Publication

Updated on 2021-11-25.

2021

  1. Marina Laplana, Matthias Bieg, Christian Faltus, Svitlana Melnik, Olga Bogatyrova, Zuguang Gu, Thomas Muley, Michael Meister, Hendrik Dienemann, Esther Herpel, Christopher I Amos, Matthias Schlesner, Roland Eils, Christoph Plass, Angela Risch, Differentially methylated regions within lung cancer risk loci are enriched in deregulated enhancers. Epigenetics 2021. PubMed.
  2. Ana Maia, Zuguang Gu, André Koch, Mireia Berdiel-Acer, Rainer Will, Matthias Schlesner, Stefan Wiemann, IFNβ1 secreted by breast cancer cells undergoing chemotherapy reprograms stromal fibroblasts to support tumour growth after treatment. Molecular oncology 2021. PubMed citescites55.
  3. Nina Hensel, Zuguang Gu, Dominik Sagar, Katharina Wieland, Janine Jechow, Sian Kemming, Emma Llewellyn-Lacey, Oezlem Gostick, Florian Sogukpinar, David A Emmerich, Bertram Price, Tobias Bengsch, Christoph Boettler, Roland Neumann-Haefelin, Christian Eils, Ralf Conrad, Dominic Bartenschlager, Naveed Grün, Robert Ishaque, Maike Thimme, Nina Hofmann, Memory-like HCV-specific CD8+ T cells retain a molecular scar after cure of chronic HCV infection. Nature immunology 2021. PubMed citescites2626.
  4. Zuguang Gu, Matthias Schlesner, Daniel Hübschmann, cola: an R/Bioconductor package for consensus partitioning through a general framework. Nucleic acids research 2021. PubMed citescites77.
  5. Daniel Hübschmann, Lea Jopp-Saile, Carolin Andresen, Stephen Krämer, Zuguang Gu, Christoph E Heilig, Simon Kreutzfeldt, Veronica Teleanu, Stefan Fröhling, Roland Eils, Matthias Schlesner, Analysis of mutational signatures with yet another package for signature analysis. Genes, chromosomes & cancer 2021. PubMed citescites99.
  6. Elisa Espinet, Zuguang Gu, Charles D Imbusch, Nathalia A Giese, Magdalena Büscher, Mariam Safavi, Silke Weisenburger, Corinna Klein, Vanessa Vogel, Mattia Falcone, Jacob Insua-Rodríguez, Manuel Reitberger, Vera Thiel, Steffi O Kossi, Alexander Muckenhuber, Karnjit Sarai, Alex Y L Lee, Elyne Backx, Soheila Zarei, Matthias M Gaida, Manuel Rodríguez-Paredes, Elisa Donato, Hsi-Yu Yen, Roland Eils, Matthias Schlesner, Nicole Pfarr, Thilo Hackert, Christoph Plass, Benedikt Brors, Katja Steiger, Dieter Weichenhan, H Efsun Arda, Ilse Rooman, Janel L Kopp, Oliver Strobel, Wilko Weichert, Martin R Sprick, Andreas Trumpp, Aggressive PDACs Show Hypomethylation of Repetitive Elements and the Execution of an Intrinsic IFN Program Linked to a Ductal Cell of Origin. Cancer discovery 2021. PubMed citescites1515.

2020

  1. Yonghe Wu, Michael Fletcher, Zuguang Gu, Qi Wang, Barbara Costa, Anna Bertoni, Ka-Hou Man, Magdalena Schlotter, Jörg Felsberg, Jasmin Mangei, Martje Barbus, Ann-Christin Gaupel, Wei Wang, Tobias Weiss, Roland Eils, Michael Weller, Haikun Liu, Guido Reifenberger, Andrey Korshunov, Peter Angel, Peter Lichter, Carl Herrmann, Bernhard Radlwimmer, Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype. Nature communications 2020. PubMed citescites77.
  2. Simon Raffel, Daniel Klimmeck, Mattia Falcone, Aykut Demir, Alireza Pouya, Petra Zeisberger, Christoph Lutz, Marco Tinelli, Oliver Bischel, Lars Bullinger, Christian Thiede, Anne Flörcken, Jörg Westermann, Gerhard Ehninger, Anthony D Ho, Carsten Müller-Tidow, Zuguang Gu, Carl Herrmann, Jeroen Krijgsveld, Andreas Trumpp, Jenny Hansson, Quantitative proteomics reveals specific metabolic features of acute myeloid leukemia stem cells. Blood 2020. PubMed citescites1717.
  3. Enoch B Antwi, Ada Olins, Vladimir B Teif, Matthias Bieg, Tobias Bauer, Zuguang Gu, Benedikt Brors, Roland Eils, Donald Olins, Naveed Ishaque, Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. Biology open 2020. PubMed citescites33.
  4. Maike Smits, Katharina Zoldan, Naveed Ishaque, Zuguang Gu, Katharina Jechow, Dominik Wieland, Christian Conrad, Roland Eils, Catherine Fauvelle, Thomas F Baumert, Florian Emmerich, Bertram Bengsch, Christoph Neumann-Haefelin, Maike Hofmann, Robert Thimme, Tobias Boettler, Follicular T helper cells shape the HCV-specific CD4+ T cell repertoire after virus elimination. The Journal of clinical investigation 2020. PubMed citescites2828.

