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Today sees the announcement of a new public–private partnership in science – the Centre for Therapeutic Target Validation – between EMBL-EBI, the Sanger Institute and GlaxoSmithKline (GSK). The collaboration is dedicated to developing a framework for biological target validation so that we can reduce the amount of time it takes to discover new therapies.

This is a really exciting initiative for me personally, both because the science is challenging and because I have been appointed as interim Head of the CTTV over the next year whilst we look for a long-term Head to steer the collaboration. It has already been a fascinating journey for me to understand the pharmaceutical industry in more depth, and really get to grips with an important scientific problem.

Continue reading “‘Big Data’, genetics and translation”

Around three years ago, I decided to use social media in order to engage – as a scientist – with a broader group of people. Since then, I’ve come to see platforms like Twitter and blogs as a way to reshape public scientific discourse – mainly for the better but with considerable adjustments. Recently, the 5000th person started following me on Twitter, which I think represents a kind of turning point and perhaps a good opportunity to reflect on the pros and cons of using these new channels to communicate with a wider audience.
Continue reading “New media for science: 3 years in.”

Last week a new paper, “Policy challenge of clinical genome sequencing,” led by Caroline Wright and Helen Firth and on which I am a co-author, was published in the British Medical Journal. It lays out the challenges of making more widespread use of genetic information in clinical practice, in particular around ‘incidental findings’. Caroline and I have a joint blog on this paper on Genome Unzipped.

This paper also marks an important watershed in my own career, as it is my first paper in an outright clinical journal. Like many other genomicists and bioinformaticians I have started to interweave my work more tightly with clinical research, as the previously mainly basic research world of molecular biology begins to gravitate towards clinical practice.

Continue reading “The Start of a Journey”

The conversation around impact factors and the assessment of research outputs, amplified by the recent ‘splash’ boycott by Randy Shekman, is turning my mind to a different aspect of science – and indeed society – and that is the use of metrics.We are becoming better and better at producing metrics: more of the things we do are digitised, and by coordinating what we do more carefully we can ‘instrument’ our lives better. Familiar examples might be monitoring household electricity meters to improve energy consumption, analysing traffic patterns to control traffic flow, or even tracking the movement of people in stores to improve sales.At the workplace it’s more about how many citations we have, how much grant funding we obtain, how many conferences we participate in, how much disk space we use… even how often we tweet. All these things usually have fairly ‘low friction’ instrumentation (with notable exceptions).

Continue reading “Making decisions: metrics and judgement”

I’ve just come back from a great meeting on Cancer Genomics, held at EMBL Heidelberg (full disclosure: I was an organiser, so no surprise I enjoyed the talks!)

The application of genomics to cancer has been progressing for a long time, but we are now in the era where “cheap enough” exome sequencing (and increasingly whole genome sequencing) is present for both fundamental cancer research and clinical research – and there is really a sense of starting to “mainstream” sequencing into clinical care (clinical care and clinical research seem closer in the Cancer field than some other areas of medicine).

Continue reading “Heterogeneity in Cancer genomics”

This September I visited CERN again, this time with a rather technical delegation from the EBI to meet with their ‘big physics data’ counterparts. Our generous hosts Ian Bird, Bob Jones and several experimental scientists showed us a great day, and gave us an extended opportunity to understand their data flow in detail. We also got a tour of the anti-matter experiments, which was very cool (though, sadly, it did not include a trip down to the main tunnels of the LHC).

CERN is a marvellous place, and it triggers some latent physics I learnt as an undergraduate. Sometimes the data challenges in CERN are used as a template for the data challenges across all of sciences in the future; I have come to learn that these analogies – unsurprisingly – are sometimes useful and sometimes not. To understand the data flow behind CERN, though, one needs to understand CERN itself in more detail.

Continue reading “CERN for molecular biologists”

Multicellular organisms are beautifully precise in the way their different component cells operate in different ways, despite each cell having the same genome. The main difference between cell types is what genes are expressed, and much of this is due to differential expression of RNA transcripts. The ability to measure all the transcripts simultaneously in a cell population with RNAseq has been very informative – but often complex. But this complexity is anchored: for most genes, there is one dominant transcript – and within an organism that major transcript is the same between tissues over half the time. This “glass-half-full” view of mRNA complexity was recently described by Alvis Brazma and his colleagues,   and integrated into a new value added resource at the EBI, the Expression Atlas.

Continue reading “Freedom of Expression”

I was discussing with a maths minded friend about the difference between “quantitative” and “non quantitative” science, mainly on how biology had to get its quantitative mojo back, and I said that a good proxy for whether someone was “quantitative” or not is whether they are at home with logarithms – do they use them, are they comfortable about logs between 0 and 1, can they read log plots?

Continue reading “5 reasons to love logarithms”