Etienne Becht

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...

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

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

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.

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...

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/...

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.

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

Thanks, will try it ! We use cells for unstained/autofluorescence and viability, for the other markers we use beads

Thanks a lot for the informative thread! Looks very exciting

Are single stained cellular controls necessary or only better ? We are using rare human samples so it's difficult to cells for single color controls, can we still hope to see improvements with AutoSpectral unmixing ?

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...

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....

🧵 (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.

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.

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

go.nature.com/45PYV6d

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...

6. found just enough strength to relay dread while being funny

That is no tiny victory.

I hope you find support until you are strong enough to support those who need it !

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.

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/...

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...

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

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...

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...

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.

🦋

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

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

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 ...

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

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

Mutations disrupting the kinase domain of IKKα lead to immunodeficiency and immune dysregulation in humans
@jem.org‪
@quentinriller.bsky.social @frl-lab.bsky.social
doi.org/10.1084/jem....

Isabelle Cremer on LinkedIn: Poste MCU immunologie-bioinformatique Un poste de maître de conférences en immunologie-bioinformatique est ouvert au concours à Sorbonne Université, au sein de la Faculté des Sciences et…

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

www.linkedin.com/posts/isabel...

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references - Genome Biology Background Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ult...

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references. #GenomeAssembly #HaplotypeResolved #Pangenomes #Genomics #GenomeBiology 🧬 🖥️
genomebiology.biomedcentral.com/articles/10....

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55

🌟 Calling all computational biology enthusiasts! 🌟 The awesome @remynicolle.bsky.social & friends created this Discord community to connect, collaborate, and share insights in this rapidly evolving field.

👉 Click here to join : discord.gg/2PzSE4dC

#Bioinformatics #ComputationalBiology

I’ve tried to put together a starter pack of immunologists/scientists exploring B Cell Repertoires and Antibody Affinities.

Please feel free to share/join!

go.bsky.app/4P64DmM