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.

Norway spruce spatiotemporal programs of conifer reproductive development
Sami Saarenpää, Nathan Zivi, Yuvarani Masarapu, Laxmi S. Mishra, Sofia Rouot, Alina Orozco, Sybil A. Herrera-Foessel, Teitur Ahlgren Kalman, Mario Liva, Sonam Yadav, Marie Englund, Nathaniel R. Street, Jens F. Sundström, Stefania Giacomello
Cell, 14 September 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

Highly resolved tumor architecture via matched spatial and nucleus transcriptomics from a single tissue section
Marcos Tito Machado, Mengxiao He, Leire Alonso Galicia, Zaneta Andrusivova, Emmanouela Perisynaki, Matthew W Myers, Sarantis Giatrellis, Sandra O’Toole, Beata Kiedik, Raphael Mauron, Sophie van der Leij, Kate Harvey, John Reeves, Javier Escudero Morlanes, Taobo Hu, Mengping Long, Mats Nilsson, Tianyi Li, Xinsong Chen, Johan Hartman, Mate Mihalffy, Taopeng Wang, Marco Vicari, Laura Savolainen, Andrew Erickson, Sandy Figiel, Alastair Lamb, Alexander Swarbrick, Joakim Lundeberg, Reza Mirzazadeh
biorxive, 10 September 2026

Spatial mapping of pediatric brain tumors across diagnoses and relapses
Javier Escudero Morlanes, Timo-Pekka Lehto, Ludvig Larsson, Leire Alonso Galicia, Annelie Mollbrink, Alia Shamikh, Elisa Basmaci, Gabriela Prochazka, Teresita Díaz De Ståhl, Johanna Sandgren, Fulya Taylan, Bianca Tesi, Ann Nordgren, Andrew Erickson, Alastair D Lamb, Klas Blomgren, Monica Nistér, Joakim Lundeberg, Reza Mirzazadeh, Linda Kvastad
biorxive, 26 August 2026

Dissecting human fetal cardiac repair using cardioids
Lavinia Ceci Ginistrelli, Tobias Ilmer, Lena Plank, Maria Novatchkova, Abhijeet Krishna, Enikő Lázár, Raphaël Mauron, Stefan H. Geyer, Lokesh Pimpale, Valeria V. Orlova, Katie McDole, Wolfgang J. Weninger, Sasha Mendjan
biorxive, 1 July 2026

Pubertal maturation and chemotherapy-associated disruption of the pediatric ovary revealed by multimodal single-cell profiling
Loren Méar, Jasmin Hassan, Matthew William Myers, Hosein Toosi, Ilmatar Rooda, Nina Boskovic, Filippa Bertilsson, Feria Hikmet, Anastasios Damdimopoulos, Rutger Schutten, Borbala Katona, Marzie Abdolhamdi, Emmanouela Perisynaki, Katri Knuus, Karin Pettersson, Kiriaki Papaikonomou, Johan Malmros, Petra Byström, Mikael Sundin, Cecilia Langenskiöld, Hartmut Vogt, Géraldine Giraud, Andres Salumets, Marjut Otala, Timo Tuuri, Joakim Lundeberg, Andrea Jurisicova, Cecilia Lindskog, Kirsi Jahnukainen, Reza Mirzazadeh, Pauliina Damdimopoulou
biorxive, 8 June 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