We currently have no open positions.

User guide contains unpublished material. Until final acceptance of the manuscript it is only available to the reviewers. Later, it can be accessed here without restrictions.


Publications in 2010 emerging with INRIA / IZBI – co-authors

  • A. Braeuning, Y. Singh, B. Rignall, A. Buchmann, S. Hammad, A. Othman, I.v. Recklinghausen, P. Godoy, S. Hoehme, D. Drasdo, J.G. Hengstler, M. Schwarz (2010) 
    Phenotype and growth behavior of residual β-catenin-positive hepatocytes in livers of β-catenin-deficient mice. Histochemistry and Cell Biology (Accepted)
  • Hoehme S and Drasdo D
    A cell-based simulation software for multicellular systems. Bioinformatics (in press) 
  • Krinner A., Hoffmann M., Loeffler M., Drasdo, D, and Galle J. (2010). 
    Individual fates of mesenchymal stem cells in vitro. BMC Systems Biology 4: 73. (IF 3.7) 
  • Hoehme, S., Brulport, M., Bauer, A., Bedawy, E., Schormann, W., Gebhardt, R., Zellmer, S., Schwarz, M., Bockamp, E., Timmel, T., G. Hengstler, J.G., and Drasdo, D. (2010). 
    Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration. PNAS. 107(23), 2010, 10371 -10376 (IF 9.4) 
  • S. Hoehme and D. Drasdo (2010). 
    Biomechanical versus nutrient control: what determines the growth dynamics of mammalian cell populations? Mathematical Population Studies
    Mathematical Population Studies, 1547-724X, Volume 17, Issue 3, 2010, 166–187.

Dipl. Biology. Géraldine Cellière

PhD Student

Research Group for Multicellular Systems Biology
Institut National de Recherche en Informatique et en Automatique (INRIA)
Equipe-projet MAMBA



Current and Former Research Interests:

I am interested in answering biological questions using appropriate mathematical models. My current work focuses on the investigation of ammonia detoxification during liver damage using an ODE-compartment model, and the metabolism of paracetamol using an agent-based model of a liver lobule combined with an ODE solver for internal cell metabolism and a transport/diffusion module for the blood flow.



Curriculum Vitae:


  • 2009 - 2010: "Classes préparatoire" in physics, maths, chemistry at Lycée Thiers, Marseille, France
  • 2007 - 2010: Engineering degree in Biology and Chemistry at Ecole Polytechnique, Palaiseau (Paris area), France
  • 2010 - 2012: Master degree in Biology at ETH Zürich, Switzerland
  • 2012 - 2015: PhD in computational biology at INRIA, Paris-Rocquencourt, France 

Work Experience

  • 2008 - 6 months: Military service in the Air Force, Aspirant grade (Base near Nice, France)
      • Managed a team of 11 people
      • Organized daily activities and evaluated my subordinates
  • 2010 - 6 months: Research internship in biochemistry, Helenius Lab and Peter Lab, ETH Zürich (Switzerland)
      • wet lab work: common genetics techniques, FACS and confocal microscopy
  • 2011 - 3+6 months: Research internship in computational biology, Iber Lab, ETH Zürich (Basel)
      • Developed and analyzed signaling pathways models (ODEs) and spatiotemporal models (PDEs) 
  • 2012 - 5 months: Product manager assistant, SoBios (start-up, Paris France)
      • Synthetized current knowledge on main signaling pathways in cells 
      • Defined requirements for a library of pathways in SBML format






Email: geraldine.celliere@inria.fr
Phone: +33 1 39 63 55 14




Dr. Hans Binder (Coordinator IZBI)
Dr. Jörg Galle
Dr. Stefan Höhme
Prof. Markus Löffler
Prof. Peter Stadler

