Mats Nilsson's Lab
@nilssonlab.org
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9 posts
Mats Nilsson's team at Stockholm University and Scilifelab, researching molecular diagnostics and in-situ spatial transcriptomics
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Mats Nilsson's Lab
@nilssonlab.org
· Jul 27
Mats Nilsson's Lab
@nilssonlab.org
· Jul 8
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
doi.org
Reposted by Mats Nilsson's Lab
Mats Nilsson's Lab
@nilssonlab.org
· Feb 14
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...
www.science.org
Mats Nilsson's Lab
@nilssonlab.org
· Feb 8
