Addressing uncertainty in genome-scale metabolic model reconstruction and analysis
The reconstruction and analysis of genome-scale metabolic models constitutes a powerful
systems biology approach, with applications ranging from basic understanding of genotype …
systems biology approach, with applications ranging from basic understanding of genotype …
[HTML][HTML] Toward modeling metabolic state from single-cell transcriptomics
Background Single-cell metabolic studies bring new insights into cellular function, which can
often not be captured on other omics layers. Metabolic information has wide applicability …
often not be captured on other omics layers. Metabolic information has wide applicability …
Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis
Over-representation analysis (ORA) is one of the commonest pathway analysis approaches
used for the functional interpretation of metabolomics datasets. Despite the widespread use …
used for the functional interpretation of metabolomics datasets. Despite the widespread use …
Single sample pathway analysis in metabolomics: performance evaluation and application
C Wieder, RPJ Lai, TMD Ebbels - BMC bioinformatics, 2022 - Springer
Background Single sample pathway analysis (ssPA) transforms molecular level omics data
to the pathway level, enabling the discovery of patient-specific pathway signatures …
to the pathway level, enabling the discovery of patient-specific pathway signatures …
Metabolic Flux Modeling in Marine Ecosystems
Ocean metabolism constitutes a complex, multiscale ensemble of biochemical reaction
networks harbored within and between the boundaries of a myriad of organisms. Gaining a …
networks harbored within and between the boundaries of a myriad of organisms. Gaining a …
Consistency, inconsistency, and ambiguity of metabolite names in biochemical databases used for genome-scale metabolic modelling
Genome-scale metabolic models (GEMs) are manually curated repositories describing the
metabolic capabilities of an organism. GEMs have been successfully used in different …
metabolic capabilities of an organism. GEMs have been successfully used in different …
Recent applications of bioinformatics in target identification and drug discovery for Alzheimer's disease
Alzheimer's disease (AD) is a complex multifactorial neurodegenerative disease
characterized by progressive memory loss. The main pathological features of the disease …
characterized by progressive memory loss. The main pathological features of the disease …
Molecular Docking in Drug Designing and Metabolism
The traditional drug discovery methods and analysis of drug target interactions and
physiological responses through biological experiments are expensive and time-consuming …
physiological responses through biological experiments are expensive and time-consuming …
Single-cell genomic profile-based analysis of tissue differentiation in colorectal cancer
H Jiang, H Zhang, X Zhang - Science China Life Sciences, 2021 - Springer
Colorectal cancer (CRC) progression is associated with cancer cell dedifferentiation and
sternness acquisition. Several methods have been developed to identify sternness …
sternness acquisition. Several methods have been developed to identify sternness …
In Silico Characterization of Natural Products in Plants
The study of natural products in plants has been revolutionized by “in silico” approaches,
combining advanced computational methods with traditional botanical study. This …
combining advanced computational methods with traditional botanical study. This …