Computational methods to identify metabolic sub-networks based on metabolomic profiles
Untargeted metabolomics makes it possible to identify compounds that undergo significant
changes in concentration in different experimental conditions. The resulting metabolomic …
changes in concentration in different experimental conditions. The resulting metabolomic …
Prediction of metabolic pathways from genome-scale metabolic networks
K Faust, D Croes, J Van Helden - Biosystems, 2011 - Elsevier
The analysis of a variety of data sets (transcriptome arrays, phylogenetic profiles, etc.) yields
groups of functionally related genes. In order to determine their biological function …
groups of functionally related genes. In order to determine their biological function …
[HTML][HTML] Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms
Background We consider the possibility of engineering metabolic pathways in a chassis
organism in order to synthesize novel target compounds that are heterologous to the …
organism in order to synthesize novel target compounds that are heterologous to the …
[HTML][HTML] DuctApe: a suite for the analysis and correlation of genomic and OmniLog™ phenotype microarray data
Addressing the functionality of genomes is one of the most important and challenging tasks
of today's biology. In particular the ability to link genotypes to corresponding phenotypes is …
of today's biology. In particular the ability to link genotypes to corresponding phenotypes is …
[HTML][HTML] Inferring branching pathways in genome-scale metabolic networks
Background A central problem in computational metabolic modelling is how to find
biochemically plausible pathways between metabolites in a metabolic network. Two …
biochemically plausible pathways between metabolites in a metabolic network. Two …
[HTML][HTML] In silico methods for linking genes and secondary metabolites: the way forward
In silico methods for linking genomic space to chemical space have played a crucial role in
genomics driven discovery of new natural products as well as biosynthesis of altered natural …
genomics driven discovery of new natural products as well as biosynthesis of altered natural …
[HTML][HTML] The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles
P Durek, D Walther - BMC systems biology, 2008 - Springer
Background The study of biological interaction networks is a central theme of systems
biology. Here, we investigate the relationships between two distinct types of interaction …
biology. Here, we investigate the relationships between two distinct types of interaction …
Metabolic pathfinding using RPAIR annotation
K Faust, D Croes, J Van Helden - Journal of molecular biology, 2009 - Elsevier
Metabolic databases contain information about thousands of small molecules and reactions,
which can be represented as networks. In the context of metabolic reconstruction, pathways …
which can be represented as networks. In the context of metabolic reconstruction, pathways …
MetaboRank: network-based recommendation system to interpret and enrich metabolomics results
Motivation Metabolomics has shown great potential to improve the understanding of
complex diseases, potentially leading to therapeutic target identification. However, no single …
complex diseases, potentially leading to therapeutic target identification. However, no single …
ECOH: an enzyme commission number predictor using mutual information and a support vector machine
Motivation: The enzyme nomenclature system, commonly known as the enzyme commission
(EC) number, plays a key role in classifying and predicting enzymatic reactions. However …
(EC) number, plays a key role in classifying and predicting enzymatic reactions. However …