Mats Nilsson's Lab
@nilssonlab.org
Mats Nilsson's team at Stockholm University and Scilifelab, researching molecular diagnostics and in-situ spatial transcriptomics
We're looking for a PhD student!
Join the team to develop new technologies for targeted spatial omics.
More info and instruction on how to apply at the following link:
su.varbi.com/what:job/job...
Join the team to develop new technologies for targeted spatial omics.
More info and instruction on how to apply at the following link:
su.varbi.com/what:job/job...
Doktorand i biokemi
Institutionen för biokemi och biofysik. SciLifeLab ( SciLifeLab ) är ett nationellt center för molekylära biovetenskaper med fokus på forskning inom hälsa och miljö. Centret kombinerar ledande
su.varbi.com
September 15, 2025 at 6:36 PM
We're looking for a PhD student!
Join the team to develop new technologies for targeted spatial omics.
More info and instruction on how to apply at the following link:
su.varbi.com/what:job/job...
Join the team to develop new technologies for targeted spatial omics.
More info and instruction on how to apply at the following link:
su.varbi.com/what:job/job...
🔬🧬🔍 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
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
"Spatially resolved microRNA expression in tissues: technologies, challenges, and opportunities"
by Agustín Robles-Remacho et al
"Recent pioneering studies demonstrate the potential of spatial miRNA profiling for translational and clinical research."
Read here:
authors.elsevier.com/sd/article/S...
by Agustín Robles-Remacho et al
"Recent pioneering studies demonstrate the potential of spatial miRNA profiling for translational and clinical research."
Read here:
authors.elsevier.com/sd/article/S...
July 27, 2025 at 12:07 PM
🔬🧬🔍 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
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
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...
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
July 8, 2025 at 11:25 AM
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...
Recent work led by our great @sergiomarcosalas.bsky.social, highlighting best practices and critical considerations when analyzing and interpreting @10xgenomics.bsky.social Xenium datasets.
🧬If you work with @10xgenomics.bsky.social Xenium, this might be of your interest.
Our new study on Xenium exploration best practice and comparing it with other commercial platforms is now out in @naturemethods.bsky.social
www.nature.com/articles/s41...
Our new study on Xenium exploration best practice and comparing it with other commercial platforms is now out in @naturemethods.bsky.social
www.nature.com/articles/s41...
Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows - Nature Methods
This study presents a comprehensive evaluation of Xenium In Situ datasets and provides recommendations on analysis workflows.
www.nature.com
March 18, 2025 at 8:08 AM
Recent work led by our great @sergiomarcosalas.bsky.social, highlighting best practices and critical considerations when analyzing and interpreting @10xgenomics.bsky.social Xenium datasets.
Reposted by Mats Nilsson's Lab
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...
www.nature.com/articles/s41...
March 13, 2025 at 6:54 PM
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...
www.nature.com/articles/s41...
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/...
www.science.org/doi/10.1126/...
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
February 14, 2025 at 12:58 PM
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/...
www.science.org/doi/10.1126/...
@agustinrobles.bsky.social writes here on the many reasons why spatial omics assays will need to integrate miRNAs.
New online! Spatial miRNomics: towards the integration of microRNAs in spatial biology
Spatial miRNomics: towards the integration of microRNAs in spatial biology
Nature Reviews Genetics, Published online: 06 February 2025; doi:10.1038/s41576-025-00819-0In this Comment, Agustín Robles-Remacho and Mats Nilsson highlight the opportunities and challenges of using spatial transcriptomics to detect and localize…
www.nature.com
February 8, 2025 at 7:43 PM
@agustinrobles.bsky.social writes here on the many reasons why spatial omics assays will need to integrate miRNAs.
Colorful dots on the ceiling as we celebrated Anastasia Magoulopoulou's defense last month, "Dissecting molecular signatures using padlock probes for deciphering pathological states".
February 4, 2025 at 8:46 AM
Colorful dots on the ceiling as we celebrated Anastasia Magoulopoulou's defense last month, "Dissecting molecular signatures using padlock probes for deciphering pathological states".
A very elegant Dr. Erik Samuelsson celebrating the successful defense of his PhD dissertation "The Definition and Applications of Transcriptomic States in Cancer"!
December 19, 2024 at 5:05 PM
A very elegant Dr. Erik Samuelsson celebrating the successful defense of his PhD dissertation "The Definition and Applications of Transcriptomic States in Cancer"!
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!
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
media.tenor.com
December 12, 2024 at 4:24 PM
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!