Publication

Updated on 2024-02-27.

Total Google Scholar citations: 12467.

2023

  1. Zuguang Gu, Daniel Hübschmann, rGREAT: an R/bioconductor package for functional enrichment on genomic regions. Bioinformatics (Oxford, England) 2023. PubMed citescites5555.
  2. Zuguang Gu, Daniel Hübschmann, simplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results. Genomics, proteomics & bioinformatics 2023. PubMed citescites9696.
  3. Zuguang Gu, On the dependency heaviness of CRAN/Bioconductor ecosystem Journal of Systems and Software 2023. PubMed.

2022

  1. Zuguang Gu, Daniel Hübschmann, Pkgndep: a tool for analyzing dependency heaviness of R packages. Bioinformatics (Oxford, England) 2022. PubMed citescites22.
  2. Josefine Radke, Naveed Ishaque, Randi Koll, Zuguang Gu, Elisa Schumann, Lina Sieverling, Sebastian Uhrig, Daniel Hübschmann, Umut H Toprak, Cristina López, Xavier Pastor Hostench, Simone Borgoni, Dilafruz Juraeva, Fabienne Pritsch, Nagarajan Paramasivam, Gnana Prakash Balasubramanian, Matthias Schlesner, Shashwat Sahay, Marc Weniger, Debora Pehl, Helena Radbruch, Anja Osterloh, Agnieszka Korfel, Martin Misch, Julia Onken, Katharina Faust, Peter Vajkoczy, Dag Moskopp, Yawen Wang, Andreas Jödicke, Lorenz Trümper, Ioannis Anagnostopoulos, Dido Lenze, Ralf Küppers, Michael Hummel, Clemens A Schmitt, Otmar D Wiestler, Stephan Wolf, Andreas Unterberg, Roland Eils, Christel Herold-Mende, Benedikt Brors, Reiner Siebert, Stefan Wiemann, Frank L Heppner, The genomic and transcriptional landscape of primary central nervous system lymphoma. Nature communications 2022. PubMed citescites5656.
  3. Zuguang Gu, Daniel Hübschmann, Improve consensus partitioning via a hierarchical procedure. Briefings in bioinformatics 2022. PubMed citescites11.
  4. Zuguang Gu, Daniel Hübschmann, Make Interactive Complex Heatmaps in R. Bioinformatics (Oxford, England) 2022. PubMed citescites7373.
  5. Zuguang Gu, Daniel Hübschmann, spiralize: an R package for visualizing data on spirals. Bioinformatics (Oxford, England) 2022. PubMed citescites77.
  6. 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 2022. PubMed citescites11.
  7. Zuguang Gu, Complex heatmap visualization iMeta 2022. PubMed citescites197197.

2021

  1. Mengyu Tu, Lukas Klein, Elisa Espinet, Theodoros Georgomanolis, Florian Wegwitz, Xiaojuan Li, Laura Urbach, Adi Danieli-Mackay, Stefan Küffer, Kamil Bojarczuk, Athanasia Mizi, Ufuk Günesdogan, Björn Chapuy, Zuguang Gu, Albrecht Neesse, Uday Kishore, Philipp Ströbel, Elisabeth Hessmann, Stephan A Hahn, Andreas Trumpp, Argyris Papantonis, Volker Ellenrieder, Shiv K Singh, TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer. Nature cancer 2021. PubMed citescites4949.
  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 citescites1313.
  3. Nina Hensel*, Zuguang Gu*, Sagar*, Dominik Wieland, Katharina Jechow, Janine Kemming, Sian Llewellyn-Lacey, Emma Gostick, Oezlem Sogukpinar, Florian Emmerich, David A Price, Bertram Bengsch, Tobias Boettler, Christoph Neumann-Haefelin, Roland Eils, Christian Conrad, Ralf Bartenschlager, Dominic Grün, Naveed Ishaque, Robert Thimme, Maike Hofmann, Memory-like HCV-specific CD8+ T cells retain a molecular scar after cure of chronic HCV infection. Nature immunology 2021. PubMed citescites105105.
  4. Zuguang Gu, Matthias Schlesner, Daniel Hübschmann, cola: an R/Bioconductor package for consensus partitioning through a general framework. Nucleic acids research 2021. PubMed citescites2727.
  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 citescites5858.
  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 citescites7272.

