Identification of bioactive metabolites using activity metabolomics

METLIN: A Technology Platform for Identifying Knowns and Unknowns

(2018) Carlos Guijas et al.   ANALYTICAL CHEMISTRY

Metabolomics and Isotope Tracing

(2018) Cholsoon Jang et al.   CELL

Time-Resolved Analysis Reveals Rapid Dynamics and Broad Scope of the CBP/p300 Acetylome

(2018) Brian T. Weinert et al.   CELL

A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication

(2018) Ilaria Piazza et al.   CELL

Metabolite-Induced Protein Expression Guided by Metabolomics and Systems Biology

(2018) Martin Giera et al.   Cell Metabolism

Palmitic Acid Hydroxystearic Acids Activate GPR40, Which Is Involved in Their Beneficial Effects on Glucose Homeostasis

(2018) Ismail Syed et al.   Cell Metabolism

Cerebrovascular β-amyloid deposition and associated microhemorrhages in a Tg2576 Alzheimer mouse model are reduced with a DHA-enriched diet

(2018) Justine Hur et al.   FASEB JOURNAL

PROMIS, global analysis of PROtein-Metabolite Interactions using Size separation inArabidopsis thaliana

(2018) Daniel Veyel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic regulation of chromatin modifications and gene expression

(2018) Juan Manuel Schvartzman et al.   JOURNAL OF CELL BIOLOGY

Metabolomics activity screening for identifying metabolites that modulate phenotype

(2018) Carlos Guijas et al.   NATURE BIOTECHNOLOGY

Biosynthesis of redox-active metabolites in response to iron deficiency in plants

(2018) Jakub Rajniak et al.   Nature Chemical Biology

Lactate in the brain: from metabolic end-product to signalling molecule

(2018) Pierre J. Magistretti et al.   NATURE REVIEWS NEUROSCIENCE

A Phase 3 Trial of l-Glutamine in Sickle Cell Disease

(2018) Yutaka Niihara et al.   NEW ENGLAND JOURNAL OF MEDICINE

MetExplore: collaborative edition and exploration of metabolic networks

(2018) Ludovic Cottret et al.   NUCLEIC ACIDS RESEARCH

Fatty acyl recognition and transfer by an integral membraneS-acyltransferase

(2018) Mitra S. Rana et al.   SCIENCE

Transaminase Inhibition by 2-Hydroxyglutarate Impairs Glutamate Biosynthesis and Redox Homeostasis in Glioma

(2018) Samuel K. McBrayer et al.   CELL

Electrophilic properties of itaconate and derivatives regulate the IκBζ–ATF3 inflammatory axis

(2018) Monika Bambouskova et al.   NATURE

Itaconate is an anti-inflammatory metabolite that activates Nrf2 via alkylation of KEAP1

(2018) Evanna L. Mills et al.   NATURE

Metabolites as regulators of insulin sensitivity and metabolism

(2018) Qin Yang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Causes and Consequences of Nonenzymatic Protein Acylation

(2018) Andrew M. James et al.   TRENDS IN BIOCHEMICAL SCIENCES

Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts

(2018) Aleksej Zelezniak et al.   Cell Systems

Cardiovascular Risk Reduction with Icosapent Ethyl for Hypertriglyceridemia

(2018) Deepak L. Bhatt et al.   NEW ENGLAND JOURNAL OF MEDICINE

The whipworm (Trichuris suis) secretes prostaglandin E2 to suppress proinflammatory properties in human dendritic cells

(2017) Lisa C. Laan et al.   FASEB JOURNAL

Treating inflammation and infection in the 21st century: new hints from decoding resolution mediators and mechanisms

(2017) Charles N. Serhan   FASEB JOURNAL

Butyrate reduces appetite and activates brown adipose tissue via the gut-brain neural circuit

(2017) Zhuang Li et al.   GUT

OpenMS – A platform for reproducible analysis of mass spectrometry data

(2017) Julianus Pfeuffer et al.   JOURNAL OF BIOTECHNOLOGY

Cytotoxic Prenylated Stilbenes Isolated from Macaranga tanarius

(2017) Tiphaine Péresse et al.   JOURNAL OF NATURAL PRODUCTS

Metabolomics-based discovery of a metabolite that enhances oligodendrocyte maturation

(2017) Brittney A Beyer et al.   Nature Chemical Biology

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

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Clinical Benefits of n-3 PUFA and ɤ-Linolenic Acid in Patients with Rheumatoid Arthritis

