Stem Cell Center of Competence ::: Uni Basel, Switzerland






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Prof. Dr. Timm Schroeder


Prof. Dr. Timm Schroeder
Group for Cell Systems Dynamics
Department of Biosystems Science and Engineering (D-BSSE), Basel
Swiss Federal Institute of Technology (ETH) Zürich
Mattenstrasse 26
CH-4058 Basel / Switzerland

E-mail timm.schroeder@
Phone +41 61 387 33 92
The Cell Systems Dynamics group studies cell fate choices and their molecular control in complex and dynamic cell systems. Due to their importance in health and disease and their potential for clinical therapy, mammalian stem and progenitor cells are of particular interest. Through a combination of purification, culture, molecular manipulation and high-throughput long-term bioimaging of cells, as well as the computer-assisted quantification of the resulting massive data sets, the molecular mechanisms controlling cell behavior are analyzed. Long-term cell tracking yields the time-resolved and quantitative single cell data that is required for a comprehensive understanding of cell fate control. The required combination of cell and molecular biology, genetics, imaging, engineering, software development, statistics and computational mathematical modelling is enabled by interdisciplinary work within the group and with collaborators. Ultimate goal is an improved understanding of the molecular mechanisms underlying stem cell behavior in health and disease, and the development of novel therapies in regenerative medicine.

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Recent publications related to stem cells:

  • Eilken HM, Nishikawa SI and Schroeder T. (2009). Continuous single-cell imaging of blood generation from haemogenic endothelium. Nature 457:896 - 900.
  • Rieger MA, Hoppe PS, Smejkal BM, Eitelhuber AC and Schroeder T. (2009). Hematopoietic cytokines can instruct lineage choice. Science 325:217-218.
  • Filipczyk A, Marr C, Hastreiter S, Feigelman J, Schwarzfischer M, Hoppe PS, Loeffler D, Kokkaliaris KD, Endele M, Schauberger B, Hilsenbeck O, Skylaki S, Hasenauer J, Anastassiadis K, Theis FJ and Schroeder T (2015) Network plasticity of pluripotency transcription factors in embryonic stem cells. Nature Cell Biology, 17: 1235-1246
  • Kokkaliaris KD, Drew E, Endele M, Loeffler D, Hoppe PS, Hilsenbeck O, Schauberger B, Hinzen C, Skylaki S, Theodorou M, Kieslinger M, Lemischka I, Moore K, Schroeder T. (2016). Identification of factors promoting ex vivo maintenance of mouse hematopoietic stem cells by long-term single-cell quantification. Blood 128:1181-92.
  • Hilsenbeck O, Schwarzfischer M, Skylaki S, Schauberger B, Hoppe PS, Loeffler D, Kokkaliaris KD, Hastreiter S, Skylaki E, Filipczyk A, Strasser M, Buggenthin F, Feigelman JS, Krumsiek J, van den Berg AJ, Endele M, Etzrodt M, Marr C, Theis FJ, Schroeder T. (2016). Software tools for single-cell tracking and quantification of cellular and molecular properties. Nat Biotechnol. 34:703-6.
  • Hoppe PS, Schwarzfischer M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Moritz N, Endele M, Filipczyk A, Gambardella A, Ahmed N, Etzrodt M, Coutu DL, Rieger MA, Marr C, Strasser MK, Schauberger B, Burtscher I, Ermakova O, Bürger A, Lickert H, Nerlov C, Theis FJ, Schroeder T. (2016). Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios. Nature 535:299-302.
  • Endele M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Skylaki S, Hoppe PS, Schambach A, Stanley ER, Schroeder T. (2017). CSF-1-induced Src signaling can instruct monocytic lineage choice. Blood 129:1691-1701.


  • Schroeder T. (2010). Hematopoietic stem cell heterogeneity: Subtypes, not unpredictable behavior. Cell Stem Cell 6:203-207.
  • Schroeder T. (2011). Long-term single-cell imaging of mammalian stem cells. Nature Methods 8:30-35.
  • Etzrodt M, Endele M, Schroeder T. (2014). Quantitative single-cell approaches to stem cell research. Cell Stem Cell 15:546-58.
  • Hoppe PS, Coutu DL, Schroeder T. (2014). Single-cell technologies sharpen up mammalian stem cell research. Nat Cell Biol. 16:919-27.
  • Hastreiter S, Schroeder T. (2016). Nanog dynamics in single embryonic stem cells. Cell Cycle 15:770-1.
  • Skylaki S, Hilsenbeck O and Schroeder T (2016) Challenges in long-term imaging and quantification of single cell dynamics Nature Biotechnology, 34: 1137-1144