2019

  1. Stephan M Tirier, Jeongbin Park, Friedrich Preußer, Lisa Amrhein, Zuguang Gu, Simon Steiger, Jan-Philipp Mallm, Teresa Krieger, Marcel Waschow, Björn Eismann, Marta Gut, Ivo G Gut, Karsten Rippe, Matthias Schlesner, Fabian Theis, Christiane Fuchs, Claudia R Ball, Hanno Glimm, Roland Eils, Christian Conrad, Pheno-seq - linking visual features and gene expression in 3D cell culture systems. Scientific reports 2019. PubMed citescites1111.
  2. Calvin Wing Yiu Chan, Zuguang Gu, Matthias Bieg, Roland Eils, Carl Herrmann, Impact of cancer mutational signatures on transcription factor motifs in the human genome. BMC medical genomics 2019. PubMed citescites1414.
  3. Nagarajan Paramasivam, Daniel Hübschmann, Umut H Toprak, Naveed Ishaque, Marian Neidert, Daniel Schrimpf, Damian Stichel, David Reuss, Philipp Sievers, Annekathrin Reinhardt, Annika K Wefers, David T W Jones, Zuguang Gu, Johannes Werner, Sebastian Uhrig, Hans-Georg Wirsching, Matthias Schick, Melanie Bewerunge-Hudler, Katja Beck, Stephanie Brehmer, Steffi Urbschat, Marcel Seiz-Rosenhagen, Daniel Hänggi, Christel Herold-Mende, Ralf Ketter, Roland Eils, Zvi Ram, Stefan M Pfister, Wolfgang Wick, Michael Weller, Rachel Grossmann, Andreas von Deimling, Matthias Schlesner, Felix Sahm, Mutational patterns and regulatory networks in epigenetic subgroups of meningioma. Acta neuropathologica 2019. PubMed citescites3232.
  4. Verena Körber, Jing Yang, Pankaj Barah, Yonghe Wu, Damian Stichel, Zuguang Gu, Michael Nai Chung Fletcher, David Jones, Bettina Hentschel, Katrin Lamszus, Jörg Christian Tonn, Gabriele Schackert, Michael Sabel, Jörg Felsberg, Angela Zacher, Kerstin Kaulich, Daniel Hübschmann, Christel Herold-Mende, Andreas von Deimling, Michael Weller, Bernhard Radlwimmer, Matthias Schlesner, Guido Reifenberger, Thomas Höfer, Peter Lichter, Evolutionary Trajectories of IDHWT Glioblastomas Reveal a Common Path of Early Tumorigenesis Instigated Years ahead of Initial Diagnosis. Cancer cell 2019. PubMed citescites107107.

2018

  1. 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, Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer. Nature communications 2018. PubMed citescites5555.
  2. Zuguang Gu, Roland Eils, Matthias Schlesner, Naveed Ishaque, EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations. BMC genomics 2018. PubMed citescites7474.

