@agustinrobles.bsky.social writes here on the many reasons why spatial omics assays will need to integrate miRNAs.
🔬🧬🔍 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
Recent work led by our great @sergiomarcosalas.bsky.social, highlighting best practices and critical considerations when analyzing and interpreting @10xgenomics.bsky.social Xenium datasets.
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...
Colorful dots on the ceiling as we celebrated Anastasia Magoulopoulou's defense last month, "Dissecting molecular signatures using padlock probes for deciphering pathological states".
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
"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...
🧬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...
New online! Spatial miRNomics: towards the integration of microRNAs in spatial biology
New work from our @mgrillo.bsky.social with @lgmartelotto.bsky.social and others. Capture somatic mutations in single-cell assays via RNA-targeted gap filling. Check it out!
This study presents a comprehensive evaluation of Xenium In Situ datasets and provides recommendations on analysis workflows.
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…
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...
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/...
Mats Nilsson's Lab
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
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...
Do you work with a strange model species and are frustrated by the lack of antibodies for immunos? Here's a web app that does some computational pre-screening for you.
sixpack-abscan.serve.scilifelab.se
