Clémence Henon

🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...

🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form
🔗 Paper: www.nature.com/articles/s42...
📖 News & Views: www.nature.com/articles/s42...
💻 Code: corneto.org
🧵 Thread 👇

Gene context drift identifies drug targets to mitigate cancer treatment resistance Jassim et al. introduce a graph-embedding computational pipeline (RECODR) that measures changes in gene co-expression context during cancer treatment. RECODR enables the design of highly effective combination treatments for aggressive brain tumors in mice and the prediction of potential new treatments for patients with medulloblastoma and triple-negative breast cancer.

Online Now: Gene context drift identifies drug targets to mitigate cancer treatment resistance

Decoding the interactions and functions of non-coding RNA with artificial intelligence Nature Reviews Molecular Cell Biology, Published online: 19 June 2025; doi:10.1038/s41580-025-00857-wStudying RNA function is constrained by limitations of traditional methods. This Roadmap discusses how artificial intelligence (AI) can enhance the study of how non-coding regions of mRNA regulate its function, and suggests how to use AI to harness publicly available data towards that goal.

ICYMI: New Online! Decoding the interactions and functions of non-coding RNA with artificial intelligence

Identification of non-canonical peptides with moPepGen - Nature Biotechnology moPepGen enables the detection of peptides across species, proteases and technologies.

Identification of non-canonical peptides with moPepGen - @uclahealth.org @uoftmedicine.bsky.social @kislingerthomas.bsky.social go.nature.com/3HYJyyz

Online Now: The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets

Teaching machines the language of biology: Scaling large language models for next-generation single-cell analysis

What if LLMs could “read” & “write” biology? 🤔
Introducing C2S‑Scale—a Yale and Google collab: we scaled LLMs (up to 27B!) to analyze & generate single‑cell data 🧬 ➡️ 📝
🔗 Blog: research.google/blog/teachin...
🔗 Preprint: biorxiv.org/content/10.1...

scPRINT: pre-training on 50 million cells allows robust gene network predictions Nature Communications - Authors present a state-of-the-art cell foundation model trained on 50 million cells. They show that the model generates a meaningful gene network and has zero-shot...

I am super happy to annonce that after 9 months under review the first paper of my PhD: scPRINT is finally available on Nature Comms! 🎉🧬
www.nature.com/artic...

Conserved spatial subtypes and cellular neighborhoods of cancer-associated fibroblasts revealed by single-cell spatial multi-omics Through integrative analyses of single-cell spatial multi-omics datasets, Liu et al. identify four distinct spatial subtypes of cancer-associated fibroblasts, conserved across cancer types and independent of platforms. These subtypes exhibit unique transcriptomic profiles, distinct interactions with neighboring cells, and correlations with tumor microenvironment characteristics and clinical outcomes.

Conserved spatial subtypes and cellular neighborhoods of cancer-associated fibroblasts revealed by single-cell spatial multi-omics

Predicting gene expression from DNA sequence using deep learning models www.nature.com/articles/s41... (read free: rdcu.be/elSrE) 🧬🖥️🧪

Dissecting regulatory syntax in human development with scalable multiomics and deep learning https://www.biorxiv.org/content/10.1101/2025.04.30.651381v1

Multimodal cell maps as a foundation for structural and functional genomics - Nature A global map of human subcellular architecture yields protein complex structures, reveals protein functions, identifies assemblies with multiple localizations or cell-type specificity and decodes paediatric cancer genomes.

Nature research paper: Multimodal cell maps as a foundation for structural and functional genomics

https://go.nature.com/3YpvALv

Towards multimodal foundation models in molecular cell biology - Nature The development of multimodal foundation models, pretrained on diverse omics datasets, to unravel the intricate complexities of molecular cell biology is envisioned.

Nature research paper: Towards multimodal foundation models in molecular cell biology

https://go.nature.com/3YvGcbJ

Toward single-molecule protein sequencing using nanopores - @unigroningen.bsky.social go.nature.com/3FL0g3k

Spatial transcriptomics holds great promise to understand biological tissue function, but the assignment of transcripts to cells has been a substantial bottleneck.

For this reason, Elyas Heidari, a student in my lab and in @steglelab.bsky.social built segger.

www.biorxiv.org/content/10.1...

So proud on our stellar medical student Florian H. Geyer for his first first-authorship paper!

Comprehensive #DSRCT multi-omics analyses unveil CACNA2D2 as a diagnostic hallmark and super-enhancer-driven EWSR1::WT1 signature gene
tinyurl.com/42fxmmud

@dkfz.bsky.social
@uniheidelberg.bsky.social

Beyond the black box with biologically informed neural networks - Nature Reviews Genetics Biologically informed neural networks promise to lead to more explainable, data-driven discoveries in genomics, drug development and precision medicine. Selby et al. highlight emerging opportunities, ...

Thrilled to share our latest publication in @natrevgenet.bsky.social. We explore how deep learning models infused with prior knowledge—biologically-informed neural networks or BINNs—offer better predictive accuracy and interpretability in multi-omics data analysis. www.nature.com/articles/s41...

SIGN! SHARE!
Wichtiger, denn je!

www.openpetition.de/petition/onl...
Hier noch Bilder aus #Essen UK-Essen und #Fortress Meeting. #Aufstehenfuerdemokratie

Ongoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution Ongoing chromothripsis shapes genomic evolution in a diverse range of sarcomas and carcinomas. High-grade osteosarcoma is predominantly driven by the mechanism of loss-translocation-amplification chro...

Ongoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution: Cell www.cell.com/cell/fulltex...

Replication Stress Is an Actionable Genetic Vulnerability in Desmoplastic Small Round Cell Tumors EWS–WT1, the unique oncogenic driver of desmoplastic small round cell tumors, confers sensitivity to PARP and ATR inhibitors, supporting the potential of these drugs in treating patients with this agg...

Congrats to the team for this great work uncovering actionable vulnerabilities in DSRCT. Let's continue efforts to improve novel target discovery and accessibility to innovation for sarcoma and rare cancer patients!
aacrjournals.org/cancerres/ar...

FEBS Press Using a mouse model that recapitulates the spread of tumor cells within the body, we have profiled paired tumors and metastasis samples using a multiomics approach combining different layers of biolo...

Multi-omics profiling reveals key factors involved in Ewing #sarcoma #metastasis

febs.onlinelibrary.wiley.com/doi/10.1002/...

RATIONALE focuses on rare cancers First multi-site study by the National Center for Tumor Diseases (NCT)

Exciting times ahead! The first joint clinical trial of the National Center for Tumor Diseases #OneNCT will address the unresolved question of whether treatment based on multi-layered molecular profiling can improve outcomes in patients with advanced #RareCancers. nct.dkfz.de/en/nct/news/...

Rare germline structural variants increase risk for pediatric solid tumors Pediatric solid tumors are a leading cause of childhood disease mortality. In this work, we examined germline structural variants (SVs) as risk factors for pediatric extracranial solid tumors using ge...

Here's our latest, led by Drs. Riaz Gillani & Ryan Collins - we studied a type of inherited genetic event (structural variants) + risk of developing certain cancers in kids:
@danafarber.bsky.social @bostonchildrens.bsky.social @broadinstitute.org @science.org

www.science.org/doi/10.1126/...