Very glad to see PROTRIDER, our protein expression outlier caller, used for establishing new rare diseased diagnoses.

Join us for our next Kipoi Seminar with Gonzalo Benegas, Yun S. Song group,UC Berkeley; Open Athena @gonzalobenegas.bsky.social 👉 Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models 📅 Wed Dec 3, 5:30pmCET 🧬 kipoi.org/seminar

scooby achieves DNA sequence-based single-cell level modeling of RNA-seq coverage and ATAC-seq insertion profiles by adapting a deep learning model that predicts bulk RNA-seq coverage. @johahi.bsky.social @lauradmartens.bsky.social @gagneurlab.bsky.social @tum.de www.nature.com/articles/s41...

Join us for our next Kipoi Seminar with Sameed Siddiqui,Sabeti lab,Broad Institute of MIT and Harvard @broadinstitute.org 👉 Lyra: An Efficient and Expressive Subquadratic Architecture for Modeling Biological Sequences 🎥❌no recording 📅 Wed Nov 5, 5:30pmCET 🧬 kipoi.org/seminar 🦋@kipoizoo.bsky.social

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.

FlashZoi is now out - our fast implementation of Borzoi. Congrats @johahi.bsky.social and enjoy all! More below.

Next Kipoi Seminar with Brendan Frey on bio foundation models and drug discovery. Attend!

Excited to share Modanovo, our transformer-based method for de novo peptide sequencing, which supports a broad range of post-translational modifications (PTMs)! www.biorxiv.org/content/10.1... #proteomics #massspectrometry #PTM

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

Congrats for the poster prize at #EMBLProtein, Xavi @xavierheal.bsky.social‬ ! Wonderful to dissect the translational response to metabolic shifts with time series of ribosome profiling and AI. Exciting multidisciplinary project. So glad to work with you and Danny Nedialkova on this.

Hani Goodarzi @genophoria.bsky.social‬ talks at the next Kipoi webinar on Evo2, a generative genomic language model trained across the tree of life. Looking forward!

2nd talk at #ISMBECCB2025 by Laura Martens @lauradmartens.bsky.social ! Laura will present Scooby tomorrow at 12:20 in the RegSys COSI. Enjoy! www.biorxiv.org/content/10.1...

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...

Join us for our next Kipoi Seminar with Yoseph Barash, University of Pennsylvania @yosephbarash.bsky.social @upenn.bsky.social 👉 From identifying UTR regulatory elements to potential RNA therapeutic targets 📅 Wed Jul 2, 5:30pm CET 🧬 kipoi.org/seminar 🦋 @kipoizoo.bsky.social

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...

Looking forward to Kathie Pollard talk on human variant interpretation this Wed. at the Kipoi seminar!

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

What a fun and amazing experience to be this year at the other side of the stage @pintofscience.de! 🙈 Thank you for organizing and everyone for participating. I think it was the most exciting and also toughest Q&A session ever! 😊 @mpibiochem.bsky.social @gagneurlab.bsky.social

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...

See you all on Wed for Lucía Barbadilla's Kipoi seminar on MPRA-trained models!

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 ;-)

STAND UP FOR SCIENCE SPEAKER ANNOUNCEMENT! ☀️ Dr. Francis Collins will be speaking at Stand Up for Science in D.C. on March 7th! More speaker announcements coming soon, stay tuned! 👀☀️

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

🚀 Exciting Career Opportunity! Helmholtz Munich & Roche are looking for an Early Career Investigator in AI for Nucleic Acid Based Medicines 🧬💡Join our innovative team and help push the boundaries of medical research. 👉 Learn more and apply: jobs.helmholtz-muenchen.de/jobposting/2...

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...

On Wed., Pedro @pedrotomazdasilva.bsky.social talks about interpreting DNA Language models through nucleotide dependency analyses. Capturing functional interactions -maps like this one for an intron- and more: RNA structures, reg motifs,... preprint: www.biorxiv.org/content/10.1...

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! 🧬😀

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/

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.