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
https://www.cs.cit.tum.de/cmm
Reposted by Gagneur lab
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...
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...
www.nature.com
October 22, 2025 at 4:48 PM
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...
www.nature.com/articles/s41...
Reposted by Gagneur lab
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
@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
October 31, 2025 at 11:03 AM
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
@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
Reposted by Gagneur lab
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.
Poster 5022W, Wed 2:30-4:30.
October 14, 2025 at 3:40 PM
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.
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.
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...
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
October 13, 2025 at 12:31 PM
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!
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
@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
September 29, 2025 at 4:37 PM
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
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
September 18, 2025 at 7:59 AM
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
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
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
September 9, 2025 at 11:42 AM
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
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.
! 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.
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 !
September 7, 2025 at 11:04 AM
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.
! 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!
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
@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
August 30, 2025 at 12:39 PM
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...
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
July 23, 2025 at 8:37 AM
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...
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
July 23, 2025 at 8:35 AM
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...
Proceedings paper:
doi.org/10.1093/bioi...
Reposted by Gagneur lab
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
@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
June 25, 2025 at 12:31 PM
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
@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...
doi.org/10.1101/2025...
June 5, 2025 at 4:44 AM
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...
doi.org/10.1101/2025...
Looking forward to Kathie Pollard talk on human variant interpretation this Wed. at the Kipoi seminar!
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
@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
June 2, 2025 at 3:05 PM
Looking forward to Kathie Pollard talk on human variant interpretation this Wed. at the Kipoi seminar!
Reposted by Gagneur lab
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
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
May 21, 2025 at 6:27 AM
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
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...
@lauradmartens.bsky.social @johahi.bsky.social @kipoizoo.bsky.social
Last preprint version:
www.biorxiv.org/content/10.1...
May 5, 2025 at 4:26 PM
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...
@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!
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
@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
March 31, 2025 at 8:54 AM
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.
March 7, 2025 at 6:57 PM
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...
March 6, 2025 at 10:00 PM
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...
doi.org/10.1101/2024...
March 6, 2025 at 9:04 PM
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...
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 ;-)
March 6, 2025 at 8:47 PM
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 ;-)
Reposted by Gagneur lab
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! 👀☀️
Dr. Francis Collins will be speaking at Stand Up for Science in D.C. on March 7th!
More speaker announcements coming soon, stay tuned! 👀☀️
March 6, 2025 at 12:00 AM
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! 👀☀️
Dr. Francis Collins will be speaking at Stand Up for Science in D.C. on March 7th!
More speaker announcements coming soon, stay tuned! 👀☀️
Reposted by Gagneur lab
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
@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
Kipoi
kipoi.org
March 1, 2025 at 7:26 PM
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
@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...
👉 Learn more and apply: jobs.helmholtz-muenchen.de/jobposting/2...
Early Career Investigator (f/m/x) in AI for Nucleic Acid Based Medicines
jobs.helmholtz-muenchen.de
February 19, 2025 at 9:16 AM
🚀 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...
👉 Learn more and apply: jobs.helmholtz-muenchen.de/jobposting/2...