(2017) Mirjana Veselinovic et al.   Nutrients

Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets

(2017) Dinesh Kumar Barupal et al.   Scientific Reports

An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma

(2016) A. Ari Hakimi et al.   CANCER CELL

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Recon 2.2: from reconstruction to model of human metabolism

(2016) Neil Swainston et al.   Metabolomics

Revealing disease-associated pathways by network integration of untargeted metabolomics

(2016) Leila Pirhaji et al.   NATURE METHODS

Metabolomics: beyond biomarkers and towards mechanisms

(2016) Caroline H. Johnson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

GAM: a web-service for integrated transcriptional and metabolic network analysis

(2016) Alexey A. Sergushichev et al.   NUCLEIC ACIDS RESEARCH

Mass spectral databases for LC/MS- and GC/MS-based metabolomics: State of the field and future prospects

(2016) Maria Vinaixa et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple ‘Omic’ Layers

(2016) Katsuyuki Yugi et al.   TRENDS IN BIOTECHNOLOGY

Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data

(2016) Robert L. Davidson et al.   GigaScience

The metabolic background is a global player in Saccharomyces gene expression epistasis

(2016) Mohammad Tauqeer Alam et al.   Nature Microbiology

A roadmap for interpreting 13 C metabolite labeling patterns from cells

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

Analysis of acetylation stoichiometry suggests that SIRT3 repairs nonenzymatic acetylation lesions

(2015) B. T. Weinert et al.   EMBO JOURNAL

Network Integration of Parallel Metabolic and Transcriptional Data Reveals Metabolic Modules that Regulate Macrophage Polarization

(2015) Abhishek K. Jha et al.   IMMUNITY

Integrated compensatory network is activated in the absence of NCC phosphorylation

(2015) P. Richard Grimm et al.   JOURNAL OF CLINICAL INVESTIGATION

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Multi-omic data analysis using Galaxy

(2015) Jorrit Boekel et al.   NATURE BIOTECHNOLOGY

Metabolic pathways promoting cancer cell survival and growth

(2015) Lindsey K. Boroughs et al.   NATURE CELL BIOLOGY

Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling

(2015) Kilian V M Huber et al.   NATURE METHODS

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

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

Predicting drug metabolism: experiment and/or computation?

(2015) Johannes Kirchmair et al.   NATURE REVIEWS DRUG DISCOVERY

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

(2015) Manish Sud 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

Glutamine-dependent α-ketoglutarate production regulates the balance between T helper 1 cell and regulatory T cell generation

(2015) Dorota Klysz et al.   Science Signaling

Brain glucose sensing in homeostatic and hedonic regulation

(2015) Laura Steinbusch et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Glutamine-dependent α-ketoglutarate production regulates the balance between T helper 1 cell and regulatory T cell generation

(2015) Dorota Klysz et al.   Science Signaling

Is Cancer a Genetic Disease or a Metabolic Disease?

(2015) David S. Wishart   EBioMedicine

Proteomic pearl diving versus systems biology in cell physiology. Focus on “Proteomic mapping of proteins released during necrosis and apoptosis from cultured neonatal cardiac myocytes”

(2014) Mark A. Knepper   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

Hexosamine Pathway Metabolites Enhance Protein Quality Control and Prolong Life

(2014) Martin S. Denzel et al.   CELL

Discovery of a Class of Endogenous Mammalian Lipids with Anti-Diabetic and Anti-inflammatory Effects

(2014) Mark M. Yore et al.   CELL

Lysine Glutarylation Is a Protein Posttranslational Modification Regulated by SIRT5

(2014) Minjia Tan et al.   Cell Metabolism

Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)-Based Strategy for Proteome-Wide Thermodynamic Analysis of Protein-Ligand Binding Interactions

(2014) Duc T. Tran et al.   MOLECULAR & CELLULAR PROTEOMICS

Intracellular α-ketoglutarate maintains the pluripotency of embryonic stem cells

(2014) Bryce W. Carey et al.   NATURE

The metabolite α-ketoglutarate extends lifespan by inhibiting ATP synthase and TOR

(2014) Randall M. Chin et al.   NATURE

Global analysis of protein structural changes in complex proteomes

(2014) Yuehan Feng et al.   NATURE BIOTECHNOLOGY

The growing landscape of lysine acetylation links metabolism and cell signalling

(2014) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Tracking cancer drugs in living cells by thermal profiling of the proteome

(2014) M. M. Savitski et al.   SCIENCE

Microfluidic platform for the quantitative analysis of leukocyte migration signatures

