Gagneur lab
@gagneurlab.bsky.social
News from the Gagneurlab@TUM -- To understand the genetic basis of gene regulation and its implication in diseases. https://www.cs.cit.tum.de/cmm
Next Kipoi webinar Wednesday by Noor Youssef from Harvard on predicting viral evolution. See you then!
Kipoi@kipoizoo.bsky.social · 3mo agoJoin us for our next Kipoi Seminar with Noor Youssef, Harvard Medical School @harvardmed.bsky.social @deboramarks.bsky.social 👉 Predicting Viral Evolution to Accelerate Vaccine and Therapeutic Design 🧬 Wed May 6, 5:30pm CET 🍃http://kipoi.org/seminar 🦋 @kipoizoo.bsky.social
Join us for our next Kipoi Seminar with Sam Boshar, Instadeep @instadeep.bsky.social 👉 A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction 🗓️ Wed Mar 4, 5:30pm CET 🧬 kipoi.org/seminar 🦋 @kipoizoo.bsky.social
Kipoi
kipoi.org
Hot off the press! Jun Cheng presents AlphaGenome at the Kipoi seminar this Wednesday. Don’t miss it.
Kipoi@kipoizoo.bsky.social · 7mo agoJoin us for our next Kipoi Seminar with Jun Cheng, DeepMind 👉 AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model 📅 Wed Feb 4, 5:30pm CET 🧬 kipoi.org/seminar 🦋 @kipoizoo.bsky.social
Great start in 2026 for the kipoi seminar with Kishore Jaganathan from Illumina! All you want to know about PromoterAI (and more?)... See you tomorrow. @kjaganatha.bsky.social
Kipoi@kipoizoo.bsky.social · 7mo agoJoin us for our next Kipoi Seminar with Kishore Jaganathan, Illumina 👉 Predicting expression-altering promoter mutations with deep learning 📅 Wed Jan 7, 5:30pm CET 🧬 kipoi.org/seminar 🦋 @kipoizoo.bsky.social
Jeremy Schwartzentruber@jeremy37.bsky.social · 9mo agoLet’s talk about rare variant association tests - we have a new method that helps you discover more with the same data! It’s called *FlexRV* to signal our approach: “flexibly modeling rare variant pathogenicity improves gene discovery for complex traits”. www.biorxiv.org/content/10.1...
Very glad to see PROTRIDER, our protein expression outlier caller, used for establishing new rare diseased diagnoses.
MS Proteomics@mspcf.bsky.social · 9mo ago(4/5) We contributed by generating the #Proteomics data and by combining our custom data analysis workflow with a supercool tool called #ProtRider (@gagneurlab.bsky.social), which has a strong potential to study #RareDiseases, or any other case in which the number of bioreps available is limited.
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
Kipoi
kipoi.org
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...
scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution - Nature Methods
scooby achieves DNA sequence-based single-cell level modeling of RNA-sequencing coverage and ATAC-sequencing insertion profiles by adapting a deep learning model that predicts bulk RNA-sequencing cove...
nature.com
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
Kipoi
kipoi.org
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.
Johannes Hingerl@johahi.bsky.social · 10mo agoHappy 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...
Next Kipoi Seminar with Brendan Frey on bio foundation models and drug discovery. Attend!
Kipoi@kipoizoo.bsky.social · 10mo agoJoin us for our next Kipoi Seminar with Brendan Frey, University of Toronto, Deep Genomics @utoronto.ca 👉 Crossing the chasm between biological foundation models and drug discovery applications 📅 Wed Oct 1, 5:30pmCET 🧬 kipoi.org/seminar 🦋@kipoizoo.bsky.social
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
Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides
Post-translational modifications (PTMs) play a central role in cellular regulation and are implicated in numerous diseases. Database searching remains the standard for identifying modified peptides fr...
biorxiv.org
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
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.
Xavier Hernandez Alias@xavierheal.bsky.social · 11mo agoExciting science at the #EMBLProtein meeting, and still one more day ahead! If you missed it, come today by my poster 130 to learn about our work at Nedialkova's @mpibiochem.bsky.social and @gagneurlab.bsky.social !
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!
Kipoi@kipoizoo.bsky.social · 12mo agoJoin us for our next Kipoi Seminar with Hani Goodarzi, Arc Institute, UCSF @arcinstitute.org @ucsfcancer.bsky.social 👉Reading and writing the language of life 📅 Wed Sep 3, 5:30pmCET 🧬 kipoi.org/seminar 🦋 @kipoizoo.bsky.social
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...
scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution
Understanding how regulatory DNA elements shape gene expression across individual cells is a fundamental challenge in genomics. Joint RNA-seq and epigenomic profiling provides opportunities to build u...
biorxiv.org
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
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
Kipoi
kipoi.org
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...
Gagneur lab@gagneurlab.bsky.social · last yr.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...
Looking forward to Kathie Pollard talk on human variant interpretation this Wed. at the Kipoi seminar!
Kipoi@kipoizoo.bsky.social · last yr.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
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...
scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution
Understanding how regulatory DNA elements shape gene expression across individual cells is a fundamental challenge in genomics. Joint RNA-seq and epigenomic profiling provides opportunities to build u...
biorxiv.org
Kipoi@kipoizoo.bsky.social · last yr.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
See you all on Wed for Lucía Barbadilla's Kipoi seminar on MPRA-trained models!
Kipoi@kipoizoo.bsky.social · last yr.Join us for our next Kipoi Seminar with Lucía Barbadilla, De Ridder Group @luciabarmar.bsky.social @umcutrecht.bsky.social 👉PARM: The regulatory grammar of human promoters uncovered by MPRA-trained deep learning 📅Wed April 2, 5:30pm CET, not recorded! 🧬kipoi.org/seminar/ 🦋 @kipoizoo.bsky.social
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.
Gagneur lab@gagneurlab.bsky.social · last yr.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...
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 ;-)
