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ECMDB: The E. coli Metabolome Database
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/jms.1777openalex-snapshot
MassBank: a public repository for sharing mass spectral data for life sciences
inferredcites →https://doi.org/10.1007/s11306-009-0168-0openalex-snapshot
Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research
inferredcites →https://doi.org/10.1016/0022-5193(70)90117-7openalex-snapshot
System theoretic analysis of models: Computer simulation of a living cell
inferredcites →https://doi.org/10.1016/j.ab.2007.07.022openalex-snapshot
Microbial metabolomics: Toward a platform with full metabolome coverage
inferredcites →https://doi.org/10.1021/ac7023409openalex-snapshot
Global Metabolic Profiling of Escherichia coli Cultures: an Evaluation of Methods for Quenching and Extraction of Intracellular Metabolites
inferredcites →https://doi.org/10.1021/cb900271ropenalex-snapshot
Exploring Disease through Metabolomics
inferredcites →https://doi.org/10.1021/ci00057a005openalex-snapshot
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
inferredcites →https://doi.org/10.1038/msb4100155openalex-snapshot
A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information
inferredcites →https://doi.org/10.1038/nchembio.186openalex-snapshot
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
inferredcites →https://doi.org/10.1073/pnas.120163297openalex-snapshot
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
inferredcites →https://doi.org/10.1093/bib/bbm030openalex-snapshot
Current Progress in computational metabolomics
inferredcites →https://doi.org/10.1093/bioinformatics/btq476openalex-snapshot
The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports
inferredcites →https://doi.org/10.1093/nar/28.1.60openalex-snapshot
EcoGene: a genome sequence database for Escherichia coli K-12
inferredcites →https://doi.org/10.1093/nar/gkh108openalex-snapshot
The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli
inferredcites →https://doi.org/10.1093/nar/gki028openalex-snapshot
EchoBASE: an integrated post-genomic database for Escherichia coli
inferredcites →https://doi.org/10.1093/nar/gkj067openalex-snapshot
DrugBank: a comprehensive resource for in silico drug discovery and exploration
inferredcites →https://doi.org/10.1093/nar/gkj405openalex-snapshot
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005
inferredcites →https://doi.org/10.1093/nar/gkn810openalex-snapshot
HMDB: a knowledgebase for the human metabolome
inferredcites →https://doi.org/10.1093/nar/gkp1002openalex-snapshot
SMPDB: The Small Molecule Pathway Database
inferredcites →https://doi.org/10.1093/nar/gkp934openalex-snapshot
T3DB: a comprehensively annotated database of common toxins and their targets
inferredcites →https://doi.org/10.1093/nar/gkq1018openalex-snapshot
Reactome: a database of reactions, pathways and biological processes
inferredcites →https://doi.org/10.1093/nar/gkq1143openalex-snapshot
EcoCyc: a comprehensive database of Escherichia coli biology
inferredcites →https://doi.org/10.1093/nar/gkr916openalex-snapshot
YMDB: the Yeast Metabolome Database
inferredcites →https://doi.org/10.1093/nar/gkr981openalex-snapshot
Reorganizing the protein space at the Universal Protein Resource (UniProt)
inferredcites →https://doi.org/10.1093/nar/gkr988openalex-snapshot
KEGG for integration and interpretation of large-scale molecular data sets
inferredcites →https://doi.org/10.1093/nar/gks060openalex-snapshot
A transposase strategy for creating libraries of circularly permuted proteins
inferredcites →https://doi.org/10.1093/nar/gks374openalex-snapshot
MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis
inferredcites →https://doi.org/10.1126/science.1132067openalex-snapshot
Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations
inferredcites →https://doi.org/10.1126/science.277.5331.1453openalex-snapshot
The Complete Genome Sequence of Escherichia coli K-12
inferredcites →https://doi.org/10.1142/9789812772435_0015openalex-snapshot
BIOSPIDER: A WEB SERVER FOR AUTOMATING METABOLOME ANNOTATIONS
inferredcites →https://doi.org/10.1186/1471-2105-9-507openalex-snapshot
MetaboMiner – semi-automated identification of metabolites from 2D NMR spectra of complex biofluids
inferredcites →https://doi.org/10.1186/1752-0509-6-30openalex-snapshot
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Introduction to Cheminformatics
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Introduction to Cheminformatics
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Positional Enrichment by Proton Analysis (PEPA): A One‐Dimensional 1H‐NMR Approach for 13C Stable Isotope Tracer Studies in Metabolomics
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High‐Throughput Metabolomics by 1D NMR
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Relationship between Protein Expression Pattern and Host Metabolome Perturbation as Monitored by Two‐Dimensional NMR Spectroscopy
