Big data analytics in healthcare

A Belle, R Thiagarajan… - BioMed research …, 2015 - Wiley Online Library
The rapidly expanding field of big data analytics has started to play a pivotal role in the
evolution of healthcare practices and research. It has provided tools to accumulate, manage …

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

NE Lewis, H Nagarajan, BO Palsson - Nature Reviews Microbiology, 2012 - nature.com
Reconstructed microbial metabolic networks facilitate a mechanistic description of the
genotype–phenotype relationship through the deployment of constraint-based …

Itaconate links inhibition of succinate dehydrogenase with macrophage metabolic remodeling and regulation of inflammation

V Lampropoulou, A Sergushichev, M Bambouskova… - Cell metabolism, 2016 - cell.com
Remodeling of the tricarboxylic acid (TCA) cycle is a metabolic adaptation accompanying
inflammatory macrophage activation. During this process, endogenous metabolites can …

Genome-scale models in human metabologenomics

A Mardinoglu, BØ Palsson - Nature Reviews Genetics, 2025 - nature.com
Metabologenomics integrates metabolomics with other omics data types to comprehensively
study the genetic and environmental factors that influence metabolism. These multi-omics …

Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism

D Machado, M Herrgård - PLoS computational biology, 2014 - journals.plos.org
Constraint-based models of metabolism are a widely used framework for predicting flux
distributions in genome-scale biochemical networks. The number of published methods for …

Metabolic network-based stratification of hepatocellular carcinoma reveals three distinct tumor subtypes

G Bidkhori, R Benfeitas, M Klevstig… - Proceedings of the …, 2018 - National Acad Sciences
Hepatocellular carcinoma (HCC) is one of the most frequent forms of liver cancer, and
effective treatment methods are limited due to tumor heterogeneity. There is a great need for …

PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases

T Liu, P Salguero, M Petek… - Nucleic Acids …, 2022 - academic.oup.com
PaintOmics is a web server for the integrative analysis and visualisation of multi-omics
datasets using biological pathway maps. PaintOmics 4 has several notable updates that …

Fast reconstruction of compact context-specific metabolic network models

N Vlassis, MP Pacheco, T Sauter - PLoS computational biology, 2014 - journals.plos.org
Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of
context-specific metabolic network models. The reconstruction of such a model from high …

Integration of expression data in genome-scale metabolic network reconstructions

AS Blazier, JA Papin - Frontiers in physiology, 2012 - frontiersin.org
With the advent of high-throughput technologies, the field of systems biology has amassed
an abundance of “omics” data, quantifying thousands of cellular components across a …

DCEO biotechnology: tools to design, construct, evaluate, and optimize the metabolic pathway for biosynthesis of chemicals

X Chen, C Gao, L Guo, G Hu, Q Luo, J Liu… - Chemical …, 2018 - ACS Publications
Chemical synthesis is a well established route for producing many chemicals on a large
scale, but some drawbacks still exist in this process, such as unstable intermediates …