Heike Siebert

A work in progress...

(Working on something more meaty and pretty... from time to time)

Heike Siebert
DFG-Research Center Matheon
Freie Universität Berlin
FB Mathematik und Informatik
Arnimallee 7
Room 103
D-14195 Berlin
Germany
Tel: +49-30-838-75862
Fax: +49-30-838-75869
e-mail: siebert at mi.fu-berlin.de


CV
Research Interests
Cooperations
Teaching
Publications

CV

08.10.1976	Born in Wilhelmshaven
07.1988 - 06.1995	Mariengymnasium Jever
09.1995 - 02.1996	Internship at the Alfred Wegener Institute for Polar and Marine Research in Bremerhaven
04.1996 - 08.2002	Study of mathematics and biology at the Christian-Albrechts-Universität Kiel
09.2002 - 02.2005	Scholarship from the German-Israeli Foundation for Scientific Research and Development,
	Christian-Albrechts-Universität Kiel,
	PhD in mathematics in December 2004
05.2005 - 03.2012	Research assistant in the group Mathematics in Life Sciences of Alexander Bockmayr at FU Berlin, Matheon member belonging to project A18
09.2008 - 10.2008	Research Fellow at the Statistical and Applied Mathematical Sciences Institute (SAMSI), N.C., USA
02.2012	Habilitation in mathematics at Freie Universität Berlin
03.2012	Professor for applied mathematics at FU Berlin, Head of the Discrete Biomathematics group, Matheon project Mathematical Systems Biology (A18) and the BMBF project MoSTNet

Research Interests

Discrete and hybrid modeling of biological regulatory networks (have a look here)


logical modeling capturing essential structural and dynamical features of a given system based on qualitative data
discrete iteration analyzing complex behavior of regulatory networks using finite dynamical systems
graph theoretical and algebraic methods modularization and classification of regulatory networks based on structural and dynamical properties
hybrid modeling approaches discrete/continuous methods, stochastic aspects

Dynamics of complex and uniformly quasiregular mappings

My first love in mathematics: beautiful theorems, beautiful proofs, beautiful pictures (take a look)

Cooperations

Here you find some of the people I have the pleasure of working with outside of my group at FU.

Alexander Heyl from Applied Genetics Institute at FU Berlin

modeling cytokinin response network of A. thaliana

Christine Sers from Institute of Pathology of Charité Berlin

modeling oncogenic RAS signaling

The former Marseille group, Denis Thieffry (now at ENS Paris), Claudine Chaouyia (now at Instituto Gulbenkian de Ciência in Portugal) and Élisabeth Remy (still at Luminy, yay)

functionality of network modules, compact representations of discrete dynamics

The BioInfo-Team at Nice Sophia Antipolis

Hybrid discrete/continuous modeling methods

Brandy Stigler from Southern Methodist University, Dallas

polynomial dynamical systems, reverse engineering

Susanna Röblitz from ZIB, Berlin

combining continuous and discrete modeling approaches

The Computational Systems Biochemistry group at Charité Berlin

combining discrete metabolic and regulatory models

Teaching

Courses in mathematics and bioinformatics at FU Berlin (for a list of courses offered by members of the group Discrete Biomathematics go here)

Interested in writing a thesis in discrete biomathematics? Just come talk to me.

Publications

Shahrad Jamshidi, Heike Siebert and Alexander Bockmayr,
Preservation of dynamic properties in qualitative modeling frameworks for gene regulatory networks,
Biosystems, to appear.

Therese Lorenz, Heike Siebert and Alexander Bockmayr,
Analysis and characterization of asynchronous state transition graphs using extremal states,
Bull. Math. Biol., (Online First) 2012. (doi)

Hannes Klarner, Adam Streck, David Safránek, Juraj Kolcák and Heike Siebert,
Parameter identification and model ranking of Thomas networks,
in Proceedings of the 10th International Conference on Computational Methods in Systems Biology, CMSB'12,
London, England, LNCS, pages 207-226, 2012. (doi)

Hannes Klarner, Heike Siebert and Alexander Bockmayr,
Time series dependent analysis of unparametrized Thomas networks,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(5), 1338 - 1351, 2012. (doi)

