Stegle Lab
@steglelab.bsky.social
Our group develops and applies computational approaches to study molecular variations and their phenotypic consequence. We are part of DKFZ and EMBL.
Website: https://steglelab.org/
Website: https://steglelab.org/
Pinned
Stegle Lab
@steglelab.bsky.social
· Dec 9
We are the Stegle Lab: A bioinformatics group advancing computational methods to study molecular variations and their impact on phenotypes. We are jointly hosted at the German Cancer Research Center (@dkfz.bsky.social) and the European Molecular Biology Laboratory (@embl.org) in Heidelberg, Germany.
How do CRISPR edits actually change cells in real tissues?
Most single-cell CRISPR screens infer edits indirectly.
We present scPT-seq, a method that directly detects CRISPR mutations and transcriptomes in the same single cells in vivo, from John Hawkins and Siamak Redhai from Boutros Lab. 1/10
Most single-cell CRISPR screens infer edits indirectly.
We present scPT-seq, a method that directly detects CRISPR mutations and transcriptomes in the same single cells in vivo, from John Hawkins and Siamak Redhai from Boutros Lab. 1/10
December 27, 2025 at 4:13 PM
How do CRISPR edits actually change cells in real tissues?
Most single-cell CRISPR screens infer edits indirectly.
We present scPT-seq, a method that directly detects CRISPR mutations and transcriptomes in the same single cells in vivo, from John Hawkins and Siamak Redhai from Boutros Lab. 1/10
Most single-cell CRISPR screens infer edits indirectly.
We present scPT-seq, a method that directly detects CRISPR mutations and transcriptomes in the same single cells in vivo, from John Hawkins and Siamak Redhai from Boutros Lab. 1/10
We are looking for a Software Developer to work on R/Python interoperability for single-cell and spatial omics methods.
🔗 Apply here: jobs.dkfz.de/en/jobs/1683...
🔗 Apply here: jobs.dkfz.de/en/jobs/1683...
Software Developer - Interoperability for Single-Cell and Spatial Omics Methods
jobs.dkfz.de
December 27, 2025 at 3:50 PM
We are looking for a Software Developer to work on R/Python interoperability for single-cell and spatial omics methods.
🔗 Apply here: jobs.dkfz.de/en/jobs/1683...
🔗 Apply here: jobs.dkfz.de/en/jobs/1683...
We’re excited to announce the "Toward Trustworthy AI Modeling for Computational Healthcare" @elsa-ai.eu workshop, a one-day in-person event focused on building private, fair, robust, reliable, and accountable AI systems for healthcare. Register now.
📅 March 9, 2026
📍 EMBL, Heidelberg, Germany
📅 March 9, 2026
📍 EMBL, Heidelberg, Germany
Registrations just opened for the workshop “TrustworthyAI4Health: Toward #TrustworthyAI Modeling for Computational #Healthcare”!🔥
Join us on March 9, 2026, to advance private, fair, robust, reliable, and accountable AI models for healthcare applications.
elsa-ai.eu/elsa-worksho...
Join us on March 9, 2026, to advance private, fair, robust, reliable, and accountable AI models for healthcare applications.
elsa-ai.eu/elsa-worksho...
December 19, 2025 at 1:42 PM
We’re excited to announce the "Toward Trustworthy AI Modeling for Computational Healthcare" @elsa-ai.eu workshop, a one-day in-person event focused on building private, fair, robust, reliable, and accountable AI systems for healthcare. Register now.
📅 March 9, 2026
📍 EMBL, Heidelberg, Germany
📅 March 9, 2026
📍 EMBL, Heidelberg, Germany
Meet Hendrik Mehrtens who recently joined our lab as a PhD student - shared with @mlolab.bsky.social 👋
Hendrik’s research focuses on reliable machine learning methods integrating large-scale EHR data with multimodal data like genomics data, with a focus on causality and uncertainty estimation.
Hendrik’s research focuses on reliable machine learning methods integrating large-scale EHR data with multimodal data like genomics data, with a focus on causality and uncertainty estimation.
December 5, 2025 at 3:41 PM
Meet Hendrik Mehrtens who recently joined our lab as a PhD student - shared with @mlolab.bsky.social 👋
Hendrik’s research focuses on reliable machine learning methods integrating large-scale EHR data with multimodal data like genomics data, with a focus on causality and uncertainty estimation.
Hendrik’s research focuses on reliable machine learning methods integrating large-scale EHR data with multimodal data like genomics data, with a focus on causality and uncertainty estimation.
