Projects and funding


Research in our group is generously supported by numerous funding initiatives. Our participation in several graduate research training schools and international collaborative projects is summarized below.



  • Computational Systems Biology

    Computational Systems Biology

    Funded by: DFG, GRK 1772/II

    Duration: 01.08.2015 - 31.01.2020

    CSB is a joint effort of the Humboldt-Universität zu Berlin, the Freie Universität Berlin, the Charité-Universitätsmedizin Berlin, the Max Planck Institute for Molecular Genetics, and the Max Delbrück Center for Molecular Medicine Berlin-Buch. Our goal is the development of new theoretical concepts and their application to current and future problems in cell biology.



    Julia Katharina Schlichting

    Andrea Auconi

  • ITZLI Institutspartnerschaft

    ITZLI Institutspartnerschaft

    Funded by: Alexander von Humboldt Foundation

    Duration: 01.01.2014 - 31.10.2017

    In this project we are trying to understand how the yeast, S. cerevisiae, progression in the cell cycle is influenced by the metabolic oscillations that arrise from the cell‘s temporal and spatial administration of the carbon source obtained as nutrient. Both metabolism and the cell division cycle are oscillating processes that are coupled in the cell. The coupling of oscillators can be represented in a mathematical model that must be fitted to experimental data in order to represent reality. Two metabolites are being used as a guide to model the metabolic dynamics in single cells: published data on NADH levels and measurments of ATP levels in our own lab through fluoresence microscopy.

    The project originated from an Institutspartnerschaft founded by the Alexander von Humboldt Foundation between the Klipp, Herrmann and Del Rio groups in Germany and Mexico.


    Paula Martinell Garcia

  • Junior research group: rxncon

    Junior research group: rxncon

    Funded by: BMBF, e:Bio Cellemental

    Duration: 01.05.2012 - 31.10.2017

    The complexity of cellular networks is an outstanding challenge for documentation, visualisation and mathematical modeling. In this project, we develop a new way to describe these networks that minimizes the combinatorial complexity and allows an automatic visualisation and export to mathematical models.



    Dr. Marcus Krantz

    Dr. Timo Lubitz

    Dr. Jesper Romers

    Dr. Magdalena Rother

    Ulrike Münzner

    Sebastian Thieme

    Mathias Wajnberg


  • LiSyM


    Funded by: BMBF

    Duration: 01.09.2016 - 31.12.2018

    LiSyM (Liver Systems Medicine) represents a research network of German centers and institutions, brought together by a 20 Million Euro funding program of the German Government, in which mathematicians, modelers, pharmacologists, molecular biologists and clinical scientists work together to develop a Systems Medicine approach to study early and advanced liver disease.

    The aim of this unique research program is to acquire and use new experimental data and data from existing data bases to build computational models that facilitate decision making at the patient's bedside and to predict the actions of new medicines in the treatment of metabolic liver disease. 



    Dr. Josch Konstantin Pauling

  • Protein Factory

    Protein Factory

    Funded by: Marie Skłodowska-Curie Innovative Training Network

    Duration: 01.01.2015 - 31.12.2018

    The ProteinFactory partnership builds new-generation platforms for bacterial protein secretion and trains a cohort of young scientists in the field of recombinant protein production.



    Ana Bulović

  • SFB 740

    SFB 740

    Funded by: DFG

    Duration: 01.01.2011 - 31.12.2014, 01.01.2015 - 31.12.2018

    Our Collaborative Research Centre (SFB 740) studies functional modules and is funded by the German Research Foundation (DFG). It was installed on January 1, 2007. The DFG granted the third four-year-funding period in November 2014. The SFB comprises 20 projects subdivided into five research areas. Participating institutions are the Charité Universitätsmedizin Berlin, the Freie Universität Berlin, the Technische Universität Berlin, the Max Delbrück Center for Molecular Medicine, the Leibniz-Institut für Molekulare Pharmakologie (FMP), and the Max Planck Institute for Molecular Genetics. 



    Severin Ehret

    Björn Goldenbogen


  • SymBioSys


    Funded by: European Union's Horizon 2020 research and innovation programme under grant agreement No 675585, Marie Curie ITN "SyMBioSys"

    Duration: 01.09.2015 - 31.08.2019

    The main objective of SyMBioSys is to train a new generation of innovative and entrepreneurial early-stage researchers (ESRs). SyMBioSys researchers will develop cutting-edge kinetic models for biological processes via systems engineering research and will exploit these for designing novel biotechnological applications. To achieve this, the ESRs projects will be integrated in such a way that all will collaboratively contribute to the building and usage of proper kinetic models of complex biological systems.



