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
Hot off the press! Jun Cheng presents AlphaGenome at the Kipoi seminar this Wednesday. Don’t miss it.
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
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!
Great work by Daniela Klaproth-Andrade and the whole team in collab with the Wilhelm lab! Thanks to Valter Bergant and Andreas Pichlmair for the application of Modanovo to the monkeypox virus.
We’re excited to see how Modanovo will push forward de novo sequencing and PTM biology!
Modanovo is open-source and available here: github.com/gagneurlab/M...
We also applied Modanovo to a dataset of human cells infected with monkeypox virus, where it complemented database-driven approaches and revealed biologically relevant phosphosites, highlighting its utility in real-world discovery.
Modanovo achieves strong performance, successfully sequencing peptides carrying biologically relevant PTMs.
Modanovo builds on Casanovo, a transformer model for peptide sequencing. We fine-tuned ot end-to-end expanding Casanovo’s token vocabulary and corresponding layers.
Why Modanovo?
Existing tools often struggle with PTMs, yet PTMs are central to protein regulation and disease. We built a model for 19 amino acid-PTM combinations, leveraging data from in vivo experiments and from PROSPECT-PTM.
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!
Finally, visit our spin-off’s stand #338 OmicsDiscoveries and have a look at the latest platform for RNA-seq oriented analysis and visit their poster P15.110.A on Sunday 1pm.
Vicente will also present the Solvathon concept—a collaborative, focused approach to accelerate diagnosis—in the session “E09 Solving Rare Disease: One for All, All for One” on Tuesday at 9am.
Vicente Yépez is discussing the added value of RNA-seq in rare disease diagnostics and practical recommendations for sequencing, analysis and interpretation, at session “W09 Mutations we almost missed” on Sunday at 14:15.
Rebeka Luknárová is showcasing the RNA-seq results in Solve-RD, which will be the basis for the work in ERDERA, at poster P16.006.A on Sunday 1pm.