Reposted by Stegle Lab
Claudia Feng's Ph.D work is now out, co-led with @brittavelten.bsky.social and @steglelab.bsky.social . Large-scale CRISPRi perturbations in genetically heterogenous iPSC lines, with single cell readout - enjoy :)
Happy to see this out now in Cell Genomics: A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines: www.cell.com/cell-genomic...
A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines
Feng et al. present the first genome-scale CRISPR interference perturbation map with
scRNA-seq readout across many genetic backgrounds in human pluripotent cells, pioneering
population-scale CRISPR pe...
www.cell.com
December 3, 2025 at 11:04 AM
Claudia Feng's Ph.D work is now out, co-led with @brittavelten.bsky.social and @steglelab.bsky.social . Large-scale CRISPRi perturbations in genetically heterogenous iPSC lines, with single cell readout - enjoy :)
Back from #scverse25 and feeling inspired by what @scverse.bsky.social has achieved over the last years. Impressive tools, a vibrant community and we even had a reunion with our two alumni Danila and Max Frank.
We also presented our latest findings from the lab 👇
We also presented our latest findings from the lab 👇
November 25, 2025 at 9:01 AM
Back from #scverse25 and feeling inspired by what @scverse.bsky.social has achieved over the last years. Impressive tools, a vibrant community and we even had a reunion with our two alumni Danila and Max Frank.
We also presented our latest findings from the lab 👇
We also presented our latest findings from the lab 👇
Reposted by Stegle Lab
The ELLIS Society welcomes its new Board. As the primary decision-making body, it will play a vital role in shaping the future of ELLIS and advancing #AI and #MachineLearning research across Europe in a time of global change.
Read the full article: ellis.eu/news/ellis-s...
Read the full article: ellis.eu/news/ellis-s...
October 27, 2025 at 9:15 AM
The ELLIS Society welcomes its new Board. As the primary decision-making body, it will play a vital role in shaping the future of ELLIS and advancing #AI and #MachineLearning research across Europe in a time of global change.
Read the full article: ellis.eu/news/ellis-s...
Read the full article: ellis.eu/news/ellis-s...
Welcome to our team, Gesa Voigt! 👋
During her molecular biology studies, Gesa developed an interest in applying mathematics and ML to understand complex biological systems. Her PhD research will focus on inferring GRNs by integrating insights from population genetics and genetic perturbation data.
During her molecular biology studies, Gesa developed an interest in applying mathematics and ML to understand complex biological systems. Her PhD research will focus on inferring GRNs by integrating insights from population genetics and genetic perturbation data.
November 12, 2025 at 12:30 PM
Welcome to our team, Gesa Voigt! 👋
During her molecular biology studies, Gesa developed an interest in applying mathematics and ML to understand complex biological systems. Her PhD research will focus on inferring GRNs by integrating insights from population genetics and genetic perturbation data.
During her molecular biology studies, Gesa developed an interest in applying mathematics and ML to understand complex biological systems. Her PhD research will focus on inferring GRNs by integrating insights from population genetics and genetic perturbation data.
Please join me in welcoming Stefanie Mantz to our lab! 👋
Steffi joins us as a PhD student after completing her Master’s at Heidelberg University. She will explore gene regulation and cell differentiation using organoid models and is excited to analyze these complex datasets and develop ML methods.
Steffi joins us as a PhD student after completing her Master’s at Heidelberg University. She will explore gene regulation and cell differentiation using organoid models and is excited to analyze these complex datasets and develop ML methods.
November 10, 2025 at 12:30 PM
Please join me in welcoming Stefanie Mantz to our lab! 👋
Steffi joins us as a PhD student after completing her Master’s at Heidelberg University. She will explore gene regulation and cell differentiation using organoid models and is excited to analyze these complex datasets and develop ML methods.
Steffi joins us as a PhD student after completing her Master’s at Heidelberg University. She will explore gene regulation and cell differentiation using organoid models and is excited to analyze these complex datasets and develop ML methods.
Are you using any of our factor models, such as MOFA? 🛵
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
November 7, 2025 at 10:29 AM
Are you using any of our factor models, such as MOFA? 🛵
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
Reposted by Stegle Lab
Thank you to everyone who joined the Life Science Thematic Workshop at the AI in Science Summit in Copenhagen.
Led by EMBL’s Oliver Stegle and Anna Kreshuk, the workshop united researchers and AI experts to explore how advanced computational approaches are shaping the future of life sciences.
#ai
Led by EMBL’s Oliver Stegle and Anna Kreshuk, the workshop united researchers and AI experts to explore how advanced computational approaches are shaping the future of life sciences.
#ai
November 4, 2025 at 12:47 PM
Thank you to everyone who joined the Life Science Thematic Workshop at the AI in Science Summit in Copenhagen.