2017

  1. Daniel B Lipka, Tania Witte, Reka Toth, Jing Yang, Manuel Wiesenfarth, Peter Nöllke, Alexandra Fischer, David Brocks, Zuguang Gu, Jeongbin Park, Brigitte Strahm, Marcin Wlodarski, Ayami Yoshimi, Rainer Claus, Michael Lübbert, Hauke Busch, Melanie Boerries, Mark Hartmann, Maximilian Schönung, Umut Kilik, Jens Langstein, Justyna A Wierzbinska, Caroline Pabst, Swati Garg, Albert Catalá, Barbara De Moerloose, Michael Dworzak, Henrik Hasle, Franco Locatelli, Riccardo Masetti, Markus Schmugge, Owen Smith, Jan Stary, Marek Ussowicz, Marry M van den Heuvel-Eibrink, Yassen Assenov, Matthias Schlesner, Charlotte Niemeyer, Christian Flotho, Christoph Plass, RAS-pathway mutation patterns define epigenetic subclasses in juvenile myelomonocytic leukemia. Nature communications 2017. PubMed.
  2. Paul A Northcott, Ivo Buchhalter, A Sorana Morrissy, Volker Hovestadt, Joachim Weischenfeldt, Tobias Ehrenberger, Susanne Gröbner, Maia Segura-Wang, Thomas Zichner, Vasilisa A Rudneva, Hans-Jörg Warnatz, Nikos Sidiropoulos, Aaron H Phillips, Steven Schumacher, Kortine Kleinheinz, Sebastian M Waszak, Serap Erkek, David T W Jones, Barbara C Worst, Marcel Kool, Marc Zapatka, Natalie Jäger, Lukas Chavez, Barbara Hutter, Matthias Bieg, Nagarajan Paramasivam, Michael Heinold, Zuguang Gu, Naveed Ishaque, Christina Jäger-Schmidt, Charles D Imbusch, Alke Jugold, Daniel Hübschmann, Thomas Risch, Vyacheslav Amstislavskiy, Francisco German Rodriguez Gonzalez, Ursula D Weber, Stephan Wolf, Giles W Robinson, Xin Zhou, Gang Wu, David Finkelstein, Yanling Liu, Florence M G Cavalli, Betty Luu, Vijay Ramaswamy, Xiaochong Wu, Jan Koster, Marina Ryzhova, Yoon-Jae Cho, Scott L Pomeroy, Christel Herold-Mende, Martin Schuhmann, Martin Ebinger, Linda M Liau, Jaume Mora, Roger E McLendon, Nada Jabado, Toshihiro Kumabe, Eric Chuah, Yussanne Ma, Richard A Moore, Andrew J Mungall, Karen L Mungall, Nina Thiessen, Kane Tse, Tina Wong, Steven J M Jones, Olaf Witt, Till Milde, Andreas Von Deimling, David Capper, Andrey Korshunov, Marie-Laure Yaspo, Richard Kriwacki, Amar Gajjar, Jinghui Zhang, Rameen Beroukhim, Ernest Fraenkel, Jan O Korbel, Benedikt Brors, Matthias Schlesner, Roland Eils, Marco A Marra, Stefan M Pfister, Michael D Taylor, Peter Lichter, The whole-genome landscape of medulloblastoma subtypes. Nature 2017. PubMed citescites530530.
  3. Marcus Winter, Loreen Thürmann, Zuguang Gu, Gerrit Schüürmann, Gunda Herberth, Denise Hinz, Martin von Bergen, Hauke Harms, Sven Olek, Stefan Röder, Michael Borte, Roland Eils, Irina Lehmann, Saskia Trump, The benzene metabolite 1,4-benzoquinone reduces regulatory T-cell function: A potential mechanism for tobacco smoke-associated atopic dermatitis. The Journal of allergy and clinical immunology 2017. PubMed citescites33.

2016

  1. Federico Vita, Cosimo Taiti, Antonio Pompeiano, Zuguang Gu, Emilio Lo Presti, Larisa Whitney, Michele Monti, Giuseppe Di Miceli, Dario Giambalvo, Paolo Ruisi, Lorenzo Guglielminetti, Stefano Mancuso, Aromatic and proteomic analyses corroborate the distinction between Mediterranean landraces and modern varieties of durum wheat. Scientific reports 2016. PubMed.
  2. Saskia Trump, Matthias Bieg, Zuguang Gu, Loreen Thürmann, Tobias Bauer, Mario Bauer, Naveed Ishaque, Stefan Röder, Lei Gu, Gunda Herberth, Christian Lawerenz, Michael Borte, Matthias Schlesner, Christoph Plass, Nicolle Diessl, Markus Eszlinger, Oliver Mücke, Horst-Dietrich Elvers, Dirk K Wissenbach, Martin von Bergen, Carl Herrmann, Dieter Weichenhan, Rosalind J Wright, Irina Lehmann, Roland Eils, Prenatal maternal stress and wheeze in children: novel insights into epigenetic regulation. Scientific reports 2016. PubMed citescites5858.
  3. Zuguang Gu, Roland Eils, Matthias Schlesner, Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics (Oxford, England) 2016. PubMed citescites22862286.
  4. Zuguang Gu, Roland Eils, Matthias Schlesner, HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data. Bioinformatics (Oxford, England) 2016. PubMed citescites2020.
  5. Zuguang Gu, Roland Eils, Matthias Schlesner, gtrellis: an R/Bioconductor package for making genome-level Trellis graphics. BMC bioinformatics 2016. PubMed citescites1212.
  6. Tobias Bauer, Saskia Trump, Naveed Ishaque, Loreen Thürmann, Lei Gu, Mario Bauer, Matthias Bieg, Zuguang Gu, Dieter Weichenhan, Jan-Philipp Mallm, Stefan Röder, Gunda Herberth, Eiko Takada, Oliver Mücke, Marcus Winter, Kristin M Junge, Konrad Grützmann, Ulrike Rolle-Kampczyk, Qi Wang, Christian Lawerenz, Michael Borte, Tobias Polte, Matthias Schlesner, Michaela Schanne, Stefan Wiemann, Christina Geörg, Hendrik G Stunnenberg, Christoph Plass, Karsten Rippe, Junichiro Mizuguchi, Carl Herrmann, Roland Eils, Irina Lehmann, Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children. Molecular systems biology 2016. PubMed citescites8282.

