Predicting Network Activity from High Throughput Metabolomics

Annotation of the Human Adult Urinary Metabolome and Metabolite Identification Using Ultra High Performance Liquid Chromatography Coupled to a Linear Quadrupole Ion Trap-Orbitrap Mass Spectrometer

(2012) Aurelie Roux et al.   ANALYTICAL CHEMISTRY

Cellular Metabolism and Disease: What Do Metabolic Outliers Teach Us?

(2012) Ralph J. DeBerardinis et al.   CELL

Orchestration of Metabolism by Macrophages

(2012) Subhra K. Biswas et al.   Cell Metabolism

Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics

(2012) Warwick B. Dunn et al.   Metabolomics

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

(2012) Aarash Bordbar et al.   Molecular Systems Biology

An accelerated workflow for untargeted metabolomics using the METLIN database

(2012) Ralf Tautenhahn et al.   NATURE BIOTECHNOLOGY

Metabolomics: the apogee of the omics trilogy

(2012) Gary J. Patti et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data

(2012) Kenneth Haug et al.   NUCLEIC ACIDS RESEARCH

Detailed Mitochondrial Phenotyping by High Resolution Metabolomics

(2012) James R. Roede et al.   PLoS One

High-performance metabolic profiling of plasma from seven mammalian species for simultaneous environmental chemical surveillance and bioeffect monitoring

(2012) Youngja H. Park et al.   TOXICOLOGY

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren et al.   PLoS Computational Biology

Constructing a fish metabolic network model

(2012) Shuzhao Li et al.   GENOME BIOLOGY

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

(2011) Aarash Bordbar et al.   BMC Systems Biology

Bridging Innate and Adaptive Immunity

(2011) William E. Paul   CELL

Riboneogenesis in Yeast

(2011) Michelle F. Clasquin et al.   CELL

Nitric oxide: A regulator of eukaryotic initiation factor 2 kinases

(2011) Lingying Tong et al.   FREE RADICAL BIOLOGY AND MEDICINE

High-performance metabolic profiling with dual chromatography-Fourier-transform mass spectrometry (DC-FTMS) for study of the exposome

(2011) Quinlyn A. Soltow et al.   Metabolomics

Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst

(2011) Jianguo Xia et al.   Nature Protocols

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

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Divergent Effects of Human Cytomegalovirus and Herpes Simplex Virus-1 on Cellular Metabolism

(2011) Livia Vastag et al.   PLoS Pathogens

Metabolomic Analysis and Visualization Engine for LC−MS Data

(2010) Eugene Melamud et al.   ANALYTICAL CHEMISTRY

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

(2010) Jing Gao et al.   BIOINFORMATICS

MetPA: a web-based metabolomics tool for pathway analysis and visualization

(2010) J. Xia et al.   BIOINFORMATICS

NeMo: Network Module identification in Cytoscape

(2010) Corban G Rivera et al.   BMC BIOINFORMATICS

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

(2010) Martin I Sigurdsson et al.   BMC Systems Biology

Systems Vaccinology

(2010) Bali Pulendran et al.   IMMUNITY

Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network

(2010) Germán Plata et al.   Molecular Systems Biology

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

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

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

Interpreting Metabolomic Profiles using Unbiased Pathway Models

(2010) Rahul C. Deo et al.   PLoS Computational Biology

Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics

(2009) M. Brown et al.   ANALYST

apLCMS—adaptive processing of high-resolution LC/MS data

(2009) Tianwei Yu et al.   BIOINFORMATICS

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Extracellular redox modulation by regulatory T cells

(2009) Zhonghua Yan et al.   Nature Chemical Biology

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

Metabolomics: A Global Biochemical Approach to Drug Response and Disease

(2008) Rima Kaddurah-Daouk et al.   Annual Review of Pharmacology and Toxicology

Identifying functional modules in protein-protein interaction networks: an integrated exact approach

(2008) M. T. Dittrich et al.   BIOINFORMATICS

Probabilistic assignment of formulas to mass peaks in metabolomics experiments

(2008) Simon Rogers et al.   BIOINFORMATICS

Metabolite identification via the Madison Metabolomics Consortium Database

(2008) Qiu Cui et al.   NATURE BIOTECHNOLOGY

Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans

(2008) Troy D Querec et al.   NATURE IMMUNOLOGY

HMDB: a knowledgebase for the human metabolome

(2008) D. S. Wishart et al.   NUCLEIC ACIDS RESEARCH

New surveyor tools for charting microbial metabolic maps

(2007) Rainer Breitling et al.   NATURE REVIEWS MICROBIOLOGY