Publications

2010

• Heinemann, M. and Sauer, U. (2010) Systems biology of microbial metabolism. Current Opinion in Microbiology, In press.
• Kotte, O., Zaugg, J. B., and Heinemann M. (2010) Bacterial adaptation through distributed sensing of metabolic fluxes. Molecular Systems Biology, 6, 355.
• Kümmel, A., Ewald, J. C., Fendt, S.M., Jol, S., Picotti, P., Aebersold, R., Sauer, U., Zamboni, N., and Heinemann M. (2010) Differential glucose repression in common yeast strains in response to a HXK2 deletion. FEMS Yeast Research, In press.

2009

• de Graaf, A. A., Freidig, A.P., de Roos, B., Jamsheedi, N., Heinemann, M., Rullmann, J.A.C., Hall, K., Adiels, M., and van Ommen, B. (2009) Nutritional systems biology modeling: from molecular mechanisms to physiology (Review). PLoS Computational Biology, 5, e1000554.
• Cook, G. M., Berney, M., Gebhard, S., Heinemann, M., Cox, R. A., Danilchanka, O., and Niederweis, M. (2009) Physiology of mycobacteria (Review). Advances in Microbial Physiology, 55, 81-184.
• Kotte, O., and Heinemann, M. (2009) A divide–and–conquer approach to analyze underdetermined biochemical models.  Bioinformatics, 25, 519-525.

2008

• Herrgård, M.J., Swainston, N., Dobson, P., Dunn, W.B., Arga, K.Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M.,  le Novère, N., Li, P., Liebermeister, W., Mo, M.L., Oliveira, A.P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasić, I., Weichart, D., Brent, R., Broomhead, D.S.,  Westerhoff, H.V., Kırdar, B., Penttilä, M., Klipp, E., Palsson, B.Ø., Sauer, U., Oliver, S.G., Mendes, P., Nielsen, J., and Kell, D.B. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.  Nature Biotechnology, 26, 1155-1160.
• Amantonico, A., Oh, J.Y., Sobek, J., Heinemann, M., and Zenobi, R. (2008) Mass spectrometric method for analyzing metabolites in yeast with single cell sensitivity. Angewandte Chemie Int. Ed., 120,5462-5465.
• Zamboni, N., Kümmel, A., and Heinemann, M. (2008) anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. BMC Bioinformatics, 9, 199.

2007

• Hübscher, J., Jansen, A., Kotte, O., Schaefer, J., Majcherczyk, P.A., Harris, L.G., Bierbaum, G., Heinemann, M., and Berger-Bächi, B. (2007) Living with an imperfect cell wall: Compensation of femAB inactivation in Staphylococcus aureus . BMC Genomics, 8, 307.
• Sauer, U., Heinemann, M., and Zamboni, N. (2007) Getting closer to the whole picture. Science, 316, 550-551.

2006

• Kümmel, A., Panke, S., and Heinemann, M. (2006) Systematic assignment of thermodynamic constraints in metabolic network models. BMC Bioinformatics, 7, 512.
• Heinemann, M., and Panke, S. (2006) Synthetic biology – putting engineering into biology. Bioinformatics, 22, 2790-2799. 
• Seggewiß, J., Becker, K., Kotte, O., Eisenacher, M., Khoschkhoi Yazdi, M.R., Fischer, A., McNamara, P., Al Naham, N., Proctor, R., Peters, G., Heinemann, M., and von Eiff, C. (2006) Reporter metabolite analysis of transcriptional profiles of a Staphylococcus aureus strain with normal phenotype and its isogenic hemB mutant displaying the small colony variant phenotype. J. Bacteriol., 188, 7765-7777.
• Kümmel, A., Panke, S., and Heinemann, M. (2006) Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol. Syst. Biol., 2, 2006.0034.

2005

• Heinemann, M., Kümmel, A., Ruinatscha, R., and Panke, S. (2005) In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network.  Biotechnol. Bioeng., 92, 850-864.

Pubmed link to other publications