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Comparing the Chemical Structure and Protein Content of ChEMBL, DrugBank, Human Metabolome Database and the Therapeutic Target Database
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Introduction to Microbial Metabolomics
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Introduction to Multi-Omics
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Reconciling Inconsistent Molecular Structures from Biochemical Databases
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Data Science Driven Drug Repurposing for Metabolic Disorders
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Computer-Aided Synthesis Planning for Biocatalysis
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A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database
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Bacteria as sensors: Real-time NMR analysis of extracellular metabolites detects sub-lethal amounts of bactericidal molecules released from functionalized materials
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Enzyme promiscuity in the field of synthetic biology applied to white biotechnology: Opportunities and weaknesses
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Isoleucyl-tRNA synthetase mutant based whole-cell biosensor for high-throughput selection of isoleucine overproducers
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Flux analysis and metabolomics for systematic metabolic engineering of microorganisms
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The metabolome of an E. coli CRISPRi library identifies benefits of minimal metabolite levels and targets for engineering
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Actinobacteria: Current research and perspectives for bioremediation of pesticides and heavy metals
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The allosteric control mechanism of bacterial glycogen biosynthesis disclosed by cryoEM
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Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery
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Early detection of bacteria in the lag phase using the distribution of relaxation times analysis
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High-Energy Ball Milling as a novel method to mecanolyze raw material for bio-H2 production by dark fermentations of Escherichia coli
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Survival of membrane-damaged Escherichia coli in a cytosol-mimicking solution
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Current state-of-the-art of separation methods used in LC-MS based metabolomics and lipidomics
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Efficient bacterial disinfection based on an integrated nanoporous titanium dioxide and ruthenium oxide bifunctional approach
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Evaluation of the metabolic response of Escherichia coli to electrolysed water by 1H NMR spectroscopy
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Recent developments and applications of metabolomics in microbiological investigations
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Applications of chromatography-ultra high-resolution MS for stable isotope-resolved metabolomics (SIRM) reconstruction of metabolic networks
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Microbial metabolomics: From novel technologies to diversified applications
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Optical phenotypic tracking: Advancing rapid toward culture-free antimicrobial susceptibility testing
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Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential
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RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli
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Multi-omic based production strain improvement (MOBpsi) for bio-manufacturing of toxic chemicals
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Credentialing Features: A Platform to Benchmark and Optimize Untargeted Metabolomic Methods
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Metabolomics Beyond Spectroscopic Databases: A Combined MS/NMR Strategy for the Rapid Identification of New Metabolites in Complex Mixtures
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nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data
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Annotation: A Computational Solution for Streamlining Metabolomics Analysis
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Expanding the Coverage of the Metabolome with Nitrogen-Based NMR
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Peak Annotation and Verification Engine for Untargeted LC–MS Metabolomics