2015

  1. Jenny Wegert, Naveed Ishaque, Romina Vardapour, Christina Geörg, Zuguang Gu, Matthias Bieg, Barbara Ziegler, Sabrina Bausenwein, Nasenien Nourkami, Nicole Ludwig, Andreas Keller, Clemens Grimm, Susanne Kneitz, Richard D Williams, Tas Chagtai, Kathy Pritchard-Jones, Peter van Sluis, Richard Volckmann, Jan Koster, Rogier Versteeg, Tomas Acha, Maureen J O’Sullivan, Peter K Bode, Felix Niggli, Godelieve A Tytgat, Harm van Tinteren, Marry M van den Heuvel-Eibrink, Eckart Meese, Christian Vokuhl, Ivo Leuschner, Norbert Graf, Roland Eils, Stefan M Pfister, Marcel Kool, Manfred Gessler, Mutations in the SIX1/2 pathway and the DROSHA/DGCR8 miRNA microprocessor complex underlie high-risk blastemal type Wilms tumors. Cancer cell 2015. PubMed citescites217217.
  2. Lei Gu, Sandra C Frommel, Christopher C Oakes, Ronald Simon, Katharina Grupp, Cristina Y Gerig, Dominik Bär, Mark D Robinson, Constance Baer, Melanie Weiss, Zuguang Gu, Matthieu Schapira, Ruprecht Kuner, Holger Sültmann, Maurizio Provenzano, Marie-Laure Yaspo, Benedikt Brors, Jan Korbel, Thorsten Schlomm, Guido Sauter, Roland Eils, Christoph Plass, Raffaella Santoro, BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence. Nature genetics 2015. PubMed citescites102102.

2014

  1. Zuguang Gu, Lei Gu, Roland Eils, Matthias Schlesner, Benedikt Brors, circlize Implements and enhances circular visualization in R. Bioinformatics (Oxford, England) 2014. PubMed citescites13161316.

2013

  1. Zuguang Gu, Jin Wang, CePa: an R package for finding significant pathways weighted by multiple network centralities. Bioinformatics (Oxford, England) 2013. PubMed citescites4444.

2012

  1. Chenfeng He, Ying-Xin Li, Guangxin Zhang, Zuguang Gu, Rong Yang, Jie Li, Zhi John Lu, Zhi-Hua Zhou, Chenyu Zhang, Jin Wang, MiRmat: mature microRNA sequence prediction. PloS one 2012. PubMed citescites2222.
  2. Zuguang Gu, Jialin Liu, Kunming Cao, Junfeng Zhang, Jin Wang, Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes. BMC systems biology 2012. PubMed citescites7676.
  3. Zuguang Gu, Chenyu Zhang, Jin Wang, Gene regulation is governed by a core network in hepatocellular carcinoma. BMC systems biology 2012. PubMed citescites1717.

2011

  1. Zuguang Gu, Jie Li, Song Gao, Ming Gong, Junling Wang, Hua Xu, Chenyu Zhang, Jin Wang, InterMitoBase: an annotated database and analysis platform of protein-protein interactions for human mitochondria. BMC genomics 2011. PubMed citescites99.

