Magnusson E.B., Halldorsson S., Fleming R.M.T. and Leosson K., Real-time optical pH measurement in a standard microfluidic cell culture system, Biomedical Optics Express, Vol. 4, Issue 9, pp. 1749-1758 (2013)
We show that by careful calibration it is possible to measure pH within microfluidic chambers with high accuracy and precision, using a direct single-pass measurement of light absorption in a commercially available phenol-red-containing cell culture medium.
Noor, E., Haraldsdóttir, H.S., Milo, R., Fleming, R.M.T., Consistent Estimation of Gibbs Energy Using Component Contributions, PLOS Computational Biology doi: 10.1371/journal.pcbi.1003098
We provide the full framework and source code for deriving estimates of standard reaction Gibbs energy, as well as confidence intervals, and believe this will facilitate the wide use of thermodynamic data for a better understanding of metabolism.
Sahoo, S., Thiele, I., ''Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells'', Human Mol Genet, In press
The impact of diet and altered genetic backgrounds on human metabolism may be studied by using computational modeling.
Edwards, L.M., Thiele, I., "Applying systems biology methods to the study of human physiology in extreme environments", Extreme Physiology & Medicine, 2:8. 2013
We propose that, in practice, systems biology rests on three pillars: computation, the omics disciplines and repeated experimental perturbation of the system of interest.
Thiele, I., Swainston, N., Fleming, R.M.T., et al. ''A community-driven global reconstruction of human metabolism'', Nat Biotech, doi:10.1038/nbt.2488 (2013).
Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling.
Aurich MK, Thiele I (2012) Contextualization Procedure and Modeling of Monocyte Specific TLR Signaling. PLoS ONE 7(12)
COBRA methods have been applied to investigate tissue-specific metabolism using omics data integration. In this study, we present ihsTLRv2, an updated TLR signaling network accounting for the association of 314 genes with 558 network reactions.
Rolfsson, O., Paglia, G., Magnusdottir, M., Palsson, B. O., Thiele, I., "Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity", Biochem Journal, Accepted (2012).
We employed a computational approach to identify human metabolites, whose metabolism is incomplete on the basis of their detection in humans...
Heinken, A., Sahoo, S., Fleming, R. M. T., Thiele, I., "Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut", Gut Microbes, 4(1):1-13 (2013).
In this study, we assembled and validated a genome-scale metabolic reconstruction of Bacteroides thetaiotaomicron (iAH991)...
Sahoo, S. ,Franzson, L., Jonsson, J.J., Thiele, I., "A compendium of inborn errors of metabolism mapped onto the human metabolic network.", Mol BioSyst, 2012.
Many IEMs are screened for in neonates through metabolomic analysis of dried blood spot samples. To enable the mapping these data onto the published human metabolic reconstruction, we added missing reactions and pathways.