jaci.2020.03.041

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

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

Acute BAF perturbation causes immediate changes in chromatin accessibility

Auteurs: 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
Publié dans: Nature Genetics, Numéro 53/3, 2021, Page(s) 269-278, ISSN 1061-4036
Éditeur: 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

Auteurs: 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
Publié dans: Circulation, Numéro 142/19, 2020, Page(s) 1831-1847, ISSN 0009-7322
Éditeur: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/circulationaha.119.044557

DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma

Auteurs: 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
Publié dans: Nature Medicine, Numéro 23/3, 2017, Page(s) 386-395, ISSN 1078-8956
Éditeur: Nature Publishing Group
DOI: 10.1038/nm.4273

An ERK-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion

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

Pooled CRISPR screening with single-cell transcriptome readout

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

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

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 46/W1, 2018, Page(s) W186-W193, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gky474

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

Auteurs: Heiko Müller, Raul Jimenez-Heredia, Ana Krolo, Tatjana Hirschmugl, Jasmin Dmytrus, Kaan Boztug, Christoph Bock
Publié dans: Nucleic Acids Research, Numéro 45/W1, 2017, Page(s) W567-W572, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkx425

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

Auteurs: 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
Publié dans: Nature Communications, Numéro 9/1, 2018, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-018-04011-3

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

Auteurs: 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,
Publié dans: Nature Medicine, Numéro in press, 2018, ISSN 1078-8956
Éditeur: Nature Publishing Group
DOI: 10.1038/s41591-018-0156-x

RnBeads 2.0: comprehensive analysis of DNA methylation data

Auteurs: Fabian Müller, Michael Scherer, Yassen Assenov, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock
Publié dans: Genome Biology, Numéro 20/1, 2019, ISSN 1474-760X
Éditeur: BMC
DOI: 10.1186/s13059-019-1664-9

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

Auteurs: 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
Publié dans: Cancer Discovery, 2019, Page(s) CD-19-0138, ISSN 2159-8274
Éditeur: American Association for Cancer Research Inc.
DOI: 10.1158/2159-8290.cd-19-0138

Combined chemosensitivity and chromatin profiling prioritizes drug combinations in CLL

Auteurs: 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
Publié dans: Nature Chemical Biology, Numéro 15/3, 2019, Page(s) 232-240, ISSN 1552-4450
Éditeur: Nature Publishing Group
DOI: 10.1038/s41589-018-0205-2

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

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

Colocalization analyses of genomic elements: approaches, recommendations and challenges

Auteurs: Chakravarthi Kanduri, Christoph Bock, Sveinung Gundersen, Eivind Hovig, Geir Kjetil Sandve
Publié dans: Bioinformatics, Numéro 35/9, 2018, Page(s) 1615-1624, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/bty835

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation

Auteurs: 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
Publié dans: Cell Stem Cell, Numéro 19/6, 2016, Page(s) 808-822, ISSN 1934-5909
Éditeur: Cell Press
DOI: 10.1016/j.stem.2016.10.019

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

Auteurs: 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
Publié dans: Nature Genetics, Numéro 51/9, 2019, Page(s) 1399-1410, ISSN 1061-4036
Éditeur: 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

Auteurs: 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
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-019-14081-6

Structural cells are key regulators of organ-specific immune responses

Auteurs: 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
Publié dans: Nature, Numéro 583/7815, 2020, Page(s) 296-302, ISSN 0028-0836
Éditeur: 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

Auteurs: 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
Publié dans: Nature Communications, Numéro 12/1, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-23445-w

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

Auteurs: Nikolaus Fortelny, Christoph Bock
Publié dans: Genome Biology, Numéro 21/1, 2020, ISSN 1474-760X
Éditeur: BioMed Central
DOI: 10.1186/s13059-020-02100-5

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

Auteurs: 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
Publié dans: Frontiers in Immunology, Numéro 12, 2021, ISSN 1664-3224
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fimmu.2021.630892

The Organoid Cell Atlas

Auteurs: 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
Publié dans: Nature Biotechnology, Numéro 39/1, 2021, Page(s) 13-17, ISSN 1087-0156
Éditeur: Nature Publishing Group
DOI: 10.1038/s41587-020-00762-x

Droits de propriété intellectuelle

METHOD FOR SEQUENCING RNA OLIGONUCLEOTIDES

Numéro de demande/publication: 20 20074985
Date: 2020-09-07

METHOD FOR SEQUENCING RNA OLIGONUCLEOTIDES

Numéro de demande/publication: 20 20074985
Date: 2020-09-07

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