Simone Reber

Simone studied Molecular Biology and Biochemistry at the University of Heidelberg, the University of Washington and the Swiss Federal Institute of Technology in Zurich (ETHZ). She obtained her PhD at the University of Heidelberg. For her postdoctoral training Simone joined Tony Hyman's laboratory at the MPI of Molecular Cell Biology and Genetics supported by a fellowship from the Max Planck Society, where she started combining her long-standing interests in molecular cell biology with quantitative theoretical analysis. In 2014/2015 Simone was a fellow at the College for Life Sciences at Wissenschaftskolleg zu Berlin.

In 2015, Simone started her independent research group ‘Quantitative Biology’ at the IRI for the Life Sciences funded by the Excellence Initiative. The research in the lab is driven by the idea that physics-based conceptual approaches can help to understand and describe living systems complexity. The Reber lab takes an interdisciplinary approach by combining expertise in cell-free biochemistry, single molecule biophysics, advanced light microscopy, quantitative image analysis, and continuum mechanics. The long-term goal is to provide important insights into the physical principles that underlie a cell’s organization, which is likely to have important implications for its function and molecular origins of diseases.

Since October 2018 Simone is Professor of Biochemistry at the University of Applied Sciences Berlin.

 

Research

Deep learning for biological imaging & image analysis
(Biological imaging, image analysis and data visualization)

Selected Publications

  • Varun Kapoor , William G Hirst , Christoph Hentschel, Stephan Preibisch, Simone Reber
    (2019). MTrack: Automated Detection, Tracking, and Analysis of Dynamic Microtubules. Sci
    Rep. 2019 Mar 7;9(1):3794. doi: 10.1038/s41598-018-37767-1
  • Reusch S, Biswas A, and Reber S (2020). Affinity-Purification of Label-free Tubulins from Xenopus Egg Extracts. STAR Protocols 1, 100151. doi.org/10.1016/j.xpro.2020.100151
  • Hirst WG, Kiefer C, Schaeffer E, and Reber S (2020). In vitro Reconstitution and Imaging of Microtubule Dynamics by TIRF and IR Microscopy. STAR Protocols 1, 100177. doi.org/10.1016/j.xpro.2020.100177

Graduate School

  • Tobias Kletter
    Biology: Spindle morphometrics during neuronal development
    Imaging: Adaptive feedback microscopy
    Image analysis: object detection, pixel classification, morphological image analysis, particle
    tracking
  • Ella de Gaulejac
    Biology: Functional biochemical adaptation of tubulins
    Imaging: Total Internal Reflection Fluorescence (TIRF) Microscopy, Expansion microscopy (ExM)
    Image analysis: video tracking, object recognition, motion estimation
  • Dominik Fachet
    Biology: Plasmodium tubulin as a potential drug target in Malaria
    Imaging: Total Internal Reflection Fluorescence (TIRF) Microscopy, Expansion microscopy (ExM)
    Image analysis: video tracking, object recognition, motion estimation

Partners

Christian Tischer, Advanced Light Microscopy Facility (ALMF), EMBL Heidelberg
Stephan Preibisch, Janelia Farm Research Campus, USA

Infrastructure

Software:

  • MTrack (https://github.com/PreibischLab/MTrack)
  • spindle3d (https://github.com/tischi/spindle3d)