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 citescites5353.
  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 citescites6767.
  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 citescites44.
  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 citescites4343.

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 citescites1919.
  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 citescites1616.
  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 citescites7575.
  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 citescites215215.

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 citescites112112.
  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 citescites164164.

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 citescites110110.
  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 citescites923923.
  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 citescites44.
  4. Kortine Kleinheinz, Isabell Bludau, Daniel Hübschmann, Michael Heinold, Philip Kensche, Zuguang Gu, Cristina López, Michael Hummel, Wolfram Klapper, Peter Möller, Inga Vater, Rabea Wagener, Benedikt Brors, Reiner Siebert, Roland Eils, Matthias Schlesner, ACEseq–allele specific copy number estimation from whole genome sequencing BioRXiv 2017. PubMed citescites3535.

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 citescites1515.
  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 citescites7171.
  3. Zuguang Gu, Roland Eils, Matthias Schlesner, Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics (Oxford, England) 2016. PubMed citescites60026002.
  4. Zuguang Gu, Roland Eils, Matthias Schlesner, HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data. Bioinformatics (Oxford, England) 2016. PubMed citescites3333.
  5. Zuguang Gu, Roland Eils, Matthias Schlesner, gtrellis: an R/Bioconductor package for making genome-level Trellis graphics. BMC bioinformatics 2016. PubMed citescites2020.
  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 citescites114114.

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 citescites314314.
  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 citescites146146.

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 citescites27712771.

2013

  1. Zuguang Gu, Jin Wang, CePa: an R package for finding significant pathways weighted by multiple network centralities. Bioinformatics (Oxford, England) 2013. PubMed citescites6767.

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 citescites2828.
  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 citescites9595.
  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 citescites113113.