2010

  1. Lingyun Zhu, Qiang Wang, Lin Zhang, Zhixiang Fang, Fang Zhao, Zhiyuan Lv, Zuguang Gu, Junfeng Zhang, Jin Wang, Ke Zen, Yang Xiang, Dongjin Wang, Chen-Yu Zhang, Hypoxia induces PGC-1α expression and mitochondrial biogenesis in the myocardium of TOF patients. Cell research 2010. PubMed citescites9595.
  1. Zuguang Gu, Roland Eils, Matthias Schlesner, Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics (Oxford, England) 2016. PubMed citescites22862286.
  2. Zuguang Gu, Lei Gu, Roland Eils, Matthias Schlesner, Benedikt Brors, circlize Implements and enhances circular visualization in R. Bioinformatics (Oxford, England) 2014. PubMed citescites13161316.
  3. Paul A Northcott, Ivo Buchhalter, A Sorana Morrissy, Volker Hovestadt, Joachim Weischenfeldt, Tobias Ehrenberger, Susanne Gröbner, Maia Segura-Wang, Thomas Zichner, Vasilisa A Rudneva, Hans-Jörg Warnatz, Nikos Sidiropoulos, Aaron H Phillips, Steven Schumacher, Kortine Kleinheinz, Sebastian M Waszak, Serap Erkek, David T W Jones, Barbara C Worst, Marcel Kool, Marc Zapatka, Natalie Jäger, Lukas Chavez, Barbara Hutter, Matthias Bieg, Nagarajan Paramasivam, Michael Heinold, Zuguang Gu, Naveed Ishaque, Christina Jäger-Schmidt, Charles D Imbusch, Alke Jugold, Daniel Hübschmann, Thomas Risch, Vyacheslav Amstislavskiy, Francisco German Rodriguez Gonzalez, Ursula D Weber, Stephan Wolf, Giles W Robinson, Xin Zhou, Gang Wu, David Finkelstein, Yanling Liu, Florence M G Cavalli, Betty Luu, Vijay Ramaswamy, Xiaochong Wu, Jan Koster, Marina Ryzhova, Yoon-Jae Cho, Scott L Pomeroy, Christel Herold-Mende, Martin Schuhmann, Martin Ebinger, Linda M Liau, Jaume Mora, Roger E McLendon, Nada Jabado, Toshihiro Kumabe, Eric Chuah, Yussanne Ma, Richard A Moore, Andrew J Mungall, Karen L Mungall, Nina Thiessen, Kane Tse, Tina Wong, Steven J M Jones, Olaf Witt, Till Milde, Andreas Von Deimling, David Capper, Andrey Korshunov, Marie-Laure Yaspo, Richard Kriwacki, Amar Gajjar, Jinghui Zhang, Rameen Beroukhim, Ernest Fraenkel, Jan O Korbel, Benedikt Brors, Matthias Schlesner, Roland Eils, Marco A Marra, Stefan M Pfister, Michael D Taylor, Peter Lichter, The whole-genome landscape of medulloblastoma subtypes. Nature 2017. PubMed citescites530530.
  4. Jenny Wegert, Naveed Ishaque, Romina Vardapour, Christina Geörg, Zuguang Gu, Matthias Bieg, Barbara Ziegler, Sabrina Bausenwein, Nasenien Nourkami, Nicole Ludwig, Andreas Keller, Clemens Grimm, Susanne Kneitz, Richard D Williams, Tas Chagtai, Kathy Pritchard-Jones, Peter van Sluis, Richard Volckmann, Jan Koster, Rogier Versteeg, Tomas Acha, Maureen J O’Sullivan, Peter K Bode, Felix Niggli, Godelieve A Tytgat, Harm van Tinteren, Marry M van den Heuvel-Eibrink, Eckart Meese, Christian Vokuhl, Ivo Leuschner, Norbert Graf, Roland Eils, Stefan M Pfister, Marcel Kool, Manfred Gessler, Mutations in the SIX1/2 pathway and the DROSHA/DGCR8 miRNA microprocessor complex underlie high-risk blastemal type Wilms tumors. Cancer cell 2015. PubMed citescites217217.
  5. Verena Körber, Jing Yang, Pankaj Barah, Yonghe Wu, Damian Stichel, Zuguang Gu, Michael Nai Chung Fletcher, David Jones, Bettina Hentschel, Katrin Lamszus, Jörg Christian Tonn, Gabriele Schackert, Michael Sabel, Jörg Felsberg, Angela Zacher, Kerstin Kaulich, Daniel Hübschmann, Christel Herold-Mende, Andreas von Deimling, Michael Weller, Bernhard Radlwimmer, Matthias Schlesner, Guido Reifenberger, Thomas Höfer, Peter Lichter, Evolutionary Trajectories of IDHWT Glioblastomas Reveal a Common Path of Early Tumorigenesis Instigated Years ahead of Initial Diagnosis. Cancer cell 2019. PubMed citescites107107.