Shahard Jamshidi, Heike Siebert and Alexander Bockmayr,
Comparing discrete and piecewise affine differential equation models of gene regulatory networks,
Information Processing in Cells and Tissues, IPCAT 2012, Cambridge, UK, LNCS 7223, 17-24, 2012. (doi)

Hannes Klarner, Heike Siebert and Alexander Bockmayr,
Parameter inference for asynchronous logical networks using discrete time series,
in Proceedings of the 9th International Conference on Computational Methods in Systems Biology, CMSB'11, Paris, France, ACM, NY, USA, pages 121-130, 2011. (doi)

Heike Siebert,
Analysis of discrete bioregulatory networks using symbolic steady states,
Bull. Math. Biol., 73 (4): 873-898, 2011. (doi) (Preprint)

Sven Twardziok, Heike Siebert and Alexander Heyl,
Stochasticity in reactions: a probabilistic Boolean modeling approach,
in Proceedings of the 8th International Conference on Computational Methods in Systems Biology, CMSB'10,
Trento, Italy, ACM, NY, USA, pages 76-85, 2010. (doi) (Preprint)

Heike Siebert,
Dynamical and structural modularity of discrete regulatory networks,
in Computational Models for Cell Processes, CompMod 2009, Eindhoven, Netherlands, volume 6 of EPTCS, pages 109-124, 2009. (arXiv)

Heike Siebert,
Deriving behavior of Boolean bioregulatory networks from subnetwork dynamics,
Math. Comput. Sci., 2(3):421-442, 2009. (doi)

Heike Siebert,
Local Structure and Behavior of Boolean Bioregulatory Networks,
in Algebraic Biology, AB 2008, Castle of Hagenberg, Austria, volume 5147 of LNCS, pages 185-199, Springer, 2008. (doi)

Heike Siebert and Alexander Bockmayr,
Temporal constraints in the logical analysis of regulatory networks,
Theoret. Comput. Sci., 391(3): 258-275, 2008. (doi)

Heike Siebert and Alexander Bockmayr,
Context sensitivity in logical modelling with time delays,
in Computational Methods in Systems Biology, CMSB 2007, Edinburgh, Scotland, volume 4695 of LNCS, Springer, 2007. (doi)

Heike Siebert and Alexander Bockmayr,
Relating attractors and singular steady states in the logical analysis of bioregulatory networks,
in Algebraic Biology, AB 2007, Castle of Hagenberg, Austria, volume 4545 of LNCS, pages 36-50, Springer, 2007. (doi)

Heike Siebert and Alexander Bockmayr,
Incorporating time delays into the logical analysis of gene regulatory networks,
in Computational Methods in Systems Biology, CMSB 2006, Trento, Italy, volume 4210 of LNBI, pages 169-183. Springer, 2006. (doi)

Heike Siebert,
Fixed points and normal families of quasiregular mappings,
J. Analyse Math. 98 (2006), 145-168. (doi, Preprint at CAU-Reports )

Miscallaneous

Heike Siebert,
Logic-based modeling in systems biology,
Habilitationsschrift, FU Berlin, 2011 (Habil)

Attila Csikasz-Nagy et al.
Analyzing various models of circadian clock and cell cycle coupling,
in Formal Methods in Molecular Biology, number 09091 of Dagstuhl Seminar Proceedings, 2009.
(DROPS)

Heike Siebert.
Symbolic steady states and dynamically essential subnetworks of discrete regulatory networks,
in Formal Methods in Molecular Biology, number 09091 of Dagstuhl Seminar Proceedings, 2009. (DROPS)

Heike Siebert.
Chaos bei den Robotern,
in Besser als Mathe, Eds. M. Grötschel, B. Lutz-Westphal, K. Biermann, Vieweg 2009. (book)

Fixpunkte und normale Familien quasiregulärer Abbildungen,
Dissertation, CAU Kiel, 2004 (E-Diss)

Vergrabene Komponenten der Juliamenge ganzer transzendenter Funktionen,
Diplomarbeit, CAU Kiel, 2002.