EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations

by Zuguang Gu, Roland Eils, Matthias Schlesner, Naveed Ishaque
Published 2018-04-01

Linker histone epitopes are hidden by in situ higher-order chromatin structure

by Vladimir B. Teif, Travis J. Gould, Christopher T. Clarkson, Logan Boyd, Enoch B. Antwi, Naveed Ishaque, Ada L. Olins, Donald E. Olins
Published 2020-06-01

Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4

by Enoch B. Antwi, Ada Olins, Vladimir B. Teif, Matthias Bieg, Tobias Bauer, Zuguang Gu, Benedikt Brors, Roland Eils, Donald Olins, Naveed Ishaque
Published 2020-02-01

Publisher Correction: A downy mildew effector evades recognition by polymorphism of expression and subcellular localization

by Shuta Asai, Oliver J. Furzer, Volkan Cevik, Dae Sung Kim, Naveed Ishaque, Sandra Goritschnig, Brian J. Staskawicz, Ken Shirasu, Jonathan D. G. Jones
Published 2019-01-01

A downy mildew effector evades recognition by polymorphism of expression and subcellular localization

by Shuta Asai, Oliver J. Furzer, Volkan Cevik, Dae Sung Kim, Naveed Ishaque, Sandra Goritschnig, Brian J. Staskawicz, Ken Shirasu, Jonathan D. G. Jones
Published 2018-12-01

Expression profiling during arabidopsis/downy mildew interaction reveals a highly-expressed effector that attenuates responses to salicylic acid.

by Shuta Asai, Ghanasyam Rallapalli, Sophie J M Piquerez, Marie-Cécile Caillaud, Oliver J Furzer, Naveed Ishaque, Lennart Wirthmueller, Georgina Fabro, Ken Shirasu, Jonathan D G Jones
Published 2014-10-01

Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy

by Teresa G. Krieger, Solange Le Blanc, Julia Jabs, Foo Wei Ten, Naveed Ishaque, Katharina Jechow, Olivia Debnath, Carl-Stephan Leonhardt, Anamika Giri, Roland Eils, Oliver Strobel, Christian Conrad
Published 2021-10-01

Author Correction: Cell segmentation-free inference of cell types from in situ transcriptomics data

by Jeongbin Park, Wonyl Choi, Sebastian Tiesmeyer, Brian Long, Lars E. Borm, Emma Garren, Thuc Nghi Nguyen, Bosiljka Tasic, Simone Codeluppi, Tobias Graf, Matthias Schlesner, Oliver Stegle, Roland Eils, Naveed Ishaque
Published 2021-06-01

Cell segmentation-free inference of cell types from in situ transcriptomics data

by Jeongbin Park, Wonyl Choi, Sebastian Tiesmeyer, Brian Long, Lars E. Borm, Emma Garren, Thuc Nghi Nguyen, Bosiljka Tasic, Simone Codeluppi, Tobias Graf, Matthias Schlesner, Oliver Stegle, Roland Eils, Naveed Ishaque
Published 2021-06-01

Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands

by Florian Haller, Matthias Bieg, Rainer Will, Cindy Körner, Dieter Weichenhan, Alexander Bott, Naveed Ishaque, Pavlo Lutsik, Evgeny A. Moskalev, Sarina K. Mueller, Marion Bähr, Angelika Woerner, Birgit Kaiser, Claudia Scherl, Marlen Haderlein, Kortine Kleinheinz, Rainer Fietkau, Heinrich Iro, Roland Eils, Arndt Hartmann, Christoph Plass, Stefan Wiemann, Abbas Agaimy
Published 2019-01-01

Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL

by Justyna A. Wierzbinska, Reka Toth, Naveed Ishaque, Karsten Rippe, Jan-Philipp Mallm, Lara C. Klett, Daniel Mertens, Thorsten Zenz, Thomas Hielscher, Marc Seifert, Ralf Küppers, Yassen Assenov, Pavlo Lutsik, Stephan Stilgenbauer, Philipp M. Roessner, Martina Seiffert, John Byrd, Christopher C. Oakes, Christoph Plass, Daniel B. Lipka
Published 2020-03-01

Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks

by Jan‐Philipp Mallm, Murat Iskar, Naveed Ishaque, Lara C Klett, Sabrina J Kugler, Jose M Muino, Vladimir B Teif, Alexandra M Poos, Sebastian Großmann, Fabian Erdel, Daniele Tavernari, Sandra D Koser, Sabrina Schumacher, Benedikt Brors, Rainer König, Daniel Remondini, Martin Vingron, Stephan Stilgenbauer, Peter Lichter, Marc Zapatka, Daniel Mertens, Karsten Rippe
Published 2019-05-01

Multiple candidate effectors from the oomycete pathogen Hyaloperonospora arabidopsidis suppress host plant immunity.

by Georgina Fabro, Jens Steinbrenner, Mary Coates, Naveed Ishaque, Laura Baxter, David J Studholme, Evelyn Körner, Rebecca L Allen, Sophie J M Piquerez, Alejandra Rougon-Cardoso, David Greenshields, Rita Lei, Jorge L Badel, Marie-Cecile Caillaud, Kee-Hoon Sohn, Guido Van den Ackerveken, Jane E Parker, Jim Beynon, Jonathan D G Jones
Published 2011-11-01

MEST mediates the impact of prenatal bisphenol A exposure on long-term body weight development

by Kristin M. Junge, Beate Leppert, Susanne Jahreis, Dirk K. Wissenbach, Ralph Feltens, Konrad Grützmann, Loreen Thürmann, Tobias Bauer, Naveed Ishaque, Matthias Schick, Melanie Bewerunge-Hudler, Stefan Röder, Mario Bauer, Angela Schulz, Michael Borte, Kathrin Landgraf, Antje Körner, Wieland Kiess, Martin von Bergen, Gabriele I. Stangl, Saskia Trump, Roland Eils, Tobias Polte, Irina Lehmann
Published 2018-04-01

Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer

by Naveed Ishaque, Mohammed L. Abba, Christine Hauser, Nitin Patil, Nagarajan Paramasivam, Daniel Huebschmann, Jörg Hendrik Leupold, Gnana Prakash Balasubramanian, Kortine Kleinheinz, Umut H. Toprak, Barbara Hutter, Axel Benner, Anna Shavinskaya, Chan Zhou, Zuguang Gu, Jules Kerssemakers, Alexander Marx, Marcin Moniuszko, Miroslaw Kozlowski, Joanna Reszec, Jacek Niklinski, Jürgen Eils, Matthias Schlesner, Roland Eils, Benedikt Brors, Heike Allgayer
Published 2018-11-01

Alternative lengthening of telomeres in childhood neuroblastoma from genome to proteome

by Sabine A. Hartlieb, Lina Sieverling, Michal Nadler-Holly, Matthias Ziehm, Umut H. Toprak, Carl Herrmann, Naveed Ishaque, Konstantin Okonechnikov, Moritz Gartlgruber, Young-Gyu Park, Elisa Maria Wecht, Larissa Savelyeva, Kai-Oliver Henrich, Carolina Rosswog, Matthias Fischer, Barbara Hero, David T. W. Jones, Elke Pfaff, Olaf Witt, Stefan M. Pfister, Richard Volckmann, Jan Koster, Katharina Kiesel, Karsten Rippe, Sabine Taschner-Mandl, Peter Ambros, Benedikt Brors, Matthias Selbach, Lars Feuerbach, Frank Westermann
Published 2021-02-01

Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration

by Hye-Jung E. Chun, Pascal D. Johann, Katy Milne, Marc Zapatka, Annette Buellesbach, Naveed Ishaque, Murat Iskar, Serap Erkek, Lisa Wei, Basile Tessier-Cloutier, Jake Lever, Emma Titmuss, James T. Topham, Reanne Bowlby, Eric Chuah, Karen L. Mungall, Yussanne Ma, Andrew J. Mungall, Richard A. Moore, Michael D. Taylor, Daniela S. Gerhard, Steven J.M. Jones, Andrey Korshunov, Manfred Gessler, Kornelius Kerl, Martin Hasselblatt, Michael C. Frühwald, Elizabeth J. Perlman, Brad H. Nelson, Stefan M. Pfister, Marco A. Marra, Marcel Kool
Published 2019-11-01