Ståhl Lab

Patrik Ståhl
Associate Professor, Principal Investigator, KTH

Research focus

We have a particular focus on spatially resolved technologies, and have propelled some of the recent international advances in the field, in particular in the context of spatial transcriptomics. We have an experimental approach to technology innovation, and are used to pushing currently known limits in our protocols.

Team members

Patrik Ståhl, associate professor, team leader, KTH
Lovisa Franzén, industrial PhD student, AstraZeneca / KTH
Margherita Zamboni, postdoc researcher
Nayanika Bhalla, PhD student, KTH

Key publications

Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium
Vickovic S, Schapiro D, Carlberg K, Lötstedt B, Larsson L, Hildebrandt F, Korotkova M, Hensvold AH, Catrina AI, Sorger PK, Malmström V, Regev A, Ståhl PL
Communications Biology (11 Feb 2022)

Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin
Bäckdahl J, Franzén L, Massier L, Li Q, Jalkanen J, Gao H, Andersson A, Bhalla N, Thorell A, Rydén M, Ståhl PL, Mejhert N
Cell Metab. 2021 Sep 7;33(9):1869-1882.e6. doi: 10.1016/j.cmet.2021.07.018. PMID: 34380013

Identification and transfer of spatial transcriptomics signatures for cancer diagnosis
Yoosuf N, Navarro JF, Salmén F, Ståhl PL, Daub CO
Breast Cancer Res. 2020 Jan 13;22(1):6. doi: 10.1186/s13058-019-1242-9. PMID: 31931856; PMCID: PMC6958738

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart
Asp M, Giacomello S, Larsson L, Wu C, Fürth D, Qian X, Wärdell E, Custodio J, Reimegård J, Salmén F, Österholm C, Ståhl PL, Sundström E, Åkesson E, Bergmann O, Bienko M, Månsson-Broberg A, Nilsson M, Sylvén C, Lundeberg J
Cell, 2019 Dec 12;179(7):1647-1660.e19. doi: 10.1016/j.cell.2019.11.025. PMID: 31835037

Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics
Carlberg K, Korotkova M, Larsson L, Catrina AI, Ståhl PL*, Malmström V*
Sci Rep. 2019 Dec 12;9(1):18975. doi: 10.1038/s41598-019-55441-y. PMID: 31831833; PMCID: PMC6908624

Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
Hård J, Al Hakim E, Kindblom M, Björklund ÅK, Sennblad B, Demirci I, Paterlini M, Reu P, Borgström E, Ståhl PL, Michaelsson J, Mold JE, Frisén J.
Genome Biol. 2019 Apr 1;20(1):68. doi: 10.1186/s13059-019-1673-8. PMID: 30935387; PMCID: PMC6444814

Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors
Salmén F, Vickovic S, Larsson L, Stenbeck L, Vallon-Christersson J, Ehinger A, Häkkinen J, Borg Å, Frisén J, Ståhl PL and Lundeberg J
Available at bioRxiv

High-density spatial transcriptomics arrays for in situ tissue profiling
Vickovic S*, Eraslan G, Salmén F, Klughammer J, Stenbeck L, Äijö T, Bonneau R, Bergenstråhle L, Fernandéz Navarro J, Gould J, Ronaghi M, Frisén J, Lundeberg J*, Regev A, Ståhl PL
Nature Methods (2019)

ST Viewer: A tool for analysis and visualization of Spatial Transcriptomics datasets
Fernández Navarro J*, Lundeberg J and Ståhl PL
Bioinformatics (2019)

Barcoded solid phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections
Salmén F†, Ståhl PL†*, Mollbrink A, Fernández Navarro J, Vickovic S, Frisén J & Lundeberg J*
Nature Protocols (2018)

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
Berglund E, Maaskola J, Schultz N, Friedrich S, Marklund M, Bergenstråhle J, Tarish F, Tanoglidi A, Vickovic S, Larsson L, Salmeń F, Ogris C, Wallenborg K, Lagergren J, Ståhl PL, Sonnhammer E, Helleday T*, Lundeberg J*
Nature Communications (2018)

ST Spot Detector: a web-based application for automatic spot and tissue detection for Spatial Transcriptomics image data sets
Wong K†, Navarro JF†*, Bergenstråhle L, Ståhl PL, Lundeberg J
Bioinformatics (2018)

Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
Asp M, Salmén F†, Ståhl PL†, Vickovic S†, Felldin U, Löfling M, Navarro JF, Maaskola J, Eriksson MJ, Persson B, Corbascio M, Persson H, Linde C, Lundeberg J*
Scientific Reports (2017)

ST Pipeline: an automated pipeline for spatial mapping of unique transcripts
Navarro J F*, Sjöstrand J, Salmén F, Lundeberg J, Ståhl PL
Bioinformatics (2017)

An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
Jemt A, Salmén F, Lundmark A, Mollbrink A, Fernández Navarro J, Ståhl PL, Tülay YL, Lundeberg J
Scientific Reports (2016)

Massive and parallel expression profiling using microarrayed single-cell sequencing
Vickovic S, Ståhl PL, Salmén F, Giatrelis S, Westholm JO, Mollbrink A, Fernández Navarro J, Custodio J, Bienko M, Sutton LA, Rosenquist R, Frisén J, Lundeberg J*
Nature Communications (2016)

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
Ståhl PL†, Salmén F†, Vickovic S, Lundmark A, Fernández Navarro J, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, PI Costea, Sahlén P, Mulder J, Bergmann O, Lundeberg J*, Frisén J
Science (2016)

* Corresponding author
† Authors contributed equally