Bessant Lab

News and Resources from the Bessant Bioinformatics Lab at QMUL

MSc Bioinformatics scholarships available

Queen Mary University of London’s shiny new MSc Bioinformatics programme starts on 22 September 2014. To help attract the very best applicants, scholarships of up to £5,000 are being offered. For all the details, see the MSc Bioinformatics course page.

Spectroscopy and machine learning – a winning combination for cancer diagnostics?

In our paper out today in TrAC Trends in Analytical Chemistry we look back on a decade of research into the application of machine learning to the diagnosis of cancer from spectral data. This combination of rapid analytical technique and automated data processing offers much promise as a fast, and in some cases non-invasive, diagnostic tool. So why isn’t it used yet in clinical practice? Our conclusion was that limited sample sizes and validation undermine the outcomes of most published studies in this area, leading us to recommend larger studies and public sharing of data to advance the field. For all the details, see the paper.

A new test for Crohn’s disease?

A few years ago, we embarked upon one of largest metabolomic profiling projects ever undertaken on gastroenterology patients. Colleagues collected and analysed blood, breath, faeces and urine from patients with a range of digestive disorders. We applied some particularly rigorous data analysis methods to the acquired data and the results have finally been published in Metabolomics. One finding stands out – Crohn’s disease appears to have a distinctive faecal metabolome. Find more details in the paper.

New MSc Bioinformatics course in London

We are launching a brand new MSc programme in bioinformatics here at Queen Mary University of London, starting in September 2014. This state-of-the-art course, taught by domain experts, aims to give biological and biomedical graduates the data analysis and coding skills that are essential in modern science. For more details, see the MSc Bioinformatics course page.

Our new textbook published

The second edition of Building Bioinformatics Solutions, the popular textbook co-authored by Conrad Bessant and former students Darren Oakley and Ian Shadforth has been published this week by Oxford University Press. This new version has been fully updated, with the web development chapter almost completely rewritten, and much new material added including a whole new chapter on software engineering (how to code properly!). For more details, see

Funded PhD studentship available

In collaboration with biomedical colleagues from the Blizard Institute, we have a fully funded Life Sciences Institute (LSI) studentship available, for October 2014 start. The project is in the area of data integration using the Galaxy platform. For more information, check out the link below.

Project details at QMUL web site

Deadline for applications is 31 January 2014.

Update: All LSI studentships for 2014 have now been filled.

Publications update

The second research paper from our Wellcome Trust project on gut disorders has recently been published in Inflammatory Bowel Disease. This project produced a lot of interesting data, and two further papers from this are in the pipeline. We’ve also been involved in a couple of recently published proteome informatics reviews – a paper about general quantitative proteomics software supporting HUPO-PSI standards and a book chapter focussing specifically on selected reaction monitoring (SRM). Proofs for the second edition of Building Bioinformatics Solutions are coming through right now, so this should be in print late this year or early 2014.

Funded PhD studentship available

We have a fully funded studentship available, for October 2013 start. The project is in the area of proteome informatics, and will link in with other activities going on in the lab and further afield. For more information, check out the link below.

PhD details on FindAPhD

Update: This position is now filled.

mzQuantML data standard published

The mzQuantML standard format for representing the results of quantitative proteomics experiments has been published in Molecular and Cellular Proteomics. This HUPO-PSI initiative should make it easier to exchange quantitative proteomics data between groups, between software, and should ultimately increase the quantity of publicly available quantitative proteomics data.

We contributed to this effort by testing and refining the standard as we built support for it into our x-Tracker tool, and are participating in the development of the mzq-lib library of software designed to simplify mzQuantML uptake in the field.

mzQuantML paper at MCP

A detailed insight into mzQuantML

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