Jonathan J. Froehlich

Portrait of Jonathan J. Froehlich

I'm an experimental-computational scientist who builds scalable perturbation and functional-genomics systems to answer complex biological questions. Previously Postdoc at Systems Epigenetics Max Planck Institute for Molecular Genetics and PhD at Systems Biology of Gene Regulatory Elements MDC-BIMSB.

Research projects

Quantitative gene regulation in stem cells

I studied how gene regulatory DNA responds to graded Oct4 levels in mouse embryonic stem cells to determine features of dose-sensitivity.

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Parallelized mutagenesis of regulatory sequences in vivo

I developed parallel CRISPR-Cas9 editing to test >1,000 regulatory mutations in C. elegans, and discovered new interactions of gene regulatory sequences.

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Regulation of chromatin and heterochromatin

I established high-content screening and found signaling pathways that regulate heterochromatin organization.

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Side projects

Papers-to-table extracts structured information from scientific publications with local LLMs.

Experience

  1. Postdoctoral researcher
    Max Planck Institute for Molecular Genetics
  2. Dr. rer. nat.Molecular Biology
    Humboldt University Berlin
  3. Doctoral researcher
    MDC · Berlin Institute for Medical Systems Biology
  4. MScBiology
    Ludwig Maximilian University Munich
  5. Master’s student
    MPI of Immunobiology and Epigenetics
  6. Intern
    Ludwig Maximilian University Munich
  7. BScMolecular Biotechnology
    FH Campus Vienna
  8. Bachelor’s student
    MPI of Immunobiology and Epigenetics
  9. Intern
    MPI of Immunobiology and Epigenetics
  10. Intern
    Institute of Molecular Pathology Vienna
  11. Intern
    Leibniz Institute of Virology

Selected publications

  1. Till Schwaemmle, Gemma Noviello, Eleni Kanata, Jonathan J. Froehlich, Melissa Bothe, Aybuge Altay, Jade Scouarnec, Vivi-Yun Feng, Martin Vingron, Edda G. Schulz. Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus. Nature Structural & Molecular Biology, 2025.
  2. Jonathan J. Froehlich and Nikolaus Rajewsky. C. elegans gene regulatory alleles and reporter bashing studies. Micropublication Biology, 2023.
  3. Jonathan J. Froehlich*, Bora Uyar*, Margareta Herzog, Kathrin Theil, Petar Glažar, Altuna Akalin, Nikolaus Rajewsky. Parallel genetics of regulatory sequences using scalable genome editing in vivo. Cell Reports, 2021. *co-first.
  4. Jonathan J. Froehlich, Nikolaus Rajewsky, Collin Ewald. Estimation of C. elegans cell- and tissue volumes. Micropublication Biology, 2021.
  5. Sylvain Maenner, Marisa Müller, Jonathan J. Froehlich, Diana Langer, Peter B. Becker. ATP-dependent roX RNA remodeling by the helicase maleless enables specific association of MSL proteins. Molecular Cell, 2013.
  6. Silvia Dambacher, Wen Deng, Matthias Hahn, Dennis Sadic, Jonathan J. Froehlich, Alexander Nuber, Christian Hoischen, Stephan Diekmann, Heinrich Leonhardt, Gunnar Schotta. CENP-C facilitates the recruitment of M18BP1 to centromeric chromatin. Nucleus, 2012.