Daniel Seaton
@danieldseaton.bsky.social
Human genetics and genomics in drug discovery.
Reposted by Daniel Seaton
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
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
November 7, 2025 at 10:29 AM
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
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
Reposted by Daniel Seaton
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
April 24, 2025 at 7:36 AM
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
Reposted by Daniel Seaton
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.
Bonus: robust, efficient interpretation of syntax
Great collab with @jengreitz.bsky.social lab.
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.
April 18, 2025 at 2:55 PM
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.
Bonus: robust, efficient interpretation of syntax
Great collab with @jengreitz.bsky.social lab.
Reposted by Daniel Seaton
📢 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)
🧵👇 (1/n)
March 24, 2025 at 7:47 AM
📢 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)
🧵👇 (1/n)
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...
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
March 6, 2025 at 8:23 PM
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...
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...
Reposted by Daniel Seaton
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
December 30, 2024 at 2:31 PM
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...
Reposted by Daniel Seaton
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/
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/
December 25, 2024 at 11:48 PM
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/
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/
Reposted by Daniel Seaton
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...
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
December 17, 2024 at 7:05 AM
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...
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...
Reposted by Daniel Seaton
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.
December 9, 2024 at 3:25 PM
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.
Reposted by Daniel Seaton
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
December 4, 2024 at 8:46 PM
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...
Reposted by Daniel Seaton
Paired CRISPR screens to map gene regulation in cis and trans https://www.biorxiv.org/content/10.1101/2024.11.27.625752v1
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
November 28, 2024 at 2:33 AM
Paired CRISPR screens to map gene regulation in cis and trans https://www.biorxiv.org/content/10.1101/2024.11.27.625752v1
Reposted by Daniel Seaton
Cross-tissue isoform switches by human transcription factors suggest a widespread regulatory mechanism https://www.biorxiv.org/content/10.1101/2024.11.28.625692v1
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
November 29, 2024 at 7:34 PM
Cross-tissue isoform switches by human transcription factors suggest a widespread regulatory mechanism https://www.biorxiv.org/content/10.1101/2024.11.28.625692v1
Reposted by Daniel Seaton
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.
The team is rapidly deploying fixes and new software to adapt. More servers in the mail.
November 20, 2024 at 9:23 PM
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.
The team is rapidly deploying fixes and new software to adapt. More servers in the mail.
Reposted by Daniel Seaton
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.
November 20, 2024 at 4:15 PM
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.
Reposted by Daniel Seaton
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...
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
November 19, 2024 at 2:18 PM
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...
Haven't heard of EMBL-EBI? Take a look at what we’re working on. www.ebi.ac.uk/about/our-im...
Reposted by Daniel Seaton
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!
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!
November 19, 2024 at 7:56 PM
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!
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!
Reposted by Daniel Seaton
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...
New preprint from a collaboration led by Grace Bower and Evgeny Kvon.
doi.org/10.1101/2024...
May 27, 2024 at 4:26 PM
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...
New preprint from a collaboration led by Grace Bower and Evgeny Kvon.
doi.org/10.1101/2024...
Reposted by Daniel Seaton
Josh Weinstock @joshweinstock.bsky.social at ASHG on inferring GRN from perturbation data
www.biorxiv.org/content/10.1...
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
November 2, 2023 at 6:46 PM
Josh Weinstock @joshweinstock.bsky.social at ASHG on inferring GRN from perturbation data
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Daniel Seaton
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!
October 31, 2023 at 10:46 PM
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!
Reposted by Daniel Seaton
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...
www.gov.uk/government/n...
October 31, 2023 at 11:39 AM
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...
www.gov.uk/government/n...
Reposted by Daniel Seaton
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:
October 29, 2023 at 1:23 PM
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:
Reposted by Daniel Seaton
Presentations from our group at ASHG next week:
October 27, 2023 at 12:25 AM
Presentations from our group at ASHG next week:
Reposted by Daniel Seaton
Reposted by Daniel Seaton
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
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
tidyomics
Open organizaion of developers creating tidy-style analysis packages in R/Bioconductor and beyond. Reach out to join. - tidyomics
github.com
October 26, 2023 at 12:54 PM
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
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
Reposted by Daniel Seaton
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...
doi.org/10.1038/s415...
October 16, 2023 at 9:36 AM
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...
doi.org/10.1038/s415...