From correlation to causation: analysis of metabolomics data using systems biology approaches

Biomedical applications of cell- and tissue-specific metabolic network models

(2017) Hamideh Fouladiha et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Age and Sex Effects on Plasma Metabolite Association Networks in Healthy Subjects

(2017) Alessia Vignoli et al.   JOURNAL OF PROTEOME RESEARCH

Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling

(2017) Maria Suarez-Diez et al.   JOURNAL OF PROTEOME RESEARCH

Review of metabolic pathways activated in cancer cells as determined through isotopic labeling and network analysis

(2017) Wentao Dong et al.   METABOLIC ENGINEERING

Navigating freely-available software tools for metabolomics analysis

(2017) Rachel Spicer et al.   Metabolomics

Characterization of poplar metabotypes via mass difference enrichment analysis

(2017) Franco Moritz et al.   PLANT CELL AND ENVIRONMENT

Compensatory metabolic networks in pancreatic cancers upon perturbation of glutamine metabolism

(2017) Douglas E. Biancur et al.   Nature Communications

Restrictions in ATP diffusion within sarcomeres can provoke ATP-depleted zones impairing exercise capacity in chronic obstructive pulmonary disease

(2016) Alexey E. Alekseev et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

WUFlux: an open-source platform for 13C metabolic flux analysis of bacterial metabolism

(2016) Lian He et al.   BMC BIOINFORMATICS

Computational methods to identify metabolic sub-networks based on metabolomic profiles

(2016) Clément Frainay et al.   BRIEFINGS IN BIOINFORMATICS

Computational approaches for systems metabolomics

(2016) Jan Krumsiek et al.   CURRENT OPINION IN BIOTECHNOLOGY

Entropy-Based Network Representation of the Individual Metabolic Phenotype

(2016) Edoardo Saccenti et al.   JOURNAL OF PROTEOME RESEARCH

Change...

(2016) John R. Yates   JOURNAL OF PROTEOME RESEARCH

Correlation Patterns in Experimental Data Are Affected by Normalization Procedures: Consequences for Data Analysis and Network Inference

(2016) Edoardo Saccenti   JOURNAL OF PROTEOME RESEARCH

iSCHRUNK – I n S ilico Approach to Ch aracterization and R eduction of Un certainty in the K inetic Models of Genome-scale Metabolic Networks

(2016) Stefano Andreozzi et al.   METABOLIC ENGINEERING

Recon 2.2: from reconstruction to model of human metabolism

(2016) Neil Swainston et al.   Metabolomics

Mitochondrial and nuclear DNA matching shapes metabolism and healthy ageing

(2016) Ana Latorre-Pellicer et al.   NATURE

Revealing disease-associated pathways by network integration of untargeted metabolomics

(2016) Leila Pirhaji et al.   NATURE METHODS

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach

(2016) Pedro A. Saa et al.   Scientific Reports

BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology

(2015) Pablo Moreno et al.   BMC BIOINFORMATICS

Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction

(2015) A Ranjitha Dhanasekaran et al.   BMC BIOINFORMATICS

A roadmap for interpreting 13 C metabolite labeling patterns from cells

(2015) Joerg M Buescher et al.   CURRENT OPINION IN BIOTECHNOLOGY

How to measure metabolic fluxes: a taxonomic guide for 13 C fluxomics

(2015) Sebastian Niedenführ et al.   CURRENT OPINION IN BIOTECHNOLOGY

Development of novel tools for thein vitroinvestigation of drug-induced liver injury

(2015) Jian Jiang et al.   Expert Opinion on Drug Metabolism & Toxicology

Covariances Simultaneous Component Analysis: a new method within a framework for modeling covariances

(2015) Age K. Smilde et al.   JOURNAL OF CHEMOMETRICS

Allostasis and Resilience of the Human Individual Metabolic Phenotype

(2015) Veronica Ghini et al.   JOURNAL OF PROTEOME RESEARCH

Effects of Sample Size and Dimensionality on the Performance of Four Algorithms for Inference of Association Networks in Metabonomics

(2015) Maria Suarez-Diez et al.   JOURNAL OF PROTEOME RESEARCH

Gender-specific pathway differences in the human serum metabolome

(2015) Jan Krumsiek et al.   Metabolomics

Multiscale characterization of ageing and cancer progression by a novel network entropy measure

(2015) Giulia Menichetti et al.   Molecular BioSystems

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

MetaboAnalyst 3.0—making metabolomics more meaningful

(2015) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

INCA: a computational platform for isotopically non-stationary metabolic flux analysis

(2014) J. D. Young   BIOINFORMATICS

Non-stationary 13C metabolic flux analysis of Chinese hamster ovary cells in batch culture using extracellular labeling highlights metabolic reversibility and compartmentation

(2014) Averina Nicolae et al.   BMC Systems Biology

Probabilistic Networks of Blood Metabolites in Healthy Subjects As Indicators of Latent Cardiovascular Risk

(2014) Edoardo Saccenti et al.   JOURNAL OF PROTEOME RESEARCH

Enzyme clustering accelerates processing of intermediates through metabolic channeling

(2014) Michele Castellana et al.   NATURE BIOTECHNOLOGY

BioModels: ten-year anniversary

(2014) Vijayalakshmi Chelliah et al.   NUCLEIC ACIDS RESEARCH

Potential metabolic mechanism of girls' central precocious puberty: a network analysis on urine metabonomics data

