Sign in

Dom Somma

@dom-somma.bsky.social
164 followers 221 following 28 posts

Molecular Immunologist, Lecturer/Senior Research Associate at Univ. Cattolica in Rome/Gemelli Hospital. Honorary Lecturer at Univ. of Glasgow. #scRNAseq #immunology #molecular #MyelidCells #nanopore #SpatialTransriptomics

PostsRepliesMedia
Reposted by Dom Somma
Yeqing Lin @yeqinglin.bsky.social · 08/05/2026
Introducing Genie 3, a generative protein model that substantially advances the state-of-the-art for binder design, increasing in silico success rates by up to 20x on hard multimeric targets. It also debuts a form of inference-time scaling unobserved in other design models. 🧵1/8
25716
Dom Somma @dom-somma.bsky.social · 13/05/2026
bsky.app
@lauradol4.bsky.social on Bluesky
Love this! #philsky #academicsky
000
Reposted by Dom Somma
Laura D'Olimpio @lauradol4.bsky.social · 10/05/2026
Love this! #philsky #academicsky
18626
Reposted by Dom Somma
Nikolai Slavov @slavov-n.bsky.social · 12/05/2026
The final version of our @annualreviews.bsky.social article is now published OA: www.annualreviews.org/content/jour...
annualreviews.org
Single-Cell Proteomic Technologies: Tools in the Quest for Principles
Over the last decade, proteomics analysis of single cells by mass spectrometry transitioned from an uncertain possibility to a set of robust and rapidly advancing technologies supporting the accurate ...
0179
Dom Somma @dom-somma.bsky.social · 10/04/2026
Interesting #10XGenomics #Flex #scRNAseq #bias
bsky.app
@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
000
Reposted by Dom Somma
Johan Duchêne @johanduchene.bsky.social · 10/04/2026
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...
biorxiv.org
0105
Reposted by Dom Somma
bioRxiv Immunology @biorxiv-immuno.bsky.social · 27/01/2026
A single-cell atlas of intestinal immune cells across the day-night cycle reveals dynamic populations www.biorxiv.org/content/10.64898/20…
021
Dom Somma @dom-somma.bsky.social · 20/01/2026
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
182
Dom Somma @dom-somma.bsky.social · 07/01/2026
#biology #assay cell migration
bsky.app
@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
010
Reposted by Dom Somma
Denis Wirtz @deniswirtz.bsky.social · 18/12/2025
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...
17337
Reposted by Dom Somma
Julia Sero @cellmorphosero.bsky.social · 04/12/2025
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
youtu.be
Introduction to CellProfiler - by a biologist, for biologists!
YouTube video by CellMorphoJSero
48433
Reposted by Dom Somma
Hao Yin @haoyin.bsky.social · 12/12/2025
#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...
0228
Reposted by Dom Somma
Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🗨️ 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)
26436
Reposted by Dom Somma
Nikolai Slavov @slavov-n.bsky.social · 12/11/2025
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.
282
Reposted by Dom Somma
Albert Vilella, PhD. @albertvilella.bsky.social · 09/09/2025
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...
1143
Reposted by Dom Somma
British Society for Immunology @britsocimm.bsky.social · 09/09/2025
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
001
Reposted by Dom Somma
Jacob Schreiber @jmschreiber91.bsky.social · 14/05/2025
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...
nature.com
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...
1172
Dom Somma @dom-somma.bsky.social · 14/06/2025
Well done everyone!! See you next year #Eular2025
030
Reposted by Dom Somma
Genes & Diseases Journal @genesndiseases.bsky.social · 13/06/2025
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
001
Dom Somma @dom-somma.bsky.social · 14/06/2025
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
051
Dom Somma @dom-somma.bsky.social · 13/06/2025
How to use multimodal datasets with #AI to make decision for patient treatment in #RA remission@stealivernini.bsky.social #Eular25
032
Reposted by Dom Somma
Shicheng Guo @shihcheng.bsky.social · 13/06/2025
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 doi.org/10.1038/s41467-025-59621-5 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
doi.org
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
032
Reposted by Dom Somma
10x Genomics @10xgenomics.bsky.social · 13/06/2025
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
042
Dom Somma @dom-somma.bsky.social · 13/06/2025
Another great talk from @laviac.bsky.social on Tenosynovium differences in pre-clinical RA #Eular2025
062
Dom Somma @dom-somma.bsky.social · 13/06/2025
Amazing presentation from @stealivernini.bsky.social on metabolites in Ra remission and flare #Eular2025
073
Dom Somma @dom-somma.bsky.social · 13/06/2025
Join us with "big data and small molecules, novel in RA mechanisms" in room F1 #Eular2025
030
Dom Somma @dom-somma.bsky.social · 13/06/2025
Interesting hands-on workshop
bsky.app
@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
000
Reposted by Dom Somma
Dr Simon Stones @simonrstones.bsky.social · 12/06/2025
Absolutely love hearing Iain McInnes speak! Time to move away from rheumatology to IMIDology! #eular2025
031
Dom Somma @dom-somma.bsky.social · 12/06/2025
Never seen a conference where they don't provide coffee to non-clinicians...we are human beings! 🤣🤣 #Eular #Eular2025 @eular.org
