Alex Geary
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alextremophile.bsky.social
Alex Geary
@alextremophile.bsky.social
570 followers 430 following 30 posts
Postdoctoral Bioinformaticial in the Computational Rare Disease Genomics group (Nicky Whiffin). univ. Oxford 🧬💻

Loves Evolution, regulation, cheese and cats. She/Her
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alextremophile.bsky.social
I am super proud to present our new manuscript “Using SpliceAI to triage splice-altering variants in 7,220 individuals with rare conditions highlights limitations of the precomputed scores”
www.medrxiv.org/content/10.1...
Using SpliceAI to triage splice-altering variants in 7,220 individuals with rare conditions highlights limitations of the precomputed scores
Background: SpliceAI is a deep learning algorithm that predicts whether genetic variants are likely to affect splicing. Precomputed spliceAI predictions for all theoretical SNVs and small indels were ...
www.medrxiv.org
August 29, 2025 at 8:57 AM
Reposted by Alex Geary
alexblakes.bsky.social
I learned so much from this work and I hope that and discoveries like this can make a real difference to the lives of people living with #RareConditions. Please do share! 😊
www.medrxiv.org/content/10.1...
Biallelic variants in the non-coding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes
Genetic variants in RNU4-2, which encodes U4, a key non-coding small nuclear RNA (snRNA) component of the major spliceosome, were recently shown to cause a prevalent neurodevelopmental disorder (NDD) ...
www.medrxiv.org
August 18, 2025 at 11:23 AM
Reposted by Alex Geary
alexblakes.bsky.social
The headlines?

1) Variants on both copies of #RNU4-2 cause a recessive neurodevelopmental disorder with prominent speech delay
2) One of the hallmarks is distinct white matter changes on MRI
3) It is clinically and genetically distinct from #ReNU syndrome

www.medrxiv.org/content/10.1...
Biallelic variants in the non-coding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes
Genetic variants in RNU4-2, which encodes U4, a key non-coding small nuclear RNA (snRNA) component of the major spliceosome, were recently shown to cause a prevalent neurodevelopmental disorder (NDD) ...
www.medrxiv.org
August 18, 2025 at 11:23 AM
alextremophile.bsky.social
An awesome piece of work by @alexblakes.bsky.social, @rociorius.bsky.social, @nickywhiffin.bsky.social and team!

I am super excited to see more emerging from this tiny, but mighty gene, and am overjoyed at the implications this has for the rare disorders community ❤️
August 18, 2025 at 11:28 AM
Reposted by Alex Geary
nechamawieder.bsky.social
3/
The review outlines how UTR variants cause disease, such as:
- Create or remove upstream AUGs (uAUGs)
- Alter splicing
- Alter polyadenylation
- Interfere with miRNA or protein binding
July 4, 2025 at 8:08 AM
alextremophile.bsky.social
This is such an awesome review paper from @nechamawieder.bsky.social!
UTRs are more than just 'buffers' for the coding sequence - they contain a wealth of important regulatory features!
July 4, 2025 at 9:41 AM
Reposted by Alex Geary
shakespeare.lol
You seem’d of late to make the law a tyrant
April 25, 2025 at 3:53 PM
alextremophile.bsky.social
Want a Friday mood boost whilst also raising awareness of rare disorders? Then this fresh drop from the band of one of the GEL participant panel members is for you! ♥️🎶♥️
Play it loud, share it widely!
(Beware - it is _extremely_ catchy!)

open.spotify.com/album/1f2CAX...
The A The C The G The T
The Rayne · Single · 2025 · 2 songs
open.spotify.com
April 25, 2025 at 11:40 AM
Reposted by Alex Geary
zjayres.bsky.social
Love to my trans sisters, always.

#TransRightsAreHumanRights
April 16, 2025 at 7:18 PM
Reposted by Alex Geary
themountaingoats.bsky.social
if you are a cis person it costs you nothing to just say today that you see & hear your trans sisters & brothers & others over in the UK today -- and around the world, too, knowing that rulings like today's ripple out in ugly ways.
April 16, 2025 at 12:18 PM
alextremophile.bsky.social
I am delighted to share with you the news that our shiny new paper has hit the shelves in Genome Medicine!!

link.springer.com/article/10.1...

Key points (A 🧵):
Systematic identification of disease-causing promoter and untranslated region variants in 8040 undiagnosed individuals with rare disease - Genome Medicine
Background Both promoters and untranslated regions (UTRs) have critical regulatory roles, yet variants in these regions are largely excluded from clinical genetic testing due to difficulty in interpre...
link.springer.com
April 14, 2025 at 5:43 PM
Reposted by Alex Geary
gregfindlay.bsky.social
We're quite excited about this story as it showcases the power of SGE to dissect non-coding genes and to uncover new disease associations and diagnoses. This has, indeed, been an excellent collaboration...
April 11, 2025 at 4:14 PM
Reposted by Alex Geary
nickywhiffin.bsky.social
🚨I could not be more excited to share our new preprint on saturation genome editing of the small nuclear RNA (snRNA) RNU4-2:
www.medrxiv.org/content/10.1...

