We are the Spatial Research lab – Welcome!
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.
Image: Ludvig Larsson, Natalie Stakenborg, Joakim Lundeberg and Guy Boeckxstaens
NEWS
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.
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. PhD student Alma Andersson 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: https://github.com/almaan/sepal.
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.
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.
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
Jonas Frisén
Professor
Karolinska Institutet,
Biomedicum B6,
Solnavägen 9,
171 65 Solna, Sweden
jonas.frisen@ki.se
Annelie Mollbrink
Lab manager, 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
spatialtranscriptomics@scilifelab.se
Patrik Ståhl
Assistant 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
Stefania Giacomello
Team Leader, 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
Human Developmental
Cell Atlas (HDCA)
Paulo Czarnewski, PhD
Scientific coordinator
HDCA Sweden website
hdca-sweden@scilifelab.se
