Christoph Kaleta

Address

Research Group Theoretical Systems Biology
Friedrich-Schiller-Universität Jena
Raum 15N10
Leutragraben 1
D-07743 Jena
Deutschland
Phone: +49-3641-949590
Fax: +49-3641-946452
Email:

Welcome to my homepage!


Christoph Kaleta

Current Position

since July 2011 Juniorprofessor (Assistant professor) of Theoretical Systems Biology at
the School of Biology and Pharmacy of the University of Jena

Education

March 2010 Ph.D. thesis "summa cum laude" entitled "Analysis of Large-Scale Metabolic Networks: Organization Theory,
Phenotype Prediction and Elementary Flux Patterns" under the supervision of Prof. Dr. Stefan Schuster
2008: Diploma thesis "Inference of Gene Regulatory Networks in Escherichia coli using
Directed Information" in the group of Reinhard Guthke at the Hans-Knöll-Institute, Jena.
2003 - 2008: Studies in Bioinformatics

Former Positions

04/2010 - 06/2011: PostDoc in the department of bioinformatics (Prof. Stefan Schuster)
10/2008 - 03/2010: Ph.D. student in the department of bioinformatics (Prof. Stefan Schuster)
2005 - 2008: Student assistant in the Biosystems Analysis Group
09/2006 - 03/2007: Internship at the IBISC, Evry, France
in the group of Jean-Louis Giavitto

Research

  • Analysis of metabolic networks
  • Integrative analysis of high-throughput experimental data (transcriptomic, fluxomic, metabolomic) in the context of metabolic networks
  • Inference of gene regulatory networks
  • Elucidation of global principles in the regulation of metabolic networks using optimality principles
  • Development of theoretical methods aimed at the improvement of microbial production sys- tems (production of amino acids and proteins)
  • Algorithm engineering

Interests

Analysis of metabolic and regulatory networks
Understanding living systems from any perspective (biology, artifical life, etc.)
Synthetic Biology

Publications

2011

A. Göhler, Ö. Kökpinar, W. Schmidt-Heck, R. Geffers, R. Guthke, U. Rinas, S. Schuster, K. Jahreis, C. Kaleta (2011)
More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli
BMC Syst. Biol. accepted.

F. Wessely, M. Bartl, R. Guthke, P. Li, S. Schuster, C. Kaleta (2011)
Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs
Molecular Systems Biology 7:515.

C. Kaleta, L.F. de Figueiredo, S. Werner, R. Guthke, M. Ristow, S. Schuster (2011)
In silico evidence for gluconeogenesis from fatty acids in humans
PLoS Comp. Biol. 7(7), e1002116.

S. Schuster, L.F. de Figueiredo, A. Schroeter, C. Kaleta (2011)
Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach.
BioSystems 105(2), 147-53.

C. Kaleta, L.F. de Figueiredo, I. Heiland, S. Klamt, S. Schuster (2011)
Special issue: Integration of OMICs datasets into metabolic pathway analysis.
BioSystems 105(2), 107-8.

G. Beuster, K. Zarse, C. Kaleta, R. Thierbach, M. Kiehntopf, P. Steinberg, S. Schuster, M. Ristow (2011)
Inhibition of alanine aminotransferase (ALAT) in silico and in vivo promotes mitochondrial metabolism to impair malignant growth.
Journal of Biological Chemistry 286(25), 22323-30.

2010

K. Bohl, L.F. de Figueiredo, O. Hädicke, S. Klamt, C. Kost, S. Schuster, C. Kaleta (2010)
CASOP GS: Computing intervention strategies targeted at production improvement in genome-scale metabolic networks
German Conference on Bioinformatics 2010, Braunschweig.

C. Kaleta, A. Göhler, S. Schuster, K. Jahreis, Reinhard Guthke, S. Nikolajewa (2010)
Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis
BMC Systems Biology, 4:116.

S. Schuster, L.F. de Figueiredo, C. Kaleta (2010)
Predicting novel pathways in genome-scale metabolic networks
Biochemical Society Transactions 38: 1202-1205.

