Andrew R. Jones

The paper presents a high-quality acetylation dataset and shows that transfer learning can achieve good performance with minimal data for identifying PTMs.

The paper creates a high-confidence human methylation atlas and develops a deep learning model for methylated peptide detection.

This study compares hepatic stress response pathways in humans and preclinical animal species, finding rodents have greater basal and adaptive capacity for mitigating chemical insults.

This study examines proteomic changes in human muscle constructs under microgravity and shows that HSP10 overexpression reduces these changes, suggesting a potential strategy for combating muscle atrophy.

This study uses AlphaFold 3 scores to assess gene model quality in three species, finding they strongly favor curated models and suggest combining scores from multiple tools improves accuracy.

The paper identifies an expansion of SUMO protease genes in cultivated rice, suggesting selective breeding pressure may drive this expansion and its potential role in stress responses.

The paper maps the functional importance of site-specific ubiquitination across the human proteome by analyzing conservation, perturbation, and machine learning scores.

This study creates the first complete SUMO Cell Atlas in eukaryotes, revealing how SUMO components vary spatially and are regulated during stress responses in Arabidopsis roots.

The paper predicts novel phosphorylation sites across eukaryotes using conservation analysis and evaluates their functional relevance by linking conservation patterns to protein functions and kinase evolution.

The paper shows ROS-induced IAA3/SHY2 multimerization regulates auxin responses during xerobranching and lateral root emergence in plants.

The paper develops a pan-gene catalogue for Asian cultivated rice by creating a reference panel of 16 cultivars and identifying core and cultivar-specific genes.

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.

The paper reanalyzes public DIA proteomics datasets to provide a baseline view of human protein expression across tissues and compares it with previous DDA results.

The paper reanalyzes public pig proteomics data to map baseline protein expression across 14 organs and compares it with human orthologs.

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.

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

The paper introduces get_pangenes to identify pangenes from genome alignments, showing it outperforms existing methods and confirms presence-absence variation in barley.

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.

The paper reanalyzes 24 public proteomics datasets to assess baseline protein abundance in 31 human organs and integrates the results into the Expression Atlas for combined proteomics and transcriptomics analysis.

The paper reanalyzes proteomics datasets from mouse and rat tissues to compare baseline protein expression across species and organs, finding high correlation among orthologs in brain, kidney, heart, and liver.

The paper estimates the false discovery rate of phosphosites in public databases and predicts a more realistic count of true phosphosites in the human proteome.

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.

The paper introduces mzMLb, a new mass spectrometry data format optimized for speed and storage, validated to outperform existing formats in performance and compatibility.

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.

VAPPER enables high-throughput analysis of variant antigen repertoires in African trypanosomes, providing profiles and comparisons with existing strains.

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.

The paper compares phosphoproteomics data from Arabidopsis and rice to identify shared phosphorylation motifs and biological processes, finding high conservation and species-specific differences.

The paper introduces two new data formats, proBAM and proBed, to integrate proteomics with genomics and transcriptomics data in proteogenomics studies.