De Bono, B. Vastrik, I., D’Eustachio, P., Schmidt, E., Gopinath, G., Croft, D., Gillespie, M., Jassal, B., Lewis, S., Matthews, L., Wu, G., Birney, E. and Stein, L. (2007) Reactome: An integrated expert model of human molecular processes and access toolkit, Journal of Integrative Bioinformatics (submitted).

Irit Gat-Viks and Ron Shamir. Refinement and expansion of signaling pathways: the osmotic response network in yeast. Genome Research 2007. 17(3):358-367. [Abstract]

Greenman et al. Patterns of somatic mutation in human cancer genomes. (2007) Nature, 7132:153-8. [Abstract]

Igor Ulitsky, Irit Gat-Viks and Ron Shamir. MetaReg: A tool for modeling, analysis and visualization of biological systems by using large-scale experimental data. Submitted.

Vastrik, I., D’Eustachio, P., Schmidt, E., Joshi-Tope, G., Gopinath, G., Croft, D., de Bono, B., Gillespie, M., Jassal, B., Lewis, S., Matthews, L., Wu, G., Birney, E. and Stein, L. (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biology, 8:R39. [Abstract]

Wierling, C., Maschke-Dutz, E., Klipp, E., Herwig, R., Lehrach, H. PyBioS - an object-oriented tool for modeling and simulation of cellular processes, submitted.

Wierling, C., Herwig, R., Lehrach H. (2007) Resources, Standards and Tools for Systems Biology. Briefings in Functional Genomics and Proteomics. In press.

Assmus, H., Herwig, R., Cho, K.H., Wolkenhauer, O. (2006) Understanding the dynamics of biological systems: roles in medical research. Expert Reviews in Molecular Diagnostics 6:891-902. [Abstract]

Borger S., Liebermeister W., Klipp E. (2006), Prediction of enzyme kinetic parameters based on statistical learning, Genome Informatics Series 17 (1).

Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir,A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks,Journal of Computational Biology. 2006, 13(2): 165-181. [Abstract]

Herwig, R., Lehrach H. (2006) Expression profiling of drug response - from genes to pathways. Dialogues in Clinical Neuroscience 8:283-293. [Abstract]

Liebermeister W., Klipp E. (2006), Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theoretical Biology and Medical Modelling 3:41 [Abstract]

Liebermeister W., Klipp E. (2006), Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data. Theoretical Biology and Medical Modelling 3:42 [Abstract]

Schmidt, E., Birney, E., Croft, D., de Bono, B., D’Eustachio, P., Gillespie, M., Gopinath, G., Jassal, B., Lewis, S., Matthews, L., Stein, L., Vastrik, I. and Wu., G. (2006) Reactome – a knowledgebase of biological pathways in R. Meersman, Z. Tari, P. Herrero et al. (Eds.): OTM Workshops 2006, LNCS 4277, pp. 710 - 719. © Springer-Verlag Berlin Heidelberg 2006 [Abstract]

Schulz M., Uhlendorf J., Klipp E., Liebermeister W. (2006), SBMLmerge, a system for combining biochemical network models, Genome Informatics Series 17 (1)

Schulz M. (2006), Dimension reduction of biochemical network models: implementation and comparison of different algorithms, BA thesis.

In German*: Wierling, C. (2006) PyBioS - ein Modellierungs- und Simulationssystem für komplexe biologische Prozesse. In Forschung und wissenschaftliches Rechnen. Beiträge zum Heinz-Billing Preis 2005 (Hrsg. K. Kremer, V. Macho), 69:53-71, Gesellschaft für wissenschaftliche Datenverarbeitung Göttingen (GWDG). Heinz-Billing Preis 2005

*This work was awarded 3^rd place at the Heinz Billing Award for the Advancement of Scientific Computation of the Max Planck Society 2005.

