Professor Andy Jones Bsc, MRes, PhD
Professor of Bioinformatics Biochemistry, Cell and Systems Biology
- Work email Andrew.Jones@liverpool.ac.uk
- Personal Websitehttps://www.liverpool.ac.uk/computational-biology-facility/
Research
Proteomics / metabolomics data analysis, software and data sharing
My group has developed several open source and one commercial software package for mass spectrometry (MS). These include:
- Proteolabels - Commercial software for label-based quantitative analysis, available from Waters Corp as an extension for Progenesis QI for proteomics
- ProteoAnnotator - free and open source software for proteogenomic analysis (mapping MS spectra against genomes) using multiple search engines
- lcmsWorld - software for high-performance 3D visualisation of LC-MS data.
I am also Chair of the Proteomics Standards Initiative and have been involved with the development of data standards for proteomics, such as mzIdentML and for metabolomics such as mzTab-M.
The group is developing approaches for understanding the profile, evolution and function of post-translational modification (PTMs) across animals, plants and eukaryotic pathogens.
Analysis of plant genomes and proteomes
My group is increasingly analysing and integrating multi-omics data on crops, particularly rice. Our first work in this area was via a BBSRC/Newton funded grant working with collaborators at BGI China, in which we developed and used a proteogenomics pipeline to provide protein-level evidence for ~8000 rice genes, discovery of over 100 novel genes not annotated in the canonical gene models, and suggested gene model revisions for ~700 genes (e.g. new splice junctions) through very large scale analysis of RNA Seq and mass spectrometry data in the public domain. We have also started to work on exploring the evolutionary conservartion of post-translational modifications (PTMs) in flowering plants, and potential discovery of crosstalk between different PTM sites.
In new work, we are interested in improving annotation of the rice genome, and particularly focussing on analysis of gene families involved in regulation (such as transcription factors) or signalling such as kinases.
Immunogenetics, adverse drug reactions and machine learning applied to biomedical data
Our group maintains and develops the popular Allele Frequency Net Database storing data on allele, haplotype and gene frequencies for immune-related genes (HLA, KIR, Cytokines) in healthy human populations, covering over 10M individuals. We have developed new portals for storing disease associations for KIR genes, and for capturing known associations between HLA alleles and adverse drug reactions (ADRs). We have also used molecular docking to understand associations between HLA protein structure and ADR mechanisms.
The group is also applying machine learning (ML) techniques for the analysis of clinical data, such as single antigen bead (SAB) technology for profiling patient antibodies prior to kidney transplants, with the Transplant Immunology lab at the Royal Liverpool hospital. We are also developing ML approaches for analysing flow cytometry data, used in blood cancer diagnosis with the Haemato Oncology Diagnostic Service (HODS).
Research Grants
Post-doctoral research assistant (PDRA) Statistical Analysis
DEFENCE SCIENCE & TECHNOLOGY LABORATORY (UK)
April 2023 - April 2026
An Integrated, Physiologically Based, Multiscale Platform to Humanise Preclinical Assessment of Fetal Drug Exposure and Toxicity During Pregnancy
WELLCOME TRUST (UK)
January 2024 - December 2031
COVID-19: Molecular mapping of SARS-Cov2 and the host response with multiomics mass spectrometry to stratify disease outcomes for therapeutic and diagnostic interventions.
