David S. Wishart

Identification of novel and known oocyte-specific genes using complementary DNA subtraction and microarray analysis in three different species.

Probing the structural determinants of type II' beta-turn formation in peptides and proteins.

Identification of a novel archaebacterial thioredoxin: determination of function through structure.

RefDB: a database of uniformly referenced protein chemical shifts.

Backbone 1H, 15N and 13C assignments for the human rhinovirus 3C protease (serotype 14).

Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts.

VADAR: a web server for quantitative evaluation of protein structure quality.

Structural and functional characterization of a thioredoxin-like protein (Mt0807) from Methanobacterium thermoautotrophicum.

The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli.

GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images.

Solution structures of reduced and oxidized bacteriophage T4 glutaredoxin.

NMR solution structure of the precursor for carnobacteriocin B2, an antimicrobial peptide from Carnobacterium piscicola.

Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations.

SuperPose: a simple server for sophisticated structural superposition.

PlasMapper: a web server for drawing and auto-annotating plasmid maps.

Dynamic relationships among type IIa bacteriocins: temperature effects on antimicrobial activity and on structure of the C-terminal amphipathic alpha helix as a receptor-binding region.

Circular genome visualization and exploration using CGView.

Synthesis and evaluation of keto-glutamine analogues as potent inhibitors of severe acute respiratory syndrome 3CLpro.

PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

BacMap: an interactive picture atlas of annotated bacterial genomes.

Complete 1H, 13C and 15N NMR assignments of MTH0776 from Methanobacterium thermoautotrophicum.

A simple method to adjust inconsistently referenced 13C and 15N chemical shift assignments of proteins.

Bioinformatics in drug development and assessment.

Dynamic cellular automata: an alternative approach to cellular simulation.

MovieMaker: a web server for rapid rendering of protein motions and interactions.

BASys: a web server for automated bacterial genome annotation.

Solution Structure of MTH0776 from Methanobacterium thermoautotrophicum.

A simple method to predict protein flexibility using secondary chemical shifts.

DrugBank: a comprehensive resource for in silico drug discovery and exploration.

Improving the accuracy of protein secondary structure prediction using structural alignment.

Accurate prediction of protein torsion angles using chemical shifts and sequence homology.

PREDITOR: a web server for predicting protein torsion angle restraints.

Automated bacterial genome analysis and annotation.

Metabolomics in monitoring kidney transplants.

HMDB: the Human Metabolome Database.

Computational systems biology in drug discovery and development: methods and applications.

NMR: prediction of protein flexibility.

The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts.

Proteomics and the human metabolome project.

Drug-target discovery in silico: using the web to identify novel molecular targets for drug action.

Current progress in computational metabolomics.

PPT-DB: the protein property prediction and testing database.

NMR solution structures of the apo and peptide-inhibited human rhinovirus 3C protease (Serotype 14): structural and dynamic comparison.

Improving early drug discovery through ADME modelling: an overview.

Application of the random coil index to studying protein flexibility.

BioSpider: a web server for automating metabolome annotations.

DrugBank: a knowledgebase for drugs, drug actions and drug targets.

Human Metabolome Database: completing the 'human parts list'.

Metabolomics: a complementary tool in renal transplantation.

Introduction to cheminformatics.

In silico drug exploration and discovery using DrugBank.

Identifying putative drug targets and potential drug leads: starting points for virtual screening and docking.

PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation.

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.

The human cerebrospinal fluid metabolome.

Protein contact order prediction from primary sequences.

CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data.

DrugBank and its relevance to pharmacogenomics.

PSA fluoroimmunoassays using anti-PSA ScFv and quantum-dot conjugates.

Applications of metabolomics in drug discovery and development.

HMDB: a knowledgebase for the human metabolome.

MetaboMiner--semi-automated identification of metabolites from 2D NMR spectra of complex biofluids.

In silico identification of genes in bacteriophage DNA.

Genomic sequence and activity of KS10, a transposable phage of the Burkholderia cepacia complex.

Exploring human metabolites using the human metabolome database.

Development of a novel virtual screening cascade protocol to identify potential trypanothione reductase inhibitors.

GeNMR: a web server for rapid NMR-based protein structure determination.

Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping.

MetaboAnalyst: a web server for metabolomic data analysis and interpretation.

Applications of machine learning in cancer prediction and prognosis.

Evidence for copurification of micronuclei in sucrose density gradient-enriched plasma membranes from cell lines.

Solid phase synthesis of acylglycine human metabolites.

T3DB: a comprehensively annotated database of common toxins and their targets.

Computational systems biology in cancer: modeling methods and applications.

SMPDB: The Small Molecule Pathway Database.

Computational approaches to metabolomics.

A probabilistic approach for validating protein NMR chemical shift assignments.

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

Transcriptional response of E. coli upon FimH-mediated fimbrial adhesion.

PROSESS: a protein structure evaluation suite and server.

Discovering drug targets through the web.

MetPA: a web-based metabolomics tool for pathway analysis and visualization.

DrugBank 3.0: a comprehensive resource for 'omics' research on drugs.

Computational strategies for metabolite identification in metabolomics.

Detailed biophysical characterization of the acid-induced PrP(c) to PrP(β) conversion process.

Interpreting protein chemical shift data.

The human serum metabolome.

Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra.

SHIFTX2: significantly improved protein chemical shift prediction.

Metabolomic data processing, analysis, and interpretation using MetaboAnalyst.

Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst.

PHAST: a fast phage search tool.

MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets.

Relative and regional stabilities of the hamster, mouse, rabbit, and bovine prion proteins toward urea unfolding assessed by nuclear magnetic resonance and circular dichroism spectroscopies.

Advances in metabolite identification.

The prion protein binds thiamine.

Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins.

Intermolecular transmission of superoxide dismutase 1 misfolding in living cells.

YMDB: the Yeast Metabolome Database.

The bacterial nanorecorder: engineering E. coli to function as a chemical recording device.

BacMap: an up-to-date electronic atlas of annotated bacterial genomes.

Prediction of skeletal muscle and fat mass in patients with advanced cancer using a metabolomic approach.

Discovery of small molecule inhibitors that interact with γ-tubulin.

Use of proteinase K nonspecific digestion for selective and comprehensive identification of interpeptide cross-links: application to prion proteins.

Exploring the essential collective dynamics of interacting proteins: application to prion protein dimers.

Development of Ecom₅₀ and retention index models for nontargeted metabolomics: identification of 1,3-dicyclohexylurea in human serum by HPLC/mass spectrometry.

Resolution-enhanced native acidic gel electrophoresis: a method for resolving, sizing, and quantifying prion protein oligomers.

Metabolomics and first-trimester prediction of early-onset preeclampsia.

Multi-platform characterization of the human cerebrospinal fluid metabolome: a comprehensive and quantitative update.

MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis.

METAGENassist: a comprehensive web server for comparative metagenomics.

Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.

Using multiple structural proteomics approaches for the characterization of prion proteins.

ECMDB: the E. coli Metabolome Database.

First-trimester metabolomic detection of late-onset preeclampsia.

HMDB 3.0--The Human Metabolome Database in 2013.

Differential metabolite profiles and salinity tolerance between two genetically related brown-seeded and yellow-seeded Brassica carinata lines.

The metabolomic profile of umbilical cord blood in neonatal hypoxic ischaemic encephalopathy.

Chapter 3: Small molecules and disease.

Metabolomic analysis for first-trimester Down syndrome prediction.

An improved method to detect correct protein folds using partial clustering.

MyCompoundID: using an evidence-based metabolome library for metabolite identification.

Nanopore analysis of wild-type and mutant prion protein (PrP(C)): single molecule discrimination and PrP(C) kinetics.

Metabolomic analysis for first-trimester trisomy 18 detection.

Translational biomarker discovery in clinical metabolomics: an introductory tutorial.

Small molecule inhibitors of ERCC1-XPF protein-protein interaction synergize alkylating agents in cancer cells.

INMEX--a web-based tool for integrative meta-analysis of expression data.

Recommendations of the wwPDB NMR Validation Task Force.

The human urine metabolome.

A simple method to measure protein side-chain mobility using NMR chemical shifts.

Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content.

Molecular docking of thiamine reveals similarity in binding properties between the prion protein and other thiamine-binding proteins.

