TY  - JOUR
A1  - Steuer, Ralf
A1  - Gross, Thilo
A1  - Selbig, Joachim
A1  - Blasius, Bernd
T1  - Structural kinetic modeling of metabolic networks
JF  - Proceedings of the National Academy of Sciences of the United States of America
N2  - To develop and investigate detailed mathematical models of metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, kinetic modeling is still often severely hampered by inadequate knowledge of the enzyme-kinetic rate laws and their associated parameter values. Here we propose a method that aims to give a quantitative account of the dynamical capabilities of a metabolic system, without requiring any explicit information about the functional form of the rate equations. Our approach is based on constructing a local linear model at each point in parameter space, such that each element of the model is either directly experimentally accessible or amenable to a straightforward biochemical interpretation. This ensemble of local linear models, encompassing all possible explicit kinetic models, then allows for a statistical exploration of the comprehensive parameter space. The method is exemplified on two paradigmatic metabolic systems: the glycolytic pathway of yeast and a realistic-scale representation of the photosynthetic Calvin cycle.
KW  - systems biology
KW  - computational biochemistry
KW  - metabolomics
KW  - metabolic regulation
KW  - biological robustness
Y1  - 2006
U6  - https://doi.org/10.1073/pnas.0600013103
SN  - 0027-8424
SN  - 1091-6490
VL  - 103
IS  - 32
SP  - 11868
EP  - 11873
PB  - National Academy of Sciences
CY  - Washington
ER  - 
TY  - JOUR
A1  - Catchpole, Gareth
A1  - Platzer, Alexander
A1  - Weikert, Cornelia
A1  - Kempkensteffen, Carsten
A1  - Johannsen, Manfred
A1  - Krause, Hans
A1  - Jung, Klaus
A1  - Miller, Kurt
A1  - Willmitzer, Lothar
A1  - Selbig, Joachim
A1  - Weikert, Steffen
T1  - Metabolic profiling reveals key metabolic features of renal cell carcinoma
JF  - Journal of cellular and molecular medicine : a journal of translational medicine
N2  - Recent evidence suggests that metabolic changes play a pivotal role in the biology of cancer and in particular renal cell carcinoma (RCC). Here, a global metabolite profiling approach was applied to characterize the metabolite pool of RCC and normal renal tissue. Advanced decision tree models were applied to characterize the metabolic signature of RCC and to explore features of metastasized tumours. The findings were validated in a second independent dataset. Vitamin E derivates and metabolites of glucose, fatty acid, and inositol phosphate metabolism determined the metabolic profile of RCC. alpha-tocopherol, hippuric acid, myoinositol, fructose-1-phosphate and glucose-1-phosphate contributed most to the tumour/normal discrimination and all showed pronounced concentration changes in RCC. The identified metabolic profile was characterized by a low recognition error of only 5% for tumour versus normal samples. Data on metastasized tumours suggested a key role for metabolic pathways involving arachidonic acid, free fatty acids, proline, uracil and the tricarboxylic acid cycle. These results illustrate the potential of mass spectroscopy based metabolomics in conjunction with sophisticated data analysis methods to uncover the metabolic phenotype of cancer. Differentially regulated metabolites, such as vitamin E compounds, hippuric acid and myoinositol, provide leads for the characterization of novel pathways in RCC.
KW  - kidney cancer
KW  - metabolism
KW  - metabolomics
KW  - metastasis
Y1  - 2011
U6  - https://doi.org/10.1111/j.1582-4934.2009.00939.x
SN  - 1582-1838
VL  - 15
IS  - 1
SP  - 109
EP  - 118
PB  - Wiley-Blackwell
CY  - Malden
ER  - 
TY  - JOUR
A1  - Lisec, Jan
A1  - Römisch-Margl, Lilla
A1  - Nikoloski, Zoran
A1  - Piepho, Hans-Peter
A1  - Giavalisco, Patrick
A1  - Selbig, Joachim
A1  - Gierl, Alfons
A1  - Willmitzer, Lothar
T1  - Corn hybrids display lower metabolite variability and complex metabolite inheritance patterns
JF  - The plant journal
N2  - We conducted a comparative analysis of the root metabolome of six parental maize inbred lines and their 14 corresponding hybrids showing fresh weight heterosis. We demonstrated that the metabolic profiles not only exhibit distinct features for each hybrid line compared with its parental lines, but also separate reciprocal hybrids. Reconstructed metabolic networks, based on robust correlations between metabolic profiles, display a higher network density in most hybrids as compared with the corresponding inbred lines. With respect to metabolite level inheritance, additive, dominant and overdominant patterns are observed with no specific overrepresentation. Despite the observed complexity of the inheritance pattern, for the majority of metabolites the variance observed in all 14 hybrids is lower compared with inbred lines. Deviations of metabolite levels from the average levels of the hybrids correlate negatively with biomass, which could be applied for developing predictors of hybrid performance based on characteristics of metabolite patterns.
KW  - heterosis
KW  - Zea mays
KW  - metabolomics
Y1  - 2011
U6  - https://doi.org/10.1111/j.1365-313X.2011.04689.x
SN  - 0960-7412
VL  - 68
IS  - 2
SP  - 326
EP  - 336
PB  - Wiley-Blackwell
CY  - Malden
ER  -