    Olufemi Bolaji

    Roman Rainer

  • SysToxChip


    Funded by: BMBF (031A303)

    Duration: 01.10.2014 - 31.03.2018

    The projects relates to the field of individualized drug safety evaluation and aims to use the methods of systems biology to develop and evaluate effective reporters embedded in diagnostic multiorgan microfluidic chips. Patient-specific induced pluripotent stem cell (iPS) technology is applied to explore liver dependent toxic effects of drugs on individual human tissues such as kidney cells. The developed technologies will be the basis for clinical-trial-on-a-chip approaches for drug and drug safety evaluation. At TBP we design and implement mathematical models for relevant signaling pathways, e.g. unfolded protein response, kidney metabolism, or DNA repair.


    Dr. Judith Wodke

    Adrian Zachariae

    Thomas Marschall

  • TRR 175

    TRR 175

    Funded by: DFG

    Duration: 01.07.2016 - 30.06.2020

    The photosystem II in Chlamydomonas reinhardtii consists of two core subunits, the D1 and the D2 subunit. The translation of these subunits is controlled via two independent pathways, which are both linked to the metabolic processes within the chloroplast. The translation of D1 is linked to the synthesis of Acetyl-CoA and therefore also to the fatty acid synthesis, while the translation of D2 is controlled by an enzyme which uses NADPH from the Oxidative Pentose Phosphate Pathway.
    The two main modulators here are NTRC, which controls the translation of the D2 subunit, and DLA2, which controls the translation of the D1 subunit. To better understand the role and activity of these two proteins, we want to build a kinetic ODE model of the system which governs the translation of subunits of Photosystem II.



    Maria Dost

  • 1


Finished Projects


Aquaglyceroporins Marie Curie Research Training Network:
Integrate Analysis of Aquaporin Structure and Function
11/2006 - 10/2010 homepage

BaSysBio Developing 'Systems Biology' Techniques to Study the Global Regulation of Gene Transcription in a Model Bacterium: Bacillus subtilis 11/2006 - 10/2010


CellComput Biological computation built on cell communication systems 03/2007 - 02/2011  

ColoNET A Systems Biology Approach for Integrating Molecular Diagnostics and Targeted Therapy in Colorectal Cancer 02/2009 - 01/2013  

DFG Sachbeihilfe Dr. Jannis Uhlendorf: Interaction of osmotic stress regulation and ion homeostasis in S. cerevisiae 10/2014 - 09/2017  

Drug-iPS Gene Regulation and Stem Cell Research 01/2009 - 12/2012  

Einstein Research Network Single Molecule RNA Biology - Dynamics and function of RNA from transcription to degradation 07/2013 - 07/2016  

ENFIN Enabling Systems Biology 10/2008 - 05/2011 homepage

EST Systems Biology Marie Curie Early Stage Training in Systems Biology: Mathematical Modeling of Aging Processes in Yeast 01/2005 - 12/2008 homepage

FinSysB Marie Curie Initial Training Network: Pathogenomics and Systems Biology of Fungal Infections - An Integrative Approach 01/2009 - 10/2012  

GerontoMitoSys Mitochondrial network of pathways in aging and lifespan control - a systems biology approach 01/2010 - 12/2012  

IMPRS International Max Planck Research School for Computational Biology and Scientific Computing 01/2005 - 12/2013  

IRTG International Research Training Group: Berlin - Boston - Kyoto. Genomics and Systems Biology of Molecular Networks

04/2006 - 09/2010

partially extended:

10/2010 - 05/2012


LGS Molecular Biophysics Leibniz Graduate School of Molecular Biophysics 01/2007 - 12/2014  

SFB 618 Collaborative Research Center for Theoretical Biology: Robustness, Modularity and Evolutionary Design of Living Systems 07/2009 - 06/2013 homepage

SysteMTb A Collaborative Project for the Establishment of a Systems Biology Framework to Understand Key Features of Mycobacterium Tuberculosis 04/2010 - 09/2014  

A systematic analysis of colorectal cancer
02/2013 - 06/2016

Translucent 1 Systems Biology of Micro Organisms: Gene Interaction Networks and Models of Cation Homeostasis in Saccharomyces cerevisiae  03/2007 - 02/2010  

Translucent 2 Modeling Ion Homeostasis in the Yeast Saccharomyces cerevisiae 05/2010 - 10/2013  

UNICELLSYS Eukaryotic Unicellular Organism Biology – Systems Biology of the Control of Cell Growth and Proliferation 04/2008 - 03/2013  


Systemvirologie von Influenza - Molekulare Signatur der permissiven Virusinfektion - Teilproject A 01/2013 - 12/2015  

YSBN The Yeast Systems Biology Network 11/2005 - 10/2008