  6. Lei Gu, Sandra C Frommel, Christopher C Oakes, Ronald Simon, Katharina Grupp, Cristina Y Gerig, Dominik Bär, Mark D Robinson, Constance Baer, Melanie Weiss, Zuguang Gu, Matthieu Schapira, Ruprecht Kuner, Holger Sültmann, Maurizio Provenzano, Marie-Laure Yaspo, Benedikt Brors, Jan Korbel, Thorsten Schlomm, Guido Sauter, Roland Eils, Christoph Plass, Raffaella Santoro, BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence. Nature genetics 2015. PubMed citescites102102.
  7. Lingyun Zhu, Qiang Wang, Lin Zhang, Zhixiang Fang, Fang Zhao, Zhiyuan Lv, Zuguang Gu, Junfeng Zhang, Jin Wang, Ke Zen, Yang Xiang, Dongjin Wang, Chen-Yu Zhang, Hypoxia induces PGC-1α expression and mitochondrial biogenesis in the myocardium of TOF patients. Cell research 2010. PubMed citescites9595.
  8. Tobias Bauer, Saskia Trump, Naveed Ishaque, Loreen Thürmann, Lei Gu, Mario Bauer, Matthias Bieg, Zuguang Gu, Dieter Weichenhan, Jan-Philipp Mallm, Stefan Röder, Gunda Herberth, Eiko Takada, Oliver Mücke, Marcus Winter, Kristin M Junge, Konrad Grützmann, Ulrike Rolle-Kampczyk, Qi Wang, Christian Lawerenz, Michael Borte, Tobias Polte, Matthias Schlesner, Michaela Schanne, Stefan Wiemann, Christina Geörg, Hendrik G Stunnenberg, Christoph Plass, Karsten Rippe, Junichiro Mizuguchi, Carl Herrmann, Roland Eils, Irina Lehmann, Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children. Molecular systems biology 2016. PubMed citescites8282.
  9. Zuguang Gu, Jialin Liu, Kunming Cao, Junfeng Zhang, Jin Wang, Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes. BMC systems biology 2012. PubMed citescites7676.
  10. Zuguang Gu, Roland Eils, Matthias Schlesner, Naveed Ishaque, EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations. BMC genomics 2018. PubMed citescites7474.
  11. Saskia Trump, Matthias Bieg, Zuguang Gu, Loreen Thürmann, Tobias Bauer, Mario Bauer, Naveed Ishaque, Stefan Röder, Lei Gu, Gunda Herberth, Christian Lawerenz, Michael Borte, Matthias Schlesner, Christoph Plass, Nicolle Diessl, Markus Eszlinger, Oliver Mücke, Horst-Dietrich Elvers, Dirk K Wissenbach, Martin von Bergen, Carl Herrmann, Dieter Weichenhan, Rosalind J Wright, Irina Lehmann, Roland Eils, Prenatal maternal stress and wheeze in children: novel insights into epigenetic regulation. Scientific reports 2016. PubMed citescites5858.
  12. 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, Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer. Nature communications 2018. PubMed citescites5555.
  13. Zuguang Gu, Jin Wang, CePa: an R package for finding significant pathways weighted by multiple network centralities. Bioinformatics (Oxford, England) 2013. PubMed citescites4444.
  14. Nagarajan Paramasivam, Daniel Hübschmann, Umut H Toprak, Naveed Ishaque, Marian Neidert, Daniel Schrimpf, Damian Stichel, David Reuss, Philipp Sievers, Annekathrin Reinhardt, Annika K Wefers, David T W Jones, Zuguang Gu, Johannes Werner, Sebastian Uhrig, Hans-Georg Wirsching, Matthias Schick, Melanie Bewerunge-Hudler, Katja Beck, Stephanie Brehmer, Steffi Urbschat, Marcel Seiz-Rosenhagen, Daniel Hänggi, Christel Herold-Mende, Ralf Ketter, Roland Eils, Zvi Ram, Stefan M Pfister, Wolfgang Wick, Michael Weller, Rachel Grossmann, Andreas von Deimling, Matthias Schlesner, Felix Sahm, Mutational patterns and regulatory networks in epigenetic subgroups of meningioma. Acta neuropathologica 2019. PubMed citescites3232.
