🔥The 9th Round of Easy Loan, Earn $40 Reward is in progress❗️ ⏰ Promotion Period: January 15th - Feburary 15th, 2025 👉 Register now and check more details at gate.io/campaigns/358

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/CELEBRI…

Today in Science Magazine, 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/sc…

Josie Bryant (Josie Bryant) 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-c… To apply: ebi.ac.uk/research/postd…

🌞🌞🌞Job alert ‼️ We have not one but two positions available with me in Ineos Oxford Institute for Antimicrobial Research Oxford Biology. More details here: ineosoxford.ox.ac.uk/careers If you're interested, get in touch. Please share/RT #AMR

I was excited by a preprint on 'PanMAN' by Yatish Turakhia and co, here's a mini-review on my initial thoughts and how it might apply to bacteria: johnlees.me/posts/panman-r…

I have written up some new notes in the intermediate programming course on parallel programming, which are available here: iprogramming.bacpop.org/parallel.html The main intro and advanced examples are in rust, but I've also added two independent sections covering python and R.

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

📢 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

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

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).

Extension to ska 'skalo' -- using local assembly to recover indels and MNPs where split k-mers mismatch biorxiv.org/content/10.110… We hope to integrate this into the main ska package in future too

Happy to announce that our (me and Yun William Yu) metagenome profiler sylph (github.com/bluenote-1577/…) is now published in Nature Biotechnology! 1/5

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/content/journa… Microbiology Society

This neat paper about rapid evolution of bacterial transformation rate by Eduardo Rocha @labXC & co takes some of its inspiration from an earlier PLOS Biology paper by Nick Croucher & Christophe Fraser Group: journals.plos.org/plosbiology/ar…

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

A mere six years after its first release, SKA is now published genome.cshlp.org/content/early/…

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

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/connectio…