Lightnews — Scholar-powered news

Reposted by Daniel Seaton

Diego del Alamo @delalamo.xyz · Apr 24

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.

1 2 12

Reposted by Daniel Seaton

Anshul Kundaje @anshulkundaje.bsky.social · Apr 18

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.

Michael Montgomery @michaeltmont.bsky.social · Apr 17

Through this analysis, we found that chromatin accessibility models outperformed the corresponding expression models for predicting effects on gene expression, similar to previous analysis of data from plasmid reporter assays and natural genetic variation.

4 25

Reposted by Daniel Seaton

Anna Cuomo @annasecuomo.bsky.social · Mar 24

📢 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)

2 31 98

Daniel Seaton @danieldseaton.bsky.social · Mar 6

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...

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.

www.linkedin.com

1 7 6

Reposted by Daniel Seaton

Kaur Alasoo @kauralasoo.bsky.social · Dec 30

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...

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...

www.biorxiv.org

1 4 21

Daniel Seaton @danieldseaton.bsky.social · Dec 27

I think the regulatory model (looping etc) first is good with examples that are less extreme and unusual than fto or limb/shh. I think hmgcr and cholesterol is a proximal regulatory effect.

5

Reposted by Daniel Seaton

Anshul Kundaje @anshulkundaje.bsky.social · Dec 25

Our ChromBPNet preprint out!

www.biorxiv.org/content/10.1...

Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

8 89 230

Reposted by Daniel Seaton

Jeff Spence @jeffspence.github.io · Dec 17

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...

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...

www.biorxiv.org

4 95 210

Reposted by Daniel Seaton

Stegle Lab @steglelab.bsky.social · Dec 9

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.

5 18

Reposted by Daniel Seaton

Na Cai @caina89.bsky.social · Dec 4

New work by Andy Dahl and Michal Sadowski on using GxE to study genetics of drug response now out in Cell Genomics www.cell.com/cell-genomic...

Characterizing the genetic architecture of drug response using gene-context interaction methods

Sadowski et al. propose a framework to study the genetics of response to commonly prescribed drugs in large biobanks. They quantify the heritability of response to statins, metformin, warfarin, and methotrexate, and identify associated genes. Their analysis also shows the importance of accounting for drug use in genetic risk prediction.

www.cell.com

1 10 26

Reposted by Daniel Seaton

bioRxiv Genomics @biorxiv-genomic.bsky.social · Nov 28

Paired CRISPR screens to map gene regulation in cis and trans https://www.biorxiv.org/content/10.1101/2024.11.27.625752v1

Recent massively-parallel approaches to decipher gene regulatory circuits have focused on the discov

www.biorxiv.org

14 36

Reposted by Daniel Seaton

bioRxiv Genomics @biorxiv-genomic.bsky.social · Nov 29

Cross-tissue isoform switches by human transcription factors suggest a widespread regulatory mechanism https://www.biorxiv.org/content/10.1101/2024.11.28.625692v1

Many human genes, including transcription factor (TF) genes, produce alternative coding isoforms. Al

www.biorxiv.org

6 22

Reposted by Daniel Seaton

Why @why.bsky.team · Nov 20

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.

1.6K 3K 38K

Reposted by Daniel Seaton

Hilary Martin @hilarycmartin.bsky.social · Nov 20

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.

7 42 120

Reposted by Daniel Seaton

EMBL-EBI @ebi.embl.org · Nov 19

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...

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.

www.ebi.ac.uk

31 79

Reposted by Daniel Seaton

Jason Buenrostro @jbuenrostro.bsky.social · Nov 19

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!

9 21 67

Reposted by Daniel Seaton

Axel Visel @axelvisel.bsky.social · May 27

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.

2 21 55

Daniel Seaton @danieldseaton.bsky.social · Dec 26

Yes, and also how it informs selection of training datasets. Selecting English language text for English language comprehension, augmenting image datasets by including rotated versions of the same images for image recognition.

1 2

Daniel Seaton @danieldseaton.bsky.social · Dec 26

I think it already has some physics (eg covalent bond lengths), just less than you might expect (no force field concept). Similar, llms have some knowledge of language (eg the concept of words), just less than you might expect (no verb/noun concept).

1 1

Reposted by Daniel Seaton

Michael Love @mikelove.bsky.social · Nov 2

Josh Weinstock @joshweinstock.bsky.social at ASHG on inferring GRN from perturbation data

www.biorxiv.org/content/10.1...

Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the g...

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

www.biorxiv.org

2 8

Reposted by Daniel Seaton

Anna Cuomo @annasecuomo.bsky.social · Oct 31

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!

1 4 13

Reposted by Daniel Seaton

Jeffrey Barrett @jeffbarrett.eu · Oct 31

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...

3 10

Reposted by Daniel Seaton

Kaur Alasoo @kauralasoo.bsky.social · Oct 29

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:

1 1 1

Reposted by Daniel Seaton

Sasha Gusev @sashagusevposts.bsky.social · Oct 27

Presentations from our group at ASHG next week:

1 2 7

Reposted by Daniel Seaton

Keith Robison @omicsomics.bsky.social · Oct 24

Catalogue of Long Read Tools - over 800 entries!

🧬🖥️

long-read-tools.org/table.html

A catalogue of long read analysis tools

Long read sequencing technologies have gained rapid popularity due to their strengths over short read sequencing technologies. Here we present a catalogue of available long read sequence analysis too...

long-read-tools.org

7 12