Questions
Research at the interface of evolution, informatics, and ecology
Exploring biology and data science through big-data DNA and automation
Biology is changing. New technology means machines to read DNA sequences hidden in living cells cost hundreds, not thousands - and produce data in hours, not weeks. Computational models and hardware to exploit this tsunami have leapt forward, too. The era of big-data biology and phylogenomics - our nascent ability to read the evolutionary and ecological history of any sample, anywhere - has begun.
Unfortunately, our ambitions haven't caught up. Projects, workflows, data pipelines and training all lag behind, and the opportunities we should be reaping are as far from reach as ever. I'm helping to fix this through my research, consulting and teaching. During COVID-19 I designed and commissioned a highly automated lab that processed nearly a million live patient samples. I've published phylogenomic analyses in Nature, the biggest journal in science. I've taught hundreds of biologists, bioinformaticians, and genomics scientists and consulted on projects for governmental and top commercial partners.
I am a Senior Research Fellow in Phylogenomics at the National Biofilms Innovation Centre in Southampton, a Lecturer in Biology at St Hilda's College, Oxford, and a Fellow of the Software Sustainability Institute. If you'd like to have a chat about research, consulting, or training - drop me a line!
Joe
The coming ubiquity of both portable DNA sequencers and cloud computation mean scenarios formerly found in sci-fi films (instant DNA analysis) are coming, soon. I'm developing methods to streamline DNA sequence analysis using cloud computation.
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Up to 80% of the microscopic organisms on the Earth exist not as solitary cells, but 'biofilms'. These are complex, three-dimensional slimy structures where bacteria (and other microorganisms) co-exist, resisting our attempts to remove or kill them with antibiotics.
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Modern DNA sequencers are highly portable, compared to lab-bound models of a decade ago. I'm trialling field-based sequencing using the MinION USB sequencer - a palm-size device with potential to revolutionise environmental metagenomics and turbotaxonomy.
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To reliably detect complex biological patterns we need big biological data. Getting there needs automated labs working orders of magnitude faster than expensive pipette-jockeys can manage. Using our COVID experience (automating hundreds of thousands of sample tests, we're rethinking lab workflows.
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Phylogenomic models accounting for uncertainty require useful metrics on tree space - the 'distance' between two or more phylogenetic trees. However few useful such measures exist and I'm hunting for more...
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The vast scale of bioinformatics datasets currently being assembled require models of asynchronous computation; meta-algorithms where model areas are updated asynchronously on separate machines.
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Development of sustainable software and open research norms is a priority for big-data empirical bioscience in the 21st centrury, to avoid the 'reproducibility crisis'. I'm a Fellow of the SSI.
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I'm interested in the parallels and divergences between the natural world (in a systems biology context) and organisation of human societies. Maybe I'll get to take a sabbatical one day!
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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 length and bias of MinION reads makes them ideal for sample ID – better than … Continue reading Rapid, raw-read reference and identification (R4IDs): A flexible platform for rapid generic species ID using long-read sequencing technology.
Talk presented at the UK-India Joint Bioinformatics Workshop, Pirbright Institute, 09 Feb 2018 [slideshare id=88051198&doc=joe-parker-pirbright-ukindia-180215141918] 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 and rapidly. One such example is the rise of Acute Oak Decline (AOD) … Continue reading 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 given at a technology/informatics company, London, Feb 2018. [slideshare id=87391225&doc=joe-parker-reak-time-phylogenomics-180207132740] An overview of contemporary advances and remaining problems in big-data biology, especially phylogenomics. Tweet this Digg Post to LinkedIn Slashdot Stumble This
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 (paywall). If you can’t read it online, my Grandad has a copy he might lend … Continue reading Read all about it!
