Clémence Henon
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clemence-henon.bsky.social
Clémence Henon
@clemence-henon.bsky.social
45 followers 92 following 3 posts
MD-PhD | Medical Oncologist & Postdoc @ DKFZ
Between Biology, Data & Care 🔬🧬
Sarcomas & rare cancers | Affiliated with Gustave Roussy
Posts Replies Media Videos
Reposted by Clémence Henon
stephenturner.us
Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion www.nature.com/articles/s41... 🧬🖥️🧪 github.com/pinellolab/D... (noncommercial)
December 23, 2025 at 7:00 PM
Reposted by Clémence Henon
cp-cell.bsky.social
Now online! Multimodal AI generates virtual population for tumor microenvironment modeling
Multimodal AI generates virtual population for tumor microenvironment modeling
GigaTIME leverages multimodal AI to generate virtual multiplex immunofluorescence (mIF) profiles from standard H&E slides, enabling comprehensive tumor immune microenvironment modeling across a large (>14,000) and diverse patient population. This virtual approach unlocks new opportunities for large-scale clinical discoveries that were previously hindered by the scarcity of mIF data.
dlvr.it
December 9, 2025 at 7:51 PM
Reposted by Clémence Henon
natcomputsci.nature.com
📢 @fionakolbinger.bsky.social and @jnkt.bsky.social characterize the discordance between metrics used to evaluate AI tools and their clinical impact, proposing a framework to reduce this disconnect. www.nature.com/articles/s43... @tudresden.bsky.social @ekfzdigital.bsky.social

🔓 rdcu.be/eQmQp
Adaptive validation strategies for real-world clinical artificial intelligence - Nature Computational Science
Technical metrics used to evaluate medical artificial intelligence tools often fail to predict their clinical impact. We characterize this discordance and propose a framework of study designs to guide...
www.nature.com
November 17, 2025 at 3:23 PM
Reposted by Clémence Henon
natcomputsci.nature.com
📢Out now! Ouyang Zhu and Jun Li from @notredame.bsky.social present Scouter, a lightweight AI method that can predict genome-wide transcriptional responses to single- and two-gene perturbations using LLM embeddings. www.nature.com/articles/s43... 🖥️ 🧬
Scouter predicts transcriptional responses to genetic perturbations with large language model embeddings - Nature Computational Science
A lightweight AI method called Scouter that predicts genome-wide transcriptional responses to single- and two-gene perturbations using large language model embeddings is presented and achieves substan...
www.nature.com
December 5, 2025 at 7:10 PM
Reposted by Clémence Henon
tommytang.bsky.social
Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq | Nature Genetics www.nature.com/articles/s4...
October 11, 2025 at 2:15 PM
Reposted by Clémence Henon
fabiantheis.bsky.social
🚀 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...
September 28, 2025 at 5:50 PM
Reposted by Clémence Henon
saezlab.bsky.social
🎉 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 👇
July 22, 2025 at 3:23 PM
Reposted by Clémence Henon
cp-cancercell.bsky.social
Online Now: Gene context drift identifies drug targets to mitigate cancer treatment resistance
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.
dlvr.it
June 27, 2025 at 6:52 PM
Reposted by Clémence Henon
natrevmcb.nature.com
ICYMI: New Online! Decoding the interactions and functions of non-coding RNA with artificial intelligence
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.
bit.ly
June 22, 2025 at 9:12 AM
Reposted by Clémence Henon
natbiotech.nature.com
Identification of non-canonical peptides with moPepGen - @uclahealth.org @uoftmedicine.bsky.social @kislingerthomas.bsky.social go.nature.com/3HYJyyz
Identification of non-canonical peptides with moPepGen - Nature Biotechnology
moPepGen enables the detection of peptides across species, proteases and technologies.
go.nature.com
June 16, 2025 at 2:38 PM
Reposted by Clémence Henon
cp-cancercell.bsky.social
Online Now: The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets
The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets
Knol et al. report a large pan-cancer proteome landscape based on high-throughput, single-shot mass spectrometry across 22 cancer types including both liquid (n = 4) and solid cancers (n = 18), revealing co-expression-based phenotypes and immune phenotypes and defining top 25 ranked proteins as potential biomarkers and drug targets for each cancer type as well as a multi-cancer classifier.
dlvr.it
May 30, 2025 at 11:52 AM
Reposted by Clémence Henon
vandijklab.bsky.social
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...
Teaching machines the language of biology: Scaling large language models for next-generation single-cell analysis
research.google
April 18, 2025 at 2:14 PM
Reposted by Clémence Henon
jkobject.com
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...
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...
www.nature.com
April 16, 2025 at 12:53 PM
Reposted by Clémence Henon
cp-cancercell.bsky.social
Conserved spatial subtypes and cellular neighborhoods of cancer-associated fibroblasts revealed by single-cell spatial multi-omics
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.
dlvr.it
May 14, 2025 at 2:18 PM
Reposted by Clémence Henon
stephenturner.us
Predicting gene expression from DNA sequence using deep learning models www.nature.com/articles/s41... (read free: rdcu.be/elSrE) 🧬🖥️🧪
May 13, 2025 at 3:30 PM
Reposted by Clémence Henon
biorxivpreprint.bsky.social
Dissecting regulatory syntax in human development with scalable multiomics and deep learning https://www.biorxiv.org/content/10.1101/2025.04.30.651381v1
May 1, 2025 at 3:33 AM
Reposted by Clémence Henon
nature.com
Nature research paper: Multimodal cell maps as a foundation for structural and functional genomics

https://go.nature.com/3YpvALv
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.
go.nature.com
April 11, 2025 at 7:49 AM
Reposted by Clémence Henon
nature.com
Nature research paper: Towards multimodal foundation models in molecular cell biology

https://go.nature.com/3YvGcbJ
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.
go.nature.com
April 21, 2025 at 10:20 AM
Reposted by Clémence Henon
natbiotech.nature.com
Toward single-molecule protein sequencing using nanopores - @unigroningen.bsky.social go.nature.com/3FL0g3k
March 18, 2025 at 1:39 PM
Reposted by Clémence Henon
moritzgerstung.bsky.social
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...
March 17, 2025 at 4:19 PM
Reposted by Clémence Henon
grunewaldlab.bsky.social
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
March 15, 2025 at 2:42 PM
Reposted by Clémence Henon
davidselby.bsky.social
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...
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, ...
www.nature.com
March 4, 2025 at 3:12 PM
clemence-henon.bsky.social
Single cell RNA-sequencing of Ewing sarcoma tumors demonstrates transcriptional heterogeneity and clonal evolution
Abstract. Purpose: Ewing sarcoma (EwS) is the second most common bone cancer in children, accounting for 2% of pediatric cancer diagnoses. Patients who present with metastatic disease at the time of d...
aacrjournals.org
March 5, 2025 at 10:15 AM
Reposted by Clémence Henon
diuta.bsky.social
SIGN! SHARE!
Wichtiger, denn je!

www.openpetition.de/petition/onl...
Hier noch Bilder aus #Essen UK-Essen und #Fortress Meeting. #Aufstehenfuerdemokratie
February 19, 2025 at 6:49 PM
clemence-henon.bsky.social
Ongoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution: Cell www.cell.com/cell/fulltex...
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...
www.cell.com
January 15, 2025 at 8:15 AM