http://dx.doi.org/10.1364/BOE.4.001749

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.

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003098

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.

http://hmg.oxfordjournals.org/content/early/2013/03/27/hmg.ddt119.full

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.

http://www.extremephysiolmed.com/content/2/1/8/abstract

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.

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2488.html

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.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049978

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.

http://www.biochemj.org/bj/imps/abs/BJ20120980.htm

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...

http://www.landesbioscience.com/journals/gutmicrobes/article/22370/?show_full_text=true

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)...

http://pubs.rsc.org/en/content/articlelanding/2012/mb/c2mb25075f

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.

slideshow 1slideshow 2slideshow 3slideshow 4
 http://dx.doi.org/10.1364/BOE.4.001749

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.

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003098

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.

http://hmg.oxfordjournals.org/content/early/2013/03/27/hmg.ddt119.full

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.

http://www.extremephysiolmed.com/content/2/1/8/abstract

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.

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2488.html

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.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049978

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.

http://www.biochemj.org/bj/imps/abs/BJ20120980.htm

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...

http://www.landesbioscience.com/journals/gutmicrobes/article/22370/?show_full_text=true

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)...

http://pubs.rsc.org/en/content/articlelanding/2012/mb/c2mb25075f

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.

Photosynthetic Micro-Algae

The convergence of light-emitting diode technology, photobioreactor design, algal biotechnology and low energy processing costs make biological fixation of this CO2 into fine chemicals feasible. The Center for Systems Biology is working on projects that are aimed at:

  1. determining the key performance characteristics of a core unit of a photobioreactor-based factory,
  2. designing and initiating scale-up of these units into versatile modules,
  3. determining the spectrum of algal strains that can be cultivated with this system.

 

Human Metabolism

Metabolism is a foundational process in all living cells. In fact, the ability to metabolize is considered as one of the criteria for being considered a living organism. Metabolism is directly or indirectly involved in essentially all cellular functions and is implicated in all major human disease states. With the state of the annotation of the human genome, it has been possible to perform an initial reconstruction of the genome-scale metabolic network in Homo sapiens. This genome-scale reconstruction opens unprecedented opportunities for basic research in human physiology and disease. The Center for Systems Biology is focused on these newly emerging opportunities and deploys the rapidly developing discipline of systems biology.

Center for Systems Biology

CSBui

The Center for Systems Biology focuses on human metabolism. In addition, the Center will establish an industrial biotechnology focused program. The systems biology of thermophilic bacteria found in Iceland will be studied. Application of such knowledge will be deployed to develop processes that will lead to the fixation of CO2, H2 and H2S that comes from geothermal well in Iceland. When developed, such processing technology could be used on a worldwide basis as geothermal energy is likely to be a part of the world’s future energy solution.

Funding

The ERC's mission is to encourage the highest quality research in Europe through competitive funding and to support investigator-initiated frontier research across all fields of research, on the basis of scientific excellence.  

Rannis administers the main public competitive funds in the field of research and innovation in Iceland, including the Research Fund, the Technical Development Fund, the Graduate Students' Fund and the Innovation Fund for Students.

http://ec.europa.eu/research/mariecurieactions/The Marie Curie Actions have long been one of the most popular and appreciated features of the Community Framework Programmes for Research and Technological Development.

The objectives of the Georg Consortium is to create a platform for entrepreneurship and export of geothermal energy resources and education, both for partners in the group and in the ensuing creative environment established through its national and international operations.

Systems Biology

Molecular systems biology represents an interdisciplinary field. To operate in this field a practitioner needs to know the basic life science disciplines (biochemistry, genetics, cell biology, physiology, etc), the genomic and high- throughput sciences, bioinformatics (statistics, algorithms and large-scale data analysis), and engineering sciences (numerics, modeling and simulation). Thus a molecular systems biology program will need participation from the natural sciences, engineering and medicine.

The Center for Systems Biology at the University of Iceland is indeed such an interdisciplinary effort. The University of Iceland will be significantly impacted by the establishment and growth of the Center and it will nucleate new research and education.

Resources

7th Systems Biology Short Course in the land of midnight sun
June 18th - 21st, 2013

 

RECON X - Reconstruction of The Human Genome

 

 

The openCOBRA Project The COnstraints Based Reconstruction and Analysis (COBRA) 

 

Courses

 

 

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