Mats Nilsson's Lab @nilssonlab.org

🔬🧬🔍 If you're interested in spatial omics and miRNAs, don’t miss our latest review!

We explore where the early field of spatial miRNomics stands, what’s missing, and why incorporating miRNAs matters for building richer spatial transcriptomic maps.

#SpatialOmics #miRNA #GeneRegulation

27.07.2025 12:07 — 👍 5 🔁 2 💬 0 📌 0

In Situ Inference of Copy Number Variations in Image-Based Spatial Transcriptomics Copy number variations (CNVs) drive cancer progression. So far, spatial CNV inference has relied on whole transcriptome-based sequencing technologies. However, advances in image‐based spatial transcriptomics (iST) now enable high-plex gene measurement in situ. Here, we introduce an approach that adapts CNV inference to iST data, enabling spatial mapping of malignant clones and the tumor microenvironment, at single-cell resolution. Additionally, we assess how panel size and detection efficiency influence CNV inference. ### Competing Interest Statement S.M.S is co-founder of spatialist AB, a spatial omics consultancy company. H.H. is co-founder and Chief Scientific Officer of Omniscope, a Scientific Advisory Board member at Nanostring/Bruker and Mirxes, a consultant for Moderna and Singularity, and has received honoraria from Genentech. M.N. is co-founder of VoxlBio AB, a spatial omics reagents company. Swedish Research Council, https://ror.org/03zttf063, 2024-02533 Cancerfonden, 24-3457 Horizon Europe Mission on Cancer, 101136552 Swiss National Science Foundation, 222136 MCIN/AEI/10.13039/501100011033 and FSE+, RYC2022-035848-I MICIU/AEI/10.13039/501100011033/ FEDER/UE, PID2023-148687OB-I00 European Unions H2020 research and innovation program, 848028 European Research Council (ERC), 810287 Ministerio de Ciencia e Innovación (MCI), PID2020-115439GB-I00, PLEC2021-007654 LaCaixa Foundation, HR22-0031, HR22-0172 Generalitat de Catalunya through the Suport Grups de Recerca AGAUR, 2021-SGR ERA-NET Neuron/Ministerio de Ciencia e Innovación (MCI), PCI2022-133012 ASPIRE Award from The Mark Foundation for Cancer Research Scientific Foundation of the Spanish Association Against Cancer U-CAN Erling Persson Foundation

Our latest work is now live on bioRxiv! We use copy number variation inference to uncover tumor clonality from imaging-based spatial transcriptomics data. Check it out: doi.org/10.1101/2025...

08.07.2025 11:25 — 👍 5 🔁 4 💬 0 📌 1

Recent work led by our great @sergiomarcosalas.bsky.social, highlighting best practices and critical considerations when analyzing and interpreting @10xgenomics.bsky.social Xenium datasets.

18.03.2025 08:08 — 👍 6 🔁 0 💬 0 📌 0

A study from @sergiomarcosalas.bsky.social @nilssonlab.org and colleagues presents a comprehensive evaluation of Xenium in situ datasets and provides recommendations on analysis workflows. @scilifelab.se

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

13.03.2025 18:54 — 👍 21 🔁 13 💬 0 📌 1

Evolutionary convergence of sensory circuits in the pallium of amniotes The amniote pallium contains sensory circuits that are structurally and functionally equivalent, yet their evolutionary relationship remains unresolved. We used birthdating analysis, single-cell RNA a...

New paper alert! Led by the great Fernando Garcia Moreno, our lab's first venture into evolutionary developmental biology is out on @science.org
www.science.org/doi/10.1126/...

14.02.2025 12:58 — 👍 8 🔁 1 💬 0 📌 0

@agustinrobles.bsky.social writes here on the many reasons why spatial omics assays will need to integrate miRNAs.

08.02.2025 19:43 — 👍 3 🔁 0 💬 0 📌 0

Colorful dots on the ceiling as we celebrated Anastasia Magoulopoulou's defense last month, "Dissecting molecular signatures using padlock probes for deciphering pathological states".

04.02.2025 08:46 — 👍 3 🔁 0 💬 0 📌 0

A very elegant Dr. Erik Samuelsson celebrating the successful defense of his PhD dissertation "The Definition and Applications of Transcriptomic States in Cancer"!

19.12.2024 17:05 — 👍 4 🔁 0 💬 0 📌 0

a cartoon of a man looking out a window at the stars ALT: a cartoon of a man looking out a window at the stars

Hello world. Our lab has a new home here on Bluesky! We will post about spatial omics, science, nice papers and lab activities. The account will be collectively managed by lab members. Happy spatial-omics everyone!

12.12.2024 16:24 — 👍 5 🔁 1 💬 1 📌 0

Mats Nilsson's Lab

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