Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

(2019) Vikash Pandey et al.   PLoS Computational Biology

Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli

(2019) Mattia Zampieri et al.   Nature Communications

Modeling metabolism of the human gut microbiome

(2018) Stefanía Magnúsdóttir et al.   CURRENT OPINION IN BIOTECHNOLOGY

Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

(2018) Erica M Forsberg et al.   Nature Protocols

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics

(2017) Zijuan Lai et al.   NATURE METHODS

Systems biology guided by XCMS Online metabolomics

(2017) Tao Huan et al.   NATURE METHODS

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

(2017) Aarash Bordbar et al.   Scientific Reports

The gut microbiota: A treasure for human health

(2016) Daotong Li et al.   BIOTECHNOLOGY ADVANCES

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Increasing selectivity and coverage in LC-MS based metabolome analysis

(2016) Karin Ortmayr et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model

(2016) Daniel A. Cuevas et al.   Frontiers in Microbiology

Metabolomics and its integration with systems biology: PSI 2014 conference panel discussion report

(2015) Tushar More et al.   Journal of Proteomics

The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics

(2015) Scarlet Beck et al.   MOLECULAR & CELLULAR PROTEOMICS

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

From next-generation sequencing to systematic modeling of the gut microbiome

(2015) Boyang Ji et al.   Frontiers in Genetics

Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses

(2014) Harsha Gowda et al.   ANALYTICAL CHEMISTRY

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

Toward ‘Omic Scale Metabolite Profiling: A Dual Separation–Mass Spectrometry Approach for Coverage of Lipid and Central Carbon Metabolism

(2013) Julijana Ivanisevic et al.   ANALYTICAL CHEMISTRY

XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data

(2012) Ralf Tautenhahn et al.   ANALYTICAL CHEMISTRY

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

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

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