Daniel Seaton
Human genetics and genomics in drug discovery.
- Reposted by Daniel SeatonAre 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
- Reposted by Daniel SeatonAn 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 SeatonSingle 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.
- 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)
- 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...
- Reposted by Daniel SeatonVery 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 SeatonOur 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/
- Reposted by Daniel SeatonWhat 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...
- Reposted by Daniel SeatonWe 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 SeatonNew 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 SeatonPaired CRISPR screens to map gene regulation in cis and trans https://www.biorxiv.org/content/10.1101/2024.11.27.625752v1
- Reposted by Daniel SeatonCross-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 SeatonTo 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.
- Reposted by Daniel SeatonMy 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.
- 📣 Big news! Our tag-team effort on common variants in rare neurodevelopmental conditions is now out in Nature 📣 Co-first authoring with the brilliant Qinqin Huang🌟—proof that teamwork does make the dream work. 💪 www.nature.com/articles/s41...
- Reposted by Daniel SeatonNot 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...
- Reposted by Daniel SeatonHey, 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!
- Reposted by Daniel SeatonREX - 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...