Led by EMBL’s Oliver Stegle and Anna Kreshuk, the workshop united researchers and AI experts to explore how advanced computational approaches are shaping the future of life sciences.
#ai
Led by EMBL’s Oliver Stegle and Anna Kreshuk, the workshop united researchers and AI experts to explore how advanced computational approaches are shaping the future of life sciences.
#ai
Looking forward to this collab with @moritzmall.bsky.social and Barbara Treutlein!
We’ll generate high-throughput multi-modal CRISPR data on ASD risk genes in 🧠 organoids & assembloids, and build an ML model of gene regulation dynamics to analyze the data and enable future in silico experiments.
We’ll generate high-throughput multi-modal CRISPR data on ASD risk genes in 🧠 organoids & assembloids, and build an ML model of gene regulation dynamics to analyze the data and enable future in silico experiments.
Presenting recipients of our 2025 Stimulator Grant:
👉TACTICS: Thalamocortical Assembloids and Computational Tools for Investigating Cellular Signatures in #Autism.
🧠How do autism-linked mutations disrupt early brain development? @moritzmall.bsky.social @steglelab.bsky.social
@dkfz.bsky.social
👉TACTICS: Thalamocortical Assembloids and Computational Tools for Investigating Cellular Signatures in #Autism.
🧠How do autism-linked mutations disrupt early brain development? @moritzmall.bsky.social @steglelab.bsky.social
@dkfz.bsky.social
October 14, 2025 at 11:42 AM
Looking forward to this collab with @moritzmall.bsky.social and Barbara Treutlein!
We’ll generate high-throughput multi-modal CRISPR data on ASD risk genes in 🧠 organoids & assembloids, and build an ML model of gene regulation dynamics to analyze the data and enable future in silico experiments.
We’ll generate high-throughput multi-modal CRISPR data on ASD risk genes in 🧠 organoids & assembloids, and build an ML model of gene regulation dynamics to analyze the data and enable future in silico experiments.
Do you want to link genomic variants to functional gene expression - cell by cell?
SDR-seq makes it possible; an experimental method connecting coding and non-coding variants to expression in single cells.
Proud to have contributed a custom FASTQ-processing tool to this great collaborative project.
SDR-seq makes it possible; an experimental method connecting coding and non-coding variants to expression in single cells.
Proud to have contributed a custom FASTQ-processing tool to this great collaborative project.
EMBL scientists have created a more sensitive single-cell sequencing tool for genomic variants and RNA in the same single cell.
Known as SDR-seq, the tool has unprecedented scale, precision, and speed to characterise variants and link them to functions and disease.
www.embl.org/news/science...
Known as SDR-seq, the tool has unprecedented scale, precision, and speed to characterise variants and link them to functions and disease.
www.embl.org/news/science...
New tool offers single-cell study of specific genetic variants | EMBL
Scientists developed a more sensitive single-cell sequencing tool linking genomic variants & RNA in the same cell uncover links to disease.
www.embl.org
October 10, 2025 at 2:42 PM
Do you want to link genomic variants to functional gene expression - cell by cell?
SDR-seq makes it possible; an experimental method connecting coding and non-coding variants to expression in single cells.
Proud to have contributed a custom FASTQ-processing tool to this great collaborative project.
SDR-seq makes it possible; an experimental method connecting coding and non-coding variants to expression in single cells.
Proud to have contributed a custom FASTQ-processing tool to this great collaborative project.
Don’t miss Manu’s poster on DeepGenoXcan, our new personalized and interpretable sequence-to-expression model, at #ASHG2025!
📅 October 16, 2:30pm-4:30pm
📍 Poster 1007T
📅 October 16, 2:30pm-4:30pm
📍 Poster 1007T
Excited to be at #ASHG2025 in Boston next week. On Thursday, I will be presenting a poster (1007T) on our latest work on Personalised sequence to expression modelling. Looking forward to meeting new folks and reconnecting with old friends and colleagues.
October 10, 2025 at 1:35 PM
Don’t miss Manu’s poster on DeepGenoXcan, our new personalized and interpretable sequence-to-expression model, at #ASHG2025!
📅 October 16, 2:30pm-4:30pm
📍 Poster 1007T
📅 October 16, 2:30pm-4:30pm
📍 Poster 1007T
Super excited for the 2nd edition of the #scverse conference!
A fantastic opportunity to showcase and discover innovative data frameworks for #singlecell analysis, and to meet the developers behind the scverse ecosystem. Looking forward to connecting with the community!
