Woah more than a year since I last posted.

Hello  

I walked into Oxford 

#compiling / #crunchingdata

https://www.youtube.com/shorts/_S28qL52h-U

2 x papers accepted between mid-Dec 2023 and mid-Jan 2024 (one as 1st author). And a sole-author paper that went through a double-hurdle to be reviewed at a fancy journal (which alone is worthy of some celebration on my end). What's in my mind (after frantically updating CV and notifying panels of the update*)?

https://www.youtube.com/shorts/ZIGZVSYoOz4

* Except those who said 'you cannot simply tell us you have two more papers'  and have my CV evaluated without my 2 now-accepted-publications.

#Bioinformatics question for readers out here: A reviewer asked to put a quantitative metric to compare a software I wrote to analyse de novo assemblies vs reference-mapped assemblies...

Feels a bit like apples vs oranges (de novo vs reference-mapped) but the question is still there. And the number of genomes to process for this is 5,032.

Any suggestions?

Too many platforms to track, but... here's another #preprint  This is a tool I built to help my colleagues in Bristol vacuum info about any gene they wanted  Because they had phenotypic data on their stuff, they are using the tool to predict phenotypes from their genomic datasets. But that's another story.

It returns a spreadsheet w/ 1) mutations in CDS, 2) mutations in promoter, 3) relative copy number. I screened 5,000+ genomes to demo it.

https://www.biorxiv.org/content/10.1101/2023.09.15.557405

Postdocs in the academic [TT] market #PostdocLife

https://www.youtube.com/shorts/KhqmsAuJyCQ

Next week I'll be presenting a poster of the pipeline I wrote. It's called Hound, and uses by default protein sequences to find AMR (and non-AMR) genes iteratively across thousands of de novoassemblies.

Given this, it was hard not to include "F--k the gene!" in the poster.

I'll show myself out now.

X: Carlos... can you run database ACME on all these isolates with your program?

Me: Of course, it's mean to give users flexibility for what they want---I said naively before checking ACME or the isolates.

X hands over a 2TB HDD.

Me: Blimey the Hound is slow today...

Then I proceed to checks server, ACME, and the isolates. So apparently I've been diggin' for more than 3,100 genes in 2,000 isolates 

Some exciting news! (or not)

I was asked to guest edit an issue about the use of #AI #Bioinformatics in #Microbiology for the journal Frontiers in Cellular and Infection Microbiology.

The goal, is to assemble a team of 3-4 editors (myself included) to shape the scope of the issue and gather a list of potential contributors. We will have the chance to write an editorial article >=4 manuscripts are accepted.

If you'd like to help me with this endeavour or would like to submit a study DM me.