  15. Maike Smits, Katharina Zoldan, Naveed Ishaque, Zuguang Gu, Katharina Jechow, Dominik Wieland, Christian Conrad, Roland Eils, Catherine Fauvelle, Thomas F Baumert, Florian Emmerich, Bertram Bengsch, Christoph Neumann-Haefelin, Maike Hofmann, Robert Thimme, Tobias Boettler, Follicular T helper cells shape the HCV-specific CD4+ T cell repertoire after virus elimination. The Journal of clinical investigation 2020. PubMed citescites2828.
  16. Nina Hensel, Zuguang Gu, Dominik Sagar, Katharina Wieland, Janine Jechow, Sian Kemming, Emma Llewellyn-Lacey, Oezlem Gostick, Florian Sogukpinar, David A Emmerich, Bertram Price, Tobias Bengsch, Christoph Boettler, Roland Neumann-Haefelin, Christian Eils, Ralf Conrad, Dominic Bartenschlager, Naveed Grün, Robert Ishaque, Maike Thimme, Nina Hofmann, Memory-like HCV-specific CD8+ T cells retain a molecular scar after cure of chronic HCV infection. Nature immunology 2021. PubMed citescites2626.
  17. Chenfeng He, Ying-Xin Li, Guangxin Zhang, Zuguang Gu, Rong Yang, Jie Li, Zhi John Lu, Zhi-Hua Zhou, Chenyu Zhang, Jin Wang, MiRmat: mature microRNA sequence prediction. PloS one 2012. PubMed citescites2222.
  18. Zuguang Gu, Roland Eils, Matthias Schlesner, HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data. Bioinformatics (Oxford, England) 2016. PubMed citescites2020.
  19. Simon Raffel, Daniel Klimmeck, Mattia Falcone, Aykut Demir, Alireza Pouya, Petra Zeisberger, Christoph Lutz, Marco Tinelli, Oliver Bischel, Lars Bullinger, Christian Thiede, Anne Flörcken, Jörg Westermann, Gerhard Ehninger, Anthony D Ho, Carsten Müller-Tidow, Zuguang Gu, Carl Herrmann, Jeroen Krijgsveld, Andreas Trumpp, Jenny Hansson, Quantitative proteomics reveals specific metabolic features of acute myeloid leukemia stem cells. Blood 2020. PubMed citescites1717.
  20. Zuguang Gu, Chenyu Zhang, Jin Wang, Gene regulation is governed by a core network in hepatocellular carcinoma. BMC systems biology 2012. PubMed citescites1717.
  21. Elisa Espinet, Zuguang Gu, Charles D Imbusch, Nathalia A Giese, Magdalena Büscher, Mariam Safavi, Silke Weisenburger, Corinna Klein, Vanessa Vogel, Mattia Falcone, Jacob Insua-Rodríguez, Manuel Reitberger, Vera Thiel, Steffi O Kossi, Alexander Muckenhuber, Karnjit Sarai, Alex Y L Lee, Elyne Backx, Soheila Zarei, Matthias M Gaida, Manuel Rodríguez-Paredes, Elisa Donato, Hsi-Yu Yen, Roland Eils, Matthias Schlesner, Nicole Pfarr, Thilo Hackert, Christoph Plass, Benedikt Brors, Katja Steiger, Dieter Weichenhan, H Efsun Arda, Ilse Rooman, Janel L Kopp, Oliver Strobel, Wilko Weichert, Martin R Sprick, Andreas Trumpp, Aggressive PDACs Show Hypomethylation of Repetitive Elements and the Execution of an Intrinsic IFN Program Linked to a Ductal Cell of Origin. Cancer discovery 2021. PubMed citescites1515.
  22. Calvin Wing Yiu Chan, Zuguang Gu, Matthias Bieg, Roland Eils, Carl Herrmann, Impact of cancer mutational signatures on transcription factor motifs in the human genome. BMC medical genomics 2019. PubMed citescites1414.
  23. Zuguang Gu, Roland Eils, Matthias Schlesner, gtrellis: an R/Bioconductor package for making genome-level Trellis graphics. BMC bioinformatics 2016. PubMed citescites1212.
  24. Stephan M Tirier, Jeongbin Park, Friedrich Preußer, Lisa Amrhein, Zuguang Gu, Simon Steiger, Jan-Philipp Mallm, Teresa Krieger, Marcel Waschow, Björn Eismann, Marta Gut, Ivo G Gut, Karsten Rippe, Matthias Schlesner, Fabian Theis, Christiane Fuchs, Claudia R Ball, Hanno Glimm, Roland Eils, Christian Conrad, Pheno-seq - linking visual features and gene expression in 3D cell culture systems. Scientific reports 2019. PubMed citescites1111.
