⭕ Just published in Bioinformatics Advances: "nVenn2: faster, simpler generalized quasi-proportional Venn diagrams"  Find it here: https://doi.org/10.1093/bioadv/vbag183

The best experiment doesn't exist - blog.turbine.ai/p/the-best-e...

The best experiment doesn't exist

as shown by an analysis of DepMap data

blog.turbine.ai

Most chromosomal mosaicisms arise after fertilization. We report a child with hepatoblastoma carrying a chromosome 18 rearrangement that instead originated before fertilization. Multi-omics analyses revealed its evolution from gametogenesis to cancer. doi.org/10.1016/j.jh...

This is a very cool work! Only saw it now. They could extract almost the entire (!) The Great Gastsby and 1984 from Claude (with some jailbreaking). But for some reason not Catch-22. I wonder why that is and what it tells us about the training data (or about Catch-22?). Catch-22 is great btw.

A. Feder Cooper@afedercooper.bsky.social · 7mo ago

We extracted (parts of) 12 books in experiments with 4 frontier-lab, production LLMs. We prompted the LLMs with a short prefix of a book and asked them to complete the rest. For Harry Potter and the Sorcerer’s Stone, we extracted 95.8% of the book from jailbroken Claude 3.7 Sonnet.

🧬💻 Attention young immunologists! Drowning in datasets? Plots feeling basic? We’ve got you! 🎓 Computational Immunology Summer School 📅 Aug 24–26, 2026 | Paris ✅ 1 day of keynotes ✅ 2 days of hands-on workshops ✅ Wholesome networking 🔗 Learn. Connect. Level up! 👉 More info: shorturl.at/PseSm

Great fun to write this review on Kupffer cells with Florent Ginhoux and Paul Kubes, covering origin, diversity and roles in immunity and metabolism, now out in @natrevimmunol.nature.com. Huge credit to Bruna Araujo David, Francesco Andreata and Camille Blériot for driving this work. t.co/rGpmTMRddV

🔬 Just published in Bioinformatics Advances: "Computational design of class II MHC binding peptide with sequence-based evolution information"  Read it here: https://doi.org/10.1093/bioadv/vbag090

Cell type composition drives patient stratification in single-cell RNA-seq cohorts www.biorxiv.org/content/10.6...

I've only skimmed the paper but this looks pretty impressive!

#SingleCell preprints@prepub-singlecell.bsky.social · 5mo ago

Integration of large, complex single-cell datasets with Harmony2 #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.03.16.711825v1

How to deal with clinical flow cytometry data with batch effects, changing markers, multiple panels per sample, incomplete cell-type labelling and large differences in cell-type proportions across patients? Mike Phuycharoen developed the UVAE method to solve this problem www.cell.com/iscience/ful...

New preprint 🧫🧬 Spatial transcriptomics (~550,000 cells, 2,432 patient-derived organoids): we map gene expression, shape, and function in space to understand cancer biology and drug response. w/ @marianna-raps.bsky.social @khomicsko.bsky.social and Maxim Norkin www.biorxiv.org/content/10.6...

I made a map of 3.4 million Bluesky users - see if you can find yourself! bluesky-map.theo.io I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail

Bluesky Map

Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.

bluesky-map.theo.io

I am just reading this paper, and it is absolutely wild. Tumor cells acquire mutations in mitochondria, and then transfer them to T-cells, and the mutant mitochondria drives dysfunction in the T-cells?! www.nature.com/articles/s41...

Immune evasion through mitochondrial transfer in the tumour microenvironment - Nature

Mitochondria with mutations in their DNA from cancer cells can be transferred to T cells in the tumour microenvironment, which leads to T cell dysfunction and impaired antitumour immunity.

nature.com

1) We recently published a multicentric study in cghjournal.org/article/S154... We analyzed using machine learning an international cohort of 1,399 pts treated for HCC with atezo/bev across 12 centers to uncover clinically meaningful subgroups. @etrepo.bsky.social

An education in tolerance: the 2025 Nobel Prize in Physiology or Medicine journals.biologists.com/dmm/article/...

As the saying goes, one man’s trash is another man’s treasure: the flow-cytometry doublets that are routinely excluded from analysis are in fact a rich source of tumor-reactive T cells. #immunology #science #tumor #immunotherapy buff.ly/pETJPEH

Tumour-reactive heterotypic CD8 T cell clusters from clinical samples

Tumour-reactive CD8+ T cells are enriched in functional clusters with tumour cells and/or antigen-presenting cells and can be isolated and expanded from clinical samples.

nature.com

Pre-print alert! And this one really is a must read for anyone that does spectral #flowcytometry. It is a complete, fully-automated spectral unmixing pipeline that reduces error up to 9000-fold. Want to get a tough sample, like lung, looking like this? Read more! www.biorxiv.org/content/10.1...

