Reference : Benchmarking procedures for high-throughput context specific reconstruction algorithms
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
http://hdl.handle.net/10993/23844
Benchmarking procedures for high-throughput context specific reconstruction algorithms
English
Pacheco, Maria Irene mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >]
Pfau, Thomas mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit > ; University of Aberdeen > Department of Physics > Institute of Complex Systems and Mathematical Biology]
Sauter, Thomas mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >]
22-Jan-2016
Frontiers in Physiology
Frontiers Research Foundation
The impact of systems medicine on human health and disease
Yes
International
1664-042X
Lausanne
Switzerland
[en] metabolic networks and pathways ; metabolic reconstruction ; constraint-based modeling ; tissue specific networks ; benchmarking ; validation
[en] Recent progress in high-throughput data acquisition has shifted the focus from data generation to processing and understanding of how to integrate collected information. Context specific reconstruction based on generic genome scale models like ReconX or HMR has the potential to become a diagnostic and treatment tool tailored to the analysis of specific individuals. The respective computational algorithms require a high level of predictive power, robustness and sensitivity. Although multiple context specific reconstruction algorithms were published in the last 10 years, only a fraction of them is suitable for model building based on human high-throughput data. Beside other reasons, this might be due to problems arising from the limitation to only one metabolic target function or arbitrary thresholding. This review describes and analyses common validation methods used for testing model building algorithms. Two major methods can be distinguished: consistency testing and comparison based testing. The first is concerned with robustness against noise, e.g., missing data due to the impossibility to distinguish between the signal and the background of non-specific binding of probes in a microarray experiment, and whether distinct sets of input expressed genes corresponding to i.e., different tissues yield distinct models. The latter covers methods comparing sets of functionalities, comparison with existing networks or additional databases. We test those methods on several available algorithms and deduce properties of these algorithms that can be compared with future developments. The set of tests performed, can therefore serve as a benchmarking procedure for future algorithms.
Researchers ; Professionals ; Students
http://hdl.handle.net/10993/23844
10.3389/fphys.2015.00410
http://journal.frontiersin.org/article/10.3389/fphys.2015.00410/full

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