Johannes Hingerl
@johahi.bsky.social
ML for regulatory genomics. PhD student @ Gagneurlab
johahi.github.io
johahi.github.io
Reposted by Johannes Hingerl
Excited to share Nona: a unifying multimodal masking framework for functional genomics.
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
November 10, 2025 at 9:01 PM
Excited to share Nona: a unifying multimodal masking framework for functional genomics.
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Reposted by Johannes Hingerl
gReLU advances deep learning based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications. @avantikalal.bsky.social @gokcen.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
gReLU: a comprehensive framework for DNA sequence modeling and design - Nature Methods
gReLU advances deep-learning-based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications.
www.nature.com
October 16, 2025 at 3:26 PM
gReLU advances deep learning based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications. @avantikalal.bsky.social @gokcen.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Johannes Hingerl
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.
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 11:53 AM
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...
Reposted by Johannes Hingerl
The Biodiversity Cell Atlas white paper is out! A bold vision to map the diversity and evolution of cell types across the tree of life 🌍
Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
September 24, 2025 at 4:53 PM
The Biodiversity Cell Atlas white paper is out! A bold vision to map the diversity and evolution of cell types across the tree of life 🌍
Reposted by Johannes Hingerl
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by Johannes Hingerl
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
September 18, 2025 at 4:14 PM
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
Reposted by Johannes Hingerl
In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance.
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
August 27, 2025 at 4:20 PM
In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance.
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
Reposted by Johannes Hingerl
tangermeme: A toolkit for understanding cis-regulatory logic using deep learning models https://www.biorxiv.org/content/10.1101/2025.08.08.669296v1
August 12, 2025 at 11:46 AM
tangermeme: A toolkit for understanding cis-regulatory logic using deep learning models https://www.biorxiv.org/content/10.1101/2025.08.08.669296v1
Reposted by Johannes Hingerl
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...
Reposted by Johannes Hingerl
Our review "Predicting gene expression from DNA sequence using deep learning models" is finally out! 🤗
Predicting gene expression from DNA sequence using deep learning models go.nature.com/3F8r0Li #Review by Lucía Barbadilla-Martínez, Noud Klaassen, Bas van Steensel & Jeroen de Ridder @nkinl.bsky.social @umcutrecht.bsky.social
Predicting gene expression from DNA sequence using deep learning models - Nature Reviews Genetics
Barbadilla-Martínez et al. review recent progress in deep-learning-based sequence-to-expression models, which predict gene expression levels solely from DNA sequence. These models are providing new in...
go.nature.com
May 14, 2025 at 3:43 PM
Our review "Predicting gene expression from DNA sequence using deep learning models" is finally out! 🤗
Reposted by Johannes Hingerl
a fundamental challenge in my field is that staring at long-running jobs, waiting for them to finish, is not seen as productive
May 12, 2025 at 1:44 PM
a fundamental challenge in my field is that staring at long-running jobs, waiting for them to finish, is not seen as productive
Reposted by Johannes Hingerl
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
🐕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
May 2, 2025 at 11:01 AM
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
🐕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
Reposted by Johannes Hingerl
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...
Reposted by Johannes Hingerl
Our preprint on designing and editing cis-regulatory elements using Ledidi is out! Ledidi turns *any* ML model (or set of models) into a designer of edits to DNA sequences that induce desired characteristics.
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Programmatic design and editing of cis-regulatory elements
The development of modern genome editing tools has enabled researchers to make such edits with high precision but has left unsolved the problem of designing these edits. As a solution, we propose Ledi...
www.biorxiv.org
April 24, 2025 at 12:59 PM
Our preprint on designing and editing cis-regulatory elements using Ledidi is out! Ledidi turns *any* ML model (or set of models) into a designer of edits to DNA sequences that induce desired characteristics.
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Reposted by Johannes Hingerl
Very proud of two new preprints from the lab:
1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...
1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...
CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species
Sequence-based deep learning models have become the state of the art for the analysis of the genomic regulatory code. Particularly for transcriptional enhancers, deep learning models excel at decipher...
www.biorxiv.org
April 4, 2025 at 9:04 AM
Very proud of two new preprints from the lab:
1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...
1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...
Reposted by Johannes Hingerl
We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...
April 3, 2025 at 2:30 PM
We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...
Reposted by Johannes Hingerl
CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species https://www.biorxiv.org/content/10.1101/2025.04.02.646812v1
April 3, 2025 at 7:34 AM
CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species https://www.biorxiv.org/content/10.1101/2025.04.02.646812v1
Reposted by Johannes Hingerl
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.
Reposted by Johannes Hingerl
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...
Reposted by Johannes Hingerl
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...
Reposted by Johannes Hingerl
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 Johannes Hingerl
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
Reposted by Johannes Hingerl
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...
PROTRIDER: Protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder
Motivation Detection of gene regulatory aberrations enhances our ability to interpret the impact of inherited and acquired genetic variation for rare disease diagnostics and tumor characterization. Wh...
doi.org
February 19, 2025 at 8:15 AM
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...