John Lees

Pathogen informatics and modelling group leader at EMBL-EBI -

[EMBL @embl]

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. 👇

https://t.co/2n6B6bfSQ0

[John Lees @johnlees6]

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

[EMBL-EBI @emblebi]

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.

https://t.co/o9QdzfUKyn

[John Lees @johnlees6]

A mere six years after its first release, SKA is now published
https://t.co/vtJGt98ged

[John Lees @johnlees6]

@TimoJMoilanen @shenwei356 @ZaminIqbal This is great!!

[Zamin Iqbal @ZaminIqbal]

This is exactly the kind of thing we wanted to happen!

[Roli Roberts @RoliRoberts]

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: https://t.co/FdyRGzNJfy

[Zamin Iqbal @ZaminIqbal]

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.
https://t.co/fG0GCYqKZO
@MicrobioSoc

[Jim Shaw @jim_elevator]

Happy to announce that our (me and @YunWilliamYu) metagenome profiler sylph (https://t.co/WGX3W1yOjT) is now published in @NatureBiotech!

1/5

[John Lees @johnlees6]

Extension to ska 'skalo' -- using local assembly to recover indels and MNPs where split k-mers mismatch
https://t.co/I4tilmrq3U
We hope to integrate this into the main ska package in future too

[Camille Marchet @[email protected] @CamilleMrcht]

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).

[John Lees @johnlees6]

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!
https://t.co/HnKRbshoVD

[John Lees @johnlees6]

We are happy to have been selected by SMBE to host a satellite meeting on Pathogen Pangenome Evolution Between and Within their Hosts:
https://t.co/HnKRbshoVD
We are expecting the meeting to be in Tokyo on 26-28th November 2024, save the date!

[John Lees @johnlees6]

Also now old Celebrimbor is a big name in rings of power s2 maybe our backronym will finally land

[John Lees @johnlees6]

Now published in bioinformatics, CELEBRIMBOR 'pangenomes from metagenomes'
https://t.co/L7FL5fekfe
I think reviewer comments helped make it better, so worth another look (at fig 1 particularly!)

[John Lees @johnlees6]

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
https://t.co/c3BZprY94E

[John Lees @johnlees6]

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
https://t.co/c3BZprY94E

[EMBL Events @EMBLEvents]

📢 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
➡️ https://t.co/iHuEvxUC9v

[John Lees @johnlees6]

A reminder that abstract submission for the SMBE satellite meeting on pathogen pangenomes and transmission closes soon (8th September, a short extension). See:
https://t.co/HnKRbshoVD

[John Lees @johnlees6]

I have written up some new notes in the intermediate programming course on parallel programming, which are available here:
https://t.co/SIdrMS8Rhn

The main intro and advanced examples are in rust, but I've also added two independent sections covering python and R.

[John Lees @johnlees6]

@yatishturakhia Yes very exciting stuff! Looking forward to seeing where you take it

[John Lees @johnlees6]

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:
https://t.co/q1vUKwAM57

[Sheppard Lab @sheppard_lab]

🌞🌞🌞Job alert ‼️ We have not one but two positions available with me in @IneosOxford @OxfordBiology. More details here: https://t.co/nAW2DFaszm
If you're interested, get in touch. Please share/RT
#AMR