Author Archives: Joe

Inference and informatics in a ‘sequenced’ world

Posted on 2 August, 2017 by Joe

Short lecture relating my recent work on real-time phylogenomics, implications for bioinformatics research and future directions of genomic/phylogenetic modelling to explicitly account for phylogeny, synteny and identity through coloured graphs. University of Reading, 2nd August 2017 Slides [SlideShare]: cc-by-nd Tweet … Continue reading →

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What is ‘real-time’ phylogenomics?

Posted on 15 June, 2017 by Joe

Over the past few years I’ve been developing research, which I collectively refer to as ‘real-time phylogenomics’ – and this is the name of our mini-site for MinION-based rapid identification-by-sequencing. Since our paper on this will hopefully be published soon, … Continue reading →

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Some aspects of BLASTing long-read data

Posted on 2 May, 2017 by Joe

Quick note to explain some of the differences we’ve observed working with long-read data (MinION, PacBio) for sample ID via BLAST. I’ll publish a proper paper on this, but for now: Long reads aren’t just a bit longer than Illumina data, … Continue reading →

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Only Corbyn can save the Left

Posted on 19 April, 2017 by Joe

Labour go into this election with the dice stacked against Corbyn, as the Tories intended. But here’s the thing – he’s only an election liability *if* you believe he can win. But in fact everyone – surely even the man … Continue reading →

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Step-by-step: Raspberry Pi as a wifi bridge, plus a (really) low-spec media centre…

Posted on 20 February, 2017 by Joe

I’ll keep this brief, really so, because this is mainly an aide-memoire for when this horrific bodge breaks in the next, ooh, month or so. But, for context: The problem: Our office/studios are in a shed at the bottom of the … Continue reading →

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‘Stretched resources’ applies to parliamentarians, too…

Posted on 2 February, 2017 by Joe

I listened to a sad story on BBCR4 today this morning – a grieving mother can’t bury her daughter, murdered, because there’s no body – in years of searching none has been found. The killer isn’t co-operating (they don’t have … Continue reading →

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Using field-based DNA sequencing to accelerate phylogenomics

Posted on 30 November, 2016 by Joe

Invited seminar at the Department of Zoology, Oxford University, 30th November 2016. Summary of our field-based real-time phylogenomics (MinION DNA sequencing) experiments this year, and applicability to broad-scale tree-of-life phylogenomics and macroevolutionary biology. Slides [SlideShare]: cc-by-nd Tweet this Digg Post … Continue reading →

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Science and (small) business

Posted on 22 October, 2016 by Joe

Over the last 10-20 years there’s been a revolution in academic science (or should that be ‘coup’?) where many aspects of the job have been professionalised and formalised, especially project management but management in general. This generally includes tools like … Continue reading →

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Making progress down the road

Posted on 15 September, 2016 by Joe

Too many laws and customs of driving make speed more important than safety, from the driving instructors’ “make good progress down the road” (e.g. “hurry the fuck up”, which most drivers internalise as “drive at least as fast as the … Continue reading →

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Single-molecule real-time (SMRT) Nanopore sequencing for Plant Pathology applications

Posted on 14 September, 2016 by Joe

A short presentation to the British Society for Plant Pathology’s ‘Grand Challenges in Plant Pathology’ workshop on the uses of real-time DNA/RNA sequencing technology for plant health applications. Doctoral Training Centre, University of Oxford, 14th September 2016. Slides [SlideShare]: cc-by-nc-nd … Continue reading →

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