Pathogen informatics and modelling https://xitter.cf/t.co/2Qg0pvaFg3 (Research group leader at EMBL-EBI - https://xitter.cf/t.co/lJdwj0idt0)
Joined December 2009
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John Lees retweeted
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…
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…
A mere six years after its first release, SKA is now published
genome.cshlp.org/content/ear…
John Lees retweeted
This is exactly the kind of thing we wanted to happen!
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
John Lees retweeted
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…
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
John Lees retweeted
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
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?
1/n
John Lees retweeted
Happy to announce that our (me and @YunWilliamYu) metagenome profiler sylph (github.com/bluenote-1577/syl…) is now published in @NatureBiotech!
1/5
Rapid species-level metagenome profiling and containment estimation with sylph go.nature.com/3BBVqDC
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
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).
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/
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!
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!)
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…
John Lees retweeted
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…
John Lees retweeted
📢 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
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/
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.
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…
John Lees retweeted
🌞🌞🌞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
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/…
John Lees retweeted
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…