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Etienne Becht

@ebecht.bsky.social
524 followers 670 following 14 posts

Computational immunologist. Interested in immunooncology, cytometry, single cell data, spatial data, T and B cell specificities...

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Reposted by Etienne Becht
Masahiro Kanai @masakanai.bsky.social · 30/09/2026
Our single-nucleus immune multiome atlas is now out in @nature.com! 🧬 10M PBMCs from 1,108 @finngen.bsky.social donors recruited by Finnish Blood Service, profiled at @broadinstitute.org with chromatin accessibility and gene expression in the same nuclei, to trace how disease variants act 🧵👇
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Mikhail Pogorelyy @pogorely.bsky.social · 25/11/2025
Excited to see our TIRTL-seq method published in Nature Methods www.nature.com/articles/s41...! Some updates after the revision: (1/4)
nature.com
TIRTL-seq: deep, quantitative and affordable paired TCR repertoire sequencing - Nature Methods
TIRTL-seq is a high-throughput method for paired T cell receptor sequencing at the cohort scale.
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Etienne Becht @ebecht.bsky.social · 27/08/2026
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#SingleCell preprints @prepub-singlecell.bsky.social · 27/08/2026
CytoGate-Bench: an LLM benchmark for cross-panel cell gating in cytometry #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20…
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Etienne Becht @ebecht.bsky.social · 26/08/2026
I've been so fortunate to teach at the 1st Parisian Immuno-Informatics Summer School, where we've taken on the (herculean) task of exposing the inner workings of bulk & scRNAseq analysis tools to mostly wet-lab students. Their interest really rewarded our efforts! See you next year 🤞
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Etienne Becht @ebecht.bsky.social · 20/08/2026
From F-Droid to independent devs, the entire Android ecosystem is under threat from Google's new mandatory registration decree. See why 67+ orgs are saying no: keepandroidopen.org
keepandroidopen.org
Keep Android Open
Your phone is about to stop being yours. In 2027, Google will block every Android app whose developer hasn't registered with them.
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Reposted by Etienne Becht
Bioinformatics Advances @bioinfoadv.bsky.social · 09/07/2026
⭕ Just published in Bioinformatics Advances: "nVenn2: faster, simpler generalized quasi-proportional Venn diagrams"  Find it here: doi.org/10.1093/bioadv/vbag183
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Valentine Svensson @nxn.se · 06/07/2026
The best experiment doesn't exist - blog.turbine.ai/p/the-best-e...
blog.turbine.ai
The best experiment doesn't exist
as shown by an analysis of DepMap data
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Theo Hirsch @tz-hirsch.bsky.social · 06/07/2026
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...
Natural history of the patient, from gametogenesis to tumorigenesis
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Dmitry Kobak @hippopedoid.bsky.social · 18/05/2026
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.
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Etienne Becht @ebecht.bsky.social · 05/05/2026
🧬💻 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
immunology-immunopathology-institute.u-pariscite.fr
Immuno-informatics Summer School Program : 24-26 August, 2026, Paris | Immunology-immunopathology-institute
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Iannacone Lab @iannaconelab.bsky.social · 08/04/2026
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
t.co
https://rdcu.be/fckoZ
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Bioinformatics Advances @bioinfoadv.bsky.social · 09/04/2026
🔬 Just published in Bioinformatics Advances: "Computational design of class II MHC binding peptide with sequence-based evolution information"  Read it here: doi.org/10.1093/bioadv/vbag090
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Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · 01/04/2026
Cell type composition drives patient stratification in single-cell RNA-seq cohorts www.biorxiv.org/content/10.6...
biorxiv.org
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Will Macnair @willmacnair.bsky.social · 19/03/2026
I've only skimmed the paper but this looks pretty impressive!
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Magnus Rattray @mrattray.bsky.social · 01/03/2026
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...
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Raphael Gottardo @rgottardo.bsky.social · 18/02/2026
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...
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Theo Sanderson @theo.io · 08/02/2026
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.theo.io
Bluesky Map
Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.
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Hunter Shain @shainlab.bsky.social · 28/01/2026
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...
nature.com
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.
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naultjc.bsky.social @naultjc.bsky.social · 27/11/2025
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
cghjournal.org
The “A-B-C” classification reveals outcome trajectories in patients with hepatocellular carcinoma under atezolizumab/bevacizumab
We aimed to identify subgroups of patients with unresectable hepatocellular carcinoma (HCC) using a non‐a priori, data‐driven machine learning approach to uncover subgroups with distinct profiles acro...
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Adrian Liston @labliston.bsky.social · 20/11/2025
