Reference genomes don't capture all genetic diversity. This is particularly true for bacteria, where one strain can have 100s kilobases a close relative lacks. This is often summarized by gene-by-gene 'bean-bag' pan-genome analysis. But genome structure matters! 1/

So excited to announce that we have a definitive program for the "QBIO - Innate and Adaptive Recognition of Antigens and Neoantigens" colloquium! Have a look at our amazing panel of speakers at sites.google.com/view/qbio-iara…. Registrations and abstract submission are open!

Since its emergence in late 2019, #SARSCoV2 has diversified into multiple distinct variants. In a new preprint, I quantify evolution within these variants and compare it to the process that gave rise to these variants. biorxiv.org/content/10.110… 1/N

Huge congrats to Richard Neher for receiving the 3rd Symposium for Emerging Viral Diseases Geneva Centre for Emerging Viral Diseases Award! So well deserved for tireless hard work during the pandemic and on Nextstrain! For his award lecture he will speak on adaptive evolution in #influenza & #SARSCoV2.

👨🏽‍🎓New PhD Opportunity👩🏿‍🎓! My new Epidemiology & Virus Evolution (EVE) group at Swiss TPH 🇨🇭is looking for a PhD student in the evolution of phylogenetics of respiratory viruses 🦠🌳. Interested? See here for more details & to apply! jobs.swisstph.ch/Vacancies/927/… Please share! 😁

👩🏻‍🔬New **PostDoc** Opportunity!👨🏾‍🔬 My new Epidemiology & Virus Evolution (EVE) group at Swiss TPH🇨🇭 is looking for a PostDoc in evolution & phylogenetics of respiratory viruses 🦠🌳 Interested? See here for more details & to apply! jobs.swisstph.ch/Vacancies/928/… Please share! 😁

I have an open postdoc in my group: embl.org/jobs/position/… To work on either modelling or method development, but with a lot of flexibility in project choice. Please contact me if you are interested

Recruiting PhD students for Oct 24 start at University of Bath. Fully funded for UK students only. If interested in developing data structures/algorithms for bacterial genomics, or exploring plasmid epidemiology, or ML/AI on bacterial/phage geno/pheno data, give me a call 1/n

ggCaller paper now out in its final form genome.cshlp.org/content/33/9/1… Call your genes, get your pangenome (and a great cover thanks to laurenbellcreative.com)

In particular we've got space on the fantastic Pathogen Phylogenetics and Nextstrain course, and would love to see you there! I've you've ever wanted to dip into phylo & learn how to run Nextstrain, here's a great chance in a beautiful place!

Two PhD positions for #plasmid evolution research are open in our group: 1) Computational evolutionary microbiology and 2) Microbial evolutionary genetics. Application deadline: 10.3.24. Details in evoldir: evol.mcmaster.ca/brian/evoldir/… TransEvo @_K_E_C

If any non-UK folk with (or soon to have) a PhD are interested in applying for a Newton International Fellowship to work with me at the University of Bath (UK) on pangenome algorithms for bacteria and/or plasmids, do get in touch! Deadline 13th March! royalsociety.org/grants-schemes…

First paper from my student Daria Frolova's PhD now on biorxiv: biorxiv.org/content/10.110… 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

Ever wondered how fast accessory genome dynamics of bacteria really is? In a new preprint we (Marco Molari, Liam Shaw) explore how rapidly E coli picks up genes horizontally, breaks genome synteny, etc.. biorxiv.org/content/10.110… For a thread by Marco see mstdn.science/@mrcmlr/112772…

It has been public for a while, but with #VoM2024 starting, today is as good as any to introduce our new tool phage genome annotation tool Phold. Phold uses structural homology to assign functions to phage proteins (1/n)

One of the reasons I've been quiet on Twitter for a few months is because I've been working on something big - something I'm really happy to share now! Pathoplexus.org A new, open-source database for pathogen sequence sharing. 👐🧬🌎 1/12

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

The Kavli Institute for Theoretical Physics QBio course on mobile elements was amazing 🩵 With excellent projects led by Paul Turner Lab, Roberto Kolter, Joanne Emerson, Richard Neher, NimwegenLab, Benjamin Good (+ me). Course began with a wetlab bootcamp, Dallas Mould demonstrating the first experiments..