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 [slideshare id=78587606&doc=2017readingbioinfforgenomics-joeparker-final3-170805084405] Tweet this Digg Post to LinkedIn Slashdot Stumble This
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 [slideshare id=69767351&doc=2016oxfordzoojoeparker-161202163931] Tweet this Digg Post to LinkedIn Slashdot Stumble This
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 [slideshare id=66051562&doc=smrt-nanopore-gcpp-joeparker-160915100855] Tweet this Digg Post to LinkedIn Slashdot Stumble This
Talk presented at the #bench16 (benchmarking) symposium at KCL, London, Wed 20th April 2016. Funded by the SSI. Slides (Slideshare – cc-by-nd) [slideshare id=61147571&doc=joe-parker-benchmarking-bioinformatics-160420140811] Tweet this Digg Post to LinkedIn Slashdot Stumble This
General science talk about the potential of real-time phylogenomics, delivered at the Jodrell Lecture Theatre, Kew Gardens, November 2nd 2015 Slides [SlideShare]: cc-by-nc-nd [slideshare id=54651010&doc=real-time-phylogenomics-joeparker-151102162613-lva1-app6892] Tweet this Digg Post to LinkedIn Slashdot Stumble This
Presentation on lightweight bioinformatics (Raspi / cloud computing) for real-time field-based analyses. Presented at iEOS2015, St. Andrews, 3-6th July 2015. Slides [SlideShare]: cc-by-nc-nd [slideshare id=50251856&doc=joeparkerlightweightbioinformatics-150707112254-lva1-app6892] Tweet this Digg Post to LinkedIn Slashdot Stumble This
In prep. SUMMARY Building on work presented previously (Parker et al., 2008), we study a number of more complex measures of phylogeny-trait association (implemented in the program Befi-BaTS / BaTS v0.10.1) which take into account the branch lengths of a phylogenetic tree in addition to the topographical relationship between taxa. Extensive simulation is performed to … Continue reading Application note: ‘Befi-BaTS’ version 0.10.1 – Error rate and statistical power of distance-based measures of phylogeny-trait association.
In prep. Manuscripts in progress (all rights reserved – you may not copy or distribute these files; content and conclusions subject to change; strictly embargoed until publication in a peer-reviewed journal/book): v1: .doc Tweet this Digg Post to LinkedIn Slashdot Stumble This
In prep. (v3 – 14 Jun 2017) Summary. The CONTEXT (COmparative Nucleotides and Trees Exploration Tool) is a phylogenomics dataset browser that consists of a Java API and an executable binary jarfile with graphical user interface (GUI) for the high-throughput analysis of phylogenomic datasets to detect convergent molecular evolution. Motivation. Comparative genomics studies have become increasingly … Continue reading Application note: CONTEXT, a Phylogenomic Dataset Browser
In prep. (v2 – 21 April 2015) Abstract Convergent evolution is a process by which neutral evolutionary processes and adaptive natural selection in response to niche specialisation lead to similar forms arising in unrelated taxa. Phenotypic convergence has been appreciated for well over a century (recognised as a confounding factor in morphological cladistics). Recently several … Continue reading Detection of molecular convergence – literature review
In prep. (v0 – 24 February 2015) Summary. Genome Convergence Pipeline consists of a Java API and an executable binary jarfile with graphical user interface (GUI) for the high-throughput analysis of phylogenomic datasets to detect convergent molecular evolution. Motivation. Although convergent phenotypes are readily observed in nature evidence that evolution can produce convergent signals in … Continue reading Application note: the Genomic Convergence Detection Pipeline
Seminar presented at the Maths Department, University of Portsmouth, 19th November 2014 Evolutionary biologists represent actual or hypothesised evolutionary relations between living organisms using phylogenies, directed bifurcating graphs (trees) that describe evolutionary processes in terms of speciation or splitting events (nodes) and elapsed evolutionary time or distance (edges). Molecular evolution itself is largely dominated by … Continue reading Interpreting ‘tree space’ in the context of very large empirical datasets
Talk presented at the 18th Evolutionary Biology Meeting At Marseille (programme), 16th-19th September 2014. (Powerpoint – note this is a draft, not the final talk, pending authorisation): EBMdraft [slideshare id=41517262&doc=ebmjoeparkerconvergencefinal-recover-nosampling-141113102943-conversion-gate01] Tweet this Digg Post to LinkedIn Slashdot Stumble This
High-throughput comparative genomics Research seminar presented for MSc students at University College Dublin, 24rd October 2013. Invited by Prof. Emma Teeling’s lab at UCD. Powerpoint: UCD_MSc_phylogenomics_joeParker_edit [slideshare id=41517492&doc=ucdmscphylogenomicsjoeparkeredit-141113103421-conversion-gate02] Tweet this Digg Post to LinkedIn Slashdot Stumble This
Exciting news from the lab this week… we’ve published in one of the leading journals, Nature!!! Much of my work in the Rossiter BatLab for the last couple of years has centred around the search for genomic signatures of molecular convergence. This means looking for similar genetic changes in otherwise unrelated organisms. We’d normally expect … Continue reading Our Nature paper! Genome-wide molecular convergence in echolocating mammals
Seminar presented at the Tropical Biodiversity in the 21st Century symposium, held at the Natural History Museum, London on the 3rd & 4th June 2013 (programme). Powerpoint: High-throughput computing and phylogenomics Tweet this Digg Post to LinkedIn Slashdot Stumble This
BMC Evol Biol. 2011 May 19;11(1):131. [Epub ahead of print] Gray RR*, Parker J*, Lemey P, Salemi M, Katzourakis A, Pybus OG. *These authors contributed equally to this article. BACKGROUND: Hepatitis C virus (HCV) is a rapidly-evolving RNA virus that establishes chronic infections in humans. Despite the virus’ public health importance and a wealth of … Continue reading The mode and tempo of hepatitis C virus evolution within and among hosts.
