JAN 11TH 2024

WRAPPING UP 2023. As we bid farewell to 2023, we reflect on a year packed with scientific achievements from our research collective. First and foremost we are extremely proud of our fantastic colleagues who successfully earned their Ph.D. degrees – Ludvig L, Zaneta, and Franziska. We are also thrilled about the scientific article output coming from our collective, covering a total of about 20 publications and eight pre-prints. To highlight a few, we started off the year with the presentation of the spatial ATAC methodology (Nat Biotechnology) and quickly followed up with the publication of the RNA-Rescue Spatial Transcriptomics method (Nat Communications). Later in the year, our hard work to demonstrate Expansion Spatial Transcriptomics (Nat Methods) and Spatial Multimodal Analysis (Nat Biotechnology) were published. During the autumn-winter our articles describing novel methods and tools also saw the light of day: Miniature spatial transcriptomics (Nat Communications), semla: a toolkit for Visium data analysis (Bioinformatics), Dual spatial transcriptomics of host and pathogens in SARS-CoV-2 lungs (Genome Biology), Spatial meta-transcriptomics (Nat Biotechnology), and Spatial VDJ (Science).

Here’s to a successful 2023 and continued scientific advances in 2024! 🎉

JUN 22ND 2023

CELEBRATING A FRUITFUL SPRING. The summer is here in Stockholm and we celebrate the eventful spring that has given us several fantastic publications and a new doctor in the team – congratulations Dr. Ludvig Larsson for successfully defending your thesis on May 26th! 🥳

Today, our most recent article was published in Nature Methods: “Expansion spatial transcriptomics“, where our collaboration with Bo Wang’s group at Stanford University led to the development of a new method based on the combination of expansion microscopy and spatial transcriptomics in order to enhance the spatial resolution of Visium

JAN 31ST 2023

STARTING 2023 WITH NEW PUBLICATIONS. We greet the new year with a new publication in Nature Communications: “Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples“. In this article, we present a modified protocol for Visium in order to improve the mRNA recovery from more challenging fresh frozen samples, an approach we call RNA-Rescue Spatial Transcriptomics (RRST) ⛑️.

In addition, we also have a new pre-print available on bioRxiv where we demonstrate combined use of Visium, to capture mRNA, and mass spectrometry imaging, to capture metabolites, on the same tissue section: “Spatial Multimodal Analysis of Transcriptomes and Metabolomes in Tissues

AUG 10TH 2022

SPATIAL CNV IN CANCER. Today, our newest publication “Spatially resolved clonal copy number alterations in benign and malignant tissue” is out it Nature! In this study, Mengxiao, Emelie, and many others from our group, embarked on a mission with our fantastic collaborators to chart the spatially resolved copy number variation in a vast number of tissue biopsies from malignant and benign tumors. Here, we demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and in nearby benign tissue using an organ-wide approach focused on the prostate, suggesting a model for how genomic instability arises in histologically benign tissue that may represent early events in cancer evolution.

Check out the paper here!

JAN 12TH 2022

A NEW YEAR OF SCIENCE. It is a brand new year and surely 2022 will deliver as much exciting science as last year did! Our Spatial Research group (AKA the “ST Collective”) was as busy as ever during 2021; Three PhD dissertations (congrats to Joseph, Konstantin, and Linda!) and more than fifteen publications and preprint. Now we look forward to a new year full of spatially resolved science!

MAR 11TH 2021

NEW PUBLICATION. Alma has developed a new tool, sepal, for identification of spatial patterns in spatial transcriptomics datasets. Th full details of the method and examples of its uses can be found in the publication “sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling” (Oxford Bioinformatics), and the code and installation details for the python package are all available on github:

The full article can be read here.

JAN 8TH 2021

SPATIAL RNA INTEGRITY NUMBER. Linda Kvastad, Ph.D student, has published her latest technical article where she and colleagues has managed to spatially measure the RNA integrity number (RIN) in a tissue section. They demonstrate the use of sRIN to identify spatial variation in tissue quality prior to more comprehensive spatial transcriptomics workflows. The article “The spatial RNA integrity number assay for in situ evaluation of transcriptome quality” was published in Communication Biology.

The full article can be read here.

JAN 6TH 2021

METHOD OF THE YEAR 2020! Nature has announced that the Method of the Year 2020 is no other than Spatially Resolved Transcriptomics! Ludvig Larsson, Jonas Frisén, and Joakim Lundeberg were given the honour of publishing their commentary “Spatially resolved transcriptomics adds a new dimension to genomics” as experts on this subject.

Read the Nature article here.

OCT 9TH 2020

NEW PUBLICATIONS.  Our research group has been very productive during 2020 and had more articles published within the last than ever. Among the latest articles published are “Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease”, a collaboration with the VIB-KU Leuven Center for Brain & Disease Research, published in Cell 20th of August. Most recently, PhD student Alma Andersson had her paper “Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography” published (Communications Biology) which described Stereoscope, a novel tool for inferring scRNA-seq data on spatial transcriptomics data.

