Tagging for the #GeroSky community - would welcome any discussion

This builds on recent work on ageing, tissue context, and interventions. Sharing in case this is of interest to others following ageing biology @agingdoc.bsky.social

This could create a challenge for therapeutics. e.g. resetting cellular states may yield transient benefits if the surrounding slow-turnover architecture remains degraded.

This drift could become locked in: coordination is encoded across substrates with different turnover rates, from fast signalling to slow architecture such as the ECM. When slower substrates degrade, they may re-specify faster ones, creating a self-stabilising coordination trap

A core issue may be a sensing bottleneck: cells have access to only a compressed, low-dimensional view of their microenvironment. Consequently, tissues may be unable to fully audit their own collective states, allowing functional drift to accumulate.

Happy to share a new preprint exploring the idea that multicellular coordination may itself be a fundamental constraint in ageing, and asking how stochastic cellular damage is translated into tissue-level decline 🧵
www.preprints.org/manuscript/2...

Tumor clone dynamics in gastro-esophageal cancer organoids reveal a non-genetic memory of neoadjuvant chemotherapy via downregulation of NFκB signaling Adenocarcinomas of the gastroesophageal junction exhibit genetic and non-genetic heterogeneity that impact clinical outcomes, though the underlying mechanisms behind drug resistance remain poorly unde...

We are happy to present a new paper on gastric tumour evolution in response to peri-operative chemotherapy. www.biorxiv.org/content/10.1... 🧵 1/6

Nice work! Do you think it would be hard to calculate perplexity for short read data?

Perplexity as a Metric for Isoform Diversity in the Human Transcriptome Long-read sequencing (LRS) has revealed a far greater diversity of RNA isoforms than earlier technologies, increasing the critical need to determine which, and how many, isoforms per gene are biologic...

New work from the lab trying to wrap our heads around the massive complexity of the human transcriptome revealed by long-read RNA-seq! Fun collab with Gloria Sheynkman. www.biorxiv.org/content/10.1...

Thank you, Francisco 🙏

Thanks Wales Bioinformatics Network 🙂

GitHub - kcleal/gw: Genome browser and variant annotation Genome browser and variant annotation. Contribute to kcleal/gw development by creating an account on GitHub.

🚨 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…

#Genomics #Bioinformatics

Very impressive work 👏

A really useful resource

@adbeggs.bsky.social Hi Andrew. Fantastic talk today at the WCRC conference! It was very inspiring 👏

🧬🖥️ 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...

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

🧬🖥️ 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 👉

🧬 🖥️

Also my first foray into rust land - lots to like I have to say!

GitHub - kcleal/superintervals: Fast interval intersection library Fast interval intersection library. Contribute to kcleal/superintervals development by creating an account on GitHub.

Hi all. Just released a fast library (C++/Rust/Python) for performing interval intersections. Uses a novel superset-index that tends to be faster than current libs, and also has a SIMD accelerated counting algorithm 👇 github.com/kcleal/super...

Thanks 👍 Could I be added? Cheers

Whole genome in 2s 😂 wow👏

Hi @robp.bsky.social, not sure if I qualify, but could I be added to the list? Cheers 👍

I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics)

go.bsky.app/TRWCnZs

BioNumpy looks really good, looking forward to giving this a try www.nature.com/articles/s41...

Genomics+Bioinformatics Starter Pack 🧬🖥️ Join the conversation

I created a genomics+bioinformatics starter pack. If I left you off, *please* reply and I'll add you! go.bsky.app/B5YYBfq

Hello world! This looks promising