J Virol. 2011 May 18. [Epub ahead of print] Clegg SR, Coyne KP, Parker J, Dawson S, Godsall SA, Pinchbeck G, Cripps PJ, Gaskell RM, Radford AD. Canine parvovirus 2 (CPV-2) is a severe enteric pathogen of dogs, causing high mortality in unvaccinated dogs. After emerging, CPV-2 spread rapidly worldwide. However, there is now some … Continue reading Molecular epidemiology and phylogeny reveals complex spatial dynamics of endemic canine parvovirus.
PLoS Pathog. 2010 Sep 2;6(9):e1001084. Ozkaya Sahin G, Bowles EJ, Parker J, Uchtenhagen H, Sheik-Khalil E, Taylor S, Pybus OG, Mäkitalo B, Walther-Jallow L, Spångberg M, Thorstensson R, Achour A, Fenyö EM, Stewart-Jones GB, Spetz AL. Neutralizing antibodies (NAb) able to react to heterologous viruses are generated during natural HIV-1 infection in some individuals. Further … Continue reading Generation of neutralizing antibodies and divergence of SIVmac239 in cynomolgus macaques following short-term early antiretroviral therapy.
J Virol. 2010 Aug;84(15):7815-21. Epub 2010 May 19. Rosario M, Fulkerson J, Soneji S, Parker J, Im EJ, Borthwick N, Bridgeman A, Bourne C, Joseph J, Sadoff JC, Hanke T Although major inroads into making antiretroviral therapy available in resource-poor countries have been made, there is an urgent need for an effective vaccine administered shortly … Continue reading Safety and immunogenicity of novel recombinant BCG and modified vaccinia virus Ankara vaccines in neonate rhesus macaques.
Humphreys I, Fleming V, Fabris P, Parker J, Schulenberg B, Brown A, Demetriou C, Gaudieri S, Pfafferott K, Lucas M, Collier J, Huang KH, Pybus OG, Klenerman P, Barnes E. J Virol. 2009 Nov;83(22):11456-66. Epub 2009 Sep 9. Hepatitis C virus subtype 3a is a highly prevalent and globally distributed strain that is often associated … Continue reading Full-Length Characterization of Hepatitis C Virus Subtype 3a Reveals Novel Hypervariable Regions under Positive Selection during Acute Infection
A research thesis submitted for the degree of Doctor of Philosophy at the University of Oxford. J Parker Funded by: Natural Environment Research Council (UK) with support from Linacre College, Oxford. Abstract: This thesis examines the evolutionary biology of the RNA viruses, a diverse group of pathogens that cause significant diseases. The focus of this … Continue reading The within- and among-host evolution of chronically-infecting human RNA viruses
Virology. 2009 Apr 25;387(1):229-34. Epub 2009 Mar 9. Tee KK, Pybus OG, Parker J, Ng KP, Kamarulzaman A, Takebe Y. HIV is capable of frequent genetic exchange through recombination. Despite the pandemic spread of HIV-1 recombinants, their times of origin are not well understood. We investigate the epidemic history of a HIV-1 circulating recombinant form … Continue reading Estimating the Date of Origin of An HIV-1 Circulating Recombinant Form
Infect Genet Evol. 2008 May;8(3):239-46. Epub 2007 Aug 21. Parker J, Rambaut A, Pybus OG. Many recent studies have sought to quantify the degree to which viral phenotypic characters (such as epidemiological risk group, geographic location, cell tropism, drug resistance state, etc.) are correlated with shared ancestry, as represented by a viral phylogenetic tree. Here, … Continue reading Correlating Viral Phenotypes With Phylogeny: Accounting for Phylogenetic Uncertainty
I'm a public-funded scientist and an advocate of Open Data and Reproducible Research. My previous work as a postdoc has been funded via a variety of means and published under multiple licenses, but source data for most of my publications is available. If you want workflow scripts and software please email me and I'll try to help where I can.
