Current status and applications of genome-scale metabolic models
Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction
associations for entire metabolic genes in an organism, and can be simulated to predict …
associations for entire metabolic genes in an organism, and can be simulated to predict …
Metabolomics and complementary techniques to investigate the plant phytochemical cosmos
Covering: up to 2021 Plants and their associated microbial communities are known to
produce millions of metabolites, a majority of which are still not characterized and are …
produce millions of metabolites, a majority of which are still not characterized and are …
Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants
Plant metabolism underpins many traits of ecological and agronomic importance. Plants
produce numerous compounds to cope with their environments but the biosynthetic …
produce numerous compounds to cope with their environments but the biosynthetic …
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants …
For over 10 years, ModelSEED has been a primary resource for the construction of draft
genome-scale metabolic models based on annotated microbial or plant genomes. Now …
genome-scale metabolic models based on annotated microbial or plant genomes. Now …
Integrated omics analysis of specialized metabolism in medicinal plants
Medicinal plants are a rich source of highly diverse specialized metabolites with important
pharmacological properties. Until recently, plant biologists were limited in their ability to …
pharmacological properties. Until recently, plant biologists were limited in their ability to …
PATtyFams: protein families for the microbial genomes in the PATRIC database
The ability to build accurate protein families is a fundamental operation in bioinformatics that
influences comparative analyses, genome annotation, and metabolic modeling. For several …
influences comparative analyses, genome annotation, and metabolic modeling. For several …
Remobilization of phytol from chlorophyll degradation is essential for tocopherol synthesis and growth of Arabidopsis
K Vom Dorp, G Hölzl, C Plohmann, M Eisenhut… - The Plant …, 2015 - academic.oup.com
Phytol from chlorophyll degradation can be phosphorylated to phytyl-phosphate and phytyl-
diphosphate, the substrate for tocopherol (vitamin E) synthesis. A candidate for the phytyl …
diphosphate, the substrate for tocopherol (vitamin E) synthesis. A candidate for the phytyl …
Updates in metabolomics tools and resources: 2014–2015
BB Misra, JJJ van der Hooft - Electrophoresis, 2016 - Wiley Online Library
Data processing and interpretation represent the most challenging and time‐consuming
steps in high‐throughput metabolomic experiments, regardless of the analytical platforms …
steps in high‐throughput metabolomic experiments, regardless of the analytical platforms …
APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data
Motivation Alternative polyadenylation (APA) has been increasingly recognized as a crucial
mechanism that contributes to transcriptome diversity and gene expression regulation. As …
mechanism that contributes to transcriptome diversity and gene expression regulation. As …
[HTML][HTML] Insights into the seed microbiome and its ecological significance in plant life
In recent years, the microbiome has attracted much attention because of the multiple roles
and functions that microbes play in plants, animals, and human beings. Seed-associated …
and functions that microbes play in plants, animals, and human beings. Seed-associated …