Author Archives: Joe

Why Trump is right on defence spending… and wrong

It’s all over the press this week: Trump wants all NATO members to spend 4% of their GDP on defence – a doubling of the previously-agreed 2% target (which many countries don’t meet). To me this seems pretty wrong, for … Continue reading

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I’m a programmer – and driverless cars scare the hell out of me

Tech-savvy developer types often ride bikes, and often instinctively back the idea of robot vehicles. After all, the subconscious asks, if I can code a computer to play a game, what’s so hard about getting it to move around a … Continue reading

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Rapid, raw-read reference and identification (R4IDs): A flexible platform for rapid generic species ID using long-read sequencing technology.

Our paper on rapid identification of samples using partial, low-coverage, MinION-sequenced reference databases for ID (at the Kew Science Festival) is in preprint. See here on BiorXiv: doi: 10.1101/281048. In it, we show (with empirical data and simulation) that the … Continue reading

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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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Read all about it!

Dead excited to say our Nature Science Reports paper on field-based DNA extraction, sequencing (and a bit of analysis) has been picked up by the BBC World Service and The Times (UK) newspaper! You can read all about it here … Continue reading

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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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