Wright, James Christopher
My work is focussed on proteomic bioinformatics, developing new tools, pipelines and methods for quantitative proteomics data analysis, proteogenomic studies, and post translational modification discovery. This has included the continued development of MascotPercolator as a tool for improving spectral identification scoring in proteomics experiments, software to align, quantify and normalise HDMSe dataset for proteomic profiling of tissues, and tools to detect and validate unexpected modifications in proteomics datasets. I am also heavily involved in the development of workflows for proteogenomic data analysis for genome annotation.
Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
Cell reports 2017;20;9;2201-2214
Flexible Data Analysis Pipeline for High-Confidence Proteogenomics.
Journal of proteome research 2016;15;12;4686-4695
DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics.
Journal of proteomics & bioinformatics 2016;9;6;176-180
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
Nature communications 2016;7;11778
Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever.
The Journal of experimental medicine 2016;213;6;1061-77
Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.
Nucleic acids research 2016;44;D1;D746-52
Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation.
Journal of proteomics 2014;103;1-14
The OMSSAPercolator: an automated tool to validate OMSSA results.
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
Molecular & cellular proteomics : MCP 2012;11;12;1682-9
Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator.
Molecular & cellular proteomics : MCP 2012;11;8;478-91
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.
Genome research 2011;21;5;756-67
Cross species proteomics.
Methods in molecular biology (Clifton, N.J.) 2010;604;123-35
Recent developments in proteome informatics for mass spectrometry analysis.
Combinatorial chemistry & high throughput screening 2009;12;2;194-202
Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger.
BMC genomics 2009;10;61