UK RESEARCH AND INNOVATION
October 2020 - April 2022
Bench Fees for Kawinnat Sue-ob (201519816)
ROYAL THAI EMBASSY
June 2021 - May 2024
2021BBSRC-NSF/BIO: “Globally harmonized re-analysis and sharing of DIA quantitative proteomics datasets and spectral library data”
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
June 2023 - May 2026
Bioinformatics resources for kinetoplastid organisms and their hosts
WELLCOME TRUST (UK)
March 2020 - February 2025
FungiDB: An integrated bioinformatics resource for fungi and oomycetes
WELLCOME TRUST (UK)
November 2018 - November 2024
SUMOcode: deciphering how SUMOylation controls environmental stress responses in plants
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
February 2021 - January 2026
GRAPPA - Global compRehensive Atlas of Peptide and Protein Abundance
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
August 2020 - July 2023
2019BBSRC-NSF/BIO - Globally coordinated pan-Oryza genomes, proteomes and pathways
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
December 2020 - November 2024
PhosphoX-db: A web-based bioinformatics platform for studying non-canonical phosphorylation
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
September 2018 - June 2020
PDRA Statistical Analysis
DEFENCE SCIENCE & TECHNOLOGY LABORATORY (UK)
January 2019 - January 2023
Non-canonical protein phosphorylation in human cancer cells
NORTH WEST CANCER RESEARCH INCORPORATING CLATTERBRIDGE CANCER RESEARCH (UK)
June 2018 - January 2022
Analysis of the dynamic sulfotyrosine proteome
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
September 2019 - February 2023
Integrating global resources for cross-species PTMs
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
October 2019 - June 2023
Big Hypotheses: A Fully Parallelised Bayesian Inference Solution
ENGINEERING & PHYSICAL SCIENCES RESEARCH COUNCIL
April 2018 - September 2024
From Pathway Discovery to Re-engineering
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
May 2016 - July 2020
Meta-Analysis
DEFENCE SCIENCE & TECHNOLOGY LABORATORY (UK)
July 2017 - February 2020
Delivering a production platform and datlas for nexr generation biomarker dicovery, validation and assay development in clinical proteomics
MEDICAL RESEARCH COUNCIL
April 2017 - March 2020
Pathfinder – exploring the commercial market for multi-omics analysis software
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
May 2017 - August 2017
Pathfinder – market research for lcmsWorld
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
April 2016 - June 2016
lcmsWorld – multi-dimensional visualisation for mass spectrometry
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
April 2016 - September 2017
NonLinear Dynamics Case award
NONLINEAR DYNAMICS LTD (UK)
September 2015 - September 2017
Bayesian Quantitative Proteomics
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
September 2015 - March 2019
Bioinformatics infrastructure for linking proteomics and genomics to support next-generation rice research
DEPARTMENT FOR BUSINESS, ENERGY AND INDUSTRIAL STRATEGY (BEIS) (UK)
January 2016 - June 2018
Biology from bioinformatics: developing a suite of data analytical and visualisations tools downstream of quantitative mass spectrometry workflows.
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL, WATERS CORPORATION (UK)
September 2015 - August 2017
Sparking Impact
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
June 2013 - July 2014
PROCESS - Proteomics data Collection, Software and Standards to support open access and long term management of data
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
November 2013 - October 2016
ProteomeXchange: International Data Exchange and Data Representation Standards for Proteomics
EUROPEAN COMMISSION
January 2011 - June 2014
An integrated open source software resource for quantitative proteomics
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
January 2011 - January 2016
The PPP-labels software for quantitative proteomics
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
September 2014 - September 2015
ProteoGenomics: dynamic linkage of genomes and proteomes through Ensembl and ProteomeXchange
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
July 2014 - December 2016
Informatics tools for exploiting ion mobility mass spectral data in proteomics
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
February 2010 - October 2010
Developing proteome-bioinformatics methods for a large scale refinement of gene models in Apicomplexan parasites
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
July 2009 - June 2012
ProteoFormer – a software toolkit for top-down proteomics
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
July 2014 - November 2015
Standards-compliant software tools for curation and public deposition of proteomics data
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
October 2010 - April 2012
NIH National Institute of allergy and infectious diseases
NATIONAL INSTITUTES OF HEALTH (USA)
November 2010 - October 2013
Open source pipelines for integrated metabolomics analysis by NMR and mass spectrometry
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
November 2015 - December 2016
A Europe-wide Strategy to enhance Transplantation of highly sensitized patients on basis of Acceptable HLA Mismatches (EUROSTAM)
ROYAL LIVERPOOL AND BROADGREEN UNIVERSITY HOSPITALS NHS TRUST (UK)
July 2013 - December 2015
Building the PTM map of the human genome through commensal computing
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
February 2014 - February 2017