SMPDB 2.0: big improvements to the Small Molecule Pathway Database.

DrugBank 4.0: shedding new light on drug metabolism.

Identification and characterization of ϕH111-1: A novel myovirus with broad activity against clinical isolates of Burkholderia cenocepacia.

Using isotopically-coded hydrogen peroxide as a surface modification reagent for the structural characterization of prion protein aggregates.

Metabolomic analysis of cold acclimation of Arctic Mesorhizobium sp. strain N33.

Metabolomic prediction of fetal congenital heart defect in the first trimester.

The food metabolome: a window over dietary exposure.

Lipopolysaccharide induced conversion of recombinant prion protein.

Brassica villosa, a system for studying non-glandular trichomes and genes in the Brassicas.

Shaking alone induces de novo conversion of recombinant prion proteins to β-sheet rich oligomers and fibrils.

In silico studies and fluorescence binding assays of potential anti-prion compounds reveal an important binding site for prion inhibition from PrP(C) to PrP(Sc).

Development of isotope labeling liquid chromatography mass spectrometry for mouse urine metabolomics: quantitative metabolomic study of transgenic mice related to Alzheimer's disease.

Salmonella phages and prophages: genomics, taxonomy, and applied aspects.

CSI 2.0: a significantly improved version of the Chemical Shift Index.

Identifying putative drug targets and potential drug leads: starting points for virtual screening and docking.

The use of metabolomics in population-based research.

Role of water in ligand binding to maltose-binding protein: insight from a new docking protocol based on the 3D-RISM-KH molecular theory of solvation.

Recombinant mouse prion protein alone or in combination with lipopolysaccharide alters expression of innate immunity genes in the colon of mice.

MetaboAnalyst 3.0--making metabolomics more meaningful.

Pathways with PathWhiz.

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

Metabolomic fingerprint of heart failure with preserved ejection fraction.

Accurate, fully-automated NMR spectral profiling for metabolomics.

NMR Exchange Format: a unified and open standard for representation of NMR restraint data.

Accessible surface area from NMR chemical shifts.

Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review.

Validation of metabolomic models for prediction of early-onset preeclampsia.

Correction: Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics.

Is Cancer a Genetic Disease or a Metabolic Disease?

A robust algorithm for optimizing protein structures with NMR chemical shifts.

Metabolome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants.

ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli.

Isolation of soluble scFv antibody fragments specific for small biomarker molecule, L-Carnitine, using phage display.

Sildenafil Therapy Normalizes the Aberrant Metabolomic Profile in the Comt(-/-) Mouse Model of Preeclampsia/Fetal Growth Restriction.

Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis.

Clinical phenotype clustering in cardiovascular risk patients for the identification of responsive metabotypes after red wine polyphenol intake.

Cancer Metabolomics and the Human Metabolome Database.

Emerging applications of metabolomics in drug discovery and precision medicine.

Introduction to Cheminformatics.

PHASTER: a better, faster version of the PHAST phage search tool.

Heatmapper: web-enabled heat mapping for all.

Using DrugBank for In Silico Drug Exploration and Discovery.

Detecting Renal Allograft Inflammation Using Quantitative Urine Metabolomics and CXCL10.

Metabolomic determination of pathogenesis of late-onset preeclampsia.

The future of NMR-based metabolomics.

Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis.

Metabolomics enables precision medicine: "A White Paper, Community Perspective".

Nano-Optomechanical Systems for Gas Chromatography.

SPLASH, a hashed identifier for mass spectra.

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.

YMDB 2.0: a significantly expanded version of the yeast metabolome database.

Improved Glucose Homeostasis in Obese Mice Treated With Resveratrol Is Associated With Alterations in the Gut Microbiome.

Role of polysaccharide and lipid in lipopolysaccharide induced prion protein conversion.

Exposome-Explorer: a manually-curated database on biomarkers of exposure to dietary and environmental factors.

Current and Future Perspectives on the Structural Identification of Small Molecules in Biological Systems.

Urinary metabolomics for noninvasive detection of antibody-mediated rejection in children after kidney transplantation.

GC-MS Metabolomics Identifies Metabolite Alterations That Precede Subclinical Mastitis in the Blood of Transition Dairy Cows.