iiinova — where your digital self keeps evolving

Reposted by Daniel Seaton

Stegle Lab @steglelab.bsky.social · 07/11/2025

Are you using any of our factor models, such as MOFA? 🛵 You might’ve found it challenging to tailor them to your specific use cases - not anymore! Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n

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Diego del Alamo @delalamo.xyz · 24/04/2025

An interesting "what have we been doing all these years?" result from this paper is how sub-optimal the widely-used uniform sampling scheme can be (cluster all @50%, sample from all clusters equally). In contrast, strategies that account for the relative differences in cluster size improve val loss

(c) Diversity of PPA-1 data distributions as measured by the CDF of 50% ID cluster sizes.
(d) Validation losses of 1.4B parameter models trained on 80B tokens from different data distributions.

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Anshul Kundaje @anshulkundaje.bsky.social · 18/04/2025

Single task, lightweight, short-context bp res. profile models often perform on par or outperform current large, multi task, long context models on counterfactual prediction. Much to do to improve. Bonus: robust, efficient interpretation of syntax Great collab with @jengreitz.bsky.social lab.

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Anna Cuomo @annasecuomo.bsky.social · 24/03/2025

📢 new preprint alert: So so excited to share our analysis on the impact of common and rare variants on single-cell gene expression in blood, using WGS and scRNA-seq data from nearly 2,000 individuals and 5.4m cells as part of TenK10K phase 1 🧬 www.medrxiv.org/content/10.1... 🧵👇 (1/n)

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Daniel Seaton @danieldseaton.bsky.social · 06/03/2025

Are you a postgraduate student interested in protein modelling and drug discovery? We have an exciting opportunity to join our team at GSK for a 6-9 months internship, working on an ambitious cross-department research project. Apply before March 14th! www.linkedin.com/jobs/view/41...

linkedin.com

GSK hiring Computational Biologist in Stevenage, England, United Kingdom | LinkedIn

Posted 11:13:48 PM. Site Name: UK - Hertfordshire - Stevenage, Heidelberg - OfficePosted Date: Feb 28 2025We create a…See this and similar jobs on LinkedIn.

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Kaur Alasoo @kauralasoo.bsky.social · 30/12/2024

Very cool paper from Eddie Park and Yi Xing studying the relationship between intron retention QTLs and expression QTLs. Predictably, genetically regulated intron retention can cause changes in gene expression via nonsense-mediated decay (NMD). www.biorxiv.org/content/10.1...

biorxiv.org

Origins and Implications of Intron Retention Quantitative Trait Loci in Human Tissues

Intron retention is a type of alternative splicing in which introns remain unspliced in mature RNA transcripts. In order to explore the landscape and consequences of genetically regulated intron reten...

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Jeff Spence @jeffspence.github.io · 17/12/2024

What do GWAS and rare variant burden tests discover, and why? Do these studies find the most IMPORTANT genes? If not, how DO they rank genes? Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬) www.biorxiv.org/content/10.1...

biorxiv.org

Specificity, length, and luck: How genes are prioritized by rare and common variant association studies

Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...

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Reposted by Daniel Seaton

Stegle Lab @steglelab.bsky.social · 09/12/2024

We are the Stegle Lab: A bioinformatics group advancing computational methods to study molecular variations and their impact on phenotypes. We are jointly hosted at the German Cancer Research Center (@dkfz.bsky.social) and the European Molecular Biology Laboratory (@embl.org) in Heidelberg, Germany.

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Reposted by Daniel Seaton

Why @why.bsky.world · 20/11/2024

To be clear, we do have plans for scaling, we just kinda expected more than a couple days notice before getting blasted with a million new users a day. The team is rapidly deploying fixes and new software to adapt. More servers in the mail.

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Reposted by Daniel Seaton

Hilary Martin @hilarycmartin.bsky.social · 20/11/2024

My group's work dissecting the contribution of common variants to rare neurodevelopmental conditions is now out at nature.com/articles/s41..., led by co-first authors Qinqin Huang (not yet on blue sky) and @emiliewigdor.bsky.social . See below for Emilie's tweetorial.

nature.com

Examining the role of common variants in rare neurodevelopmental conditions - Nature

Patients with neurodevelopmental conditions without a monogenic diagnosis have a higher polygenic burden than those with a monogenic diagnosis. Non-transmitted common all...

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Reposted by Daniel Seaton

EMBL-EBI @ebi.embl.org · 19/11/2024

Not enough bioinformatics in your Bluesky feed? We’ve got you covered. Follow us for our latest news, exciting life science research, updates from our data resources, new tools and training resources. Haven't heard of EMBL-EBI? Take a look at what we’re working on. www.ebi.ac.uk/about/our-im...

ebi.ac.uk

Our impact

We provide open data that helps scientists understand life and that informs solutions to real-world problems, such as infectious diseases, climate change and food security.

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Jason Buenrostro @jbuenrostro.bsky.social · 19/11/2024

Hey, a question for the genetics community. Does genetic fine-mapping work well? How often does it miss? We usually find that most fine-mapped variants do not fall within coding or regulatory regions. Is it a limitation of epigenomics or a limitation of fine-mapping? Please share your thoughts!

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Axel Visel @axelvisel.bsky.social · 27/05/2024

REX - a mammalian "range extender" element that can turn short-distance enhancers into long-distance enhancers. New preprint from a collaboration led by Grace Bower and Evgeny Kvon. doi.org/10.1101/2024...

Schematic overview of the proposed mode of action of the newly discovered REX element. Top: An enhancer can activate a gene at a short distance, but not at at long range. Middle: Presence of (C/T)AATTA motifs within an enhancer enable it to act over long distances. Bottom: Coupling a short-range enhancer to the REX element containing the same motifs turns it into a long-range enhancer.

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Anna Cuomo @annasecuomo.bsky.social · 31/10/2023

Sad to be missing #ASHG23, but check out the talk by the brilliant Wei Zhou talk on Saturday on our new scalable & efficient method for single-cell eQTL mapping!

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Jeffrey Barrett @jeffbarrett.eu · 31/10/2023

This is tremendous news, and the quote that "UK Biobank is the world’s most significant resource for health research" is not an exaggeration. Very happy to see it continue to be sustained, especially as we're doing a workshop tomorrow at #ASHG23 on how to use these data! www.gov.uk/government/n...

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Kaur Alasoo @kauralasoo.bsky.social · 29/10/2023

Unfortunately I have to miss #ASHG23 this year, but if you are interested in our group's work, do check out these two posters from Ralf Tambets and Krista Freimann:

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Sasha Gusev @sashagusevposts.bsky.social · 27/10/2023

Presentations from our group at ASHG next week:

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Michael Love @mikelove.bsky.social · 26/10/2023

Abdullah @abdnahid.bsky.social first #Bioconductor package {easylift} is released in Bioc 3.18 Facilitates genomic liftover using existing Bioc tools: ranges |> easylift("hg38") Abdullah is one of the group that signed up for #tidyomics open challenges: github.com/tidyomics

github.com

tidyomics

Open organizaion of developers creating tidy-style analysis packages in R/Bioconductor and beyond. Reach out to join. - tidyomics

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Pau Badia i Mompel @paubadiam.bsky.social · 16/10/2023

Very happy to see that our review on gene regulatory networks is being featured by Nature Reviews Genetics and that it inspired its cover! 🥳 doi.org/10.1038/s415...

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