130
Reposted by Dom Somma
Gherman Novakovsky @gnovakovsky.bsky.social · 30/05/2025
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/)
15921
Reposted by Dom Somma
BioMassSpec @realbiomassspec.bsky.social · 28/05/2025
hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments #MolSystBiol #MassSpec www.embopress.org/doi/full/10....
embopress.org
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 ...
0128
Reposted by Dom Somma
British Society for Cell Biology @bscb-official.bsky.social · 15/04/2025
We are sponsoring the Scottish Cell Biology Meeting on 18th Sept. Save the date!
0109
Reposted by Dom Somma
Pedro Beltrao @pedrobeltrao.bsky.social · 02/05/2025
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...
nature.com
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.
313451
Reposted by Dom Somma
Cell Reports @cp-cellreports.bsky.social · 14/05/2025
Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification
dlvr.it
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.
0127
Reposted by Dom Somma
Rafeeque Mavoor @rafeequemavoor.bsky.social · 13/05/2025
🧵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!
32679350
Reposted by Dom Somma
Waggoner Lab @labwaggoner.bsky.social · 26/04/2025
Review @annualreviews.bsky.social @cincyresearch.bsky.social Bidirectional Communication Between the Innate and Adaptive Immune Systems www.annualreviews.org/content/jour...
0103
Dom Somma @dom-somma.bsky.social · 24/04/2025
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
130
Reposted by Dom Somma
Azura Biosciences @azurabio.bsky.social · 11/04/2025
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:
101
Reposted by Dom Somma
Tamim Ahsan @tamim-ahsan.bsky.social · 21/04/2025
🚨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/...
doi.org
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
101
Reposted by Dom Somma
Tamim Ahsan @tamim-ahsan.bsky.social · 21/04/2025
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)
111
Reposted by Dom Somma
Shicheng Guo @shihcheng.bsky.social · 23/04/2025
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 doi.org/10.1016/j.cell.2025.03.037 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
doi.org
Redirecting
No description available
011
Reposted by Dom Somma
Shicheng Guo @shihcheng.bsky.social · 10/02/2025
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 doi.org/10.1038/s41467-025-56553-y
001
Reposted by Dom Somma
Shicheng Guo @shihcheng.bsky.social · 10/02/2025
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 doi.org/10.1038/s41467-024-55746-1
001
Reposted by Dom Somma
European Journal of Immunology @eurjimmunol.bsky.social · 15/01/2025
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
bit.ly
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...
11212
Reposted by Dom Somma
@PhysGenCenter @physgencenter.bsky.social · 14/01/2025
There’s a lot to unpack in our recent Science Advances paper - come check it out! Here’s a thread on what we found. #chromatin #genomics #biophotonics #dna #epigenetics #imaging #northwestern #science #biology #aging #longevity #biomedicine #cpge www.science.org/doi/10.1126/...
science.org
Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system
Gene transcription is an emergent phenomenon of packing domain geometry in situ.
11911
Reposted by Dom Somma
Matthew Sinton 🏳️‍🌈 @mcsinton.bsky.social · 14/01/2025
Delighted to have had the opportunity to write this spotlight with @juanquintana.bsky.social and the lab, on the recent @lydialynch.bsky.social paper, showing rhythmicity of IL-17 expression in adipose! Fascinating paper, which raises loads of cool questions #immunosky www.cell.com/immunity/ful...
cell.com
Interleukin-17 and fat: Timing is everything
Interleukin-17 plays a major role in controlling adipose tissue homeostasis. In a recent study published in Nature, Douglas et al. demonstrate that time-of-day-dependent expression of interleukin-17 b...
59725
Reposted by Dom Somma
Slavov Laboratory @slavovlab.bsky.social · 13/01/2025
The X and Y chromosomes each encodes homologous RNA helicases, DDX3X & DDX3Y. They negatively cross-regulate each other via mRNA destabilization. ◼️ This buffers the protein levels of DDX3X and DDX3Y. genome.cshlp.org/content/earl...
genome.cshlp.org
Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
082
Reposted by Dom Somma
Shicheng Guo @shihcheng.bsky.social · 13/01/2025
Discover how #metabolism shapes protein #PTMs! Unveil the intricate dance of modifications & feedback loops that regulate cellular functions. Dive into the 'modification of a modification' phenomenon! #science PMID:39775169, Nat Chem Biol 2025, @nchembio
buff.ly
Mechanisms of metabolism-coupled protein modifications
This Perspective highlights how metabolic states regulate diverse protein modifications that affect physiology. In addition, the roles of subcellular localization of metabolic enzymes and the importance...
031
Dom Somma @dom-somma.bsky.social · 20/12/2024
That's all for this year! Have a nice break! #LabLife #HappyHolidays
000
Reposted by Dom Somma
Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 17/12/2024
Checkout out these two bombshell papers from @possuhuanglab.bsky.social @stanfordmedicine.bsky.social, computational design of antigen-specific binders to MHC-I or -II, with applications to next gen targeted therapeutics 🤯
08922