🧵 (1/2) Interested in tertiary lymphoid structures (TLSs)? Check out our latest review, where we chart how TLSs form across organs and contexts — from lung to liver, CNS, skin, gut & more — and their dual roles in protection vs. pathology.

Tertiary Lymphoid Structures Across Organs: Context, Composition, and Clinical Levers

Tertiary lymphoid structures (TLSs) arise in non-lymphoid tissues in response to persistent antigen stimulation and chronic inflammation. Spanning organs from lung and liver to meninges, skin, and be....

onlinelibrary.wiley.com

Nature research paper: One mother for two species via obligate cross-species cloning in ants go.nature.com/45PYV6d

One mother for two species via obligate cross-species cloning in ants - Nature

In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same mother having distinct genomes and morphologies.

go.nature.com

Your yearly reminder to acknowledge the core facilities you use and their staff scientists in your papers. These scientists are a crucial part of the scientific ecosystem and to continue to exist they need tangible credit for their work. Plus their associated expertise adds credibility to your work.

🧪💻 We're hiring ! Post-doctoral position open for a data scientist 👉 Come work with us on high-throughput single cell protein expression data : drive.google.com/file/d/1w8Zv...

Unbelievable news. Pancreatic is one of the deadliest cancers. New paper shows personalized mRNA vaccines can induce durable T cells that attack pancreatic cancer, with 75% of patients cancer free at three years—far, far better than standard of care. www.nature.com/articles/s41...

Our paper is out! LCK–co-receptor association ensures T cell lineage fidelity and maximizes epitope-specific TCR diversity | Science Immunology www.science.org/doi/10.1126/...

LCK–co-receptor association ensures T cell lineage fidelity and maximizes epitope-specific TCR diversity

LCK-mutant mice help define the role of LCK–co-receptor association in T cell development and immune responses.

science.org

Flow cytometry batch effect correction without requiring normalization controls 🤩 onlinelibrary.wiley.com/doi/full/10....

CytoNorm 2.0: A flexible normalization framework for cytometry data without requiring dedicated controls

Cytometry is a single cell, high-dimensional, high-throughput technique that is being applied across a range of disciplines. However, many elements alongside the data acquisition process might give r...

onlinelibrary.wiley.com

Excited to share this new work led by postdoc Brendan Floyd, deep mapping of cell-surface protein interactomes of T and B cells reveals maverick mitochondrial proteins and immune modulatory complexes. www.biorxiv.org/content/10.1...

Mapping the nanoscale organization of the human cell surface proteome reveals new functional associations and surface antigen clusters

The cell surface is a dynamic interface that controls cell-cell communication and signal transduction relevant to organ development, homeostasis and repair, immune reactivity, and pathologies driven b...

biorxiv.org

Thanks to those who politely pointed out we initially made a list of Metastasis Researchers... we've now made a starter pack! ☺️ go.bsky.app/KasKkhK Drop us a message or reply here to be added. More to follow over the coming days. 🦋

Our collaborators @rgottardo.bsky.social and Ken Stuart (+ others) describe tagtango, an application to compare #single-cell annotations. #bioinformatics academic.oup.com/bioinformati...

tagtango: an application to compare single-cell annotations

AbstractSummary. In this article, we present tagtango, an innovative R package and web application designed for robust and intuitive comparison of single-c

academic.oup.com

So THAT'S what Granzyme K does-- cleave complement and promote inflammation in the airway. Fascinating! #ImmunoSky #AsthmaSky #InflammationSky www.nature.com/articles/s41...

GZMK-expressing CD8+ T cells promote recurrent airway inflammatory diseases - Nature

Comparing T cells in nasal polyps from repeated surgeries shows that effector memory-like persistent clones colonize the mucosal tissue during disease recurrence and promote inflammation by producing ...

nature.com

La FHU* MOSAIC² relabellisée pour 5 ans ! Félicitations à la Pr Valérie Paradis et ses équipes qui portent ce FHU, illustrant l’engagement de l'Institut du Cancer en faveur de la recherche ! Plus d'informations sur le projet prochainement. @hopitalbeaujon.bsky.social @ap-hp.bsky.social

Luo et al. developed ATLAS-seq (Aptamer-based T-Lymphocyte Activity Screening and Sequencing), a microfluidic-based high-throughput platform for isolating and profiling antigen-reactive T cells. bit.ly/4fThnwo