Register now! 👇
A fantastic opportunity to showcase and discover innovative data frameworks for #singlecell analysis, and to meet the developers behind the scverse ecosystem. Looking forward to connecting with the community!
Register now! 👇
🎉 scverse conference 2025 Registration & Call for Abstracts NOW OPEN! 🎉
We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025!
Details in thread!
🧵 1/3
We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025!
Details in thread!
🧵 1/3
August 28, 2025 at 3:59 PM
Super excited for the 2nd edition of the #scverse conference!
A fantastic opportunity to showcase and discover innovative data frameworks for #singlecell analysis, and to meet the developers behind the scverse ecosystem. Looking forward to connecting with the community!
Register now! 👇
A fantastic opportunity to showcase and discover innovative data frameworks for #singlecell analysis, and to meet the developers behind the scverse ecosystem. Looking forward to connecting with the community!
Register now! 👇
A scalable framework enabling the induction and spatial genotyping ➡ phenotyping of hundreds of tumors in mouse liver. #CHOCOLAT-G2P
Check out the publication for the nuts and bolts of 🍫-G2P: doi.org/10.1038/s415...
Check out the publication for the nuts and bolts of 🍫-G2P: doi.org/10.1038/s415...
This is a great set of methods for studying combinatorial effects of cancer mutations on spatial phenotypes.
Clever experimental design by @breinigmarco.bsky.social hijacking Visium and elegant analysis by @lomakinai.bsky.social and @elihei.bsky.social
www.nature.com/articles/s41...
Clever experimental design by @breinigmarco.bsky.social hijacking Visium and elegant analysis by @lomakinai.bsky.social and @elihei.bsky.social
www.nature.com/articles/s41...
Integrated in vivo combinatorial functional genomics and spatial transcriptomics of tumours to decode genotype-to-phenotype relationships - Nature Biomedical Engineering
A method integrates perturbation mapping with 10X Visium spatial transcriptomics to map tumour genetic complexity and heterogeneity.
www.nature.com
August 7, 2025 at 7:27 AM
A scalable framework enabling the induction and spatial genotyping ➡ phenotyping of hundreds of tumors in mouse liver. #CHOCOLAT-G2P
Check out the publication for the nuts and bolts of 🍫-G2P: doi.org/10.1038/s415...
Check out the publication for the nuts and bolts of 🍫-G2P: doi.org/10.1038/s415...
We're seeking a PhD student passionate about ML, biology, and driving impact in healthcare!
You'll be working on multi-omics factorization models for personalized medicine, co-supervised by @junyanlu.bsky.social.
👉 Project: www.helmholtz.de/assets/hidss...
✍️ Apply: hidss4health.de/application
You'll be working on multi-omics factorization models for personalized medicine, co-supervised by @junyanlu.bsky.social.
👉 Project: www.helmholtz.de/assets/hidss...
✍️ Apply: hidss4health.de/application
Application - Helmholtz Information & Data Science Academy
hidss4health.de
August 5, 2025 at 8:08 AM
We're seeking a PhD student passionate about ML, biology, and driving impact in healthcare!
You'll be working on multi-omics factorization models for personalized medicine, co-supervised by @junyanlu.bsky.social.
👉 Project: www.helmholtz.de/assets/hidss...
✍️ Apply: hidss4health.de/application
You'll be working on multi-omics factorization models for personalized medicine, co-supervised by @junyanlu.bsky.social.
👉 Project: www.helmholtz.de/assets/hidss...
✍️ Apply: hidss4health.de/application
Reposted by Stegle Lab
🌐 EMBL’s new initiative is set to transform life science research through full AI integration – from genomics to drug discovery.
💡 Funding from the Hector Foundation is dedicated to attracting interdisciplinary talent, boosting infrastructure, training, & innovation.
www.embl.org/news/connect...
💡 Funding from the Hector Foundation is dedicated to attracting interdisciplinary talent, boosting infrastructure, training, & innovation.
www.embl.org/news/connect...
August 1, 2025 at 7:15 AM
🌐 EMBL’s new initiative is set to transform life science research through full AI integration – from genomics to drug discovery.
💡 Funding from the Hector Foundation is dedicated to attracting interdisciplinary talent, boosting infrastructure, training, & innovation.
www.embl.org/news/connect...
💡 Funding from the Hector Foundation is dedicated to attracting interdisciplinary talent, boosting infrastructure, training, & innovation.
www.embl.org/news/connect...
Reposted by Stegle Lab
To all post-docs: The Genome Biology dept @embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Group Leader - Genome Biology Unit
Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...
embl.wd103.myworkdayjobs.com
July 30, 2025 at 1:41 PM
To all post-docs: The Genome Biology dept @embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
This year, our lab has a great representation at the ISMB/ECCB 2025 conference in Liverpool! Every day at the conference, you’ll have the chance to hear at least one talk or explore a poster by one of our incredible lab members.
