Katy Brown
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thekatybrown.bsky.social
Katy Brown
@thekatybrown.bsky.social
Postdoc in computational genomics studying RNA viruses at Cambridge. She/Her https://orcid.org/0000-0002-8400-6922
Reposted by Katy Brown
I cherish this mug so much that I don't even use it for liquids..
And it's from the 1993 my beloved paper by Dolja and Koonin. I will forever be grateful for @thekatybrown.bsky.social for such a thoughtful gift! :)

Their work was also what got me into virology without any hesitation:)
February 12, 2026 at 7:12 PM
Reposted by Katy Brown
🧬 Data scientists and enablers with experience in UK biomedical research: Your experience matters! MRC-funded research to tackle isolation & career barriers in biomedical data science roles.

app.onlinesurveys.jisc.ac.uk/s/oxford/bio...
πŸ“… Closes: 6/3/26
Β£50 Prize draw
Contact: integrate@imm.ox.ac.uk
January 15, 2026 at 12:04 PM
I have a new preprint! www.biorxiv.org/content/10.6... I found this endogenous retrovirus as a PhD student with @rtarlinton.bsky.social back in 2012 - a mere 14 years later we've written it up! This ERV is expressed in guinea pig lymphomas and might explain their high rate of lymphoma/leukemia. πŸ’»πŸ§ͺ
Expression of Retroviruses in Guinea Pig Lymphomas
Retroviruses commonly cause neoplasia in many species but have not been described in guinea pigs. While historical evidence exists for the presence of an active retrovirus in domestic guinea pigs ( Cavia porcella), there has been no description of the sequence of these viruses or their role in disease in guinea pigs. This paper uses genome mining of the published domestic and wild ( Cavia aperea) guinea pig genomes for retroviral sequences to identify the gamma and beta-retroviral complement of the Cavia genome, describing eight groups of viruses with evidence of recombination between virus groups. The most intact group, gamma-like retroviruses related to HERV-T (integration estimates of 855,000 to 3.8 million years ago), has five near full length loci that are likely capable of active infection. RNA-Scope In-situ Hybridisation of archived formalin-fixed, paraffin embedded (FFPE) guinea pig lymphoma sections with a probe for one of these loci demonstrated viral RNA expression in lymphoma tissue, strengthening the case for a role of these viruses in the high incidence of leukaemia and lymphoma in this species. ### Competing Interest Statement The authors have declared no competing interest. University of Nottingham, https://ror.org/01ee9ar58
www.biorxiv.org
January 20, 2026 at 2:27 PM
It would be interesting to look! But it’s hard to find them.
December 17, 2025 at 4:54 PM
Perfect summary!
December 17, 2025 at 4:53 PM
Reposted by Katy Brown
also the post at the ToL slack was captioned

barger badger badger badger
virus virus
AAAAAAAHHH sponge sponge it's a sponge
December 17, 2025 at 4:39 PM
Thank you! This is amazing!
December 17, 2025 at 4:35 PM
Reposted by Katy Brown
really nice talk by @thekatybrown.bsky.social on fishing for viruses in our Darwin Tree of Life @sangerinstitute.bsky.social datasets 🎣🦠

#SciArt #sketchnote
December 17, 2025 at 2:24 PM
Proud to have been a part of this! www.cell.com/cell/fulltex...
November 17, 2025 at 10:41 AM
October 28, 2025 at 1:27 PM
+ all kinds of EVEs in arthropods! I also found a bunch of viral pathogens mislabelled as bacterial and explored "near miss" proteins - with probably coincidental similarity to RdRp. 5/5
October 28, 2025 at 1:27 PM
I love EVEs so I spent time exploring and found orbivirus like EVEs in nematodes which pre-date species divergence and with a likely infectious counterpart, loads of diverse mitovirus-like regions in plants, and the first EVEs in the Perkinozoa phylum of protists 4/5
October 28, 2025 at 1:27 PM
Initially I wanted to explore how complicated it is to use database proteins as a negative control when looking for viruses because so many are unlabelled viral sequences. But then I unexpectedly found hundreds of RdRp-like endogenous viral elements 3/5
October 28, 2025 at 1:27 PM
I dug into proteins labelled as e.g. "unchacterised protein", "hypothetical protein" without any named function from any species in the NCBI protein and UniProt databases to find proteins related to RdRp 2/5
October 28, 2025 at 1:27 PM
My paper is out! Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterised sequences in public protein databases. doi.org/10.1093/ve/v... πŸ’»πŸ§¬ 1/5 🧡
October 28, 2025 at 1:27 PM
Reposted by Katy Brown
I translated "Jeff Jet: Abenteuer InfoHighway" as "Jeff Jet: Adventure on the InfoHighway" archive.org/details/jeff... - a German promotional adventure game for Hewlett Packard from 1995.
September 22, 2025 at 4:47 PM
Come to the BOKR session at 2:20 and see Charlotte Tumescheit @schnamo.bsky.social give a super interesting talk about improving prediction of molecular properties by incorporating ontologies. #ISMBECCB2025
July 23, 2025 at 1:30 PM
Someone needs to implement an LLM to help select which talks to go to at #ISMBECCB2025
July 23, 2025 at 1:22 PM
Come and see me in the ice rink if you want to plot phylogenies in matplotlib! Poster 206. GitHub.com/KatyBrown/plot_phylo #ISMBECCB2025
July 22, 2025 at 9:13 AM
You ring the doorbell on Oncology, just show any card, they won't check, then go down two floors in the lift, around the corner and then up one floor, once you get outside climb over the fence, scrabble up the verge, sign in as a visitor and you're there.
July 21, 2025 at 8:39 PM
It's the same in the UK. They specialise in roads which look like they link together but there's a huge fence or mysterious ditch blocking the way, or they've joined two buildings across the gap but not added a door to let people through.
July 21, 2025 at 8:33 PM
Reposted by Katy Brown
I reformatted the #ISMBECCB2025 schedule a bit - in case anyone else wants to use it this way - ordered by day and start time:

csv: drive.google.com/file/d/1JyhT...

xlsx:
docs.google.com/spreadsheets...
ISMBECCB_2025_All_Detailed_Schedule.csv
drive.google.com
July 21, 2025 at 8:05 AM
Thank you! This is amazing.
July 21, 2025 at 8:09 AM
Excited for the ISMB/ECCB conference! I have two posters A520 today about an endogenous and exogenous virus I found in nematodes - and B206 tomorrow about my tool plot_phylo for drawing phylogenies in matplotlib. #ISMBECCB2025
July 21, 2025 at 8:04 AM
And the same colour!
July 9, 2025 at 11:14 AM