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steglelab.bsky.social
Stegle Lab
@steglelab.bsky.social
660 followers 130 following 50 posts
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/
steglelab.org
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steglelab.bsky.social
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.
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Aug 28
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! 👇
scverse.bsky.social
scverse @scverse.bsky.social · Aug 2
🎉 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!
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Aug 7
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...
moritzgerstung.bsky.social
Moritz Gerstung @moritzgerstung.bsky.social · Jul 29
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...
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
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Aug 5
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
Application - Helmholtz Information & Data Science Academy
hidss4health.de
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Reposted by Stegle Lab
embl.org
EMBL @embl.org · Aug 1
🌐 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...
Caption+Credit: EMBL’s AI Strategy aims to transform life sciences by integrating AI across research areas like genomics, drug discovery, and imaging. Creative team/ EMBL
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Reposted by Stegle Lab
eileen-furlong.bsky.social
Eileen Furlong @eileen-furlong.bsky.social · Jul 30
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...
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
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 19
Hakime, as part of @elsa-ai.eu, is organizing a dedicated Health Privacy Session which will feature a keynote talk, a panel discussion, and the recap of the Health Privacy Challenge with contributed presentations from the challenge participants. #CAMDA
📅 July 24 | 🕑 11:20-15:00 | 📍 Room 01C
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 19
@vitaliikl.bsky.social will discuss how biophysical deep learning improves understanding of embryogenesis. He applied cell2state, his new method leveraging TF-motif interactions and biophysical constraints, on an unpublished multimodal sc and spatial atlas.
#RegSys
📅 July 23 | 🕑 14:40 | 📍 Room 11BC
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 19
John will share how to achieve higher throughput and fidelity in screening via flexible, high-accuracy barcode decoding. He presents a principled, information theory-based software solution that unifies diverse, demanding decoding tasks within one robust framework.
#HiTSeq
📅 July 23 | 📍 Poster C-192
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 19
@elihei.bsky.social is gonna present our new tool segger, developed in collaboration with Moritz Gerstung and @danapeer.bsky.social, for fast and accurate segmentation of spatial transcriptomics using attention-based graph neural networks. #MLCSB
📅 July 22 | 🕑 15:50 | 📍 Room 01A
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 19
@thbec.bsky.social is going to share preliminary results on Meta-DeepRVAT, a new approach for deep learning based meta-analysis improving the power of rare variant association studies using population scale external control cohorts. #MLCSB
📅 July 21 |📍 Poster A-312
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 19
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. 👇
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Reposted by Stegle Lab
euripsconf.bsky.social
EurIPS Conference @euripsconf.bsky.social · Jul 16
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
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 4
Please spread the word and be sure to register here until July 31: event.sdu.dk/mopitas-scho...

We, Richard Röttger, Jakub Sedzinski, @itisalist.bsky.social, @oliverstegle.bsky.social and all the other members from the MOPITAS team, look forward to welcoming you to Munich!
MOPITAS Autumn School
event.sdu.dk
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 4
And a lot of hands-on formats organized by tool developers that guide you through the process with the latest tools and approaches. We will cover data pre-processing, multi-omics matrix factorization, single-cell spatial transcriptomics, cell fate analysis and much more!
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 4
Join us for a series of presentations from leading data science experts, including @francescafinotello.bsky.social, @dominicgrun.bsky.social, Johanna Klughammer, Malte Lücken, @fabiantheis.bsky.social and @jwrth.genomic.social.ap.brid.gy.
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 4
The Autumn School will feature a dynamic, hands-on format. Mornings will be dedicated to insightful talks and lectures, while afternoons will focus on collaborative mini-projects, allowing participants to apply what they’ve learned in a practical setting.
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 4
📢 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.
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 4
Expect a keynote talk, invited team presentations, and a panel discussion on privacy in health with leading experts. Don’t miss it! 🧑‍⚕️🔒

🗓️ CAMDA Programme:
www.iscb.org/ismbeccb2025...

🧪 More on the Health Privacy Challenge:
benchmarks.elsa-ai.eu?ch=4
CAMDA
ISCB - International Society for Computational Biology
www.iscb.org
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 4
The workshop brought together researchers from academia and industry to brainstorm ideas for the next edition of the Health Privacy Challenge. 🤝

What’s next for the Health Privacy Challenge?
It will feature a dedicated session at CAMDA during ISMB/ECCB 2025 in Liverpool!

#ELSAAI #ISMBECCB
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 4
#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. 🛡️
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jul 4
Deadline in 9 days - apply now!
oliverstegle.bsky.social
Oliver Stegle @oliverstegle.bsky.social · Jun 26
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...
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
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brittavelten.bsky.social
Britta Velten @brittavelten.bsky.social · Jun 25
🚀 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
Bioinformatics Software Engineer
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
shorturl.at
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Reposted by Stegle Lab
elsa-ai.eu
ELSA – European Lighthouse on Secure and Safe AI @elsa-ai.eu · Jun 17
ELSA will be extended!🎉
The European Commission decided to extend the duration of our Lighthouse on Secure and Safe AI. We will now run for an additional 12 months until August 2026.

Find more details in the official press release:
elsa-ai.eu/official-ext...
Congratulations to the network!
ELSA – European Lighthouse on Secure and Safe AI extended until August 2026
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Reposted by Stegle Lab
saezlab.bsky.social
Saez-Rodriguez Group @saezlab.bsky.social · Jun 12
🔧 decoupler 2.0.6 is out thanks to @paubadiam.bsky.social‬, now as a core @scverse.bsky.social package scverse.org

This release includes a streamlined API aligned with scverse standards, updated vignettes, and a new one on pseudotime enrichment analysis 👇
decoupler.readthedocs.io/en/latest/
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steglelab.bsky.social
Stegle Lab @steglelab.bsky.social · Jun 5
Great opportunity for early-career students. We also offer an internship project at the intersection of machine learning and healthcare - exploring privacy risks in pre-trained AI models.
embl.org
EMBL @embl.org · Jun 4
Applications open for the EMBL #TechDev Internship!

Engineers, physicists, coders & more — join EMBL labs across Europe to build cutting-edge tools for life sciences.

Apply now: www.embl.org/about/info/s...

#STEM #LifeSciences #Internship #Research
A man is working on a scientific instrument. Text box says: "EMBL TechDev Internship Programme. Training opportunities available at the interface of engineering and biology across EMBL!"
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