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.

ProbeST: a custom probe design pipeline for dual host-pathogen Spatial Transcriptomics
Sofia Rouot, Ireen van Dolderen, Patrick Rosendahl Andreassen, Solène Frapard, Sybil A Herrera-Foessel, Hailey Sounart, Sami Saarenpää, Julia A Vorholt, Stefania Giacomello
BMC Genomics, 25 June 2026

Rare regulatory mutations disrupt mesenchymal molecular programs driving endocardial cushion formation in bicuspid aortic valve
Artemy Zhigulev, Andrey Buyan, Enikő Lázár, Nikita Gryzunov, Karin Lång, Raphaël Mauron, Vladimir Nozdrin, Rapolas Spalinskas, Sailendra Pradhananga, Madeleine Petersson Sjögren, Doreen Schwochow, Anders Franco-Cereceda, Joakim Lundeberg, Ivan V. Kulakovskiy, Per Eriksson, Hanna M. Björck, Pelin Sahlén
Nature Communications, 18 April 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

Single-cell spatial multi-omics molecular pathology enabled by SuperFocus
Yao Lu, Xiaolong Tian, Marco Vicari, Archibald Enninful, Shuozhen Bao, Zhiliang Bai, Chen Liu, Xuchen Zhang, Per E. Andrén, Joakim Lundeberg, Mina L. Xu, Rong Fan, Yang Xiao, Zongming Ma
biorxive, 23 March 2026

Spatial single-cell atlas reveals regional variations in healthy and diseased human lung
Alexandra B. Firsova, Sergio Marco Salas, Louis B. Kuemmerle, Xesús M. Abalo, Alexandros Sountoulidis, Ludvig Larsson, Krishnaa T. Mahbubani, Jonas Theelke, Zaneta Andrusivova, Leire Alonso Galicia, Andreas Liontos, Tamás Balassa, Ferenc Kovacs, Peter Horvath, Yuexin Chen, Janine Gote-Schniering, Mircea-Gabriel Stoleriu, Jürgen Behr, Kerstin B. Meyer, Wim Timens, Herbert B. Schiller, Malte D. Luecken, Fabian J. Theis, Joakim Lundeberg, Mats Nilsson, Martijn C. Nawijn, Christos Samakovlis
Nature Communication, 5 November 2025

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

Spatiotemporal gene expression and cellular dynamics of the developing human heart
Enikő Lázár, Raphaël Mauron, Žaneta Andrusivová, Julia Foyer, Mengxiao He, Ludvig Larsson, Nick Shakari, Sergio Marco Salas, Christophe Avenel, Sanem Sariyar, Jan Niklas Hansen, Marco Vicari, Paulo Czarnewski, Emelie Braun, Xiaofei Li, Olaf Bergmann, Christer Sylvén, Emma Lundberg, Sten Linnarsson, Mats Nilsson, Erik Sundström, Igor Adameyko, Joakim Lundeberg
Nature Genetics, 29 October 2025

Spatial architecture of development and disease
Enikő Lázár, Joakim Lundeberg
Nature Review Genetics, 30 September 2025

Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data
Li T, Yang Q, Acs B, Sifakis E, Toosi H, Engblom C, Thrane K, Lin Q, Mold J, Sun W, Boyaci C, Steen S, Frisén J, Largergren J, Lundeberg J, Chen X, Hartman J
Nature Precision Oncology, 9 September 2025

adiposetissue.org: A knowledge portal integrating clinical and experimental data from human adipose tissue
Zhong J, Zareifi D, Weinbrenner S, Hansen M, Klingelhuber F, Nono Nankam PA, Frendo-Cumbo S, Bhalla N, Cordeddu L, de Castro Barbosa T, Arner P, Dahlman I, Muniandy M, Heinonen S, Pietiläinen KH, Hoffmann A, Ghosh A, John D, Tönjes A, Ståhl PL, Böttcher Y, Keller M, Kovacs P, Kerr AG, Langin D, Wolfrum C, Blüher M, Krahmer N, Massier L, Mejhert N, Rydén M
Cell Metabolism, 14 February 2025