Joakim Lundeberg
Professor, Principal Investigator, KTH
Email: joakim.lundeberg@scilifelab.se
Research Focus
Our research is focused on developing and exploring spatially resolved gene expression tools and their applications. The basic concept is that we first place thin tissue sections onto barcoded microarrays, after which the tissue is stained and RNA is extracted while maintaining positional information within the tissue.
Many of our projects focus on building large scale interdisciplinary molecular atlases, including human development, where we are integrating spatial transcriptomics data with other technological platforms.
Team members
Joakim Lundeberg, professor, team leader, KTH
Enikö Lazar, Postdoc, KTH
Kim Thrane, PhD, Postdoc, KTH
Reza Mirzazadeh, PhD, Postdoc, KTH
Eva Gracia Villacampa, PhD student, KTH
Leire Alonso Galicia, PhD student, KTH
Ludvig Bergenstråhle, PhD, KTH
Marco Vicari, PhD student, KTH
Markus Ekvall, PhD student, KTH
Matthew William Myers, research engineer, KTH
Mengxiao He, PhD student, KTH
Emmanouela Perisynaki, research engineer, KTH
Javier Escudero Morlanes, PhD student, KTH
Marcos Abreu Machado, PhD student, KTH
Raphaël Mauron, PhD student, KTH
Key publications
Spatially resolved clonal copy number alterations in benign and malignant tissue
Andrew Erickson, Mengxiao He, Emelie Berglund, Maja Marklund, Reza Mirzazadeh, Niklas Schultz, Linda Kvastad, Alma Andersson, Ludvig Bergenstråhle, Joseph Bergenstråhle, Ludvig Larsson, Leire Alonso Galicia, Alia Shamikh, Elisa Basmaci, Teresita Díaz De Ståhl, Timothy Rajakumar, Dimitrios Doultsinos, Kim Thrane, Andrew L. Ji, Paul A. Khavari, Firaz Tarish, Anna Tanoglidi, Jonas Maaskola, Richard Colling, Tuomas Mirtti, Freddie C. Hamdy, Dan J. Woodcock, Thomas Helleday, Ian G. Mills, Alastair D. Lamb & Joakim Lundeberg
Nature 608, 360–367 (2022)
SnapShot: Spatial transcriptomics.
Larsson L, Bergenstråhle L, He M, Andrusivova Z, Lundeberg J.
Cell. 2022 Jul 21;185(15):2840-2840.e1. doi: 10.1016/j.cell.2022.06.002.
PMID: 35868280
Super-resolved spatial transcriptomics by deep data fusion.
Bergenstråhle L, He B, Bergenstråhle J, Abalo X, Mirzazadeh R, Thrane K, Ji AL, Andersson A, Larsson L, Stakenborg N, Boeckxstaens G, Khavari P, Zou J, Lundeberg J, Maaskola J.
Nat Biotechnol. 2022 Apr;40(4):476-479. doi: 10.1038/s41587-021-01075-3. Epub 2021 Nov 29.
PMID: 34845373
Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.
Ratz M, von Berlin L, Larsson L, Martin M, Westholm JO, La Manno G, Lundeberg J, Frisén J.
Nat Neurosci. 2022 Mar;25(3):285-294. doi: 10.1038/s41593-022-01011-x. Epub 2022 Feb 24.
PMID: 35210624 Free PMC article
Spatially resolved transcriptomics adds a new dimension to genomics
Larsson L, Frisén J, Lundeberg J*
Nature Methods (2021 Jan), DOI: 10.1038/s41592-020-01038-7
Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
Ji AL, Rubin AJ, Thrane K, Jiang S, Reynolds DL, Meyers RM, Guo MG, George BM, Mollbrink A, Bergenstråhle J, Larsson L, Bai Y, Zhu B, Bhaduri A, Meyers JM, Rovira-Clavé X, Hollmig ST, Aasi SZ, Nolan GP, Lundeberg J, Khavari PA*
Cell (2020 Sep), DOI: 10.1016/j.cell.2020.08.043
Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease
Chen WT, Lu A, Craessaerts K, Pavie B, Sala Frigerio C, Corthout N, Qian X, Laláková J, Kühnemund M, Voytyuk I, Wolfs L, Mancuso R, Salta E, Balusu S, Snellinx A, Munck S, Jurek A, Fernandez Navarro J, Saido TC, Huitinga I, Lundeberg J, Fiers M*, De Strooper B*
Cell (2020 Aug), DOI: 10.1016/j.cell.2020.06.038
Spatially Resolved Transcriptomes-Next Generation Tools for Tissue Exploration
Asp M, Bergenstråhle J, Lundeberg J*
Bioessays (2020 Oct), DOI: 10.1002/bies.201900221
Integrating spatial gene expression and breast tumour morphology via deep learning
He B, Bergenstråhle L, Stenbeck L, Abid A, Andersson A, Borg Å, Maaskola J*, Lundeberg J*, Zou J*
Nature Biomedical Engineering (2020 Aug), DOI: 10.1038/s41551-020-0578-x
Molecular atlas of the adult mouse brain
Ortiz C, Navarro JF, Jurek A, Märtin A, Lundeberg J*, Meletis K*
Science Advances (2020 Jun), DOI: 10.1126/sciadv.abb3446
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)
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)
Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis
Maniatis S, Äijö T, Vickovic S, Braine C, Kang K, Mollbrink A, Fagegaltier D, Andrusivova Z, Saarenpää S, Saiz-Castro G, Cuevas M, Watters A, Lundeberg J*, Bonneau R*, Phatnani H*
Science (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)
Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays
Giacomello S* and 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 P, Sonnhammer E, Helleday T*, Lundeberg J*
Nature Communications (2018)
The Human Cell Atlas
Regev A*, Teichmann SA*, Lander ES*, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Péer D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.
Elife (2017)
Spatially resolved transcriptome profiling in model plant species
Giacomello S*, Salmén F, Terebieniec B K, Vickovic S, Navarro J F, Alexeyenko A, Reimegård J, McKee L S, Mannapperuma C, Bulone V, Ståhl P L, Sundström J F, Street N R, Lundeberg J*
Nature Plants (2017)
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