Published in Ther Drug Monit on December 01, 2005
HMDB: the Human Metabolome Database. Nucleic Acids Res (2007) 13.38
HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res (2008) 11.23
HMDB 3.0--The Human Metabolome Database in 2013. Nucleic Acids Res (2012) 9.21
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics (2012) 5.95
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics (2010) 5.77
MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res (2009) 5.70
The human serum metabolome. PLoS One (2011) 5.55
Mass spectrometry-based metabolomics. Mass Spectrom Rev (2006) 5.23
Innovation: Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol (2012) 5.19
Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc (2011) 4.13
FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal Chem (2009) 3.71
Mass spectral molecular networking of living microbial colonies. Proc Natl Acad Sci U S A (2012) 3.56
MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res (2012) 3.32
Discovery of a class of endogenous mammalian lipids with anti-diabetic and anti-inflammatory effects. Cell (2014) 3.03
An accelerated workflow for untargeted metabolomics using the METLIN database. Nat Biotechnol (2012) 2.56
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res (2010) 2.32
Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research. Metabolomics (2009) 2.21
Global metabolic profiling procedures for urine using UPLC-MS. Nat Protoc (2010) 2.18
XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal Chem (2008) 2.10
Colonic contribution to uremic solutes. J Am Soc Nephrol (2011) 1.98
Metabolite annotations based on the integration of mass spectral information. Plant J (2008) 1.97
Nutritional metabolomics: progress in addressing complexity in diet and health. Annu Rev Nutr (2012) 1.89
Activity-based protein profiling for biochemical pathway discovery in cancer. Nat Rev Cancer (2010) 1.84
Dividing cells regulate their lipid composition and localization. Cell (2014) 1.84
Advances in structure elucidation of small molecules using mass spectrometry. Bioanal Rev (2010) 1.76
How large is the metabolome? A critical analysis of data exchange practices in chemistry. PLoS One (2009) 1.73
Metabolomic analysis of the cerebrospinal fluid reveals changes in phospholipase expression in the CNS of SIV-infected macaques. J Clin Invest (2008) 1.66
xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data. BMC Bioinformatics (2013) 1.61
Molecular networking as a dereplication strategy. J Nat Prod (2013) 1.57
MetaboLights: towards a new COSMOS of metabolomics data management. Metabolomics (2012) 1.53
Multiple organic anion transporters contribute to net renal excretion of uric acid. Physiol Genomics (2008) 1.53
Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nat Protoc (2010) 1.51
Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses. Anal Chem (2014) 1.49
Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nat Protoc (2013) 1.49
Acylcarnitines are anticoagulants that inhibit factor Xa and are reduced in venous thrombosis, based on metabolomics data. Blood (2015) 1.44
Predicting network activity from high throughput metabolomics. PLoS Comput Biol (2013) 1.44
X13CMS: global tracking of isotopic labels in untargeted metabolomics. Anal Chem (2014) 1.43
A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice. ISME J (2013) 1.42
Discovery of Metabolic Biomarkers for Duchenne Muscular Dystrophy within a Natural History Study. PLoS One (2016) 1.39
ECMDB: the E. coli Metabolome Database. Nucleic Acids Res (2012) 1.38
Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence. Proc Biol Sci (2016) 1.38
Molecular formula and METLIN Personal Metabolite Database matching applied to the identification of compounds generated by LC/TOF-MS. J Biomol Tech (2008) 1.38
LC-MS-based metabolomics. Mol Biosyst (2011) 1.36
Molecular cartography of the human skin surface in 3D. Proc Natl Acad Sci U S A (2015) 1.32
Variability analysis of human plasma and cerebral spinal fluid reveals statistical significance of changes in mass spectrometry-based metabolomics data. Anal Chem (2009) 1.30
Understanding and classifying metabolite space and metabolite-likeness. PLoS One (2011) 1.29
Lipidomics at the interface of structure and function in systems biology. Chem Biol (2011) 1.29
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol (2016) 1.27
The Drosophila foraging gene mediates adult plasticity and gene-environment interactions in behaviour, metabolites, and gene expression in response to food deprivation. PLoS Genet (2009) 1.25
Metabolite identification and quantitation in LC-MS/MS-based metabolomics. Trends Analyt Chem (2012) 1.23
