Ryan Tewhey
@tewhey.bsky.social
Associate Professor at The Jackson Laboratory -- Studying gene regulation, genetic variation & human complex traits.
New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...
Please consider attending and RT. Great lineup of speakers!
Stowers Institute@stowersinstitute.bsky.social · 8mo agoRegistration is OPEN for #SRCKC26: Development, Regulatory Genomics & AI! Organized by Neşet Özel, @juliazeitlinger.bsky.social, & @saukaspengler.bsky.social. Join us April 22–24 in #KansasCity to explore cis-regulatory logic, genomics & #AI. 📅 Register now: bit.ly/4rMvVoI
I’ll be attending #ASHG25! I’m currently hiring for (i) a Senior Research Scientist or (ii) a Postdoc position in my lab. If you’re interested, please reach out to arrange a time to meet and discuss.
Excited to finally present the lab's latest work in defining candidate causal genetic variants that drive autoimmune diseases and their effects on primary human T cell expression and function! www.nature.com/articles/s41...
Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks - Nature Genetics
Massively parallel reporter assay in primary human CD4+ T cells and bulk and single-cell CRISPR-interference screens identify candidate causal variants linked to autoimmune disease risk that modulate ...
nature.com
Exited to share our recent work on viral cis-regulatory elements in collaboration with @tewhey.bsky.social! We identified >2000 CREs across the genomes of 27 human-infecting dsDNA viruses from the Herpesvirus, Adenovirus, Papillomavirus, and Polyomavirus families. www.biorxiv.org/content/10.1... 1/8
Interested in using functional data to understand clinical variants? Been hunting for a good review of the topic? We just wrote one! rdcu.be/exaEU
Multiplexed assays of variant effect for clinical variant interpretation
Nature Reviews Genetics - Multiplexed assays of variant effect (MAVEs) are highly scalable experimental approaches used to generate functional data for genetic variants. In this Review, McEwen et...
nature.com
Our "Atlas of Variant Effects 2030 Roadmap" is live: zenodo.org/records/1542... 1/n
Atlas of Variant Effects 2030 Roadmap: resolving human variants of uncertain significance
At the Clinical Atlas of Variant Effects meeting (CLAVE meeting, July 2024, Pittsburgh USA), we developed recommendations for a draft atlas that can be realized by 2030, with a focus on empowering gen...
zenodo.org
1/n 🚨Very excited to share our recent work!🚨 To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro. www.biorxiv.org/content/10.1...
Proud to share our lab’s first student preprint!🚀@j-c-butts.bsky.social, @alwaysrong.bsky.social, @sagergosai.bsky.social leveraged our MPRA models to predict variant effects, providing scores for the complete catalog of human variation. Grateful for another fun collab with @stevereilly.bsky.social.
John Butts@j-c-butts.bsky.social · last yr.Excited to share our MPAC preprint, a scalable ensemble of ML models for genome-wide non-coding variant effect prediction and our findings from 575M predictions across databases including @ukbiobank.bsky.social, GTEx, ClinVar, COSMIC, and @gnomad-project.bsky.social www.biorxiv.org/content/10.1...
In 15 yrs of reporting, I've never had so many health & biomed researchers & outreach orgs tell me they're afraid to talk w/press or barred from speaking bc of new comms policies. I understand the fear of losing funds. I don't know if silence does more harm than good. If you can speak up, pls do.
A special Bluetorial about one of my mentors Ruth Kirschstein Among Ruth Kirschstein’s many contributions to American science was the development and expansion of programs intended to increase participation of people from groups underrepresented in biomedical research.
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
Super excited to announce our latest flagship model Borzoi: major props to Johannes & David Kelley et al for advancing it. It's been a long journey from our prior Enformer model into this one. A few innovations: i) longer DNA context, ii) adaptation to predict RNA-seq abundance and splice isoforms,
Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation - Nature Genetics
Borzoi adapts the Enformer sequence-to-expression model to directly predict RNA-seq coverage, enabling the in-silico analysis of variant effects across multiple layers of gene regulation.
nature.com
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/
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...
biorxiv.org
Anshul Kundaje@anshulkundaje.bsky.social · 2y agoAiming to release our long awaited ChromBPNet preprint by early next week as well. I'm recovering from back to back infections for the past 6 weeks. But we're almost there. We have some solid variant prediction benchmarks in there against large supervised models and lots more. Stay tuned.