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List of works by Andrew Jones

16(th) IHIW: extending the number of resources and bioinformatics analysis for the investigation of HLA rare alleles.

scientific article

A DIGE study on the effects of salbutamol on the rat muscle proteome - an exemplar of best practice for data sharing in proteomics

scientific article

A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: application to emerging infectious diseases

scientific article published on 25 January 2015

A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis

scientific article published on 17 July 2012

A database for curating the associations between killer cell immunoglobulin-like receptors and diseases in worldwide populations

scientific article published on 12 April 2013

A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum

scientific article published on 15 May 2015

A software toolkit and interface for performing stable isotope labeling and top3 quantification using Progenesis LC-MS

scientific article

A standardized framing for reporting protein identifications in mzIdentML 1.2

scientific article

A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group

scientific article published on January 2006

A toolkit for capturing and sharing FuGE experiments

scientific article published on 17 September 2008

A tutorial for software development in quantitative proteomics using PSI standard formats

scientific article

Allele Frequencies Net Database: Improvements for storage of individual genotypes and analysis of existing data

scientific article

Allele frequencies database

scientific article

Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations

scientific article

Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations

scientific article

An analysis of extensible modelling for functional genomics data

scientific article

An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ

scientific article (publication date: February 2007)

An object model and database for functional genomics

scientific article published on 14 May 2004

An update on data standards for gel electrophoresis

scientific article

Annual spring meeting of the Proteomics Standards Initiative

scientific article published in October 2009

Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain

scientific article published in October 2008

Bioinformatics Challenges and Solutions in Proteomics as Quantitative Methods Mature ⬇️

scientific article published on July 17, 2012

Capture and analysis of quantitative proteomic data

scientific article

Computational phosphoproteomics: from identification to localization

scientific article

Controlled vocabularies and ontologies in proteomics: overview, principles and practice

scientific article

Data Access and Integration in the ISPIDER Proteomics Grid

Development of data representation standards by the human proteome organization proteomics standards initiative

scientific article

Embedding standards in metabolomics: the Metabolomics Society data standards task group

FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines

scientific article published on 21 February 2011

Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France

scientific article

FuGE: Functional Genomics Experiment Object Model

scientific article published on January 2006

FuGEFlow: data model and markup language for flow cytometry

scientific article

Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics.

scientific article published on 12 August 2015

Guidelines for reporting quantitative mass spectrometry based experiments in proteomics.

scientific article published on 14 March 2013

Guidelines for reporting the use of column chromatography in proteomics

Guidelines for reporting the use of gel electrophoresis in proteomics.

scientific article

Guidelines for reporting the use of gel image informatics in proteomics

scientific article published on 01 July 2010

How to submit MS proteomics data to ProteomeXchange via the PRIDE database

scientific article

IPeak: An open source tool to combine results from multiple MS/MS search engines

scientific article published on 6 May 2015

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

scientific article published on March 2009

In silico analysis of HLA associations with drug-induced liver injury: use of a HLA-genotyped DNA archive from healthy volunteers

scientific article

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

scientific article published on 17 June 2022

Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites

scientific article

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany

scientific article published on 9 October 2014

Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome

scientific article published in 2024

Minimum Reporting Guidelines for Proteomics Released by the Proteomics Standards Initiative

scientific article published on 01 October 2008

Modeling and managing experimental data using FuGE.

scientific article

Modulation of the host cell proteome by the intracellular apicomplexan parasite Toxoplasma gondii

scientific article

Numerical compression schemes for proteomics mass spectrometry data

scientific article

Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.

scientific article published in October 2013

Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation

scientific article published on 09 May 2022

Proposal for a standard representation of two-dimensional gel electrophoresis data

scientific article

ProteoAnnotator--open source proteogenomics annotation software supporting PSI standards.

scientific article

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

scientific article (publication date: March 2014)

Representation of selected-reaction monitoring data in the mzQuantML data standard

scientific article published on 5 June 2015

Semi-automatic tool to describe, store and compare proteomics experiments based on MIAPE compliant reports

scientific article published on 01 March 2010

Software for analysing ion mobility mass spectrometry data to improve peptide identification

scientific article

Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea

scientific article published in September 2010

Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA

scientific article (publication date: September 2012)

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

article

The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006.

scientific article published in April 2007

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

scientific article (publication date: 2013)

The PSI semantic validator: a framework to check MIAPE compliance of proteomics data

scientific article

The ProteoRed MIAPE web toolkit: a user-friendly framework to connect and share proteomics standards

scientific article

The Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

scientific article

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative

scientific article (publication date: September 2010)

The jmzQuantML programming interface and validator for the mzQuantML data standard

scientific article

The mzIdentML data standard for mass spectrometry-based proteomics results

scientific article (publication date: July 2012)

The mzIdentML data standard version 1.2, supporting advances in proteome informatics.

scientific article

The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics

scientific article (publication date: August 2013)

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

scientific article

The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.

scientific article published on 2 June 2015

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

scientific article published on 31 January 2018

The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation

scientific article published on 21 July 2008

Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML

scientific article (publication date: November 2013)

VAPPER: High-throughput variant antigen profiling in African trypanosomes of livestock

scientific article published on 01 September 2019

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

scientific article published on 28 October 2021

Visualisation and analysis of proteomic data from the procyclic form of Trypanosoma brucei

scientific article

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments

scientific article

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data

scientific article (publication date: March 2012)

jmzTab: a java interface to the mzTab data standard

scientific article

lcmsWorld: High-Performance 3D Visualization Software for Mass Spectrometry

scientific article published on 12 March 2021

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics

scientific article published on 13 February 2019

nmrML: a community supported open data standard for the description, storage, and exchange of NMR data

scientific article published on 16 October 2017

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