Lipidomics profiling by high-resolution LC-MS and high-energy collisional dissociation fragmentation: focus on characterization of mitochondrial cardiolipins and monolysocardiolipins. Anal Chem (2010) 1.23
Primer on agar-based microbial imaging mass spectrometry. J Bacteriol (2012) 1.22
Radiation metabolomics and its potential in biodosimetry. Int J Radiat Biol (2011) 1.20
Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis. Anal Chim Acta (2012) 1.20
A statistically rigorous test for the identification of parent-fragment pairs in LC-MS datasets. Anal Chem (2010) 1.20
Untargeted metabolomics identifies enterobiome metabolites and putative uremic toxins as substrates of organic anion transporter 1 (Oat1). J Proteome Res (2011) 1.18
Microbial metabolomics. Curr Genomics (2011) 1.17
Metabolomics: beyond biomarkers and towards mechanisms. Nat Rev Mol Cell Biol (2016) 1.14
Metabolic differentiation of neuronal phenotypes by single-cell capillary electrophoresis-electrospray ionization-mass spectrometry. Anal Chem (2011) 1.14
LC-MS based serum metabolomics for identification of hepatocellular carcinoma biomarkers in Egyptian cohort. J Proteome Res (2012) 1.14
Identification of noninvasive biomarkers for alcohol-induced liver disease using urinary metabolomics and the Ppara-null mouse. J Proteome Res (2010) 1.13
Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Res (2015) 1.13
A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis. Nat Chem Biol (2012) 1.13
Global metabolic profiling of animal and human tissues via UPLC-MS. Nat Protoc (2012) 1.13
Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules. Proc Natl Acad Sci U S A (2013) 1.12
CASMI: And the Winner is . . . Metabolites (2013) 1.12
Qualitative analysis of algal secretions with multiple mass spectrometric platforms. J Chromatogr A (2012) 1.10
An untargeted metabolomic workflow to improve structural characterization of metabolites. Anal Chem (2013) 1.10
Serum lipidomics profiling using LC-MS and high-energy collisional dissociation fragmentation: focus on triglyceride detection and characterization. Anal Chem (2011) 1.09
Mass spectrometry of natural products: current, emerging and future technologies. Nat Prod Rep (2014) 1.09
PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools. BMC Bioinformatics (2012) 1.08
High-performance metabolic profiling of plasma from seven mammalian species for simultaneous environmental chemical surveillance and bioeffect monitoring. Toxicology (2012) 1.08
Identification of serum biomarkers of hepatocarcinoma through liquid chromatography/mass spectrometry-based metabonomic method. Anal Bioanal Chem (2011) 1.07
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des (2008) 1.07
In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids. Bioinformatics (2012) 1.06
Patch clamp electrophysiology and capillary electrophoresis-mass spectrometry metabolomics for single cell characterization. Anal Chem (2014) 1.06
Discovery of candidate serum proteomic and metabolomic biomarkers in ankylosing spondylitis. Mol Cell Proteomics (2011) 1.06
Development of Ecom₅₀ and retention index models for nontargeted metabolomics: identification of 1,3-dicyclohexylurea in human serum by HPLC/mass spectrometry. J Chem Inf Model (2012) 1.06
UPLC-MS-based urine metabolomics reveals indole-3-lactic acid and phenyllactic acid as conserved biomarkers for alcohol-induced liver disease in the Ppara-null mouse model. J Proteome Res (2011) 1.05
Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models. Biophys J (2010) 1.04
Untargeted metabolomics from biological sources using ultraperformance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS). J Vis Exp (2013) 1.03
Biomonitoring in the Era of the Exposome. Environ Health Perspect (2016) 1.03
Review: toxicometabolomics. J Appl Toxicol (2013) 1.03
Credentialing features: a platform to benchmark and optimize untargeted metabolomic methods. Anal Chem (2014) 1.03
Cancer cells incorporate and remodel exogenous palmitate into structural and oncogenic signaling lipids. Biochim Biophys Acta (2013) 1.02
Shotgun metabolomics approach for the analysis of negatively charged water-soluble cellular metabolites from mouse heart tissue. Anal Chem (2007) 1.02
Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification. Anal Chem (2014) 1.02
From differentiating metabolites to biomarkers. Anal Bioanal Chem (2009) 1.01
Targeted, LCMS-based Metabolomics for Quantitative Measurement of NAD(+) Metabolites. Comput Struct Biotechnol J (2013) 1.01
Computational mass spectrometry for small molecules. J Cheminform (2013) 1.01
Ion mobility derived collision cross sections to support metabolomics applications. Anal Chem (2014) 1.00
Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks. Plant Cell (2014) 1.00
CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. Nucleic Acids Res (2014) 1.00
Statistical methods for the analysis of high-throughput metabolomics data. Comput Struct Biotechnol J (2013) 1.00
Plasma metabolomics in human pulmonary tuberculosis disease: a pilot study. PLoS One (2014) 0.99
Personal genomes, quantitative dynamic omics and personalized medicine. Quant Biol (2013) 0.98
The intestinal metabolome: an intersection between microbiota and host. Gastroenterology (2014) 0.98
Upregulation of the phthiocerol dimycocerosate biosynthetic pathway by rifampin-resistant, rpoB mutant Mycobacterium tuberculosis. J Bacteriol (2012) 0.98
MetaboSearch: tool for mass-based metabolite identification using multiple databases. PLoS One (2012) 0.98
Qualitative and quantitative metabolomic investigation of single neurons by capillary electrophoresis electrospray ionization mass spectrometry. Nat Protoc (2013) 0.97
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem (2006) 15.00
Generation of induced pluripotent stem cells using recombinant proteins. Cell Stem Cell (2009) 11.65
Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science (2010) 10.30
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci U S A (2009) 5.86
Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease. Science (2007) 5.49
Innovation: Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol (2012) 5.19
Structure of the human histamine H1 receptor complex with doxepin. Nature (2011) 3.48
Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. Chem Biol (2010) 3.38
An assembly landscape for the 30S ribosomal subunit. Nature (2005) 3.33
Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des (2003) 3.29
A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury. Nat Med (2005) 3.26
XCMS Online: a web-based platform to process untargeted metabolomic data. Anal Chem (2012) 3.24
Assignment of endogenous substrates to enzymes by global metabolite profiling. Biochemistry (2004) 3.10
Metabolic oxidation regulates embryonic stem cell differentiation. Nat Chem Biol (2010) 3.06
Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics (2005) 2.83
Immunization with HIV-1 gp41 subunit virosomes induces mucosal antibodies protecting nonhuman primates against vaginal SHIV challenges. Immunity (2011) 2.82
Metabolomics implicates altered sphingolipids in chronic pain of neuropathic origin. Nat Chem Biol (2012) 2.76
Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. J Am Chem Soc (2010) 2.62
Microbial metalloproteomes are largely uncharacterized. Nature (2010) 2.62
An accelerated workflow for untargeted metabolomics using the METLIN database. Nat Biotechnol (2012) 2.56
Using siRNA in prophylactic and therapeutic regimens against SARS coronavirus in Rhesus macaque. Nat Med (2005) 2.55
Systemic gut microbial modulation of bile acid metabolism in host tissue compartments. Proc Natl Acad Sci U S A (2010) 2.52
Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol (2008) 2.38
Metabolomics identifies perturbations in human disorders of propionate metabolism. Clin Chem (2007) 2.31
The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming. Cell Res (2011) 2.30
Expanding coverage of the metabolome for global metabolite profiling. Anal Chem (2011) 2.28
Short telomeres and prognosis of hypertension in a chinese population. Hypertension (2009) 2.18
Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure (2011) 2.11
Clathrate nanostructures for mass spectrometry. Nature (2007) 2.10
From exogenous to endogenous: the inevitable imprint of mass spectrometry in metabolomics. J Proteome Res (2007) 2.08
Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes. J Mol Recognit (2009) 2.05
Nuclear hormone receptor targeted virtual screening. J Med Chem (2003) 2.05
Colonization-induced host-gut microbial metabolic interaction. MBio (2011) 2.04
The expanding role of mass spectrometry in metabolite profiling and characterization. Chembiochem (2005) 2.04
Solvent-dependent metabolite distribution, clustering, and protein extraction for serum profiling with mass spectrometry. Anal Chem (2006) 2.04
Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists. J Med Chem (2010) 1.88
Nonlinear data alignment for UPLC-MS and HPLC-MS based metabolomics: quantitative analysis of endogenous and exogenous metabolites in human serum. Anal Chem (2006) 1.81
Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol (2004) 1.79
Membrane cofactor protein is a receptor for adenoviruses associated with epidemic keratoconjunctivitis. J Virol (2004) 1.77
Toward 'omic scale metabolite profiling: a dual separation-mass spectrometry approach for coverage of lipid and central carbon metabolism. Anal Chem (2013) 1.76