(2014) Leo Boneschansker et al.   Nature Communications

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

Proteasome Regulation by ADP-Ribosylation

(2013) Park F. Cho-Park et al.   CELL

Posttranscriptional RNA Modifications: Playing Metabolic Games in a Cell’s Chemical Legoland

(2013) Mark Helm et al.   CHEMISTRY & BIOLOGY

Oncometabolites: linking altered metabolism with cancer

(2013) Ming Yang et al.   JOURNAL OF CLINICAL INVESTIGATION

Meta-analysis of global metabolomic data identifies metabolites associated with life-span extension

(2013) Gary J. Patti et al.   Metabolomics

Density-dependent Lectin–Glycan Interactions as a Paradigm for Conditional Regulation by Posttranslational Modifications

(2013) James W. Dennis et al.   MOLECULAR & CELLULAR PROTEOMICS

Understanding Metabolic Regulation and Its Influence on Cell Physiology

(2013) Christian M. Metallo et al.   MOLECULAR CELL

Metabolite turns master regulator

(2013) Joshua D. Rabinowitz et al.   NATURE

SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database

(2013) Timothy Jewison et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Molecular recognition and function of riboswitches

(2012) Alexander Serganov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Inhibition of  -KG-dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors

(2012) M. Xiao et al.   GENES & DEVELOPMENT

A framework for human microbiome research

(2012)   NATURE

Metabolic control of adult neural stem cell activity by Fasn-dependent lipogenesis

(2012) Marlen Knobloch et al.   NATURE

The circadian clock: a framework linking metabolism, epigenetics and neuronal function

(2012) Selma Masri et al.   NATURE REVIEWS NEUROSCIENCE

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

(2012) Kenneth Haug et al.   NUCLEIC ACIDS RESEARCH

HMDB 3.0—The Human Metabolome Database in 2013

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

Epigenetic regulation in pluripotent stem cells: a key to breaking the epigenetic barrier

(2012) A. Watanabe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Epigenetic control on cell fate choice in neural stem cells

(2012) Xiao-Ling Hu et al.   Protein & Cell

Cross Talk Between O-GlcNAcylation and Phosphorylation: Roles in Signaling, Transcription, and Chronic Disease

(2011) Gerald W. Hart et al.   Annual Review of Biochemistry

Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA

(2011) Atanas Kamburov et al.   BIOINFORMATICS

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

(2011) Alla Karnovsky et al.   BIOINFORMATICS

Renal Cyst Formation in Fh1-Deficient Mice Is Independent of the Hif/Phd Pathway: Roles for Fumarate in KEAP1 Succination and Nrf2 Signaling

(2011) Julie Adam et al.   CANCER CELL

Regulation of Immune Responses by Prostaglandin E2

(2011) P. Kalinski   JOURNAL OF IMMUNOLOGY

Birmingham Metabolite Library: a publicly accessible database of 1-D 1H and 2-D 1H J-resolved NMR spectra of authentic metabolite standards (BML-NMR)

(2011) Christian Ludwig et al.   Metabolomics

α-ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition

(2011) Christopher D Doucette et al.   Nature Chemical Biology

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

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

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

Differential radial capillary action of ligand assay for high-throughput detection of protein-metabolite interactions

(2011) K. G. Roelofs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Investigating the plant response to cadmium exposure by proteomic and metabolomic approaches

(2011) Florent Villiers et al.   PROTEOMICS

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

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses

(2010) Xiyan Li et al.   CELL

RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage

(2010) M. Schaefer et al.   GENES & DEVELOPMENT

MassBank: a public repository for sharing mass spectral data for life sciences

(2010) Hisayuki Horai et al.   JOURNAL OF MASS SPECTROMETRY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

mTOR: from growth signal integration to cancer, diabetes and ageing

(2010) Roberto Zoncu et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data

(2010) J. Xia et al.   NUCLEIC ACIDS RESEARCH

Integrating multiple 'omics' analysis for microbial biology: application and methodologies

(2009) W. Zhang et al.   MICROBIOLOGY-SGM

Amino-acid imbalance explains extension of lifespan by dietary restriction in Drosophila

(2009) Richard C. Grandison et al.   NATURE

Coupling HPLC to on-line, post-column (bio)chemical assays for high-resolution screening of bioactive compounds from complex mixtures

(2009) Shu-Yun Shi et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

(2008) Markus W. Covert et al.   BIOINFORMATICS

Update of the LIPID MAPS comprehensive classification system for lipids

(2008) Eoin Fahy et al.   JOURNAL OF LIPID RESEARCH