Dom Somma

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...

Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification Guerin et al. present a highly resolved timeline of chromatin and DNA methylation dynamics during early neural progenitor cell differentiation. Their approach demonstrates that chromatin and DNA methylation mechanisms operate on different timescales to mediate short- and long-term gene enhancer regulation.

Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification

🧵5 Top Free Alternatives to BioRender for Scientific Illustrations!

These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.

Save and share the post!

Review @annualreviews.bsky.social @cincyresearch.bsky.social
Bidirectional Communication Between the Innate and Adaptive Immune Systems
www.annualreviews.org/content/jour...

After 10yrs @uofglasgow.bsky.social , I'm thrilled to start as Lecturer @unicatt.bsky.social + Senior Research Associate at Gemelli Hospital. Grateful for Glasgow's brilliant colleagues and delighted to stay connected as Honorary Lecturer. New chapter, but Glasgow isn’t a goodbye!
#AcademicJourney

Here's our take:
We LOVE ST ❤️. But we get the skepticism. Too often, spatial data is treated like single-cell data with coordinates slapped on. That's like buying lemons and forgetting to make lemonade!

👇 Here are 3 spatially-aware analyses to get the most out of your ST data:

Benchmarking computational methods for detecting spatial domains and domain-specific spatially variable genes from spatial transcriptomics data Abstract. Advances in spatially resolved transcriptomics (SRT) have led to the emergence of numerous computational methods for identifying spatial domains

🚨New benchmarking study!

Benchmarking computational methods for detecting spatial domains and domain-specific spatially variable genes from spatial transcriptomics data

#SpatialBiology #SpatialTranscriptomics #SpatialDomain #SpatiallyVariableGene #clustering 🧪

(1/9)

doi.org/10.1093/nar/...

Results

- No single method was found to be optimum under all conditions.

- GraphST, BayesSpace, SpaGCN, and STAGATE yielded more robust results.

- The methods performed best on 10X Visium datasets, but poorly on Slide-seqV2 and STARmap datasets.

(6/9)

Researchers used single-cell multi-omics to trace human blood vessel organoid development, revealing key fate decisions and gene networks. PMID:40250419, CELL 2025, @Cell https://doi.org/10.1016/j.cell.2025.03.037 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

Deep mutational scanning of RBP6 in Trypanosoma brucei identifies an essential disordered region rich in positive residues! Key for metacyclogenesis. #Trypanosoma PMID:39885181, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-025-56553-y

Discover cutting-edge scSPOT: a novel method using a 52-marker CyTOF panel to profile Treg function at the single-cell level. Unveil true immune dynamics! #ImmunologyRevolution PMID:39900891, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-024-55746-1

Researcher Reflections—Inspiring Paths in Academia The journey of early-career researchers (ECRs) in immunology is marked by many challenges but also exciting prospects. Here we bring a snapshot of the recent ECR workshop organized by the Young Europ...

Dive into career journeys of PIs in immunology, from mastering lab techniques, securing tenure, to navigating moves and balancing family with research🧗
Based on @yefis-immunology.bsky.social ECR workshop at #ECI2024
A must-read for aspiring immunologists and ECRs!👉 bit.ly/4fXeUkC