Author Archives: Joe

Field-based, real-time metagenomics and phylogenomics for responsive pathogen detection: lessons from nanopore analyses of Acute Oak Decline (AOD) sites in the UK.

Talk presented at the UK-India Joint Bioinformatics Workshop, Pirbright Institute, 09 Feb 2018 Abstract: In a globalised world of increasing trade, novel threats to animal and plant health, as well as human diseases, can cross political and geographical borders spontaneously … Continue reading

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Real-time phylogenomics or ‘Some interesting problems in genomic big data’

Talk given at a technology/informatics company, London, Feb 2018. An overview of contemporary advances and remaining problems in big-data biology, especially phylogenomics. Tweet this Digg Post to LinkedIn Slashdot Stumble This

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Tent-seq: the paper (aka ‘field-based, real-time phylogenomics’)

Really proud to report that the first of our bona fide real-time phylogenomics papers is now out in Scientific Reports! In the paper we managed to show a number of things that are potentially really exciting, and I’ll get to … Continue reading

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Inference and informatics in a ‘sequenced’ world

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?

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

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

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…

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…

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

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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