Garan Jones
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sanejargon.bsky.social
Garan Jones
@sanejargon.bsky.social
76 followers 170 following 1 posts
Cancer and Ageing research; Pancreatic cancer transcriptomics; Bioinformatics; Long-read sequencing. CReST research fellow @ Cardiff University.
Posts Replies Media Videos
Reposted by Garan Jones
mikeinouye.bsky.social
I’m in Oxford this Monday and Tuesday (morning). Looking forward to seeing many old friends and colleagues… and hopefully meet some new ones! talks.ox.ac.uk/talks/id/b6e...
Genetic prediction and multi-omics: Towards disease prevention
The last 10 years have seen the emergence of predictive models based on genetics which quantify an individual’s genetic predisposition for a specific trait or disease. In this talk, I will present our...
talks.ox.ac.uk
November 2, 2025 at 8:49 PM
Reposted by Garan Jones
nickywhiffin.bsky.social
While I was taking a holiday last week, 2 super exciting preprints dropped, adding to another posted 6 days prior.

These papers describe a remarkable role for *recessive* variants in *RNU2-2* causing developmental and epileptic encephalopathy

🧵 by the amazing @christeldepienne.bsky.social 👇

1/3
September 8, 2025 at 8:43 AM
Reposted by Garan Jones
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 Garan Jones
mikeinouye.bsky.social
Sept is approaching & I can already hear initial chats/enquiries for potential PhD studies happening!

If you're interested in a PhD, check out our department @cam.ac.uk www.phpc.cam.ac.uk/education-an...

We've a super interdisciplinary faculty spanning primary care, data science, epidemiology etc
Doctoral Training | Department of Public Health and Primary Care (PHPC)
Course Code – MDPU22 A doctorate from the University of Cambridge is primarily a research degree based on a research programme developed in conjunction with a supervisor.
www.phpc.cam.ac.uk
August 27, 2025 at 12:35 PM
Reposted by Garan Jones
nickywhiffin.bsky.social
🚨 New preprint led by amazing duo @rociorius.bsky.social and @alexblakes.bsky.social in collaboration with @cassimons.bsky.social, @dgmacarthur.bsky.social and many other amazing folks! ❤️

We describe the clinical phenotype of a recessive NDD associated with biallelic variants in RNU4-2 🧬

See 🧵👇
August 18, 2025 at 11:46 AM
Reposted by Garan Jones
rjhfmstr.bsky.social
🚨 Our parent-of-origin study is out in Nature! 🧬
Maternal and paternal alleles can have distinct — even opposite — effects on human traits, revealing a hidden layer of genetic architecture that standard GWAS miss.
🔗 www.nature.com/articles/s41...

Highlights below!
August 6, 2025 at 6:27 PM
Reposted by Garan Jones
mikeinouye.bsky.social
IMHO green computing & green software engineering are becoming even very important.

Check out our Green Algorithms Initiative for more tools and information www.green-algorithms.org

And the GREENER Principles which lay the foundation for a sustainability roadmap www.nature.com/articles/s43...
Green Algorithms
Towards environmentally sustainable computational science
www.green-algorithms.org
August 4, 2025 at 3:44 PM
Reposted by Garan Jones
Our new draft V0.4 clonal/truncal somatic SV+CNV/CNA benchmark is at 42basepairs.com/browse/web/g.... Let us know if you have feedback to improve future versions!
data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.4-20250714 - Genome in a Bottle (FTP) - 42basepairs
42basepairs.com
July 21, 2025 at 3:20 PM
Reposted by Garan Jones
Our paper about extensive genomic data for a new broadly-consented pancreatic cancer cell line and matched normal tissue is now published at doi.org/10.1038/s415...! Stay tuned for draft GIAB benchmarks for somatic variants, and assemblies from these data coming soon! 1/2
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair - Scientific Data
Scientific Data - Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair
doi.org
July 21, 2025 at 3:20 PM
Reposted by Garan Jones
lifesciencescymru.bsky.social
Ydych chi ar LinkedIn? Rydym newydd lansio ein #cylchlythyr LinkedIn a fydd yn trafod #GwyddorauBywyd yng Nghymru!🧬✉️

Cael y diweddaraf am ddatblygiadau a straeon ysbrydoledig sy’n siapio dyfodol #arloesi ym maes #iechyd a #GofalCymdeithasol yng Nghymru a’r tu hwnt: www.linkedin.com/feed/update/...
Rydym yn gyffrous i gyhoeddi lansiad ein cylchlythyr LinkedIn sy'n ymroddedig i wyddorau bywyd yng Nghymru! | Life Sciences Hub Wales
Rydym yn gyffrous i gyhoeddi lansiad ein cylchlythyr LinkedIn sy'n ymroddedig i wyddorau bywyd yng Nghymru! 🧬✉️ Sicrhewch eich bod yn gwybod y diweddaraf am ddatblygiadau, prosiectau, a straeon y...
www.linkedin.com
July 3, 2025 at 11:05 AM
Reposted by Garan Jones
lifesciencescymru.bsky.social
Oeddech chi’n gwybod bod gennym ni gylchlythyr misol sy’n cynnwys y #newyddion diweddaraf ym maes #arloesi, yn ogystal â blogiau a digwyddiadau ar draws yr ecosystem #iechyd a #GofalCymdeithasol yng Nghymru a’r tu hwnt?