The IZBI (www.izbi.uni-leipzig) was established as Central Facility of the University of Leipzig in 2001 and founded from a successful grant initiative in Bioinformatics by the German Research Society as one of five funded centers in Germany. Scientific director is Prof. Markus Löffler, chair of the Institute for Medical Informatics, Statistics and Epidemiology. The Center coordinates interdisciplinary research between the faculties of Informatics, Physics, Biology and Medicine of the University and other research institutes of the region (MPI MIS, MPI EVA, Helmholtz UfZ, Fraunhofer IZI). It has currently 10 permanent or long-term experienced researchers on PR, DR or CR-equivalent level and 25 PhD-students. The IZBI activities concentrate on: a) databases and data integration, b) tissue organisation and multi-cellular systems, c) image analysis and cell tracking, d) signal transduction and gene expression, e) evolution. The objective of group (a) is the flexible management and integration of diverse molecular biology data and annotation sources. Group (b) develops mathematical models for the predictive simulation of multicellular organisation processes on the base of experimental results. Group (c) provides an advanced image analysis methods. Group (d) works on modelling of transcriptional and signalling networks integrating functional genomics data and provides a service platform for gene expression analysis and functional annotation. Group (e) pursues projects to analyse genetic diversity and to use this knowledge for discerning the evolutionary relationships among species (i.e. phylogeny reconstruction), comparisons between humans and chimpanzees and understanding complexities of biological processes (e.g. evolution of genetic regulation. This group is lead by Prof. Peter Stadler, chair for bioinformatics and external scientific member of the Max-Planck Institute for Mathematics in the Sciences in Leipzig. 
The IZBI has an outstanding expertise in analyzing and modeling stem cell behavior and multi-cellular organization, processing high-throughput data and analyzing genetic diversity. On the directly tissue-related topics, IZBI and its partner, IMISE (www.imise.uni-leipzig.de) is co-ordinating or participating in several BMBF and EU-funded projects related to stem cell biology. 

PhD Students and PostDocs (IZBI):

  • Axel Krinner (PostDoc on BMBF-HepatoSys)
  • 1 PhD-student and 1 postdoc and one student which will be hired on BMBF-LungSys
  • 3 students/postdocs that will be hired on the BMBF-Virtual Liver grant


Dr. Marie-Odile Bristerau
Dr. Jean Clairambault
Dr. Marie Doumic-Jouffret
Dr. Dirk Drasdo (Coordinator INRIA)
Prof.  Benoit Perthame

BANG was has been created 5 years ago and is headed by Prof. Benoit Perthame, who also holds a chair position at University Pierre and Marie Currie. BANG has currently about 20 members, 8 of them permanent researchers at INRIA or Universities. Current topics of BANG are Geophysical flows, Biological growth processes, Modelling, Control, Agent-based models, Differential equations (ODEs and PDEs). Within the subject of biological systems, the topics pursued are: (i) Bacterial communities and their self-organization, (ii) prion dynamics, and (iii) Continuous and agent-based models of tumor and healthy tissue growth and organization (growth dynamics in time and space, cell cycle, circadian rhythms, PK-PD, therapeutic optimization in oncology, liver regeneration, developmental biology). The last topic includes cell cycle, circadian rhythms, PK-PD, therapeutic optimization in oncology, where the main goal is to understand several aspects of anticancer therapy in strong connection with medical teams (e.g. INSERM U 776, F. Leevi, Villejuif, for solid tumors; UMRs UPMC-INSERM 872,  J.-P. Marie, Paris, for leukaemias). Based on standard ODE or PDE models of cell proliferation, effects of circadian rhythms, toxicity on healthy cells, molecular aspects of drug effects (pharmacokinetics-pharmacodynamics) were included to optimize chemotherapy, and obtain a better understanding of the efficiency of chronotherapeutics. 
Quantitative agent (agent=single cell)-based models of tissues are developed to mimic tissue growth and regeneration phenomena quantitatively. This includes multi-scale models of tissues that link molecular concentrations of signal transduction or metabolic pathway components to cell states, cell properties and cell behavior, and eventual to the tissue phenotype. 
The BANG team is internationally recognized for the different research axes aforementioned; BANG-researchers participated or participate in several EU-projects (HYKE, M3CSTGT, BIOSIM, TEMPO, CANCERSYS, PASSPORT, NOTOX), and ANR-projects (Macbac, Toppaz, Method, Cosinus) and acquired positions from other competitive initiatives (e.g. Ecole doctorales etc). In his function as simultaneous member of IZBI Leipzig DD has further been PI within the BMBF-grants Hepatosys and is currently PI of the BMBF grants LungSys and Virtual Liver Network. Two axes are pursued within BANG/INRIA: one along method development including rigorous mathematical proofs. Another axis are mathematical model applications in close collaboration with various national and international experimental biological or clinical partners.

PhD Students (BANG / INRIA):
  • Chadha Chettaoui
  • Nick Jagiella
  • William Weens
  • Emanuele Leoncini