Welcome to the Spatial Research lab!
Our research focuses on developing innovative experimental methods as well as novel computational tools for spatially resolved omics in mammalian and plant tissue sections.
You can find out more about our team and our academic research activities under the Research section.
NEWS
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.
Contact
Joakim Lundeberg
Professor
Science for Life Laboratory
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health, Dept. of Gene Technology
Tomtebodavägen 23 A
171 65 Solna, Sweden
joakim.lundeberg@scilifelab.se
Stefania Giacomello
Associate Professor, Ph.D
Science for Life Laboratory
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health, Dept. of Gene Technology
Tomtebodavägen 23 A
171 65 Solna, Sweden
stefania.giacomello@scilifelab.se
Patrik Ståhl
Associate Professor, Ph.D
Science for Life Laboratory
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health, Dept. of Gene Technology
Tomtebodavägen 23 A
171 65 Solna, Sweden
patrik.stahl@scilifelab.se
Jonas Frisén
Professor
Karolinska Institutet,
Biomedicum B6,
Solnavägen 9,
171 65 Solna, Sweden
jonas.frisen@ki.se
