The metabolome 18 years on: a concept comes of age

Development and Application of Ultra-Performance Liquid Chromatography-TOF MS for Precision Large Scale Urinary Metabolic Phenotyping

(2016) Matthew R. Lewis et al.   ANALYTICAL CHEMISTRY

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

The microbiota in adaptive immune homeostasis and disease

(2016) Kenya Honda et al.   NATURE

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

A novel methodology for in vivo endoscopic phenotyping of colorectal cancer based on real-time analysis of the mucosal lipidome: a prospective observational study of the iKnife

(2016) James Alexander et al.   SURGICAL ENDOSCOPY AND OTHER INTERVENTIONAL TECHNIQUES

MetMaxStruct: A Tversky-Similarity-Based Strategy for Analysing the (Sub)Structural Similarities of Drugs and Endogenous Metabolites

(2016) Steve O'Hagan et al.   Frontiers in Pharmacology

Point-and-shoot: rapid quantitative detection methods for on-site food fraud analysis – moving out of the laboratory and into the food supply chain

(2015) David I. Ellis et al.   Analytical Methods

MetaMapR: pathway independent metabolomic network analysis incorporating unknowns: Fig. 1.

(2015) Dmitry Grapov et al.   BIOINFORMATICS

A Call for Systematic Research on Solute Carriers

(2015) Adrián César-Razquin et al.   CELL

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

(2015) Andrew Currin et al.   CHEMICAL SOCIETY REVIEWS

Retention projection enables accurate calculation of liquid chromatographic retention times across labs and methods

(2015) Daniel Abate-Pella et al.   JOURNAL OF CHROMATOGRAPHY A

Cheaper faster drug development validated by the repositioning of drugs against neglected tropical diseases

(2015) K. Williams et al.   Journal of the Royal Society Interface

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

(2015) Reza M. Salek et al.   Metabolomics

Data standards can boost metabolomics research, and if there is a will, there is a way

(2015) Philippe Rocca-Serra et al.   Metabolomics

Human-level control through deep reinforcement learning

(2015) Volodymyr Mnih et al.   NATURE

Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis

(2015) Douglas B. Kell et al.   TRENDS IN BIOTECHNOLOGY

Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly

(2015) Pedro Mendes et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

What would be the observable consequences if phospholipid bilayer diffusion of drugs into cells is negligible?

(2015) Douglas B. Kell   TRENDS IN PHARMACOLOGICAL SCIENCES

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

(2015) James G Jeffryes et al.   Journal of Cheminformatics

The apparent permeabilities of Caco-2 cells to marketed drugs: magnitude, and independence from both biophysical properties and endogenite similarities

(2015) Steve O’Hagan et al.   PeerJ

Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer

(2015) Andy Kilianski et al.   GigaScience

MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis

(2014) James Bradbury et al.   BIOINFORMATICS

A ‘rule of 0.5’ for the metabolite-likeness of approved pharmaceutical drugs

(2014) Steve O′Hagan et al.   Metabolomics

Molecular phenotyping of a UK population: defining the human serum metabolome

(2014) Warwick B. Dunn et al.   Metabolomics

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

The solute carrier SLC35F2 enables YM155-mediated DNA damage toxicity

(2014) Georg E Winter et al.   Nature Chemical Biology

XTMS: pathway design in an eXTended metabolic space

(2014) Pablo Carbonell et al.   NUCLEIC ACIDS RESEARCH

Taking your breath away: metabolomics breathes life in to personalized medicine

(2014) Nicholas J.W. Rattray et al.   TRENDS IN BIOTECHNOLOGY

Predicting complex phenotype-genotype interactions to enable yeast engineering:Saccharomyces cerevisiaeas a model organism and a cell factory

(2013) Duygu Dikicioglu et al.   Biotechnology Journal

Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it

(2013) Douglas B. Kell   FEBS Journal

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database

(2013) Zheng-Jiang Zhu et al.   Nature Protocols

Intraoperative Tissue Identification Using Rapid Evaporative Ionization Mass Spectrometry

(2013) J. Balog et al.   Science Translational Medicine

Applications of the InChI in cheminformatics with the CDK and Bioclipse

(2013) Ola Spjuth et al.   Journal of Cheminformatics

InChI - the worldwide chemical structure identifier standard

(2013) Stephen Heller et al.   Journal of Cheminformatics

The role of reporting standards for metabolite annotation and identification in metabolomic studies

(2013) Reza M Salek et al.   GigaScience

Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast

(2012) Karin Lanthaler et al.   BMC BIOLOGY

The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so

(2012) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

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

(2012) Warwick B. Dunn et al.   Metabolomics

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

Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of “Unknown Function”

(2012) Stephanie M. Quanbeck et al.   Frontiers in Plant Science

Characterization of Isotopic Abundance Measurements in High Resolution FT-ICR and Orbitrap Mass Spectra for Improved Confidence of Metabolite Identification

(2011) Ralf J. M. Weber et al.   ANALYTICAL CHEMISTRY

The volatile compound BinBase mass spectral database

(2011) Kirsten Skogerson et al.   BMC BIOINFORMATICS

Pharmaceutical drug transport: the issues and the implications that it is essentially carrier-mediated only

(2011) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

(2011) Zeneng Wang et al.   NATURE

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry

(2011) Warwick B Dunn et al.   Nature Protocols

YMDB: the Yeast Metabolome Database

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

Human-competitive results produced by genetic programming

(2010) John R. Koza   Genetic Programming and Evolvable Machines

Robust Early Pregnancy Prediction of Later Preeclampsia Using Metabolomic Biomarkers

(2010) Louise C. Kenny et al.   HYPERTENSION

Uncultured microorganisms as a source of secondary metabolites

(2010) Kim Lewis et al.   JOURNAL OF ANTIBIOTICS

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

(2009) M. Brown et al.   ANALYST

Development and Performance of a Gas Chromatography−Time-of-Flight Mass Spectrometry Analysis for Large-Scale Nontargeted Metabolomic Studies of Human Serum

(2009) Paul Begley et al.   ANALYTICAL CHEMISTRY

Development of a Robust and Repeatable UPLC−MS Method for the Long-Term Metabolomic Study of Human Serum

(2009) Eva Zelena et al.   ANALYTICAL CHEMISTRY

Implications of the Dominant Role of Transporters in Drug Uptake by Cells (Supplementary Material)

(2009) Paul Dobson et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Environmental metabolomics: a critical review and future perspectives

(2009) Jacob G. Bundy et al.   Metabolomics

13C-based metabolic flux analysis

(2009) Nicola Zamboni et al.   Nature Protocols

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites

(2009) W. R. Wikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Automation of Science

(2009) Ross D. King et al.   SCIENCE

‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries

(2008) Paul D. Dobson et al.   DRUG DISCOVERY TODAY

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule?

(2008) Paul D. Dobson et al.   NATURE REVIEWS DRUG DISCOVERY