David Fenyo

RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database.

A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis.

Informatics and data management in proteomics.

A modular cross-linking approach for exploring protein interactions.

A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes.

Probity: a protein identification algorithm with accurate assignment of the statistical significance of the results.

The statistical significance of protein identification results as a function of the number of protein sequences searched.

A proteomics approach to the study of absorption, distribution, metabolism, excretion, and toxicity.

Phosphotyrosine signaling networks in epidermal growth factor receptor overexpressing squamous carcinoma cells.

Protein identification in complex mixtures.

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis.

Optimizing search conditions for the mass fingerprint-based identification of proteins.

SwePep, a database designed for endogenous peptides and mass spectrometry.

Reproducibility of LC-MS-based protein identification.

Detection of artifacts and peptide modifications in liquid chromatography/mass spectrometry data using two-dimensional signal intensity map data visualization.

Determining the overall merit of protein identification data sets: rho-diagrams and rho-scores.

Neuropeptidomics strategies for specific and sensitive identification of endogenous peptides.

Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs.

An automated method for scanning LC-MS data sets for significant peptides and proteins, including quantitative profiling and interactive confirmation.

Informatics development: challenges and solutions for MALDI mass spectrometry.

Use of DNA ladders for reproducible protein fractionation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for quantitative proteomics.

Rapid isolation and identification of bacteriophage T4-encoded modifications of Escherichia coli RNA polymerase: a generic method to study bacteriophage/host interactions.

Efficient identification of phosphorylation by mass spectrometric phosphopeptide fingerprinting.

Finding protein sequences using PROWL.

Validation of endogenous peptide identifications using a database of tandem mass spectra.

Screening for EphB signaling effectors using SILAC with a linear ion trap-orbitrap mass spectrometer.

Evaluation of the variation in sample preparation for comparative proteomics using stable isotope labeling by amino acids in cell culture.

Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei.

Rapid sensitive analysis of cysteine rich peptide venom components.

Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.

GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome.

The Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative. Preparation and characterisation of the carbonate-washed membrane standard.

Mass spectrometric protein identification using the global proteome machine.

Protein quantitation using mass spectrometry.

Modeling experimental design for proteomics.

Modeling mass spectrometry-based protein analysis.

High-Capacity Ion Trap Coupled to a Time-of-Flight Mass Spectrometer for Comprehensive Linked Scans with no Scanning Losses.

Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding.

Strategy for identifying dendritic cell-processed CD4+ T cell epitopes from the HIV gag p24 protein.

Comparative proteomic analysis of the ATP-sensitive K+ channel complex in different tissue types.

Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium.

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.

Atypical and classical memory B cells produce Plasmodium falciparum neutralizing antibodies.

Developments in biobanking workflow standardization providing sample integrity and stability.

Super-resolution fluorescence microscopy of the cardiac connexome reveals plakophilin-2 inside the connexin43 plaque.

Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines.

Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels.

Super-resolution imaging reveals that loss of the C-terminus of connexin43 limits microtubule plus-end capture and NaV1.5 localization at the intercalated disc.

A robust pipeline for rapid production of versatile nanobody repertoires.

Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome.

Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study.

The GPMDB REST interface.