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Dr. Daniel Ibrahim

Anschrift:BIH Center for Regenerative Therapies
Augustenburger Platz 1

13353 Berlin
Telefon:030 450 569147

Research focus

The precise control of gene expression underlies all cell differentiation during an organism’s life. The information regulating gene expression is encoded in cis-regulatory elements (aka enhancers), short stretches of DNA that are bound by transcription factors, which lie somewhat randomly skattered in the genomic area surrounding the target gene. We are interestend in all aspects related to this process.

Is the position of the enhancer relevant for its function? How does the enhancer identify it’s target gene? How do enhancers coopereate with each other? What is the influence of the surrounding DNA – the inter-enhancer­sequence – on its function? 

We investigate these questions through systematic genome engineering. We create specific mutations in the genome and then study how they alter expression level, pattern, or any other aspect of gene regulation. To do so, we apply cutting-edge functional genomic and epigenetic analyses in cell types and tissues of clinical relevance.

A synthetic approach to studying gene regulation

Our strength is a synthetic biology derived workflow to studying gene regulation. Through combination of methods from microbiology with integrase-based genome engineering for mESCs and human iPSCs we are able to synthesize any DNA sequences of dozens to hundreds of kb and integrate them site-specific into the mESCs and human iPSCs. By combining this genome engineering approach with cell, organoid, and in vivo model systems we characterize and investigate how gene regulatory information is encoded in the regulatory genome.

Models and applications

We study gene regulation in mESCs, mouse embryos and cell differentiation models (NPCs), as well as human iPSCs and iPSC-derived organoids. We use these models to understand how cell type specific gene expression patterns and expression levels are encoded in genomic DNA sequences. 

Together with our colleagues at the Berlin Institute of Health, we apply this knowledge to elucidate disease pathomechanisms, and at the same time develop technologies that lay the foundation for future gene and cell therapies.

Selected publications


Individual research projects

Team members

  • Milan Antonovic, PhD Student
  • Blanka Majchrzycka, PhD Student
  • Andreas Magg, PhD Student
  • Hannah Wieler, PhD Student
  • Mikie Phan, PhD Student
  • Ania Pitas, MSc Student


  • Alexandra Despang, PhD Student
  • Salaheddne Ali, MSc Student
  • Henrike Sczakiel, Clinician Scientist
  • Vinzenz May, MSc Student