Memory genes are enriched in CAR T cells that persist and control tumors in patients. But which transcription factors drive beneficial memory programs? We answer this in our lab’s first paper in nature led by Alex Doan Kat Mueller, PhD Andy Chen. 1/ nature.com/articles/s4158…

I’m happy to share our manuscript led by David Glass investigating the endogenous and neoplastic responses to anti-PD-1 monotherapy or anti-PD-1 + IFNg combination therapy in patients with cutaneous T cell lymphoma at Cell Reports Medicine. (1/10) cell.com/cell-reports-m…

Using in situ spatial transcriptomics? Try Proseg, @danielcjones’s new cell segmentation method based on probabilistic and Cellular Potts modeling. Great for Vizgen Merscope, 10x Genomics Xenium, and @nanostringtech CosMx data. Preprint & code: (1/n) doi.org/10.1101/2024.0…

Scientists identify the brain cells that regulate inflammation, and pinpoint how they keep tabs on the immune response go.nature.com/3y9hO5o

Reminder! Today at 18:00 CEST will be another community meeting! Quentin BLAMPEY will talk about about scyan, a method for fast cell population annotation, using only biological knowledge prior. Zoom link can be found here: scverse.zulipchat.com/#narrow/stream… See you all there!

Our multimodal model to combine TCR sequences with scRNA-seq is finally out. The most interesting part for me was observing a clear case where the combination of TCR sequence and cell state (RNA) preserved both clonotype and cell type information, leading to a more holistic cell

Paper is out! Deconvolve cellular composition from bulk gene expression nature.com/articles/s4146…

3rd edition of the Health Data Challenge (Hadaca) hackathon are open : hadaca3.sciencesconf.org/?lang=en If you're interested in collaboratively tackling challenging bioinformatics problems (in Winter in the French Alps 👀), consider attending !

We're hiring an 🧑‍🔬Assistant-Engineer for our #AgenceRecherche-funded Cytometry Augmented by Machine Learning project ! 🗒️Clinical samples processing, flow cytometry data generation and close collaboration with 💻data scientists and 🏥medical doctors. 👉 docs.google.com/document/d/1mo…

A new research article was published in ImmunoInformatics 👇 Lessons learned from the IMMREP23 TCR-epitope prediction challenge sciencedirect.com/science/articl…

It's happening again! 🤩 Join us for a hands-on program designed for those interested in advancing their skills in computational cytometry data analysis. Find the program and apply here: t.ly/49QQe #CompCyto2025 🙏 to our sponsors Sony Biotechnology and BD Biosciences

Excited to finally see this work in print! Big thanks to everyone who made it happen! 🔥 Doherty Institute UniMelb MDHS For more, check out a related study from Hongbo Chi on pathways regulating gut TRM formation via nutrient sensing: cell.com/immunity/fullt…

So proud of Dr Kevin Mulder! The one and only ! Congratulations Kevin

Fascinating talk by Rémy Nicolle on the development of expression/histology based predictive signatures for #pancreatic cancer ChampalimaudF

How does #RetinoicAcid (RA) affect immunosurveillance? Andreas Obers (Andreas Obers), @MaxEvrard, & Laura Mackay (Mackay Lab) showed that RA mediates tissue-resident memory T cell maintenance by limiting retrograde migration. 💬 bit.ly/4fxHaL1 x.com/LMackayLab/sta…

TCR lovers, we are delighted to share our benchmarking of TCR specificity tools using an harmonized aggregation of public databases. biorxiv.org/content/10.110…

Missed a comma in my code, made this

I recently wrote a primer on UMAP for Nature Reviews Primers. If you are looking for an overview of the method, a getting started primer, or best practices it is a good place to start. rdcu.be/d0YZT

🌟 Calling all computational biology enthusiasts! 🌟 The awesome Rémy Nicolle & friends created this Discord community to connect, collaborate, and share insights in this rapidly evolving field. 👉 Click to join : discord.gg/2PzSE4dC #Bioinformatics #ComputationalBiology

Permanent position (research and teaching) for a bioinformatician immunologist available in a great lab and institute, in a beautiful campus in the center of Paris linkedin.com/posts/isabelle…