JULY 25TH 2020

SPATIAL GENE EXPRESSION IN FFPE TISSUE. The much anticipated protocol for performing Spatial Transcriptomics using formalin fixed paraffin embedded (FFPE) tissue is now available as a preprint: “Genome-wide Spatial Expression Profiling in FFPE Tissues”. This work was led by PhD student Eva Gracia Villacampa, and together with other members of our group, they were able generate high quality data from clinical FFPE samples after much hard work and tedious protocol optimisations. We hope this new approach will open up for the use of ST on the large clinical biobanks of FFPE tissues!

Read the full bioRxiv preprint here.

JULY 14TH 2020

STUTILITY: A NEW R PACKAGE FOR ST/VISIUM DATA ANALYSIS. The R package we have all been waiting for when it comes to analysis of spatial transcriptomics (ST, Visium) data is finally here! In this package called STUtility, Ludvig Larsson and Joseph Bergenstråhle have built upon Satija lab’s Seurat toolkit to enable visualisation and user-friendly handling of ST data. Starting from count matrices and tissue images, you can now perform quality control, normalisation, dimensionality reduction, factor analysis, and much more, all covered within the STUtility framework. Awesome, right?

Read their fresh publication, Seamless integration of image and molecular analysis for spatial transcriptomics workflows, for more information.

JUNE 23-26TH 2020

THREE NEW PUBLICATIONS. The Swedish summer is here and June continues to deliver; we are happy to see three more articles from our group published between 23-26th of June. First out was a fantastic work on squamous cell carcinoma, a research project born from a collaboration between members of the Lundeberg group and Stanford University, and now published in Cell. It was followed by another collaborative project where deep learning was applied to breast tumour spatial transcriptomics data (Nature biomedical engineering). Lastly, the preprint “Molecular Atlas Of The Adult Mouse Brain” has now made its way to be a peer-reviewed publication in Science advances. We are thankful to all the involved people making these publications possible and look forward to more great research being published in the future!

All publications can be viewed under Resources / Publications.

JUNE 5TH 2020

CONGRATULATIONS DR. BERGLUND! Emelie Berglund successfully defended her thesis with the title “Molecular and Spatial Profiling of Prostate Tumors” on June 5th. We are all proud of her great achievement and wish her all the best in her future endeavours!

Her thesis can be read online here and a list of the publications she has authored can be found here.

MAY 4TH 2020

NEW REVIEW OUT. “Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration” is new review article written by our own Michaela, Joseph, and Joakim! In this publication you can read about the different spatially resolved transcriptomics technologies available as of today, how they compare against each other, and what we may expect from the future.

Read the review here.

APR 29TH 2020

SPATIALCPIE FOR ST ANALYSIS. “SpatialCPie” is a new R/Bioconductor package, developed by Joseph and Ludvig Bergenstråhle, which can be used for visualization of clusters at multiple resolutions and proportions for your spatial transcriptomics data. Read more about the tool on GitHub, Bioconductor, or the BMC Genomics publication “SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation”.

The full open access article can be read here.

APR 15TH 2020

PUBLICATION ALERT! Today you can read about “Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues” in BMC Genomics. If you are interested in automating you spatial transcriptomics library prep pipeline then Emelie, Sami, and the other co-authors have it all figured out for you!

The full publication can be read here.

FEB 23-26TH 2020

MEET US AT AGBT! Our group will be present at the Advances in Genome Biology and Technology (AGBT) 2020 conference on Marco Island, Florida. Check out the posters presented by Alma (#901), Lovisa (#7001), Linnea (#6008), Kim (#610), and Joseph (#110)! #AGBT20

Visit the AGBT website for more information about the conference.

DEC 12TH 2019

NEW PUBLICATION OUT IN CELL! ✨ After much hard work, Michaela Asp’s and Stefania Giacomello’s article “A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart” is now in print! Together with co-authors Ludvig Larsson and others, they have mapped the cellular organisation of the developing human heart. We hope this will be a great resource for many researchers who wish to explore the heart development. ❤️

The full article can be read here.

SPATIAL TRANSCRIPTOMICS IN RHEUMATOID ARTHRITIS. Today is a great day – our group did not only get one article published, but two! Konstantin Carlberg, PhD student, has worked together with Vivianne Malmström and her group at Karolinska Institutet to study the spatial signatures of inflammation in arthritic joints. The article entitled “Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics” was published in Scientific Reports.

SEP 27TH 2019

MOLECULAR ATLAS OF THE ADULT MOUSE BRAIN. A pre-print of Jose Fernandez Navarro’s fantastic work together with members from Dinos Meletis‘ group is now available on bioRxiv.

SEP 24-26TH 2019

SINGLE CELL GENOMICS CONFERENCE IN STOCKHOLM. Several people in our research group attended the SCG conference at Djurönäset in Stockholm. Our own Emelie Berglund was one of the speakers!

SEP 9TH 2019

NEW PUBLICATION OUT IN NATURE METHODS. Our article “High-definition spatial transcriptomics for in situ tissue profiling” is out in Nature Methods! Read about the new 2-μm resolution spatial arrays by following the link.

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Our news updates started in September 2019.

Please go to the Publication page for a list of all our published articles,
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