Wodke J. (2006), Qualitative Modelling of the Human Cell Cycle, MSc thesis

Adjaye, J., Huntriss, J., Herwig, R., BenKahla, A., Brink, T.C., Wierling, C., Hultschig, C., Groth, D., Yaspo, M.-L., Picton, H.M., Lanzendorf, S., Gosden, R.G., and Lehrach, H.(2005)Primary differentiation in the human blastocyst: Comparative molecular portraits of inner cell mass and trophectoderm cells. Stem Cells, in press.

Borger S., Liebermeister W., Klipp E. (2005), Distribution of a bifurcation parameter in a genetic network with uncertain parameters, Proceedings of the 4th workshop on computation of biochemical pathways and genetic networks, Logos-Verl., Berlin, 95-101.

Irit Gat-Viks, Amos Tanay, Daniela Raijman, and Ron Shamir. The factor graph network model for biological systems. . Proc. RECOBM 2005, pp. 31-47, Lecture Notes in Bioinformatics 3500, Springer, Berlin, 2005. [Abstract]

Joshi-Tope, G., Gillespie, M., Vastrik, I., D'Eustachio, P., Schmidt, E., de Bono, B., Jassal, B., Gopinath, G.R., Wu, G.R., Matthews, L., Lewis, S., Birney, E., Stein, L. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Research 33 Database Issue:D428-32. [Abstract]

Klipp, E., Herwig, R., Kowald, A., Wierling, C., and Lehrach H. (2005) Systems Biology in Practice: Concepts, Implementation and Application. Wiley-VCH, Weinheim. [Abstract]

Liebermeister W., Baur U., Klipp E. (2005), Biochemical network models simplified by balanced truncation, FEBS Journal, 272 (16) 4034 - 4043. [Abstract]

Liebermeister W. (2005), Dimension reduction by balanced truncation applied to a model of glycolysis, Proceedings of the 4th workshop on computation of biochemical pathways and genetic networks, Logos-Verl., Berlin, 21-28.

Liebermeister W. (2005), Predicting physiological concentrations of metabolites from their molecular structure, J. Comp. Biol 12 (10), 1307-1315. [Abstract]


W. Liebermeister (2005), Response to temporal parameter fluctuations in biochemical networks, J. Theor. Biol. 234, 423 [Abstract]

Liebermeister W., Klipp E. (2005), Biochemical networks with uncertain parameters, IEE Proc. Systems Biology 152 (3) 97-107 [Abstract]

Gat-Viks, I., Tanay, A., and Shamir, R. (2004) Modeling and Analysis of Heterogeneous Regulation in Biological Networks. Journal of Computational Biology 11: 1034-1049. [Abstract]

Hakenberg J., Schmeier S., Kowald A., Klipp E., and Leser U. (2004) Finding Kinetic Parameters Using Text Mining. OMICS: A Journal of Integrative Biology 8(2):131-152. Invited submission. Special Issue on Data Mining meets Integrative Biology – A Symbiosis in the Making. [Abstract]

Kahlem, P., Sultan, M., Herwig, R., Steinfath, M., Balzereit, D., Eppens, B., Saran, N.G., Pletcher, M.T., South, S.T., Stetten, G., Lehrach, H., Reeves. R.H., and Yaspo, M.-L. (2004) Transcript Level Alterations Reflect Gene Dosage Effects Across Multiple Tissues in a Mouse Model of Down Syndrome. Genome Research, 14:1258-1267. [Abstract]

Schmeier, S., Hakenberg, J., Kowald, A., Klipp, E. and Leser, U. (2003) Text Mining for Systems Biology Using Statistical Learning Methods. Proc 3. Workshop AKKD, Karlsruhe, Germany [Abstract]

PyBioS:http://pybios.molgen.mpg.de/Pybios

Metabolic network toolbox: http://www.molgen.mpg.de/~lieberme/pages/mnt.html

MetaReg: http://www.cs.tau.ac.il/~rshamir/metareg/

SemanticSBML: http://sysbio.molgen.mpg.de/sbmlmerge