Multiple ionization mass spectrometry strategy used to reveal the complexity of metabolomics. Anal Chem (2007) 1.75
Pathogenesis of emerging severe fever with thrombocytopenia syndrome virus in C57/BL6 mouse model. Proc Natl Acad Sci U S A (2012) 1.71
The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. PLoS Biol (2006) 1.70
Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins (2005) 1.69
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics (2006) 1.68
An animal model of MERS produced by infection of rhesus macaques with MERS coronavirus. J Infect Dis (2013) 1.67
miR-34a, a microRNA up-regulated in a double transgenic mouse model of Alzheimer's disease, inhibits bcl2 translation. Brain Res Bull (2009) 1.66
Metabolomic analysis of the cerebrospinal fluid reveals changes in phospholipase expression in the CNS of SIV-infected macaques. J Clin Invest (2008) 1.66
Statistical analysis and prediction of protein-protein interfaces. Proteins (2005) 1.65
ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins (2003) 1.63
Increased enzymatic O-GlcNAcylation of mitochondrial proteins impairs mitochondrial function in cardiac myocytes exposed to high glucose. J Biol Chem (2008) 1.62
Sepsis plasma protein profiling with immunodepletion, three-dimensional liquid chromatography tandem mass spectrometry, and spectrum counting. J Proteome Res (2006) 1.61
Soft protein-protein docking in internal coordinates. Protein Sci (2002) 1.60
GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins (2010) 1.57
Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics (2002) 1.56
Disseminating structural genomics data to the public: from a data dump to an animated story. Trends Biochem Sci (2006) 1.55
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem (2009) 1.54
Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking. Proc Natl Acad Sci U S A (2003) 1.53
Multiple organic anion transporters contribute to net renal excretion of uric acid. Physiol Genomics (2008) 1.53
Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science (2002) 1.52
Antioxidant or neurotrophic factor treatment preserves function in a mouse model of neovascularization-associated oxidative stress. J Clin Invest (2009) 1.51
The GPCR Network: a large-scale collaboration to determine human GPCR structure and function. Nat Rev Drug Discov (2012) 1.50
Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses. Anal Chem (2014) 1.49
Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nat Protoc (2013) 1.49
Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators. J Comput Aided Mol Des (2009) 1.48
Endothelial targeting of cowpea mosaic virus (CPMV) via surface vimentin. PLoS Pathog (2009) 1.47
The human early-life exposome (HELIX): project rationale and design. Environ Health Perspect (2014) 1.44
Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform (2004) 1.42
Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem (2008) 1.38
RGS9-2 negatively modulates L-3,4-dihydroxyphenylalanine-induced dyskinesia in experimental Parkinson's disease. J Neurosci (2007) 1.35
Docking and scoring with ICM: the benchmarking results and strategies for improvement. J Comput Aided Mol Des (2012) 1.34
Structure based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology (2010) 1.31
Variability analysis of human plasma and cerebral spinal fluid reveals statistical significance of changes in mass spectrometry-based metabolomics data. Anal Chem (2009) 1.30
Optimization and evaluation of metabolite extraction protocols for untargeted metabolic profiling of liver samples by UPLC-MS. Anal Chem (2010) 1.30
Meta-analysis of untargeted metabolomic data from multiple profiling experiments. Nat Protoc (2012) 1.29
Detection of viral agents in fecal specimens of monkeys with diarrhea. J Med Primatol (2007) 1.29
Liquid chromatography-mass spectrometry based global metabolite profiling: a review. Anal Chim Acta (2011) 1.29
Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins (2006) 1.29
Modeling of the aryl hydrocarbon receptor (AhR) ligand binding domain and its utility in virtual ligand screening to predict new AhR ligands. J Med Chem (2009) 1.28
Novel avian-origin human influenza A(H7N9) can be transmitted between ferrets via respiratory droplets. J Infect Dis (2013) 1.28
The structure of apo human glutamate dehydrogenase details subunit communication and allostery. J Mol Biol (2002) 1.27
Nanostructure-initiator mass spectrometry: a protocol for preparing and applying NIMS surfaces for high-sensitivity mass analysis. Nat Protoc (2008) 1.27
A nanostructure-initiator mass spectrometry-based enzyme activity assay. Proc Natl Acad Sci U S A (2008) 1.27