Tag Archives: real-time phylogenomics

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

Posted on 6 February, 2018 by Joe

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!

Posted on 2 October, 2017 by Joe

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’)

Posted on 1 September, 2017 by Joe

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

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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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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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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More MinION – the ‘1D rapid’ prep

Posted on 29 March, 2016 by Joe

My last MinION post described our first experiments with this really cool new technology. I mentioned then that their standard library prep was fairly involved, and we heard that the manufacturers, Oxford Nanopore, were working on a faster, simpler library prep. We … Continue reading →

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Messing about with the MinION

Posted on 20 December, 2015 by Joe

Molecular phylogenetics – uncovering the history of evolution using signals in organisms’ genetic sequences – is a powerful science, the latest expression of the human desire to understand our common origins. But for all its achievements, I’d always felt something … Continue reading →

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