@johanduchene.bsky.social on Bluesky If you’re using 10x Genomics (Flex v1) for scRNA-seq, this study is a must-read. 🧪 It uncovers a key artefact: • Probe barcodes themselves introduce bias • Some barcodes systematically alter gene expression signals • Apparent DEGs may be technical, not biological https://www.biorxiv.org/content/10.64898/2026.04.06.716804v1

Interesting #10XGenomics #Flex #scRNAseq #bias

If you’re using 10x Genomics (Flex v1) for scRNA-seq, this study is a must-read. 🧪

It uncovers a key artefact:
• Probe barcodes themselves introduce bias
• Some barcodes systematically alter gene expression signals
• Apparent DEGs may be technical, not biological

www.biorxiv.org/content/10.6...

A single-cell atlas of intestinal immune cells across the day-night cycle reveals dynamic populations www.biorxiv.org/content/10.64898/2026.01...

We built a containerised workflow that handles QC, doublet detection, CITE‑seq for scRNA‑seq data, and outputs a ready‑to‑use #Seurat object. One command, #reproducible results—ideal for labs without dedicated bioinformatics support.

Our new pre‑print is out!

scReady – an automated and accessible pipeline for single‑cell RNA‑Seq preprocessing: Empowering novice bioinformaticians

wellcomeopenresearch.org/articles/11-43

@haessar.bsky.social @fionan-a.bsky.social @yiyicheng@mastodon.social

#scRNAseq #bioinformatics

@deniswirtz.bsky.social on Bluesky We wrote two reviews on cell migration, published today in Nature Methods. They provides practical guidelines how to select a cell-migration assay and how to analyze cell-migration data Review 1: https://nature.com/articles/s41592-025-02935-5 Review 2: https://nature.com/articles/s41592-025-02890-1

#biology #assay cell migration

We wrote two reviews on cell migration, published today in Nature Methods.

They provides practical guidelines how to select a cell-migration assay and how to analyze cell-migration data

Review 1: nature.com/articles/s41...

Review 2: nature.com/articles/s41...

Introduction to CellProfiler - by a biologist, for biologists! YouTube video by CellMorphoJSero

If you or your trainees are just getting started with image analysis of cells & are #CellProfiler -curious, here is a fairly thorough walk-through demo I did recently. Loading files, extracting metadata (fun with Regex!), identifying objects, measuring, filtering, QC, exporting:
youtu.be/fO5nJdhj_7I

#SpatialTranscriptomics

STcompare
github.com/JEFworks-Lab...

Test your gene of interest if it is differentially spatially patterned (r, p, s)🤠
Spatial correlation
Spatial fold change
Control for spatial autocorrelation

@jef.works bioRxiv 2025
www.biorxiv.org/content/10.1...

🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)

The protein and mRNA abundance voronoi diagrams offer remarkably different perspectives.

Each tile in the maps represents a gene product; its size is proportional to the fraction of the gene product in hepatocytes.

A few more #SingleCell and #SpatialBiology methods have been published recently, making it a total of 362 in the table I compiled over the years. lookerstudio.google.com/reporting/c3...

Our flow cytometry course starts in just 8 days! There's still time to register ⏰

Tailored for immunologists, you'll learn to design multiparameter panels, run complex experiments & interpret data - all online and only across 2 days!

Register today: bit.ly/43N86mG

Generating specificity in genome regulation through transcription factor sensitivity to chromatin - Nature Reviews Genetics In this Review, Isbel et al. describe our current understanding of how transcription factors navigate features of chromatin — particularly DNA methylation and nucleosomes — and how this contributes to...

This is an amazing review. I'd encourage everyone to read it.

Generating specificity in genome regulation through transcription factor sensitivity to chromatin

www.nature.com/articles/s41...

Well done everyone!! See you next year #Eular2025

Exploring advances in #SingleCellSequencing methods, such as #SingleCell #genomic & #transcriptomic sequencing, to understand the #TumorMicroenvironment, their application in single-cell #MultiOmics, as well as their advantages & limitations. #medsky
#OpenAccess:
buff.ly/sOEOxPq

Super interesting talk from @azizaelmesmari.bsky.social, showing how to make and use human organoid synovial tissue to replace animal models for experiment and treatment validation!
#Eular2025

How to use multimodal datasets with #AI to make decision for patient treatment in #RA remission@stealivernini.bsky.social #Eular25

USP2 inhibition unleashes CD47-restrained phagocytosis and enhances anti-tumor immunity | Nature Communications The CD47/SIRPα axis conveys a ‘don’t eat me’ signal, thereby thwarting the phagocytic clearance of tumor cells. Although blocking antibodies targeting CD47 have demonstrated promising anti-tumor effects in preclinical models, clinical trials involving human cancer patients have not yielded ideal results. Exploring the regulatory mechanisms of CD47 is imperative for devising more efficacious combinational therapies. Here, we report that inhibiting USP2 prompts CD47 degradation and reshapes the tumor microenvironment (TME), thereby enhancing anti-PD-1 immunotherapy. Mechanistically, USP2 interacts with CD47, stabilizing it through deubiquitination. USP2 inhibition destabilizes CD47, thereby boosting macrophage phagocytosis. Single-cell RNA sequencing shows USP2 inhibition reprograms TME, evidenced by increasing M1 macrophages and CD8+ T cells while reducing M2 macrophages. Combining ML364 with anti-PD-1 reduces tumor burden in mouse models. Clinically, low USP2 expression predicts a bett

USP2 inhibition leads to CD47 degradation, boosting phagocytosis and anti-tumor immunity. Novel therapeutic avenue—improves on previous antibody trials! PMID:40379682, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-025-59621-5 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

Huge thanks to everyone who joined us at the 3rd Basel Single Cell & Spatial Day at Novartis on June 10, 2025! 🧬 Inspired by the science, thrilled by the connections. Special thanks to Novartis, our speakers & attendees! Stay tuned for more. #10xGenomics #Novartis #SingleCell #SpatialBiology

Another great talk from @laviac.bsky.social on Tenosynovium differences in pre-clinical RA #Eular2025

Amazing presentation from @stealivernini.bsky.social on metabolites in Ra remission and flare #Eular2025

Join us with "big data and small molecules, novel in RA mechanisms" in room F1 #Eular2025

@bioconductor.bsky.social on Bluesky 🎓 Sharpen your RNA-seq skills at EuroBioC2025 Workshops! 📍 Barcelona | Bulk & Single-cell RNA-seq 📅 Sept 15–16 | Hands-on training 🎟️ Limited spots. Register now: eurobioc2025.bioconductor.org #Bioinformatics #EuroBioC2025

Interesting hands-on workshop

Absolutely love hearing Iain McInnes speak! Time to move away from rheumatology to IMIDology! #eular2025

Never seen a conference where they don't provide coffee to non-clinicians...we are human beings! 🤣🤣

#Eular #Eular2025 @eular.org

Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)

hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments | Molecular Systems Biology imageimagehu.MAP3.0 integrates mass spectrometry experiments to identify human protein complexes. Using this resource, this study characterizes covariation of complexes, identifies mutually exclusive ...

hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments #MolSystBiol #MassSpec www.embopress.org/doi/full/10....

We are sponsoring the Scottish Cell Biology Meeting on 18th Sept. Save the date!

A tissue-specific atlas of protein–protein associations enables prioritization of candidate disease genes - Nature Biotechnology Protein–protein interactions specific to 11 individual tissues are presented in a comprehensive resource.

Our work on deriving protein-protein (functional) associations across different human tissues from proteomics data is now published. There is quite a lot in this paper, so I will just touch on a few highlights:
www.nature.com/articles/s41...