Dept. of Systems Biology and Bioinformatics is a part of the University of Rostock, Germany Universität Rostock

Dr. Holger Hennig

Image: Dr. Holger Hennig

Research Interest

Short biography

I'm a research scientist at the Dept. of Systems Biology and Bioinformatics at the University of Rostock, Germany and an affiliate at the Imaging Platform at the Broad Institute of Harvard and MIT, USA. My main area of research is the analysis of cellular images in high-throughput with a focus on Imaging Flow Cytometry (IFC). Recently, we applied cutting-edge machine learning to develop label-free cell cycle analysis for high-throughput IFC [Blasi et al., Nature Communications (2016). Hennig et al., Methods (2017)]. Now, in several ongoing research projects on immune system cells, we study blood stem cell differentiation, and investigate diseases such as leukemia and severe allergies in clinical studies. We strive to advance precision medicine by applying the latest machine learning techniques, including deep learning, which is recently achieving impressive successes, to identify signatures of various disease states in the data.

Keywords: machine learning, deep learning, biomedical image analysis, imaging flow cytometry, systems medicine


27 publications in peer-reviewed journals. H-index: 12
View all publications (google scholar profile):

Selected Publications

  • J. Caicedo,…,H. Hennig,…, A.E. Carpenter. Data analysis strategies for image-based cell profiling. Nature Methods 14, 849 (2017) [download]
  • G. Steinhoff,…, H. Hennig,…, O. Wolkenhauer. Cardiac Function Improvement and Bone Marrow Response – Outcome Analysis of the Randomized PERFECT Phase III Clinical Trial of Intramyocardial CD133+ Application After Myocardial Infarction. EBioMedicine 22, 208-224 (2017) [download]
  • H. Hennig, P. Rees, T. Blasi, L. Kamentsky, J. Hung, D. Dao, A.E. Carpenter, and A. Filby. An open-source solution for advanced imaging flow cytometry data analysis using machine learning. Methods 112, 201 (2017) [download]
  • T. Blasi, H. Hennig, H.D. Summers, F.J. Theis, D. Davies, A. Filby, A.E. Carpenter, P. Rees. Label-free cell cycle analysis for high-throughput imaging flow cytometry. Nature Communications 7, 10256 (2016) [download]
  • Y.-M. Jeong, A. Samanta, H. Hennig, Z. Duanting, B. K. Agrawalla, M.-A. Bray, A. E. Carpenter, Y.-T. Chang. A novel lysosomal-targeted CDy11 probe for real-time live imaging of mitosis and proliferating cells. Chemistry and Biology 22, 299-307 (2015) [download]
  • H. Hennig. Synchronization in human musical rhythms and mutually interacting complex systems. PNAS 111, 12974-12979 (2014) [download]


  • Dr. Anne Carpenter, Director, Imaging Platform, Broad Institute of Harvard and MIT (I'm affiliated with the Broad Institute since 2013)
  • Prof. Paul Rees, Swansea University, Wales, UK
  • Prof. Huw Summers, Swansea University, Wales, UK 
  • Prof. Fabian Theis, Director, Institute of Computational Biology, Helmholtz Centre Munich, Germany
  • Dr. Andrew Filby, Director of Flow Cytometry Core Facility, Faculty of Medical Sciences, Newcastle University, UK

Awards and grants

  • Amnis Travel Stipend from Merck-Millipore (09/2016)
  • Postdoctoral Fellowship (DFG) for research at Harvard University. Grant no. HE 6312/1-2 (06/2012)
  • Postdoctoral Fellowship (DFG) for research at Harvard University. Grant no. HE 6312/1-1 (06/2011)
  • Research stipend from Boston University (05/2008 – 09/2008)
  • Otto-Haxel award from the University of Heidelberg, awarded for an outstanding diplom/master thesis in theoretical physics (07/2004)

Academic Background

Contact Details

Dept. of Systems Biology and Bioinformatics
Ulmenstrasse 69 (building 3, 3rd floor)
18057 Rostock, Germany
Room 403

phone: +49 381 498-7683
fax: +49 381 498-7572
mail: holger.hennig(at)