For my own work I now use GitHub extensively to document and version-control my analyses; I also use Endnote a lot and complete notebooks will be published with each publication.
Obviously truly reproducible research is quite a large step on from 'give us your short reads and executables' - a complete bioinformatics analysis might include several people on multiple machines - and documenting all these steps is a kew challenge for reproducibility, a cornerstone of empirical research. I'm exploring the use of Docker containers, iPython notebooks and Research Objects to make it simpler for me to document, reproduce and communicate my research.
I am moving a substantial proportion of my compute load to cloud resources, in particular Amazon's EC2. At present one machine image is available, from my 'lightweight bioinformatics' project. Search AWS AMIs for 'ami-90296be7'.
My work with field-based MinION DNA sequencing is supported by a Pilot Study Fund grant from the Kew Foundation.
The Phylo-Hackathon project is supported by a Fellowship grant from the Software Sustainability Institute.
Previous work as a postdoc and PhD student has been funded by NERC, the BBSRC, the MRC, the European Research Council, the Royal Society and the Daiwa Foundation.
I am currently employed in the Biodiversity Informatics & Spatial Analysis department of the Science Directorate at the Royal Botanic Gardens, Kew in London.
Current collaborators include:
I'm also available to provide consultancy services to private partners on big-data projects in genomics, phylogenomics, bioinformatics/informatics and statistics. This work is delivered via Kitson Consulting.
I was inspired to give my sad-looking Wordpress site the boot (and a kick up my own arse) by the very, very excellent Bedford Lab website. However, although that site uses loads of cool technologies (like CMS/source code control managed directly on GitHub, compiled to static HTML via Jekyll, all served up on a Heroku instance...) I reckoned it was overkill for me.
Instead I've nicked some ideas from that site (layouts in Bootstrap, fonts from Typekit) but haven't completely jettisoned the old (Wordpress) CMS running on LAMP yet - partly because I haven't got the time to write a good parser for all that legacy content, and partly because I still blog there about non-science things.
So the site you see is generated simply from a (largely) static HTML file with a couple of bits of PHP pulling in Wordpress posts to populate the blog and publications. Parallax effects use Aen Tan's Parallax-Scroll code and I figured out the integration with Bootstrap (actually pretty simple) with a lot of help from this tutorial. The whole site probably took less than 20 hours to put together including design, parsing WP, and deployment and testing - I think that's pretty good, on balance.
At some point I might add a couple of sub-pages for projects, etc, as well as some server-side stuff to update publication counts and Github commits on the fly. But that's tomorrow, and tomorrow's a long way away. Lastly, my existing web host is a pretty good deal so I'll probably only move the big bandwidth stuff to S3, and then only if the server logs show I really need to! Suggestions welcome.
This is part 3 in a series of posts this summer conference season. It isn’t aimed at one particular LOC – I know how hard they all work – but intended as a general reflection. I’ve been to god-knows how many academic conferences in the last 15-20 years, but I can only really remember a … Continue reading Conference season thoughts #3 – Hosting a conference
There are good chairs and bad. Surprisingly (or not, this is academia, after all..) there’s little guidance. I’ve put together a list: Start as you mean to go on. Remind speakers to keep to time (see next point) and encourage questions from all attendees (see point 3) Control time with an iron fist – and let … Continue reading Conference thoughts #2: Chairs, earn your ticket!
Summer conference season is nearly over. This is the first of three posts, informed by some reflections about the nature of scientific conferences. Students often feel under a lot of pressure when giving their first public presentations. PIs, for whom a conference is as much a chance to strike deals and go drinking with old mates … Continue reading Conference thoughts #1: PIs, support your students!
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 length and bias of MinION reads makes them ideal for sample ID – better than … Continue reading Rapid, raw-read reference and identification (R4IDs): A flexible platform for rapid generic species ID using long-read sequencing technology.
Talk presented at the UK-India Joint Bioinformatics Workshop, Pirbright Institute, 09 Feb 2018 [slideshare id=88051198&doc=joe-parker-pirbright-ukindia-180215141918] 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 and rapidly. One such example is the rise of Acute Oak Decline (AOD) … Continue reading 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 given at a technology/informatics company, London, Feb 2018. [slideshare id=87391225&doc=joe-parker-reak-time-phylogenomics-180207132740] An overview of contemporary advances and remaining problems in big-data biology, especially phylogenomics. Tweet this Digg Post to LinkedIn Slashdot Stumble This
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 (paywall). If you can’t read it online, my Grandad has a copy he might lend … Continue reading Read all about it!
