Ståhl Lab

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Team members

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Key publications

Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue
Jutta Jalkanen, Jiawei Zhong, Pamela A Nono Nankam, Nayanika Bhalla, Merve Elmastas, Jiaxin Luo, Sophie Weinbrenner, Scott Frendo-Cumbo, Benedek Pesti, William Gourash, Anita Courcoulas, Zinger Yang Loureiro, Arne Dietrich, Jesper Bäckdahl, Anders Thorell, Marcus Buggert, Joanna Kalucka, Margo P Emont, Evan D Rosen, Matthias Blüher, Peter Kovacs, Patrik L Ståhl, Lucas Massier, Mikael Rydén, Niklas Mejhert
Cell Metabolism (3 February 2026)

Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies
Eleanor C. Williams, Lovisa Franzén, Martina Olsson Lindvall, Gregory Hamm, Steven Oag, Muntasir Mamun Majumder, James Denholm, Azam Hamidinekoo, Javier Escudero Morlanes, Marco Vicari, Joakim Lundeberg, Laura Setyo, Trevor M. Godfrey, Livia S. Eberlin, Aleksandr Zakirov, Jorrit J. Hornberg, Marianna Stamou, Patrik L. Ståhl, Anna Ollerstam, Jennifer Y. Tan, Irina Mohorianu
Nature Communications (7 January 2026)

Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction
Simon K. Dahlberg, David Fernández Bonet, Lovisa Franzén, Patrik L. Ståhl, Ian T. Hoffecker
Nature Communications (31 October 2025)

Standalone single- and bi-layered human skin 3D models supported by recombinant silk feature native spatial organization
Gkouma S, Bhalla N, Frapard S, Jönsson A, Gürbüz H, Dogan AA, Giacomello S, Duvfa M, Ståhl PL, Widhe M, Hedhammar M
Biofabrication (5 November 2024)

Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis
Franzén L, Olsson Lindvall M, Hühn M, Ptasinski V, Setyo L, Keith BP, Collin A, Oag S, Volckaert T, Borde A, Lundeberg J, Lindgren J, Belfield G, Jackson S, Ollerstam A, Stamou M, Ståhl PL, Hornberg JJ.
Nature Genetics (1 July 2024) 

Gene expression of single cells mapped in tissue sections
Ståhl PL
Nature (13 Dec 2023)

Solid-phase capture and profiling of open chromatin by spatial ATAC
Llorens-Bobadilla E, Zamboni M, Marklund M, Bhalla N, Chen X, Hartman J, Frisén J, Ståhl PL
Nature Biotechnology (5 Jan 2023) (bioRxiv 2022)

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