July, 2015.. Our paper on nanopore assembly was published in Nature Methods. It got lots of attention from the press and was featured as a Nature Reviews Microbiology highlight.

April, 2015. We have been collaborating with Jared Simpson in Ontario on a new method for nanopore-only de novo assembly and polishing. We found it was possible to assemble E. coli into a single contig using nanopore data alone. The method is described in a preprint which we have deposited in bioRxiv. Our work on nanopore sequencing in outbreaks was recently featured in Wired UK. Nick wrote a News and Reviews article for Nature Methods in collaboration with Mick Watson about the recent exciting progress with nanopore sequencing. Nick did an interview with BioMedCentral's Biome magazine about nanopore sequencing. A manuscript from Del Besra's team was recently published on drug discovery in tuberculosis. Our group performed whole-genome sequencing and mutation detection in order to confirm the predicted drug target. We are planning a Balti and Bioinformatics meeting on the 5th of May in Birmingham, and a CLIMB Hackathon on Public Health Microbiology the following weekend. We launched our new BBSRC-funded microbial genome sequencing and strain archiving service, MicrobesNG, at the SGM meeting in Birmingham.

January, 2015. Happy New Year! Some recent papers have been featured as research highlights: see Rob Knight's piece at Genome Biology on kit contamination, Nature Method's article on poretools and our recent nanopore data release and Susannah Salter writing in Nature Reviews Microbiology on our recent P. aeruginosa in hospital water study. Our nanopore read on FigShare was the 8th most popular post in 2014. Aaron Krol from Bio-IT World did a cracking write-up of the recent nanopore buzz.

So far this year I have been giving the Omicsmaps a lick of paint.

November, 2014. Our paper on the kitome is published today in BMC Biology. It has had great coverage from Ed Yong in National Geographic, Nature News, Science, Scientific American's 60-second science podcast, The Scientist and BioMed Central Blog. It has even been covered on The Science Web, a true metric of impact!

Our paper, tracking the spread of Pseudomonas aeruginosa from hospital water outlets to patients, using genomics and metagenomics sequencing is now out in BMJ Open. It has been covered by the PHG Foundation think tank.

October, 2014. The first manuscript describing a genome sequenced by nanopore technology, in this case E. coli K-12, is published in GigaScience. The poretools manuscript is published in Bioinformatics. The CONCOCT manuscript is publised in Nature Methods. Work has begun on unifying my blog, lab notebook and this lab website in Github. There may be bugs and gotchas for a while as this is a slow process.

July, 2014. Two new preprints were deposited in bioRxiv. The first looks at the vexing problem of DNA contamination in commonly used extraction kits. We find that when looking at low biomass samples this contamination has the potential to affect results of microbiome studies. The second details a toolkit for analysis of Oxford Nanopore MinION data. The accompanying Github repository is here. Finally, a new paper in Molecular Microbiology looking at in-vitro evolution for acid resistance in E. coli in collaboration with Pete Lund in Biosciences.

June, 2014. We got up and running with the Oxford Nanopore MinION and were the first group to publish a read from this instrument, see press coverage at Bio-IT World and GenomeWeb. Lots of exciting samples to try out now!

May, 2014. We received our Oxford Nanopore MinIONs!. New Genome Announcement of Elizabethkingia meningoseptica. The MRC CLIMB website for cloud computing in microbial genomics is now live. We received notification that our grant proposal to the BBSRC for our MicrobesNG service was funded. I gave an interview to Keith Bradnam's series on interviews with bioinformaticians.

February, 2014. I was proud to be part of the awesome Evomics 2014 course held in Cesky Krumlov. There are some great presentations and tutorials available on their site.

We have been accepted onto the first wave of the Oxford Nanopore MinION access programme!

The Medical Research Council announced that a consortium for medical microbial bioinformatics consisting of the Universities of Warwick, Birmingham, Swansea and Cardiff will be funded! This will provide an investment of nearly >£4m in server hardware and storage in Birmingham, as well as a five-year fellowship for me.

January, 2013. I had a lot of fun instructing and learning at C. Titus Brown's "Assembly Masterclass". If you are interested in assembly, there are lots of useful new tutorials and guides posted on the course website.

A collaboration with Chris Quince (Glasgow) and Anders Andersson (SciLifeLab, Sweden) on a novel algorithm for genome binning we call CONCOCT has reached maturity, and a preprint is now available in the arXiv.

A new paper in PLoS ONE from a collaboration with Waltham Petcare (part of Mars) was published on the oral microbiota of dogs.

November, 2013. Mick Watson and I have penned a commentary in Nature Biotechnology which may be of interest entitled: So you want to be a computational biologist?. I've also updated this page to add some details of upcoming training courses.