Systems Biology

Gene Network Engineering

Group Structure

This group is part of the EMBL/CRG Research Unit in Systems Biology
Mark Isalan
Mireia Garriga, Carmen Agustin Pavon, Yolanda Schaerli, Manjunatha Kogenaru, Luis Diambra
Diego Barcena, Vivek Senthivel
Rebecca Baumstark, Maria Lluisa Gili


The primary aim of the group is to study the interactions between biological components with a view to having a predictive understanding of biological networks. Ultimately, we would like to be able to build functional gene networks that behave in the ways we would anticipate. To achieve this, the group has been structured to combine: (1) reconstructing small networks from the bottom-up (synthetic patterning networks), (2) studying large-scale networks from the top-down (bacterial shuffle networks) and (3) protein engineering for genome editing and network engineering.
Figure 1 Figure 1

Research Projects

  • A synthetic patterning system in 3D cell culture
    We designed a toolkit for engineering cell–cell communication networks in 3D cell culture (ACS Synthetic Biology, DOI: 10.1021/sb400053b, 2013). Using the MDCK cell line we were able to use secreted activators or repressors to control gene expression in neighbouring cells.
  • How many ways can you make a stripe?
    We have engineered stripe patterns in bacteria in response to a morphogen gradient, as in the classical “French Flag” paradigm of developmental pattern formation. A computational approach identified all possible different mechanisms of stripe formation, some not yet discovered in nature, which we then built synthetically (paper submitted).

Selected Publications

  1. Carvalho A, Barcena Menendez D, Senthivel VR, Zimmermann T, Diambra L and Isalan M.
    “Genetically Encoded Sender-Receiver System in 3D Mammalian Cell Culture.”
    ACS Synthetic Biology, 2013 Dec 20. [Epub ahead of print].
  2. Sanders PGT, Cotterell J, Sharpe J and Isalan M.
    “Transfecting RNA quadruplexes results in few transcriptome perturbations.”
    RNA Biology, 10(2):205-10 (2013).
  3. Schaerli Y and Isalan M.
    “Building synthetic gene circuits from combinatorial libraries: screening and selection strategies”
    Molecular Biosystems, 9(7):1559-1567(2013).
  4. Isalan M.
    “Zinc Fingers.”
    In: Encyclopedia of Biological Chemistry (Second Edition), pp. 575–579, Academic Press (2013).