More details below. 👇
More details below. 👇
July 19, 2025 at 5:33 PM
This year, our lab has a great representation at the ISMB/ECCB 2025 conference in Liverpool! Every day at the conference, you’ll have the chance to hear at least one talk or explore a poster by one of our incredible lab members.
More details below. 👇
More details below. 👇
Reposted by Stegle Lab
EurIPS is coming! 📣 Mark your calendar for Dec. 2-7, 2025 in Copenhagen 📅
EurIPS is a community-organized conference where you can present accepted NeurIPS 2025 papers, endorsed by @neuripsconf.bsky.social and @nordicair.bsky.social and is co-developed by @ellis.eu
eurips.cc
EurIPS is a community-organized conference where you can present accepted NeurIPS 2025 papers, endorsed by @neuripsconf.bsky.social and @nordicair.bsky.social and is co-developed by @ellis.eu
eurips.cc
July 16, 2025 at 10:01 PM
EurIPS is coming! 📣 Mark your calendar for Dec. 2-7, 2025 in Copenhagen 📅
EurIPS is a community-organized conference where you can present accepted NeurIPS 2025 papers, endorsed by @neuripsconf.bsky.social and @nordicair.bsky.social and is co-developed by @ellis.eu
eurips.cc
EurIPS is a community-organized conference where you can present accepted NeurIPS 2025 papers, endorsed by @neuripsconf.bsky.social and @nordicair.bsky.social and is co-developed by @ellis.eu
eurips.cc
📢 Announcing the MOPITAS Autumn School on Spatial Transcriptomics Data Analysis – taking place November 12–14, in Munich. Don't miss this excellent opportunity to deepen your expertise in data science and multi-OMICS analysis - especially as a PhD student in the data science community.
July 4, 2025 at 7:20 PM
📢 Announcing the MOPITAS Autumn School on Spatial Transcriptomics Data Analysis – taking place November 12–14, in Munich. Don't miss this excellent opportunity to deepen your expertise in data science and multi-OMICS analysis - especially as a PhD student in the data science community.
#ELSAGeneralAssembly Flashback: At last week’s ELSA General Assembly in Brussels, our lab member Hakime represented the @embl.org partnership in the @elsa-ai.eu project. 🧬✨
Hakime shared reflections on the recently concluded Health Privacy Challenge and also organized a follow-up workshop. 🛡️
Hakime shared reflections on the recently concluded Health Privacy Challenge and also organized a follow-up workshop. 🛡️
July 4, 2025 at 10:21 AM
#ELSAGeneralAssembly Flashback: At last week’s ELSA General Assembly in Brussels, our lab member Hakime represented the @embl.org partnership in the @elsa-ai.eu project. 🧬✨
Hakime shared reflections on the recently concluded Health Privacy Challenge and also organized a follow-up workshop. 🛡️
Hakime shared reflections on the recently concluded Health Privacy Challenge and also organized a follow-up workshop. 🛡️
Deadline in 9 days - apply now!
Job alert: Join us for a postdoc in AI in genetics at @EMBL Heidelberg! Great collaboration with @Adrian Cortes @GSK, aiming to develop new tools to elucidate genetic effects using population-scale cohorts and single-cell readouts. Please share!
embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
Postdoctoral Researcher in Computational Genetics
The research group of Oliver Stegle looks for a postdoctoral researcher to join a collaborative project with GSK with the goal to apply computational methods to investigate the effects of rare variant...
embl.wd103.myworkdayjobs.com
July 4, 2025 at 9:36 AM
Deadline in 9 days - apply now!
Reposted by Stegle Lab
🚀 Job opportunity: Bioinformatics Software Engineer
Join a young and passionate team at Heidelberg University to advance bioinformatics software that drive biological discovery.
Learn more & apply 👉 shorturl.at/GCpg7
Join a young and passionate team at Heidelberg University to advance bioinformatics software that drive biological discovery.
Learn more & apply 👉 shorturl.at/GCpg7
Bioinformatics Software Engineer
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
shorturl.at
June 25, 2025 at 1:21 PM
🚀 Job opportunity: Bioinformatics Software Engineer
Join a young and passionate team at Heidelberg University to advance bioinformatics software that drive biological discovery.
Learn more & apply 👉 shorturl.at/GCpg7
Join a young and passionate team at Heidelberg University to advance bioinformatics software that drive biological discovery.
Learn more & apply 👉 shorturl.at/GCpg7