Every time I submit files to ENA I forget how I did it the previous time. So I have written up a guide to my future myself of how I normally approach it. Maybe it might be useful for someone else. padpadpadpad.netlify.app/posts/ena_fi...

Amazing resource! Thanks for this :)

Our latest paper is out. The brainchild of @drrebeccajhall.bsky.social We had shown how different E. coli strains respond to the same MDR plasmid. Here we show how one strain responds to different MDR plasmids

journals.asm.org/doi/10.1128/...

Our latest on phage-plasmids(PP) is out! Two main findings. PP recombine more with (other) plasmids and phages than the latter, thereby connecting them. PP can become just phages or plasmids, which may then transition to be conjugative. All the world’s an MGE! www.nature.com/articles/s41...

Check out our latest preprint! We explore the application of Nanopore Adaptive Sampling (NAS) for serotyping Streptococcus pneumoniae, and develop a new graph-based tool, GNASTy (pronounced ‘nasty’), to increase NAS sensitivity for detecting novel unobserved serotypes.

We have published a manuscript describing a software tool to reduce ambiguity and improve interpretability in microbial GWAS, called panfeed. Here's a quick explainer: www.microbial-pangenomes-lab.org/2023/11/09/M...

And here's the link to the paper: www.microbiologyresearch.org/content/jour...

A rugged yet easily navigable fitness landscape

-in Science from Andreas Wagner

www.science.org/doi/10.1126/...

Our latest paper is out now. The brilliant Chris Connor’s entire PhD in one paper. And I hope a new avenue of research opened in MDR E. coli

journals.plos.org/plosbiology/...

1/n

Fantastic! Let's stay in touch!

Have you wondered if some E. clones are so successful because of their plasmids? www.biorxiv.org/content/10.1...

A combination of bioinf and lab work showed that some plasmids have coexisted for centuries, and that a specific colicin gene is able to kill other clones paving their way for success!

I'm 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!

bioRxiv goes big on Bluesky: accounts for all subject categories now available (Please Reskeet) connect.biorxiv.org/news/2023/09...

We should treat methods in computational biology more like the wet lab, with positive and negative controls, and 'replication' with different inputs and parameters.
Many methods rely on heuristics and even if not, objectives are typically so nuanced that provable correctness/optimality do not help.

We have two Prof-level posts open at IMI Birmingham:

Microbial Genomics www.jobs.ac.uk/job/DBJ457/c...

Respiratory Infection Biology www.jobs.ac.uk/job/DBJ427/c...

Deadline is 30 Sept!

Email @alanmcn1.bsky.social or me with questions

skANI looks like an impressive drop-in replacement for FastANI:
www.nature.com/articles/s41...

github.com/bluenote-157...

A reminder we have two completely open search prof posts going the IMI at Birmingham

Microbial Genomics: www.jobs.ac.uk/job/DBJ457/c...

Infection Biology: www.jobs.ac.uk/job/DBJ427/c...

I see the geNomad paper is out!

www.nature.com/articles/s41...