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Reposted by Gagneur lab

Shubhankar Londhe @slondhe.bsky.social · 23h

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.

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Gagneur lab @gagneurlab.bsky.social · 2d

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

Johannes Hingerl @johahi.bsky.social · 2d

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...

Flashzoi: an enhanced Borzoi for accelerated genomic analysis

AbstractMotivation. Accurately predicting how DNA sequence drives gene regulation and how genetic variants alter gene expression is a central challenge in

doi.org

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Gagneur lab @gagneurlab.bsky.social · 15d

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

Kipoi @kipoizoo.bsky.social · 16d

Join 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

Kipoi

kipoi.org

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Gagneur lab @gagneurlab.bsky.social · 27d

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!

Gagneur lab @gagneurlab.bsky.social · 27d

Modanovo is open-source and available here: github.com/gagneurlab/M...

GitHub - gagneurlab/Modanovo

Contribute to gagneurlab/Modanovo development by creating an account on GitHub.

github.com

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Gagneur lab @gagneurlab.bsky.social · 27d

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.

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Gagneur lab @gagneurlab.bsky.social · 27d

Modanovo achieves strong performance, successfully sequencing peptides carrying biologically relevant PTMs.

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Gagneur lab @gagneurlab.bsky.social · 27d

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.

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Gagneur lab @gagneurlab.bsky.social · 27d

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.

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Gagneur lab @gagneurlab.bsky.social · 27d

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...

www.biorxiv.org

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Gagneur lab @gagneurlab.bsky.social · Sep 9

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

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Gagneur lab @gagneurlab.bsky.social · Sep 7

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 · Sep 6

Exciting 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 !

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Gagneur lab @gagneurlab.bsky.social · Aug 30

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 · Aug 26

Join 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

Kipoi

kipoi.org

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Gagneur lab @gagneurlab.bsky.social · Jul 23

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...

www.biorxiv.org

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Gagneur lab @gagneurlab.bsky.social · Jul 23

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

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Reposted by Gagneur lab

Kipoi @kipoizoo.bsky.social · Jun 25

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

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Gagneur lab @gagneurlab.bsky.social · Jun 5

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...

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Gagneur lab @gagneurlab.bsky.social · Jun 2

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

Kipoi @kipoizoo.bsky.social · May 28

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

https://kipoi.org/seminar/🦋kipoizoo.bsky

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Gagneur lab @gagneurlab.bsky.social · May 24

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.

Gagneur lab @gagneurlab.bsky.social · May 24

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.

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Gagneur lab @gagneurlab.bsky.social · May 24

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.

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Gagneur lab @gagneurlab.bsky.social · May 24

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.

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Gagneur lab @gagneurlab.bsky.social · May 24

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)

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Gagneur lab @gagneurlab.bsky.social · May 24

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

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Gagneur lab @gagneurlab.bsky.social · May 24

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

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