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Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics
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Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships
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Metabolomic Coverage of Chemical-Group-Submetabolome Analysis: Group Classification and Four-Channel Chemical Isotope Labeling LC-MS
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Advanced Methods for MALDI-MS Imaging of the Chemical Communication in Microbial Communities
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Quinone Reductase 2 Dimerization is Dynamically Driven by Ligand Binding
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In Silico Exploration of Metabolite-Derived Soft Materials Using a Chemical Reaction Network
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NMR-Based Serum Metabolomics Discriminates Takayasu Arteritis from Healthy Individuals: A Proof-of-Principle Study
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Qualitative Alterations of Bacterial Metabolome after Exposure to Metal Nanoparticles with Bactericidal Properties: A Comprehensive Workflow Based on 1H NMR, UHPLC-HRMS, and Metabolic Databases
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Continuous, Nondestructive Detection of Microorganism Growth at Buried Interfaces with Vascularized Polymers
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Electrostatically Regulated Active Site Assembly Governs Reactivity in Nonheme Iron Halogenases
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Reaction pathway engineering converts a radical hydroxylase into a halogenase
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Plant and microbial sciences as key drivers in the development of metabolomics research
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The tRNA A76 Hydroxyl Groups Control Partitioning of the tRNA-dependent Pre- and Post-transfer Editing Pathways in Class I tRNA Synthetase
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Quantitative Proteomics Analysis Reveals the Min System of Escherichia coli Modulates Reversible Protein Association with the Inner Membrane
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Applied Metabolomics for Plant Biotechnology
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ChemDistiller: an engine for metabolite annotation in mass spectrometry
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The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
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ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli
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PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more
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PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database
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Regioselective control of biocatalytic C–H activation and halogenation
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Bacterially produced GABA protects neurons from degeneration
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Evolution of the analytical scattering model of live Escherichia coli
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Defining metabolic niches for marine microbial heterotrophs
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Impact of Antibiotics with Various Target Sites on the Metabolome of Staphylococcus aureus
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Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate
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Single-Cell Approach Reveals Intercellular Heterogeneity in Phage-Producing Capacities
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Rapid SERS Detection of Thiol-Containing Natural Products in Culturing Complex
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Application of string similarity ratio and edit distance in automatic metabolite reconciliation comparing reconstructions and models
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Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes
inferred← citeshttps://doi.org/10.1186/s12934-019-1156-3openalex-snapshot
Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data
inferred← citeshttps://doi.org/10.1186/s12934-021-01557-8openalex-snapshot
Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae
inferred← citeshttps://doi.org/10.1186/s13321-016-0174-yopenalex-snapshot
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy
inferred← citeshttps://doi.org/10.1186/s13321-022-00587-7openalex-snapshot
An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts
inferred← citeshttps://doi.org/10.1186/s13578-015-0018-xopenalex-snapshot