An education in tolerance: the 2025 Nobel Prize in Physiology or Medicine journals.biologists.com/dmm/article/...
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David Usharauli @davidusharauli.bsky.social · 19/11/2025
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
nature.com
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.
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Adrian Liston @labliston.bsky.social · 28/10/2025
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...
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Iannacone Lab @iannaconelab.bsky.social · 26/09/2025
🧵 (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.
onlinelibrary.wiley.com
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....
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Nature @nature.com · 05/09/2025
Nature research paper: One mother for two species via obligate cross-species cloning in ants go.nature.com/45PYV6d
go.nature.com
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.
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Rita Strack @ritastrack.bsky.social · 10/04/2025
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.
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Etienne Becht @ebecht.bsky.social · 11/03/2025
🧪💻 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...
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Derek Thompson @dkthomp.bsky.social · 27/02/2025
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...
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Nicole La Gruta @niclag.bsky.social · 21/02/2025
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/...
science.org
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.
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Etienne Becht @ebecht.bsky.social · 20/02/2025
Flow cytometry batch effect correction without requiring normalization controls 🤩 onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com
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...
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 18/02/2025
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...
biorxiv.org
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...
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Metastasis Research Society @metastasisresearch.bsky.social · 18/02/2025
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. 🦋
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HIPC @hipcproject.bsky.social · 17/02/2025
Our collaborators @rgottardo.bsky.social and Ken Stuart (+ others) describe tagtango, an application to compare #single-cell annotations. #bioinformatics academic.oup.com/bioinformati...
academic.oup.com
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
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Alexander Dent @follicular.bsky.social · 13/02/2025
So THAT'S what Granzyme K does-- cleave complement and promote inflammation in the airway. Fascinating! #ImmunoSky #AsthmaSky #InflammationSky www.nature.com/articles/s41...
nature.com
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 ...
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Institut du Cancer AP-HP. Nord @cancerparisnord.bsky.social · 23/01/2025
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
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ACIR @acir-org.bsky.social · 16/01/2025
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
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Waggoner Lab @labwaggoner.bsky.social · 15/01/2025
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....
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Etienne Becht @ebecht.bsky.social · 07/01/2025
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...
linkedin.com
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…
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Javier Santoyo @jsantoyo.bsky.social · 19/12/2024
Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references. #GenomeAssembly #HaplotypeResolved #Pangenomes #Genomics #GenomeBiology 🧬 🖥️ genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com
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...
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Michael Fischbach @mfgrp.bsky.social · 11/12/2024
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
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Etienne Becht @ebecht.bsky.social · 10/12/2024
🌟 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
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Dr Debbie Burnett @debburnett.bsky.social · 03/12/2024
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
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Tomàs Montserrat Ayuso @tmontsay.bsky.social · 03/12/2024
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨 We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research! Read more: bmcgenomics.biomedcentral.com/articles/10.... 1/8
bmcgenomics.biomedcentral.com
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
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Will Macnair @willmacnair.bsky.social · 07/11/2024
I made a starter pack for single cell and spatial people on BlueSky! 🧬🧪🥳 I’m certain it’s very incomplete, so please just let me know if you’d like to be included 😊 go.bsky.app/U57Mar8
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Raphael Gottardo @rgottardo.bsky.social · 25/11/2024
Thanks @tsanglab.bsky.social for putting this together! #immunology #datascience go.bsky.app/PjH2Fuj
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Raphael Gottardo @rgottardo.bsky.social · 24/11/2024
Ok, I tried to create my own list of people working on developing statistical or machine learning models applied to omics data. I am sure I missed a lot of cool people. If you'd like to be added, let me know. #Stats #ML #Omics go.bsky.app/73rcuJn
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