Katie O'Mahony
@aforestsomewhere.bsky.social
Postdoc at Teagasc, Microbial Genomics
Reposted by Katie O'Mahony
🚨Update: Our analysis of global APC expenditure has now been expanded to cover more publishers (7 -> 14) and more years (2019-2025).
We estimate $15B in APCs paid over seven years, $3.7B in 2025 alone. Elsevier crosses the $1B threshold by itself in 2025.
arxiv.org/abs/2608.16322 #ScholComm
We estimate $15B in APCs paid over seven years, $3.7B in 2025 alone. Elsevier crosses the $1B threshold by itself in 2025.
arxiv.org/abs/2608.16322 #ScholComm
August 31, 2026 at 1:16 PM
🚨Update: Our analysis of global APC expenditure has now been expanded to cover more publishers (7 -> 14) and more years (2019-2025).
We estimate $15B in APCs paid over seven years, $3.7B in 2025 alone. Elsevier crosses the $1B threshold by itself in 2025.
arxiv.org/abs/2608.16322 #ScholComm
We estimate $15B in APCs paid over seven years, $3.7B in 2025 alone. Elsevier crosses the $1B threshold by itself in 2025.
arxiv.org/abs/2608.16322 #ScholComm
Reposted by Katie O'Mahony
I love that this is how I found out Starmer stepped down as an MP
Can't get a moment's peace on this bloody planet.
September 1, 2026 at 11:36 AM
I love that this is how I found out Starmer stepped down as an MP
Reposted by Katie O'Mahony
Stop paying predatory publishers of academic journals - A policy proposal to restore scientific integrity and transparency (via @febsletters.bsky.social)
doi.org/10.1002/1873...
doi.org/10.1002/1873...
August 29, 2026 at 9:53 PM
Stop paying predatory publishers of academic journals - A policy proposal to restore scientific integrity and transparency (via @febsletters.bsky.social)
doi.org/10.1002/1873...
doi.org/10.1002/1873...
Reposted by Katie O'Mahony
Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...
May 5, 2026 at 8:06 AM
Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...
Reposted by Katie O'Mahony
We've been looking at how to compare and cluster large numbers of genomes, such as those in large isolate databases such as AllTheBacteria, and metagenome assemblies (e.g. SPIRE, MGnify).
On a combined dataset of 5.6 million assemblies, we can now cluster/dereplicate everything in under a day!
On a combined dataset of 5.6 million assemblies, we can now cluster/dereplicate everything in under a day!
🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
June 16, 2026 at 4:07 PM
We've been looking at how to compare and cluster large numbers of genomes, such as those in large isolate databases such as AllTheBacteria, and metagenome assemblies (e.g. SPIRE, MGnify).
On a combined dataset of 5.6 million assemblies, we can now cluster/dereplicate everything in under a day!
On a combined dataset of 5.6 million assemblies, we can now cluster/dereplicate everything in under a day!
Reposted by Katie O'Mahony
R.I.P. Yayoi Kusama
August 29, 2026 at 2:23 PM
R.I.P. Yayoi Kusama