M. Bartl, M. Kötzing, C. Kaleta, S. Schuster, P. Li (2010)
Just-in-time activation of a glycolysis inspired metabolic network - solution with a dynamic optimization approach.
Proc. 55nd International Scientific Colloquium. 2010. Ilmenau, Germany.

F. Centler, C. Kaleta, P. S. di Fenizio, P. Dittrich (2010)
A parallel algorithm to compute chemical organizations in biological networks
Bioinformatics, 26(14):1788-9.

C. Kaleta, D. Kenanov, A. Petzold, C. Hoischen, S. Diekmann, R. Siddiqui, S. Schuster (2010)
Theoretical study of lipid biosynthesis in wild type Escherichia coli and in a protoplast-type L-form using elementary flux mode analysis
FEBS Journal, 277(4):1023-34.

2009

L. F. de Figueiredo, S. Schuster, C. Kaleta, D. A. Fell (2009)
Response to comment on 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'
Bioinformatics, 25(24):3330-1.

L. F. de Figueiredo, A. Podhorski, A. Rubio, C. Kaleta, J. E. Beasley, S. Schuster, F. J. Planes (2009)
Computing the shortest elementary flux modes in genome-scale metabolic networks
Bioinformatics, 25 (23):3158-3165.

C. Kaleta, L. F. de Figueiredo, J. Behre, S. Schuster (2009)
EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks.
In I. Grosse, S. Neumann, S. Posch, F. Schreiber, P. Stadler (editors), Lecture Notes in Informatics - Proceedings , volume P-157, Gesellschaft für Informatik, Bonn 2009, pp 179-189.

C. Kaleta, L. F. de Figueiredo, S. Schuster (2009)
Can the Whole Be Less Than the Sum of its Parts? Pathway Analysis in Genome-Scale Metabolic Networks Using Elementary Flux Patterns
Genome Research, 19 (10), 1872-83.

C. Kaleta, Stephan Richter, P. Dittrich (2009)
Using Chemical Organization Theory for Model-Checking
Bioinformatics, 25 (15), 1955-22.

C. Kaleta, L.F. de Figueiredo, S. Schuster (2009)
Detecting Metabolic Conversions in Genome-Scale Metabolic Networks on the Basis of Elementary Flux Patterns in Subnetworks.
In I. Troch and F. Breitenecker, editors, Proceedings of the Vienna Conference on Mathematical Modelling, volume 2 of ARGESIM Reports, pp 748-759.

L.F. de Figueiredo, S. Schuster, C. Kaleta, D. A. Fell (2009)
Can sugars be produced from fatty acids? A test case for pathway analysis tools
Bioinformatics, 25 (1), 152-158.

2008

C. Kaleta, F. Centler, P. S. di Fenizio, P. Dittrich (2008)
Phenotype prediction in regulated metabolic networks
BMC Systems Biology, 2, 37.

F. Centler, C. Kaleta, P. S. di Fenizio, P. Dittrich (2008)
Computing Chemical Organizations in Biological Networks
Bioinformatics, 24(14), 1611 - 1618.

2007

R. Schwarz, C. Liang, C. Kaleta, M. Kühnel, E. Hoffmann, S. Kuznetsov, M. Hecker, G. Griffith, S. Schuster and T. Dandekar (2007)
Integrated network reconstruction, visualization and analysis using YANAsquare.
BMC Bioinformatics, 8, 313.

2006

C. Kaleta, F. Centler, P. Dittrich (2006)
Analyzing Molecular Reaction Networks: From Pathways to Chemical Organizations
Molecular Biotechnology, 34(2): 117-123.

Book Chapters

S. Schäuble, S. Schuster, C. Kaleta (2011)
Hands-on metabolism: Analysis of complex biochemical networks using elementary flux modes
Methods in Systems Biology- MIE Volume 500, in press

J. Behre, L. F. de Figueiredo, S. Schuster, C. Kaleta (2011)
Detecting structural invariants in metabolic networks.
Methods in Molecular Biology, in press

C. Kaleta (2010)
From Artificial Chemistry to Systems Biology: Software for Chemical Organization Theory
A. Adamatzky and M. Komosinski (eds.), Artificial Life Models in Software Vol. II, Springer, in print.