Metabolomic profiling of Burkholderia pseudomallei using UHPLC-ESI-Q-TOF-MS reveals specific biomarkers including 4-methyl-5-thiazoleethanol and unique thiamine degradation pathway
inferred← citeshttps://doi.org/10.1371/journal.pbio.3000638openalex-snapshot
Bacterially produced metabolites protect C. elegans neurons from degeneration
inferred← citeshttps://doi.org/10.1371/journal.pone.0100385openalex-snapshot
IIS – Integrated Interactome System: A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a Variety of Data Sources and Tools
inferred← citeshttps://doi.org/10.1371/journal.pone.0177233openalex-snapshot
Relationship between recombinant protein expression and host metabolome as determined by two-dimensional NMR spectroscopy
inferred← citeshttps://doi.org/10.1371/journal.ppat.1004104openalex-snapshot
Combined Systems Approaches Reveal Highly Plastic Responses to Antimicrobial Peptide Challenge in Escherichia coli
inferred← citeshttps://doi.org/10.15252/embr.201338283openalex-snapshot
Metabolomic strategies for the identification of new enzyme functions and metabolic pathways
inferred← citeshttps://doi.org/10.18174/416473openalex-snapshot
Metabolic modeling to understand and redesign microbial systems
inferred← citeshttps://doi.org/10.2478/amns-2024-0885openalex-snapshot
Biotechnological for improving maize grain storage tolerance: progress and prospects
inferred← citeshttps://doi.org/10.3136/fstr.fstr-d-25-00114openalex-snapshot
Molecular network analysis of food materials: workflow and applications
inferred← citeshttps://doi.org/10.32657/10356/69468openalex-snapshot
Identification of potential common cyclic-di-GMP regulated biomarkers among three gram negative bacteria via transcriptomic and metabolomic profiling
inferred← citeshttps://doi.org/10.3389/fceng.2023.1142226openalex-snapshot
Central carbon metabolite profiling reveals vector-associated differences in the recombinant protein production host Escherichia coli BL21
inferred← citeshttps://doi.org/10.3390/ijms24044219openalex-snapshot
E. coli Secretome Metabolically Modulates MDA-MB-231 Breast Cancer Cells’ Energy Metabolism
inferred← citeshttps://doi.org/10.3390/metabo10020074openalex-snapshot
Absolute Quantification of the Central Carbon Metabolome in Eight Commonly Applied Prokaryotic and Eukaryotic Model Systems
inferred← citeshttps://doi.org/10.3390/metabo13080938openalex-snapshot
Metabolic Alteration of MCF-7 Cells upon Indirect Exposure to E. coli Secretome: A Model of Studying the Microbiota Effect on Human Breast Tissue
inferred← citeshttps://doi.org/10.3390/metabo13091010openalex-snapshot
In Search of Complementary Extraction Methods for Comprehensive Coverage of the Escherichia coli Metabolome
inferred← citeshttps://doi.org/10.3390/metabo4020166openalex-snapshot
Stable Isotope Tracer Analysis in Isolated Mitochondria from Mammalian Systems
inferred← citeshttps://doi.org/10.3390/metabo8010021openalex-snapshot
Nanoparticle-Assisted Metabolomics
inferred← citeshttps://doi.org/10.3390/metabo9080169openalex-snapshot
Advances of Metabolomics in Fungal Pathogen–Plant Interactions
inferred← citeshttps://doi.org/10.3390/mps1040045openalex-snapshot
Influence of Metabolite Extraction Methods on 1H-NMR-Based Metabolomic Profiling of Enteropathogenic Yersinia
inferred← citeshttps://doi.org/10.3945/ajcn.113.076133openalex-snapshot
The food metabolome: a window over dietary exposure
inferred← citeshttps://doi.org/10.4172/2153-0769.1000e137openalex-snapshot
Ontologies in Metabolomics
inferred← citeshttps://doi.org/10.52403/ijhsr.20210560openalex-snapshot
Comparison of the Amount of Escherichia Coli in Refilled Drinking Water at the Depot with Bottled Drinking Water
inferred← citeshttps://doi.org/10.6084/m9.figshare.14189592openalex-snapshot
Additional file 1 of Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae
inferred← citeshttps://doi.org/10.6084/m9.figshare.14189595openalex-snapshot
Additional file 2 of Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae
inferred← citeshttps://doi.org/10.64898/2026.06.04.730285openalex-snapshot
Structural and Catalytic Architecture of the Cysteine Synthase Cys1a
inferred← citeshttps://doi.org/10.70675/94ed4222z29f1z4fc3z9b7bzcef000259383openalex-snapshot
Exploration de la face cachée du métabolisme bactérien chez Acinetobacter baylyi ADP1
inferred← citeshttps://doi.org/10.70675/a9f2181az8cd4z498dz87adz398d98df9f99openalex-snapshot
Impacts d'une exposition prénatale au bisphénol A sur la fonction thyroïdienne et le métabolome du système nerveux central fœtal
inferred← citeshttps://doi.org/10.7554/elife.54207openalex-snapshot
Underground isoleucine biosynthesis pathways in E. coli
inferred← citeshttps://doi.org/10.7939/r3tt3qopenalex-snapshot
The use of modern metabolomics and proteomics to address the health challenges facing the Canadian cattle industry
inferred← citeshttps://doi.org/10.7939/r3vd6pj8bopenalex-snapshot
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