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

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...

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

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.

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 👇

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...

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.

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.

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

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

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.

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.

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

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 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...

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

🌐 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...

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...

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. 👇

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

📢 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. 🛡️

Deadline in 9 days - apply now!

🚀 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

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!

🔧 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/

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.

@brianfclarke.bsky.social and @thbec.bsky.social will present their latest work at the @helmholtzai.bsky.social conference in Karlsruhe this week! Two exciting posters on rare variant genetics — both on Wednesday at 16:00. Details below 👇 #HelmholtzAI #Genomics #RareVariants #DeepRVAT #HAICON

Great team, great science, great opportunity. 🚀 @brianfclarke.bsky.social is hiring a PhD student to develop deep learning methods for rare variant genetics @dkfz.bsky.social in Heidelberg. 🎯 ⏳ 1 week left to apply: jobs.dkfz.de/en/jobs/167772 #PhD #Genomics #AI

Passionate about machine learning and healthcare? Join us for a TechDev Internship @embl.org to explore the privacy risks in pre-trained models! Help uncover vulnerabilities and develop safer and trustworthy healthcare ML. 🔐🧬👩🏻‍💻 Apply here: embl.wd103.myworkdayjobs.com/de-DE/EMBL/j... Please share 🙏

Happy Birthday! 🎉 We're proud to contribute to this global initiative, working together to build and sustain foundational tools for omics data analysis in the life sciences. Here's to open science and long-term impact! 🌍

How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 new studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. multimodal cell atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵

🚨 Impressive PhD work by Manu! Our new method scDORI decodes plasticity regulators at single-cell multi-omic resolution — scaling to millions of cells and uncovering the regulatory logic driving glioblastoma heterogeneity. 🔍 Dive into the thread below and the preprint for all the insights!

We are pleased to present our position paper outlining EMBL’s recommendations for European Commission’s upcoming ‘Strategy for European Life Sciences'. Our recommendations span several interconnected areas, e.g. research infrastructures, data resources, AI & training. www.embl.org/news/embl-an...

Our lab members recently attended the @www.helmholtz.de - @ellis.eu workshop on #FoundationModels in science, where academia and industry united in Berlin to explore AI’s role in genomics and more. Exciting insights fueling innovation! 🧠 Huge thanks to the organizers for such a fantastic event! 🙌

Starting off day 2 of #RNGS25 with another insightful talk by Oliver Stegle from @dkfz.bsky.social. He emphasized the importance of computational methods, tackling problems like cell segmentation in spatial data and multimodal integration. Look out for recent tools from his lab - Segger, PRIMSO.

Postdoc Opportunity at @embl.org ! 🧬🌍 Interested in unraveling gene-environment interactions in human traits? Join our project with @vrmlnroel.bsky.social to study how environmental factors influence human health at the molecular level! 🔗 Apply: tinyurl.com/ca7d6c4y @humanecosystems.bsky.social

The next selection round for the DKFZ International PhD Program has started. Please consider applying to this really excellent program! I'll be proposing projects, as will many other outstanding PIs.

1/ New preprint! 🍳 @elihei.bsky.social and our team at @embl.org , @dkfz.bsky.social, and @mskcancercenter.bsky.social built #segger - a fast, accurate cell segmentation tool for spatial transcriptomics that assigns transcripts to their cell origins! doi.org/10.1101/2025...

Want to map the origins and trajectories of cells in development and disease? Cell2Fate is here to help you! 🚀 🔗 Learn more: doi.org/10.1038/s415... 🖥️ Try it on your own datasets: github.com/BayraktarLab/cell2fate

Exciting News! 🚀 We’re pleased to launch Track II of the Health Privacy Challenge 🫐🍅, focused on single-cell data! We invite the participants to explore the privacy and utility of synthetic single-cell RNA-seq data! #CAMDAConference Register to participate: benchmarks.elsa-ai.eu?ch=4

EMBL International PhD Programme - summer recruitment 2025! 👀 Research groups across EMBL are recruiting now! www.embl.org/about/info/e... Don’t miss this opportunity to receive dedicated mentoring while doing interdisciplinary research. 🧪#AcademicSky #MolBiol #PhDSky #careers @ebi.embl.org

Thrilled to share that our work from Trumpp Lab @hi-stem @dkfz.bsky.social is out in Nature. We provide the first single-cell data on neurons infiltrating pancreatic tumors, offering new insights into cancer therapy. #cancerneuroscience @cn-hd.bsky.social www.nature.com/articles/s41...

📢 Bring your computational expertise to our cutting-edge research team at @embl.org! Join us together with experts from GSK to explore the effects of rare variants using population-scale cohorts and single-cell readouts. Please share 🙏 🔗 Apply now: embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...

Participation in The Privacy Challenge is still open! 🫐🍅 Join us in advancing our understanding of privacy in gene-expression datasets at the intersection of computational healthcare and privacy in AI research. #CamdaConference #ISMB/ECCB2025 Register to participate: benchmarks.elsa-ai.eu?ch=4

We are delighted to announce The Health Privacy Challenge, an interactive opportunity for advancement at the intersection of computational biology and privacy research, brought to you as a part of CAMDA Conference at #ISMB/ECCB2025 🫐🍅 Register to participate: benchmarks.elsa-ai.eu?ch=4

EMBL and @ellis.eu signed a Memorandum of Understanding to drive AI in European science research, training and tech. The agreement will promote interdisciplinary training and develop innovative projects that address pressing challenges in human and planetary health. www.embl.org/news/connect...

✍️ New Bioconductor blog post on the SpatialData hackathon and workshop, organized by https://buff.ly/4j1UidT with Bioconductor participation. Check it out: https://buff.ly/4fM1qrH Thanks @arturmansl.bsky.social‬ ! #Bioconductor #SpatialData #scverse #Bioinformatics #OpenScience #RStats

Two new @natureportfolio.bsky.social publications: 1️⃣ Multi-omic profiling of medulloblastoma characterizes subclonal variation of chromothripsis (doi.org/10.1038/s414...) 2️⃣ Spatio-temporal profiling explores mechanisms of treatment resistance (doi.org/10.1038/s414...) Thanks to all involved! 🙌