  1. Zuguang Gu, Roland Eils, Matthias Schlesner, Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics (Oxford, England) 2016. PubMed citescites60026002.
  2. Zuguang Gu, Lei Gu, Roland Eils, Matthias Schlesner, Benedikt Brors, circlize Implements and enhances circular visualization in R. Bioinformatics (Oxford, England) 2014. PubMed citescites27712771.
  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 citescites923923.
  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 citescites314314.
  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 citescites215215.
  6. Zuguang Gu, Complex heatmap visualization iMeta 2022. PubMed citescites197197.
  7. Zuguang Gu, Roland Eils, Matthias Schlesner, Naveed Ishaque, EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations. BMC genomics 2018. PubMed citescites164164.
  8. 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 citescites146146.
  9. 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 citescites114114.
  10. 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 citescites113113.
  11. 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 citescites112112.
  12. 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 citescites110110.
  13. Nina Hensel*, Zuguang Gu*, Sagar*, Dominik Wieland, Katharina Jechow, Janine Kemming, Sian Llewellyn-Lacey, Emma Gostick, Oezlem Sogukpinar, Florian Emmerich, David A Price, Bertram Bengsch, Tobias Boettler, Christoph Neumann-Haefelin, Roland Eils, Christian Conrad, Ralf Bartenschlager, Dominic Grün, Naveed Ishaque, Robert Thimme, Maike Hofmann, Memory-like HCV-specific CD8+ T cells retain a molecular scar after cure of chronic HCV infection. Nature immunology 2021. PubMed citescites105105.
  14. Zuguang Gu, Daniel Hübschmann, simplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results. Genomics, proteomics & bioinformatics 2023. PubMed citescites9696.
  15. 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 citescites9595.
  16. 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 citescites7575.
  17. Zuguang Gu, Daniel Hübschmann, Make Interactive Complex Heatmaps in R. Bioinformatics (Oxford, England) 2022. PubMed citescites7373.
  18. 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 citescites7272.
  19. 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 citescites7171.
  20. 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 citescites6767.
  21. Zuguang Gu, Jin Wang, CePa: an R package for finding significant pathways weighted by multiple network centralities. Bioinformatics (Oxford, England) 2013. PubMed citescites6767.
  22. 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 citescites5858.
  23. Josefine Radke, Naveed Ishaque, Randi Koll, Zuguang Gu, Elisa Schumann, Lina Sieverling, Sebastian Uhrig, Daniel Hübschmann, Umut H Toprak, Cristina López, Xavier Pastor Hostench, Simone Borgoni, Dilafruz Juraeva, Fabienne Pritsch, Nagarajan Paramasivam, Gnana Prakash Balasubramanian, Matthias Schlesner, Shashwat Sahay, Marc Weniger, Debora Pehl, Helena Radbruch, Anja Osterloh, Agnieszka Korfel, Martin Misch, Julia Onken, Katharina Faust, Peter Vajkoczy, Dag Moskopp, Yawen Wang, Andreas Jödicke, Lorenz Trümper, Ioannis Anagnostopoulos, Dido Lenze, Ralf Küppers, Michael Hummel, Clemens A Schmitt, Otmar D Wiestler, Stephan Wolf, Andreas Unterberg, Roland Eils, Christel Herold-Mende, Benedikt Brors, Reiner Siebert, Stefan Wiemann, Frank L Heppner, The genomic and transcriptional landscape of primary central nervous system lymphoma. Nature communications 2022. PubMed citescites5656.
  24. Zuguang Gu, Daniel Hübschmann, rGREAT: an R/bioconductor package for functional enrichment on genomic regions. Bioinformatics (Oxford, England) 2023. PubMed citescites5555.
  25. 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 citescites5353.
  26. Mengyu Tu, Lukas Klein, Elisa Espinet, Theodoros Georgomanolis, Florian Wegwitz, Xiaojuan Li, Laura Urbach, Adi Danieli-Mackay, Stefan Küffer, Kamil Bojarczuk, Athanasia Mizi, Ufuk Günesdogan, Björn Chapuy, Zuguang Gu, Albrecht Neesse, Uday Kishore, Philipp Ströbel, Elisabeth Hessmann, Stephan A Hahn, Andreas Trumpp, Argyris Papantonis, Volker Ellenrieder, Shiv K Singh, TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer. Nature cancer 2021. PubMed citescites4949.
  27. 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 citescites4343.
  28. Kortine Kleinheinz, Isabell Bludau, Daniel Hübschmann, Michael Heinold, Philip Kensche, Zuguang Gu, Cristina López, Michael Hummel, Wolfram Klapper, Peter Möller, Inga Vater, Rabea Wagener, Benedikt Brors, Reiner Siebert, Roland Eils, Matthias Schlesner, ACEseq–allele specific copy number estimation from whole genome sequencing BioRXiv 2017. PubMed citescites3535.
  29. Zuguang Gu, Roland Eils, Matthias Schlesner, HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data. Bioinformatics (Oxford, England) 2016. PubMed citescites3333.
  30. 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 citescites2828.
  31. Zuguang Gu, Matthias Schlesner, Daniel Hübschmann, cola: an R/Bioconductor package for consensus partitioning through a general framework. Nucleic acids research 2021. PubMed citescites2727.
  32. Zuguang Gu, Roland Eils, Matthias Schlesner, gtrellis: an R/Bioconductor package for making genome-level Trellis graphics. BMC bioinformatics 2016. PubMed citescites2020.
  33. 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 citescites1919.
  34. Zuguang Gu, Chenyu Zhang, Jin Wang, Gene regulation is governed by a core network in hepatocellular carcinoma. BMC systems biology 2012. PubMed citescites1717.
  35. 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 citescites1616.
  36. 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 citescites1515.
  37. 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 citescites1313.
  38. 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.
  39. Zuguang Gu, Daniel Hübschmann, spiralize: an R package for visualizing data on spirals. Bioinformatics (Oxford, England) 2022. PubMed citescites77.
  40. 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 citescites44.
  41. 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 citescites44.
  42. Zuguang Gu, Daniel Hübschmann, Pkgndep: a tool for analyzing dependency heaviness of R packages. Bioinformatics (Oxford, England) 2022. PubMed citescites22.
  43. Zuguang Gu, Daniel Hübschmann, Improve consensus partitioning via a hierarchical procedure. Briefings in bioinformatics 2022. PubMed citescites11.
  44. 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 2022. PubMed citescites11.
  45. Zuguang Gu, On the dependency heaviness of CRAN/Bioconductor ecosystem Journal of Systems and Software 2023. PubMed.