Not being able to access the @ukbiobank.ac.uk is becoming a significant issue for a PhD student in our group and I can only imagine this is mirrored in many other places. It would be fantastic to at least have a timeline we could work with.

Why be satisfied with coding variant gene impairments? Check out Eva’s poster to learn how we scale DeepRVAT to the WGS UKBiobank. It’s been great fun being a part of this project! #ASHG25

Eva Holtkamp@evaholtkamp.bsky.social · 10mo ago

DeepRVATv2 is in the making! We learn from >60M WGS variants, >90 features, and 500k UKB participants to predict gene impairment beyond coding regions and showcase how DeepRVAT can advance rare disease diagnostics and gene constraint measurement. Learn more at my Poster 5058W, Wed 2:30pm #ASHG25

Excited to share UKBBGym at #ASHG25, a new benchmark for variant effect predictors using WGS, proteomics and phenotypes from 500K UKBiobank participants. Stop by for insights on the impact of non-coding variants and how computational scores stack up against exp assays. Poster 5022W, Wed 2:30-4:30.

The Solvathons have been one of our most exciting research community experiences: Hands-on, effective – solving real cases during the events, and multidisciplinary – from clinicians to bioinformaticians. Thumbs up to the SolveRD community. Looking for more now with @erdera.bsky.social rdcu.be/eFaqO

The Solve-RD Solvathons as a pan-European interdisciplinary collaboration to diagnose patients with rare disease

Nature Genetics - This Perspective presents the Solve-RD Solvathon model, an innovative, pan-European framework uniting clinical and bioinformatics experts to diagnose rare diseases through...

rdcu.be

[1/8] *New Open-Access Long Read Resource*. We sequenced 1,019 genomes from the 1000 Genomes Project sample cohort using @nanoporetech.com long-read sequencing (LRS) to median 17x coverage. Publication at go.nature.com/4ffPb8f. @hhu.de @crg.eu @embl.org @impvienna.bsky.social

Today at 12:20 in the HIT-Seq COSI, @lauradmartens.bsky.social Laura Martens will present her results on spatial chromatin accessibility data deconvolution #ISMBECCB2025. Great collab with Sarah Ouologuem and @fabiantheis.bsky.social Proceedings paper: doi.org/10.1093/bioi...

Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data

AbstractMotivation. Spatially resolved chromatin accessibility profiling offers the potential to investigate gene regulatory processes within the spatial c

doi.org

@thbec.bsky.social is going to share preliminary results on Meta-DeepRVAT, a new approach for deep learning based meta-analysis improving the power of rare variant association studies using population scale external control cohorts. #MLCSB 📅 July 21 |📍 Poster A-312

Join us for our next Kipoi Seminar with Katherine Pollard, Gladstone Institute of Data Science & Biotechnology,UCSF, Biohub @gladstoneinst.bsky.social @czbiohub.bsky.social 👉Human variant interpretation with sequence-to-activity models 📅Wed June 4,5:30pm CET🧬 kipoi.org/seminar/🦋@kipoizoo.bsky.social

Excited to present at #eshg2025. Catch my talk on improving rare variant association studies using functional gene embeddings, on Monday at 11:45am (C26.06).

Gagneur lab@gagneurlab.bsky.social · last yr.

Shubhankar Londhe @slondhe.bsky.social presents his work on RVAT in the talk “Functional gene embeddings improve rare variant polygenic risk scores” at session C26 – Computational models in human genetics. Catch it on Monday at 11:45am. 2/n

Excited to be back at #eshg2025! Come by my poster today to check out fresh results on how rare high impact variants influence gene expression across immune cells—analyzed in 5,000 UK Biobank participants

Gagneur lab@gagneurlab.bsky.social · last yr.

Eva Holtkamp @evaholtkamp.bsky.social shares insights on rare variant effects on cell type-specific gene expression in immune cells across 4,978 UK Biobank participants - catch poster P18.066.A (Sunday, 1pm)

Tomorrow Johannes Hingerl @johahi.bsky.social gives a talk on scooby at #probgen25. Enjoy learning in the legendary CSHL auditorium how to model RNA-seq and ATAC-seq profiles in individual cells from half a megabase of genomic sequence. Preprint: doi.org/10.1101/2024...

Excited to share that PROTRIDER, our method to call outliers on mass spectrometry-based proteomics data, is out now!! #proteomics #massspectrometry #raredisease doi.org/10.1101/2025...

PROTRIDER: Protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder

Motivation Detection of gene regulatory aberrations enhances our ability to interpret the impact of inherited and acquired genetic variation for rare disease diagnostics and tumor characterization. Wh...

doi.org

Join us for our next Kipoi Seminar with with Pedro Tomaz da Silva @pedrotomazdasilva.bsky.social @gagneurlab.bsky.social @TU_Muenchen! 👉Nucleotide dependency analysis of DNA language models reveals genomic functional elements 📅Wed Feb 5, 5:30pm CET 🧬https://kipoi.org/seminar/ 🦋kipoizoo.bsky

Hey reg genomics folks, here is our little x-mas present: Flashzoi. Borzoi. Just as good. 3x faster. Thumbs up to @johahi.bsky.social for the great initiative, conception & implementation. Big thanks to Johannes Linder, David Kelley and colleagues to have created Borzoi and shared it freely.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 2y ago

Flashzoi: An enhanced Borzoi model for accelerated genomic analysis https://www.biorxiv.org/content/10.1101/2024.12.18.629121v1