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 them in a minute. First though, this is the first paper I’ve published where I … Continue reading Tent-seq: the paper (aka ‘field-based, 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, it’s probably worth defining what I hope this term denotes now, what it does not … Continue reading What is ‘real-time’ phylogenomics?
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, but two, three, four or possibly even five orders of magnitude longer (up to 10^6 … Continue reading Some aspects of BLASTing long-read data
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 GANTTs, milestones, workload models, targets and many other things previously unmentionable in academia but common … Continue reading Science and (small) business
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 [slideshare id=66051562&doc=smrt-nanopore-gcpp-joeparker-160915100855] Tweet this Digg Post to LinkedIn Slashdot Stumble This
Talk presented at the #bench16 (benchmarking) symposium at KCL, London, Wed 20th April 2016. Funded by the SSI. Slides (Slideshare – cc-by-nd) [slideshare id=61147571&doc=joe-parker-benchmarking-bioinformatics-160420140811] Tweet this Digg Post to LinkedIn Slashdot Stumble This
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 got in touch and managed to get an early prototype of this kit for developers*, … Continue reading More MinION – the ‘1D rapid’ prep
Quick one this, as it’s a tricky problem I keep having to Google/SO. So I’m posting here for others but mainly myself too! Here’s the situation: you have a folder (with, ooh, let’s say 140,000 separate MinION reads, for instance…) which contains a subset of files you want to move or copy somewhere else. Normally, … Continue reading Copying LOADS of files from a folder of LOADS *AND* LOADS more in OSX
I've recorded and toured as 'Lonely Joe Parker' since 2006, hence my username on Twitter - and various other social platforms - and this website's URL. For related enquiries please contact Sotones Records. You can hear music and whatnot over on the music bits of this site.
I'm a big fan of bombay mix, Red Stripe and cycling. Not so crazy about early mornings.
I was born and raised in Southampton, one of the biggest commercial ports in the world, next to the New Forest National Park. That, and some great teachers, gave me an interest in evolution, ecology, and exploring the wide goddamn world.
I studied general biology at Imperial College, University of London (2001-2004; tutors including Andy Purvis, Mike Tristem, Tim Barraclough and Alfreid Vogler), gaining first-class honours. Subsequently I completed a D.Phil at Linacre College, University of Oxford, based in the Zoology department under Andrew Rambaut and Oliver G. Pybus (2004-2008). I developed novel phylogenetic strategies and bioinformatics pipelines for the analysis of viral pathogens' evolution, including hepatitis C virus (HCV) and human immunodeficiency virus (HIV).
From 2009-2011 I worked at the Weatherall Institute of Molecular Medicine (John Radcliffe Hospital: Univ. Oxford / Medical Research Council (UK)), developing phylogenetic and machine-learning methods for the detection of correlates between antigenicity and sequence evolution. This integrated clinical, structural, evolutionary and population genetic data leading to immunogen design and assessment in silico, trialled in vivo for the EU-funded NGIN vaccine consortium.
Between 2011-2015 I worked with Stephen Rossiter at Queen Mary, University of London on large-scale phylogenomics projects looking for signals of molecular natural selection (particularly adaptive convergent evolution) in mammals as the focal taxonomic group. I developed a rich Java API for phylogenomic analyses and authored publications including Nature (2013) and Current Biology (2013).
I currently hold an Early-Career Research Fellowship in Phylogenomics at the Royal Botanic Gardens, Kew. This post allows me wide freedom pursue my research into real-time phylogenomics, field-based DNA sequencing for turbotaxonomy and metagenomics, and integrated alignment & phylogeny models of molecular evolution.
I also lead the Informatics workpackage for the Plant & Fungal Trees Of Life project, a Kew-led initiative to reconstruct a genus-level supertree for 80% of all plant and fungal genera by 2020.
I'm available to provide consultancy services to private partners on big-data projects in genomics, phylogenomics, bioinformatics/informatics and statistics through Kitson Consulting...
...and I'm always excited by new collaborations, particularly across other domains. So if you have an idea for a project or would like to explore a PhD or masters' degree at Kew, get in touch!
*These authors contributed equally to this article.
My full academic CV is also available.