  25. Daniel Hübschmann, Lea Jopp-Saile, Carolin Andresen, Stephen Krämer, Zuguang Gu, Christoph E Heilig, Simon Kreutzfeldt, Veronica Teleanu, Stefan Fröhling, Roland Eils, Matthias Schlesner, Analysis of mutational signatures with yet another package for signature analysis. Genes, chromosomes & cancer 2021. PubMed citescites99.
  26. Zuguang Gu, Jie Li, Song Gao, Ming Gong, Junling Wang, Hua Xu, Chenyu Zhang, Jin Wang, InterMitoBase: an annotated database and analysis platform of protein-protein interactions for human mitochondria. BMC genomics 2011. PubMed citescites99.
  27. Zuguang Gu, Matthias Schlesner, Daniel Hübschmann, cola: an R/Bioconductor package for consensus partitioning through a general framework. Nucleic acids research 2021. PubMed citescites77.
  28. Yonghe Wu, Michael Fletcher, Zuguang Gu, Qi Wang, Barbara Costa, Anna Bertoni, Ka-Hou Man, Magdalena Schlotter, Jörg Felsberg, Jasmin Mangei, Martje Barbus, Ann-Christin Gaupel, Wei Wang, Tobias Weiss, Roland Eils, Michael Weller, Haikun Liu, Guido Reifenberger, Andrey Korshunov, Peter Angel, Peter Lichter, Carl Herrmann, Bernhard Radlwimmer, Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype. Nature communications 2020. PubMed citescites77.
  29. Ana Maia, Zuguang Gu, André Koch, Mireia Berdiel-Acer, Rainer Will, Matthias Schlesner, Stefan Wiemann, IFNβ1 secreted by breast cancer cells undergoing chemotherapy reprograms stromal fibroblasts to support tumour growth after treatment. Molecular oncology 2021. PubMed citescites55.
  30. Enoch B Antwi, Ada Olins, Vladimir B Teif, Matthias Bieg, Tobias Bauer, Zuguang Gu, Benedikt Brors, Roland Eils, Donald Olins, Naveed Ishaque, Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. Biology open 2020. PubMed citescites33.
  31. Marcus Winter, Loreen Thürmann, Zuguang Gu, Gerrit Schüürmann, Gunda Herberth, Denise Hinz, Martin von Bergen, Hauke Harms, Sven Olek, Stefan Röder, Michael Borte, Roland Eils, Irina Lehmann, Saskia Trump, The benzene metabolite 1,4-benzoquinone reduces regulatory T-cell function: A potential mechanism for tobacco smoke-associated atopic dermatitis. The Journal of allergy and clinical immunology 2017. PubMed citescites33.
  32. Marina Laplana, Matthias Bieg, Christian Faltus, Svitlana Melnik, Olga Bogatyrova, Zuguang Gu, Thomas Muley, Michael Meister, Hendrik Dienemann, Esther Herpel, Christopher I Amos, Matthias Schlesner, Roland Eils, Christoph Plass, Angela Risch, Differentially methylated regions within lung cancer risk loci are enriched in deregulated enhancers. Epigenetics 2021. PubMed.
  33. Daniel B Lipka, Tania Witte, Reka Toth, Jing Yang, Manuel Wiesenfarth, Peter Nöllke, Alexandra Fischer, David Brocks, Zuguang Gu, Jeongbin Park, Brigitte Strahm, Marcin Wlodarski, Ayami Yoshimi, Rainer Claus, Michael Lübbert, Hauke Busch, Melanie Boerries, Mark Hartmann, Maximilian Schönung, Umut Kilik, Jens Langstein, Justyna A Wierzbinska, Caroline Pabst, Swati Garg, Albert Catalá, Barbara De Moerloose, Michael Dworzak, Henrik Hasle, Franco Locatelli, Riccardo Masetti, Markus Schmugge, Owen Smith, Jan Stary, Marek Ussowicz, Marry M van den Heuvel-Eibrink, Yassen Assenov, Matthias Schlesner, Charlotte Niemeyer, Christian Flotho, Christoph Plass, RAS-pathway mutation patterns define epigenetic subclasses in juvenile myelomonocytic leukemia. Nature communications 2017. PubMed.
  34. Federico Vita, Cosimo Taiti, Antonio Pompeiano, Zuguang Gu, Emilio Lo Presti, Larisa Whitney, Michele Monti, Giuseppe Di Miceli, Dario Giambalvo, Paolo Ruisi, Lorenzo Guglielminetti, Stefano Mancuso, Aromatic and proteomic analyses corroborate the distinction between Mediterranean landraces and modern varieties of durum wheat. Scientific reports 2016. PubMed.