(2013) Linlin Yang et al.   BMC Systems Biology

Path2Models: large-scale generation of computational models from biochemical pathway maps

(2013) Finja Büchel et al.   BMC Systems Biology

Isotopically non-stationary metabolic flux analysis: complex yet highly informative

(2013) Wolfgang Wiechert et al.   CURRENT OPINION IN BIOTECHNOLOGY

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks

(2013) Natalie J. Stanford et al.   PLoS One

Global test for metabolic pathway differences between conditions

(2012) Diana M. Hendrickx et al.   ANALYTICA CHIMICA ACTA

influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labelling experiments

(2012) S. Sokol et al.   BIOINFORMATICS

13CFLUX2—high-performance software suite for 13C-metabolic flux analysis

(2012) Michael Weitzel et al.   BIOINFORMATICS

Comparison of co-expression measures: mutual information, correlation, and model based indices

(2012) Lin Song et al.   BMC BIOINFORMATICS

MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity

(2012) Dinesh K Barupal et al.   BMC BIOINFORMATICS

Compartmentation of glycogen metabolism revealed from 13C isotopologue distributions

(2012) Igor Marin de Mas et al.   BMC Systems Biology

Parallel labeling experiments and metabolic flux analysis: Past, present and future methodologies

(2012) Scott B. Crown et al.   METABOLIC ENGINEERING

Urinary metabolic network analysis in trauma, hemorrhagic shock, and resuscitation

(2012) Elizabeth R. Lusczek et al.   Metabolomics

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

(2012) Ida Schomburg et al.   NUCLEIC ACIDS RESEARCH

HMDB 3.0—The Human Metabolome Database in 2013

(2012) David S. Wishart et al.   NUCLEIC ACIDS RESEARCH

MPEA—metabolite pathway enrichment analysis

(2011) Matti Kankainen et al.   BIOINFORMATICS

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data

(2011) Alla Karnovsky et al.   BIOINFORMATICS

Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach

(2011) Atsushi Fukushima et al.   BMC Systems Biology

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

(2011) Jan Krumsiek et al.   BMC Systems Biology

Human metabolic profiles are stably controlled by genetic and environmental variation

(2011) G. Nicholson et al.   Molecular Systems Biology

SABIO-RK--database for biochemical reaction kinetics

(2011) U. Wittig et al.   NUCLEIC ACIDS RESEARCH

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Stable isotope-resolved metabolomics and applications for drug development

(2011) Teresa W.-M. Fan et al.   PHARMACOLOGY & THERAPEUTICS

Weighted Correlation Network Analysis (WGCNA) Applied to the Tomato Fruit Metabolome

(2011) Matthew V. DiLeo et al.   PLoS One

G q and Phospholipase C- : Turn On, Turn Off, and Do It Fast

(2011) E. M. Ross   Science Signaling

Metabolome in progression to Alzheimer's disease

(2011) M Orešič et al.   Translational Psychiatry

Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks

(2010) Jing Gao et al.   BIOINFORMATICS

Pathway Activity Profiling (PAPi): from the metabolite profile to the metabolic pathway activity

(2010) Raphael B. M. Aggio et al.   BIOINFORMATICS

Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data

(2010) F. Garcia-Alcalde et al.   BIOINFORMATICS

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

13C metabolic flux analysis in complex systems

(2010) Nicola Zamboni   CURRENT OPINION IN BIOTECHNOLOGY

Weighted Gene Coexpression Network Analysis: State of the Art

(2010) Wei Zhao et al.   Journal of Biopharmaceutical Statistics

Reverse engineering of metabolic networks, a critical assessment

(2010) Diana M. Hendrickx et al.   Molecular BioSystems

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

(2010) L. Cottret et al.   NUCLEIC ACIDS RESEARCH

BRENDA, the enzyme information system in 2011

(2010) M. Scheer et al.   NUCLEIC ACIDS RESEARCH

Insights into plant metabolic networks from steady-state metabolic flux analysis

(2009) Nicholas J. Kruger et al.   BIOCHIMIE

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example

(2009) Heiko Neuweger et al.   BMC Systems Biology

Metabolic network discovery through reverse engineering of metabolome data

(2009) Tunahan Çakır et al.   Metabolomics

OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis

(2009) Lake-Ee Quek et al.   Microbial Cell Factories

Stability of Metabolic Correlations under Changing Environmental Conditions in Escherichia coli – A Systems Approach

(2009) Jedrzej Szymanski et al.   PLoS One

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A correlation network approach to metabolic data analysis for tomato fruits

(2008) Remco Ursem et al.   EUPHYTICA

Quantifying Reductive Carboxylation Flux of Glutamine to Lipid in a Brown Adipocyte Cell Line

(2008) Hyuntae Yoo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Integrated Transcriptomics, Proteomics, and Metabolomics Analyses To Survey Ozone Responses in the Leaves of Rice Seedling

(2008) Kyoungwon Cho et al.   JOURNAL OF PROTEOME RESEARCH

Human metabolic phenotype diversity and its association with diet and blood pressure

(2008) Elaine Holmes et al.   NATURE

Systems biology: Metabonomics

(2008) Jeremy K. Nicholson et al.   NATURE

MassTRIX: mass translator into pathways

(2008) K. Suhre et al.   NUCLEIC ACIDS RESEARCH

Evidence of different metabolic phenotypes in humans

(2008) M. Assfalg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The implications of human metabolic network topology for disease comorbidity

(2008) D.- S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

(2008) Jong Min Lee et al.   PLoS Computational Biology