ArticleBMC bioinformatics2011
Reconstructing phylogeny from metabolic substrate-product relationships.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Reliable Inference of Phylogenomic Relationship via Assembly-Based Strategy Accommodating Raw Reads and Proteins.Molecular ecology resources · 2026Article
- Reconstructing Phylogeny by Aligning Multiple Metabolic Pathways Using Functional Module Mapping.Molecules (Basel, Switzerland) · 2018Article
- The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data.PloS one · 2017Article
- Novel Approach to Classify Plants Based on Metabolite-Content Similarity.BioMed research international · 2017Article
- The utility of metabolomics in natural product and biomarker characterization.Biochimica et biophysica acta · 2014Review
- A tree of cellular life inferred from a genomic census of molecular functions.Journal of molecular evolution · 2014Article
- Reconstruction of phyletic trees by global alignment of multiple metabolic networks.BMC bioinformatics · 2013Article
- Metabolic classification of microbial genomes using functional probes.BMC genomics · 2012Article
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Authors and funding
3 authors.
Funding
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Abstract
backgroundMany approaches utilize metabolic pathway information to reconstruct the phyletic tree of fully sequenced organisms, but how metabolic networks can add information to original genomic annotations has remained open.
methodsWe translated enzyme reactions assigned in 1075 organisms into substrate-product relationships to represent the metabolic information at a finer resolution than enzymes and compounds. Each organism was represented as a vector of substrate-product relationships and the phyletic tree was reconstructed by a simple hierarchical method. Obtained results were compared with several other approaches that use genome information and network properties.
resultsPhyletic trees without consideration of network properties can already extract organisms in anomalous environments. This efficient method can add insights to traditional genome-based phylogenetic reconstruction.
conclusionsStructural relationship among metabolites can highlight parasitic or symbiont species such as spirochaete and clamydia. The method assists understanding of species-environment interaction when used in combination with traditional phylogenetic methods.
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