I am interested in the mechanism of gene regulation in eukaryotes, which underlies processes like the adaptation of organisms to new environments or differentiation in multicellular organisms. In particular, I aim to understand the molecular basis for the function of transcription factors, ranging from target search to gene activation or repression, and the role that chromatin, especially histone dynamics, plays during gene regulation.

For this, I work on the eukaryotic model organism S. cerevisiae and combine cutting edge experimental techniques, like CRIPSR-Cas9 gene editing and Next-Generation-Sequencing, with computational data analysis. With the bigger picture in mind, potential projects in my lab will focus on diverse questions ranging from the evolution of transcription factors, over the role of spatial organization in gene regulation, to structure-function studies of chromatin remodelers.

If you are interested in Gene Regulation and Systems Biology in General, do not hesitate to contact me, I am always looking for motivated students to join the lab for Internships, B.SC Thesis or PhD projects.

• Jonas, F, Vidavski, M., Benuck, E., Barkai, N., Yaakov, G (2023). Nucleosome retention by histone chaperones and remodelers occludes pervasive DNA–protein binding. Nucleic Acids Research. 10.1093/nar/gkad615
• Dunjić, M., Jonas, F., Yaakov, G., More, R., Mayshar, Y., Rais, Y., Orenbuch, A.-H., Cheng, S., Barkai, N., and Stelzer, Y. (2023). Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells. Nature Communications 14, 1-19. doi:10.1038/s41467-023-39477-3
• Kumar DK*, Jonas F*, Jana T, Brodsky S, Carmi M, Barkai N.: “Complementary strategies for directing in vivo transcription factor binding through DNA binding domains and intrinsically disordered regions” Mol. Cell (2023, DOI: 10.1016/j.molcel.2023.04.002 )
• Jonas F*, Carmi M*, Krupkin B*, Steinberger J, Brodsky S, Jana T, Barkai N.: “The molecular grammar of protein disorder guiding genome-binding locations” Nucleic Acid Res. (2023, DOI: 10.1093/nar/gkad184)
• Yaakov G*., Jonas F*., Barkai N.: “Measurement of histone replacement dynamics with genetically encoded exchange timers in yeast” Nature Biotechnology (2021, DOI:10.1038/s41587-021-00959-8)
• Gera T.*, Jonas F.*, More R., Barkai N.: “Evolution of binding preferences among whole-genome duplicated transcription factors” Elife  (2022, DOI:10.7554/eLife.73225)
• Jonas F.*, Yaakov G.*, Barkai N.: “Rtt109 promotes nucleosome replacement ahead of the replicating fork” Genome Research (2022, DOI:10.1101/gr.276674.122)
• Carmon S.*, Jonas F.*, Barkai N., Schejter E., Shilo B.: “Generation and timing of graded responses to morphogen gradients” Development (2022, 10.1242/dev.199991)
• Frenkel N.*, Jonas F.*, Barkai N.: “Rtt109 slows replication speed by histone N-teminus acetylation” Genome Research (2021, DOI:10.1101/gr.266510.120)
• Jonas F., Soifert I, Barkai N: “A Visual Framework for Classifying Determinants of Cell Size” Cell Reports (2018, DOI: 10.1016/j.celrep.2018.11.087)
• Jonas F., Royle K., Aw R., Stan G., Polizzi K.:  “Investigating the consequences of asymmetric endoplasmic reticulum inheritance in Saccharomyces cerevisiae under stress using a combination of single-cell measurements and mathematical modelling.” Synth Syst Biotechnol. (2018. DOI:10.1016/j.synbio.2018.01.001)