A super fun collaboration with incredible duo @gregfindlay.bsky.social @joachimdejonghe.bsky.social from @crick.ac.uk
🧬🖥️🩺

🧵1/12
Saturation genome editing of RNU4-2 reveals distinct dominant and recessive neurodevelopmental disorders
Recently, de novo variants in an 18 nucleotide region in the centre of RNU4-2 were shown to cause ReNU syndrome, a syndromic neurodevelopmental disorder (NDD) that is predicted to affect tens of thous...
www.medrxiv.org
April 11, 2025 at 10:00 AM
alextremophile.bsky.social
This is excruciatingly painful to read, and also a really powerful reminder that the participants are always the heart of any study ♥️
carolinefwright.bsky.social Caroline Wright @carolinefwright.bsky.social · Apr 10
"Remember that it's not only scientists that read your papers" - sage advice from author of a beautiful poem 'Proband', which began life as a response to our DDD NEJM paper, linking genomic science and its patients. www.consilience-journal.com/issue-17-pro...
Proband — Consilience
www.consilience-journal.com
April 10, 2025 at 12:50 PM
alextremophile.bsky.social
Super late to rare disease weekend, but how awesome is this lady! A stellar scientist, advocate for the rare disease community, mentor, & person. As a rare human, I’m so glad that people like Nicky are doing their absolute best for the rare condition community ♥️ @nickywhiffin.bsky.social
Photo of Nicky Whiffin, the principal investigator of the Rare Disease Genomics group at the university of Oxford. She is smiling in front of a lush green hedge, wearing an excellent teal dress. The caption reads “Nicky Whiffin, whose team at Oxford University discovered ReNU syndrome’
March 2, 2025 at 9:48 PM
alextremophile.bsky.social
I had the honour of accompanying the wonderful Yuyang Chen to the Genetic Alliance #rareDiseaseDay2025 reception today.
It was fantastic to meet so many incredible people, and hear such powerful stories. Read the anthology “More than you can imagine” here: geneticalliance.org.uk/campaigns-an...
February 27, 2025 at 9:09 PM
alextremophile.bsky.social
Non Science post -
I tried to book a GP appointment. They now use an online system requiring an online consultation. This includes a bot that suggests some vaguely horrifying possible diagnoses, and many irrelevant questions. I did submit it - many won't. I still don't have an appointment.
November 28, 2024 at 3:49 PM
Reposted by Alex Geary
gabriellebrewer.bsky.social
If you have any questions about working as an editor at Nature Portfolio, please don't hesitate to reach out.
November 26, 2024 at 11:17 AM
Reposted by Alex Geary
prokaryota.bsky.social
Failure is a cornerstone of scientific research, but it still feels bad. Here is a short article I wrote on how to mentally deal with "failed" experiments. Does a truly "failed" experiment actually exist?? @academic-chatter.bsky.social #academicsky #microsky elisagranato.com/phd-tips-dea...
PhD Tips – Dealing with “failed” experiments - Elisa Granato
PhD Tips - Dealing with "failed" experiments "PhD Tips" is a series of articles aimed at graduate students at the University of Oxford (Department of Biology). I wrote this in April 2021. [This articl...
elisagranato.com
November 26, 2024 at 11:34 AM
alextremophile.bsky.social
Wonderful - absolutely wonderful!
Can we replace her FRS with an award? 🏆
www.theguardian.com/technology/2...
Oxford scientist resigns from Royal Society over Elon Musk’s continuing fellowship
Prof Dorothy Bishop said fellowship was ‘a contradiction of all the values’ of UK’s national academy of sciences
www.theguardian.com
November 25, 2024 at 10:32 PM
alextremophile.bsky.social
I often think it, but it is worth saying aloud - every day I am thankful for beepr ❤️
www.r-project.org/nosvn/pandoc...
November 7, 2023 at 7:53 PM
Reposted by Alex Geary
klewis.bsky.social
🧬 🖥️ For our genetics/genomics friends visiting #ASHG23, you can follow the conference's conversation on this feed:

bsky.app/profile/did:...

Just use #ASHG23 (or #ASHG2023) to post to the feed.
October 27, 2023 at 1:13 PM
Reposted by Alex Geary
biorxiv-genomic.bsky.social
Replication stress underlies genomic instability at CTCF/cohesin-binding sites in cancer https://www.biorxiv.org/content/10.1101/2023.10.24.563697v1
Replication stress underlies genomic instability at CTCF/cohesin-binding sites in cancer https://www.biorxiv.org/content/10.1101/2023.10.24.563697v1
CCCTC-binding factor (CTCF) and cohesin play a significant role in the formation of chromatin loops
www.biorxiv.org
October 27, 2023 at 2:35 PM
Reposted by Alex Geary
lorrainesanty.bsky.social
Penn State BMB is hiring! Two tenure-track/tenured positions.
One in Gene Regulation: psu.wd1.myworkdayjobs.com/PSU_Academic...
Second in Cryo-EM/Cryo-ET
psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...

#WomenInSTEM
October 18, 2023 at 2:40 PM