Kerry A. Ramsbottom

Searching for Sulfotyrosines (sY) in a HA(pY)STACK

The paper identifies sulfotyrosine (sY) sites in the human phosphoproteome by distinguishing them from phosphorylation using mass error shifts and filters out false positives, finding 31 convincing sY sites.

Phosphorylation in the Plasmodium falciparum proteome: A meta-analysis of publicly available data sets

This paper performs a meta-analysis of 11 phosphoproteomics datasets to identify phosphorylated sites in Plasmodium falciparum and related species, revealing sequence motifs, conservation patterns, and structural context of phosphosites.

A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome

This study analyzes rice phosphoproteomics data to identify phosphosite variations across the rice pan-genome and their functional implications.

Assessing multiple evidence streams to decide on confidence for identification of post-translational modifications, within and across data sets

The paper introduces a pipeline to improve phosphosite identification confidence by combining multiple data sets and using decoy amino acids to estimate false localisation rates, resulting in more confident identifications.

A method for independent estimation of false localisation rate for phosphoproteomics

The paper introduces a method to independently estimate the false localisation rate in phosphoproteomics using decoy amino acids, showing that alanine and leucine provide reliable results.

Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles

The paper investigates sequence and structural differences between HLA-B alleles associated with anti-thyroid drug-induced agranulocytosis and control alleles to identify molecular mechanisms.

Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with Adverse Drug Reactions

This study evaluates four molecular docking programs to assess their ability to predict drug-HLA interactions for known adverse drug reactions, finding variable accuracy and highlighting limitations of homology models and receptor flexibility.