Excited to share Nona: a unifying multimodal masking framework for functional genomics. Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM). Can these be unified under a single paradigm? 1/15

gReLU advances deep learning based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications. @avantikalal.bsky.social @gokcen.bsky.social www.nature.com/articles/s41...

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.

Happy to share that Flashzoi is now published! We enhanced Borzoi with RoPE & FlashAttention for >3x faster training/inference & 2.4x reduction in memory usage. This brings large-scale genomic analysis and fine-tuning within reach of academic budgets. 📄: doi.org/10.1093/bioi...

The Biodiversity Cell Atlas white paper is out! A bold vision to map the diversity and evolution of cell types across the tree of life 🌍

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome: The E2G Portal! e2g.stanford.edu This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues. Uses cases 👇 1/

In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance. While undoubtedly important, how we *use* these models after training is potentially even more important. tangermeme v1.0.0 is out now. Hope you find it useful!

tangermeme: A toolkit for understanding cis-regulatory logic using deep learning models https://www.biorxiv.org/content/10.1101/2025.08.08.669296v1

Update of our protein outlier caller PROTRIDER. We now handle missing values, a widespread issue for mass spec where missing values are not a random -- and this improves outlier detection on non-missing data! Thumbs up to Daniela and George for the great work. doi.org/10.1101/2025...

This year, the lab has a great representation at the #eshg2025: 3 talks, 2 posters, 1 spin-off stand ! 1/n

Our review "Predicting gene expression from DNA sequence using deep learning models" is finally out! 🤗

a fundamental challenge in my field is that staring at long-running jobs, waiting for them to finish, is not seen as productive

Join us for our next Kipoi Seminar with Laura Martens, Gagneur lab, TUM @lauradmartens.bsky.social @gagneurlab.bsky.social @tum.de 🐕scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution 📅Wed May 7, 5:30pm CET 🧬https://kipoi.org/seminar/ 🦋kipoizoo.bsky

Many of you enjoy our sequence-based model of single-cell RNA and ATAC data scooby... Don't miss Laura Marten's talk at the upcoming Kipoi seminar about it this Wed! @lauradmartens.bsky.social @johahi.bsky.social @kipoizoo.bsky.social Last preprint version: www.biorxiv.org/content/10.1...

Our preprint on designing and editing cis-regulatory elements using Ledidi is out! Ledidi turns *any* ML model (or set of models) into a designer of edits to DNA sequences that induce desired characteristics. Preprint: www.biorxiv.org/content/10.1... GitHub: github.com/jmschrei/led...

Very proud of two new preprints from the lab: 1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...

We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...

CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species https://www.biorxiv.org/content/10.1101/2025.04.02.646812v1

In today's poster session #probgen25. To the pop gen folks, interesting observation: The influence of a nucleotide on reconstructing others, rather than its own reconstructability, is a better predictor of function. This metric makes DNA LMs beat conservation in several benchmarks.

and @pedrotomazdasilva.bsky.social will present tomorrow at #probgen25 poster 128 on dependency analysis of DNA language models. Come and see what functional relationships DNA LMs capture, from regulatory code to RNA structures. Preprint: doi.org/10.1101/2024...

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...

Hello #probgen25! We have 3 contribs this year @lauradmartens.bsky.social starts today, poster 87, presenting scooby modeling scRNA-seq and sc-ATAC-seq profiles from DNA and applications. Shhh... don't tell it further... rumour says there are awesome cute scooby stickers to win ;-)

Join us for our next Kipoi Seminar with with Alexander Sasse @lxsasse.bsky.social @zmbh.uni-heidelberg.de 👉Advanced training strategies for genomic sequence-to-function models 📅 Wed March 5, 5:30pm CET 🧬 kipoi.org/seminar/ 🦋 @kipoizoo.bsky.social

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...

Just very happy to have our paper out today! A big thanks to all our co-authors, and to Nikolai and @steinaerts.bsky.social for the teamwork over the past years. If you are interested in using our models for cross-species enhancer studies, check out crested.readthedocs.io/en/stable/mo... 🙂

Can DNA sequence models predict mutations affecting human traits? We introduce TraitGym, a curated benchmark of causal regulatory variants for 113 Mendelian & 83 complex traits, and evaluate functional genomics and DNA language models. Joint work w/ Gökcen Eraslan and @yun-s-song.bsky.social 🧵👇

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

Join us in our next #MunichRNA19F! 📍 @mpibiochem.bsky.social 📅 19/02/2025 We will hear amazing talks from Shuyao Sha (@kusterlab.bsky.social), @lauradmartens.bsky.social (@gagneurlab.bsky.social), @michaelkugler.bsky.social (@hopfnerlab.bsky.social), Marc Schmitt-Supprian. Don't miss it! 🧬😀

Super excited to share our new study from the @jbuenrostro.bsky.social Lab in @nature.com! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning. Paper: www.nature.com/articles/s41...

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,

Congrats to Johannes Linder, David Kelley et al. on the journal publication of Borzoi - a long context sequence models of RNA-seq coverage profiles with many nice applications for transcriptional & post-transcriptional regulation & variant effect prediction. www.nature.com/articles/s41... 1/

Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/ www.encodeproject.org/single-cell/...

A DNA language model based on multispecies alignment predicts the effects of genome-wide variants - @yun-s-song.bsky.social go.nature.com/4gWppWg

Introducing Flashzoi⚡! We’ve upgraded the Borzoi model with rotary pos. encodings and FlashAttention, resulting in a significant speedup with similar or better accuracy for faster variant effect prediction, quicker model development and more efficient genomic analysis www.biorxiv.org/content/10.1...

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.

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

The Kipoi seminar is now also on BlueSky! 🎉 Follow @kipoizoo.bsky.social for announcements of upcoming speakers