Joined December 2009
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Have you ever thought of doing a sabbatical at EMBL?
It’s a great opportunity for scientific exchange and growth, and for learning advanced technologies and top-notch science!
Three scientists shared their experiences on their research visits at EMBL. 👇
embl.org/news/connections/sa…
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If you're a a master's student studying at a French university interested in these we're a possible host group -- send me an email to discuss
Are you a student in France studying computer science, statistics, or bioinformatics?
@FranceintheUK has opened a new round of internships hosted at EMBL-EBI.
Find out more and apply.
ebi.ac.uk/about/jobs/interns…
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16 Oct 2024
A mere six years after its first release, SKA is now published
genome.cshlp.org/content/ear…
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John Lees retweeted
16 Oct 2024
This is exactly the kind of thing we wanted to happen!
16 Oct 2024
A cool upcoming feature: When you upload a sample to Solu Platform, we’ll search all public NCBI samples for related genomes. This is built on the awesome AllTheBacteria database by Martin Hunt, Leandro Lima, @shenwei356, @johnlees6 & @ZaminIqbal
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John Lees retweeted
15 Oct 2024
This neat paper about rapid evolution of bacterial transformation rate by @eprocha @labXC & co takes some of its inspiration from an earlier @PLOSBiology paper by Nick Croucher & @ChristoPhraser: journals.plos.org/plosbiolog…
15 Oct 2024
Why do #bacterial species' #TransformationRates vary so dramatically? @epcrocha @labXC &co show that #Legionella & #Acinetobacter transformation rates evolve by sudden changes, likely caused by conflicts between #MGEs and the host bacterium #PLOSBiology plos.io/4dMviTR
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John Lees retweeted
15 Oct 2024
Daria Frolova's paper in plasmid relatedness now out in MGen! She uses rearrangement distances & shared seq content to build a relatedness network of plasmids, identifies hubs which are likely transposons, and then clusters related plasmids.
microbiologyresearch.org/con…
@MicrobioSoc
13 Jun 2024
First paper from my student Daria Frolova's PhD now on biorxiv:
biorxiv.org/content/10.1101/…
The key question: plasmids change structurally ~as fast as they mutate, so how can we decide whether 2 plasmids are "the same plasmid" for epi purposes?
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John Lees retweeted
8 Oct 2024
Happy to announce that our (me and @YunWilliamYu) metagenome profiler sylph (github.com/bluenote-1577/syl…) is now published in @NatureBiotech!
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Rapid species-level metagenome profiling and containment estimation with sylph go.nature.com/3BBVqDC
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4 Oct 2024
Extension to ska 'skalo' -- using local assembly to recover indels and MNPs where split k-mers mismatch
biorxiv.org/content/10.1101/…
We hope to integrate this into the main ska package in future too
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John Lees retweeted
I'm looking for a know fusion signature in a graph that contains annotated human transcripts (from Refseq) and samples, including prone to fusion (human carcinoma samples).
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2 Oct 2024
There is still time to register for our SMBE satellite meeting on pangenomes and transmission in Tokyo (until 31st October)
See our website for more details, and now a provisional schedule too!
smbepangenomes.bacpop.org/
22 Jan 2024
We are happy to have been selected by SMBE to host a satellite meeting on Pathogen Pangenome Evolution Between and Within their Hosts:
smbepangenomes.bacpop.org/
We are expecting the meeting to be in Tokyo on 26-28th November 2024, save the date!
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25 Sep 2024
Now published in bioinformatics, CELEBRIMBOR 'pangenomes from metagenomes'
academic.oup.com/bioinformat…
I think reviewer comments helped make it better, so worth another look (at fig 1 particularly!)
10 Apr 2024
Sam has then wrapped it all up in a nice snakemake pipeline CELEBRIMBOR (Core ELEment Bias Removal In Metagenome Binned ORthologs) which lets you go from MAGs to pangenome
github.com/bacpop/CELEBRIMBO…
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25 Sep 2024
Also now old Celebrimbor is a big name in rings of power s2 maybe our backronym will finally land
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John Lees retweeted
10 Apr 2024
Sam has then wrapped it all up in a nice snakemake pipeline CELEBRIMBOR (Core ELEment Bias Removal In Metagenome Binned ORthologs) which lets you go from MAGs to pangenome
github.com/bacpop/CELEBRIMBO…
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John Lees retweeted
9 Sep 2024
📢 Only a week left to submit your abstract for #EMBLInfectionBiology 🦠
The event is a platform for late-stage postdoctoral scientists in infection biology to connect with the leading European institutions in the field. It is fully virtual for the ease of access 💻
Discuss your research and network in a friendly setting to step up your career! 🧑🏻🔬🫱🏾🫲🏻
📜 Submit your abstract by 15 Sep
➡️ s.embl.org/inb24-01
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27 Aug 2024
A reminder that abstract submission for the SMBE satellite meeting on pathogen pangenomes and transmission closes soon (8th September, a short extension). See:
smbepangenomes.bacpop.org/
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27 Aug 2024
I have written up some new notes in the intermediate programming course on parallel programming, which are available here:
iprogramming.bacpop.org/para…
The main intro and advanced examples are in rust, but I've also added two independent sections covering python and R.
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15 Aug 2024
I was excited by a preprint on 'PanMAN' by @yatishturakhia and co, here's a mini-review on my initial thoughts and how it might apply to bacteria:
johnlees.me/posts/panman-rev…
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John Lees retweeted
9 Aug 2024
🌞🌞🌞Job alert ‼️ We have not one but two positions available with me in @IneosOxford @OxfordBiology. More details here: ineosoxford.ox.ac.uk/careers
If you're interested, get in touch. Please share/RT
#AMR
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8 Aug 2024
Josie Bryant (@Josie_M_B) and I have a 3yr joint postdoc project at Sanger & EBI (ESPOD)
Topic: Developing new bioinformatic and modelling approaches for exciting new longitudinal microbiome datasets
Project details: embl.org/editorhub/wp-conten…
To apply: ebi.ac.uk/research/postdocs/…
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John Lees retweeted
4 Jul 2024
Today in @ScienceMagazine, we report how a bacteria has evolved into a major human pathogen over the last 200 years. Read on, this is going to be an adventurous ride 1/n! science.org/doi/10.1126/scie…
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