Prof. Joachim Schultze
Platform for Single Cell Genomics and Epigenomics
Prof. Dr. Joachim L. Schultze
Group Leader
Venusberg-Campus 1/99
53127  Bonn
 +49 228 43302-410

Areas of investigation/research focus

Innovation arises at the interface of different areas of science. We specialize in the interface between neurosciences, immunology and metabolic research on one side and genomics and bioinformatics on the other side. High-throughput sequencing down to single-cell resolution plays a pivotal role in our research at the Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn.

Our research comprises both, lab-based experimental approaches as well as computer-based analyses. We are thus in an excellent position to address questions of systems biological nature. However, our expert knowledge is also applied to assist collaborators in neurobiological and immunological research at the DZNE and worldwide.

Our own research is particularly focused on:

  • Systems biological approaches for improved characterization of immune cells and the regulation of immune cells and neurocytes
  • Single-cell RNA-Seq for enhanced functional characterization of immune cells and neurocytes
  • Understanding neuronal heterogeneity at a single-cell level across species in health and disease (Human Brain Project)
  • Genetic and epigenetic reprogramming of immune cells during aging and in age related diseases, e.g. Alzheimer’s Disease (AMPro - Aging and Metabolic Programming)
  • Nervous-immune system interactions (Immunosensation2 – Cluster of Excellence)
  • Genomics of blood and discovery of biomarkers
  • Development and application of bioinformatics and computational biology based approaches to improve our understanding of regulation in immune cells
  • New approaches to handle large, zero-inflated/sparse data sets as generated by single-cell sequencing (Sparse2Big)
  • Additionally, we work on adapting existing genomics applications to novel computational architectures (memory-driven computing)

Our research group is also involved in a variety of national and international research initiatives:

And serves as a counselling and overflow management entity in the West German Genome Center (WGGC)

  • Memory Driven Computing

    Memory-driven computing is a paradigm shift, that puts memory at the center of the compute infrastructure to support todays data-driven applications. System components are connected through a fabric, Gen-Z.

    For more information, click here.


    The "Platform for Single Cell Genomics and Epigenomics" is a joint Venture between the University of Bonn and the German Center for Neurodegenerative Diseases (DZNE). Both institutions seek to conjointly increase their expert knowledge in the areas of genomics and bioinformatics. Particular focus lies on the development and application of tools and technologies for single-cell genomics and on providing these technologies for internal and external collaborators.

    The laboratory space of the platform is situated in the new DZNE building B, the bioinformatics unit is located at the LIMES Institute. Both units are closely collaborating.

    For more information, click here.

Key Publications

Schulte-Schrepping J*, Reusch N*, Paclik D*, Baßler K*, Schlickeiser S*, Zhang B*, Krämer B*, Krammer T*, Brumhard S*, Bonaguro L*, De Domenico E*, Wendisch D*, Grasshoff M, Kapellos TS, Beckstette M, Pecht T, Saglam A, Dietrich O, Mei HE, Schulz AR, Conrad C, Kunkel D, Vafadarnejad E, Xu C-J, Horne A, Herbert M, Drews A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, Müller-Redetzky H, Heim K-M, Machleidt F, Uhrig A, Bosquillon de Jarcy L, Jürgens L, Stegemann M, Glösenkamp CR, Volk H-D, Goffinet C, Landthaler M, Wyler E, Georg P, Schneider M, Dang-Heine C, Neuwinger N, Kappert K, Tauber R, Corman V, Raabe J, Kaiser KM, Vinh MT, Rieke G, Meisel C, Ulas T, Becker M, Geffers R, Witzenrath M, Drosten C, Suttorp N, von Kalle C, Kurth F, Händler K, Schultze JL+, Aschenbrenner AC+, Li Y+, Nattermann J+, Sawitzki B+, Saliba A-E+, Sander LE+, Deutsche COVID-19 OMICS Initiative (DeCOI). (*shared first, + senior author). Severe COVID-19 is marked by a dysregulated myeloid cell compartment. Cell. 2020 Aug 01; doi: 10.1016/j.cell.2020.08.001
Camell CD*, Sander J*, Spadaro O, Lee A, Nguyen KY, Wing A, Goldberg EL, Youm YH, Brown CW, Elsworth J, Rodeheffer MS, Schultze JL, Dixit VD. (* shared first). Inflammasome-driven catecholamine catabolism in macrophages blunts lipolysis during ageing. Nature. 2017 Oct 05; 550:119-123. doi: 10.1038/nature24022
See P, Dutertre CA, Chen J, Günther P, McGovern N, Irac SE, Gunawan M, Beyer M, Händler K, Duan K, Sumatoh HRB, Ruffin N, Jouve M, Gea-Mallorquí E, Hennekam RCM, Lim T, Yip CC, Wen M, Malleret B, Low I, Shadan NB, Fen CFS, Tay A, Lum J, Zolezzi F, Larbi A, Poidinger M, Chan JKY, Chen Q, Rénia L, Haniffa M, Benaroch P, Schlitzer A, Schultze JL, Newell EW, Ginhoux F. Mapping the human DC lineage through the integration of high-dimensional techniques. Science. 2017 Jun 09; 356:pii: eaag3009.
Beyer M, Abdullah Z, Chemnitz JM, Maisel D, Sander J, Lehmann C, Thabet Y, Shinde PV, Schmidleithner L, Köhne M, Trebicka J, Schierwagen R, Hofmann A, Popov A, Lang KS, Oxenius A, Buch T, Kurts C, Heikenwalder M, Fätkenheuer G, Lang PA, Hartmann P, Knolle PA, Schultze JL. Tumor-necrosis factor impairs CD4(+) T cell-mediated immunological control in chronic viral infection. Nat Immunol. 2016 May 01; 17:593-603. doi: 10.1038/ni.3399
Jia Xue, Susanne V. Schmidt, Jil Sander, Astrid Draffehn, Wolfgang Krebs, Inga Quester, Dominic DeNardo, Trupti D. Gohel, Martina Emde, Lisa Schmidleithner, Hariharasudan Ganesan, Andrea Nino-Castro, Michael R. Mallmann, Larisa Labzin, Heidi Theis, Michael Kraut, Marc Beyer, Eicke Latz, Tom C. Freeman, Thomas Ulas, Joachim L. Schultze. Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation. Immunity. 2014 Feb 19; 40:274-288. doi: 10.1016/j.immuni.2014.01.006


Thursdays 1:30-4:30 pm

Patients +49 800-7799001

(free of charge)

Professionals +49 180-779900

(9 Cent/Min. German landline, mobile and out of Germany possibly more expensive)

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