Tanysgrifiwch i Hwb Heddiw: lshubwales.com/cy/our-newsl...
July 8, 2025 at 7:51 AM
Reposted by Garan Jones
lifesciencescymru.bsky.social
Did you know we have a monthly #newsletter which features the latest #innovation news, blogs and events across the #health and #SocialCare ecosystem in #Wales and beyond?

Subscribe to Hub Highlights today: lshubwales.com/our-newsletter
July 8, 2025 at 7:52 AM
Reposted by Garan Jones
lifesciencescymru.bsky.social
Are you on LinkedIn? We’ve just launched our LinkedIn #newsletter dedicated to #LifeSciences in #Wales! 🧬✉️

Stay in the loop with developments, projects, and inspiring stories shaping the future of #health and #SocialCare #innovation across Wales and beyond: www.linkedin.com/feed/update/...
We’re excited to announce the launch of our LinkedIn newsletter dedicated to life sciences in Wales! | Life Sciences Hub Wales
We’re excited to announce the launch of our LinkedIn newsletter dedicated to life sciences in Wales! 🧬✉️ Stay in the loop with the latest developments, projects, and inspiring stories shaping the fut...
www.linkedin.com
July 3, 2025 at 11:06 AM
Reposted by Garan Jones
stephenturner.us
BiocPy brings Bioconductor's data structures and analysis tools to Python github.com/BiocPy #Rstats

Workshop materials: biocpy.github.io/BiocWorkshop...

Book: biocpy.github.io/tutorial/
July 4, 2025 at 3:30 PM
Reposted by Garan Jones
albertvilella.bsky.social
Beta access to the hyper base calling models for Oxford @nanoporetech.com sequencing register.nanoporetech.com/hyper-baseca...
Emerging Hyper Basecalling | Oxford Nanopore
This form allows you to confirm your interest in emerging hyper basecalling.
register.nanoporetech.com
July 2, 2025 at 7:21 PM
Reposted by Garan Jones
kezc.bsky.social
🚨 Our GW paper is out in Nature Methods!🥲

GW is a fast genomics browser (up to 100x faster!)
github.com/kcleal/gw

Also, just released a Python interface for GW
github.com/kcleal/gwplot

📝 nature.com/articles/s4159…#Genomicsc#Bioinformaticscs
GitHub - kcleal/gw: Genome browser and variant annotation
Genome browser and variant annotation. Contribute to kcleal/gw development by creating an account on GitHub.
github.com
June 26, 2025 at 2:47 PM
Reposted by Garan Jones
nickywhiffin.bsky.social
It's time!!!

An entire session of #eshg2025 on snRNA genes ❤️🤓
May 25, 2025 at 8:32 AM
Reposted by Garan Jones
alanlparker.bsky.social
Join our new Wales Applied Virology Unit as a Lecturer in Infectious Disease Epidemiology / Behavioural Science!

See the advert here:

krb-sjobs.brassring.com/TGnewUI/Search…

And contact WAVU co-director David Gillespie for informal enquiries.

#NewPI #Lecturer #GroupLeader #Job #Opportunity
April 16, 2025 at 6:23 AM
Reposted by Garan Jones
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
Reposted by Garan Jones
minomatt.bsky.social
Great to be visiting @nanoporetech.com as part of a cns Nanopore symposium meeting with pathologists and clinical scientists to discuss the application of nanopore sequencing in the clinic.
March 5, 2025 at 10:51 AM
Reposted by Garan Jones
kezc.bsky.social
🧬🖥️ Just released Dysgu v1.8 which now supports phasing of structural variants when using long reads. Makes SV calling much more sensitive - see PacBio benchmark 👉 github.com/kcleal/SV_Be... dysgu repo github.com/kcleal/dysgu...
February 26, 2025 at 11:37 AM
Reposted by Garan Jones
lcpilling.bsky.social
Minor-ish update to {ukbrapR} to v0.2.9 to fix 2 bugs and improve behaviour of some internal functions

github.com/lcpilling/uk...
GitHub - lcpilling/ukbrapR: R package for working in the UK Biobank Research Analysis Platform (RAP)
R package for working in the UK Biobank Research Analysis Platform (RAP) - lcpilling/ukbrapR
github.com
January 13, 2025 at 9:03 AM
Reposted by Garan Jones
Our first curated draft somatic structural variant benchmark for the new GIAB PDAC tumor cell line HG008-T is at ftp-trace.ncbi.nlm.nih.gov/ReferenceSam..., based on extensive short+long read sequencing data described in doi.org/10.1101/2024.... Feedback to improve future versions is very welcome!
Index of /ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar_DraftBenchmark_V0.1-20241219
ftp-trace.ncbi.nlm.nih.gov
December 20, 2024 at 6:04 PM
Reposted by Garan Jones
kezc.bsky.social
🧬🖥️ Sharing an update to my SV benchmark repo. More callers have been added for the CMRG/GIAB benchmarks. github.com/kcleal/SV_Be.... Also now uses #Nextflow and tests the newest #PacBio Vega data, along with #ONT kit14. Results are on the GitHub page 👉
GitHub - kcleal/SV_Benchmark_CMRG_GIAB: Structural variant benchmark of challenging medically relevant genes
Structural variant benchmark of challenging medically relevant genes - kcleal/SV_Benchmark_CMRG_GIAB
github.com
November 29, 2024 at 1:40 PM
Reposted by Garan Jones
minomatt.bsky.social
This is worth looking at. Trying some genomes we have assembled with earlier versions of hifiasm, hifiasm plus herro and then this new version of hifiasm. The early assembly results suggest that now hifiasm alone is equivalent to what we got with herro but with less compute!
November 28, 2024 at 12:58 PM