Joakim Lundeberg

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 70

Top Topics

Trypanosoma Cruzi

Amyotrophic Lateral Sclerosis

Gene Expression

Top Venues

Nature communications

Nature neuroscience

Nature genetics

This page only lists publications with an associated author ORCID identifier.

Publications

Lovisa Franzén, Martina Olsson Lindvall, Michael Hühn, Victoria A Ptasinski, Laura Setyo, Benjamin P Keith, Astrid Collin, Steven Oag, Thomas Volckaert, Annika Borde, Joakim Lundeberg, Julia Lindgren, Graham Belfield, Sonya Jackson, Anna Ollerstam, Marianna Stamou, Patrik L Ståhl, Jorrit J Hornberg
Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis. Nature genetics 56 (8) (2024)
Markus Ekvall, Ludvig Bergenstråhle, Alma Andersson, Paulo Czarnewski, Johannes Olegård, Lukas Käll, Joakim Lundeberg
Spatial landmark detection and tissue registration with deep learning. Nature methods 21 (4) (2024)
Joachim De Jonghe, James W Opzoomer, Amaia Vilas-Zornoza, Peter Crane, Benedikt S Nilges, Marco Vicari, Hower Lee, David Lara-Astiaso, Torsten Gross, Jörg Morf, Kim Schneider, Juliana Cudini, Lorenzo Ramos-Mucci, Dylan Mooijman, Katarína Tiklová, Sergio Marco Salas, Christoffer Mattsson Langseth, Nachiket D Kashikar, Charles E S Roberts, null null, Joakim Lundeberg, Mats Nilsson, Alex K Shalek, Adam P Cribbs, Jake P Taylor-King
A community effort to track commercial single-cell and spatial 'omic technologies and business trends. Nature biotechnology 42 (7) (2024)
Lovisa Franzén, Martina Olsson Lindvall, Michael Hühn, Victoria A Ptasinski, Laura Setyo, Benjamin P Keith, Astrid Collin, Steven Oag, Thomas Volckaert, Annika Borde, Joakim Lundeberg, Julia Lindgren, Graham Belfield, Sonya Jackson, Anna Ollerstam, Marianna Stamou, Patrik L Ståhl, Jorrit J Hornberg
Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis. Nature genetics 56 (8) (2024)
Lovisa Franzén, Martina Olsson Lindvall, Michael Hühn, Victoria A Ptasinski, Laura Setyo, Benjamin P Keith, Astrid Collin, Steven Oag, Thomas Volckaert, Annika Borde, Joakim Lundeberg, Julia Lindgren, Graham Belfield, Sonya Jackson, Anna Ollerstam, Marianna Stamou, Patrik L Ståhl, Jorrit J Hornberg
Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis. Nature genetics 56 (8) (2024)
Franziska Hildebrandt, Miren Urrutia Iturritza, Christian Zwicker, Bavo Vanneste, Noémi K M van Hul, Elisa Semle, Jaclyn Quin, Tales Pascini, Sami Saarenpää, Mengxiao He, Emma Rachel Andersson, Charlotte L Scott, Joel Vega-Rodríguez, Joakim Lundeberg, Johan Ankarklev
Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution. Nature communications 15 (1) (2024)
Franziska Hildebrandt, Miren Urrutia Iturritza, Christian Zwicker, Bavo Vanneste, Noémi K M van Hul, Elisa Semle, Jaclyn Quin, Tales Pascini, Sami Saarenpää, Mengxiao He, Emma Rachel Andersson, Charlotte L Scott, Joel Vega-Rodríguez, Joakim Lundeberg, Johan Ankarklev
Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution. Nature communications 15 (1) (2024)
Joachim De Jonghe, James W Opzoomer, Amaia Vilas-Zornoza, Peter Crane, Benedikt S Nilges, Marco Vicari, Hower Lee, David Lara-Astiaso, Torsten Gross, Jörg Morf, Kim Schneider, Juliana Cudini, Lorenzo Ramos-Mucci, Dylan Mooijman, Katarína Tiklová, Sergio Marco Salas, Christoffer Mattsson Langseth, Nachiket D Kashikar, Charles E S Roberts, null null, Joakim Lundeberg, Mats Nilsson, Alex K Shalek, Adam P Cribbs, Jake P Taylor-King
A community effort to track commercial single-cell and spatial 'omic technologies and business trends. Nature biotechnology 42 (7) (2024)
Markus Ekvall, Ludvig Bergenstråhle, Alma Andersson, Paulo Czarnewski, Johannes Olegård, Lukas Käll, Joakim Lundeberg
Spatial landmark detection and tissue registration with deep learning. Nature methods (2024)
Franziska Hildebrandt, Miren Urrutia Iturritza, Christian Zwicker, Bavo Vanneste, Noémi K M van Hul, Elisa Semle, Jaclyn Quin, Tales Pascini, Sami Saarenpää, Mengxiao He, Emma Rachel Andersson, Charlotte L Scott, Joel Vega-Rodríguez, Joakim Lundeberg, Johan Ankarklev
Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution. Nature communications 15 (1) (2024)
Franziska Hildebrandt, Miren Urrutia Iturritza, Christian Zwicker, Bavo Vanneste, Noémi K M van Hul, Elisa Semle, Jaclyn Quin, Tales Pascini, Sami Saarenpää, Mengxiao He, Emma Rachel Andersson, Charlotte L Scott, Joel Vega-Rodríguez, Joakim Lundeberg, Johan Ankarklev
Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution. Nature communications 15 (1) (2024)
Gustavo Monasterio, Rodrigo A Morales, David Alejandro Bejarano, Xesús M Abalo, Jennifer Fransson, Ludvig Larsson, Andreas Schlitzer, Joakim Lundeberg, Srustidhar Das, Eduardo J Villablanca
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract. Nature protocols (2024)
Lovisa Franzén, Martina Olsson Lindvall, Michael Hühn, Victoria A Ptasinski, Laura Setyo, Benjamin P Keith, Astrid Collin, Steven Oag, Thomas Volckaert, Annika Borde, Joakim Lundeberg, Julia Lindgren, Graham Belfield, Sonya Jackson, Anna Ollerstam, Marianna Stamou, Patrik L Ståhl, Jorrit J Hornberg
Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis. Nature genetics (2024)
Markus Ekvall, Ludvig Bergenstråhle, Alma Andersson, Paulo Czarnewski, Johannes Olegård, Lukas Käll, Joakim Lundeberg
Spatial landmark detection and tissue registration with deep learning. Nature methods 21 (4) (2024)
Markus Ekvall, Ludvig Bergenstråhle, Alma Andersson, Paulo Czarnewski, Johannes Olegård, Lukas Käll, Joakim Lundeberg
Spatial landmark detection and tissue registration with deep learning. Nature methods 21 (4) (2024)
Lovisa Franzén, Martina Olsson Lindvall, Michael Hühn, Victoria A Ptasinski, Laura Setyo, Benjamin P Keith, Astrid Collin, Steven Oag, Thomas Volckaert, Annika Borde, Joakim Lundeberg, Julia Lindgren, Graham Belfield, Sonya Jackson, Anna Ollerstam, Marianna Stamou, Patrik L Ståhl, Jorrit J Hornberg
Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis. Nature genetics (2024)
Markus Ekvall, Ludvig Bergenstråhle, Alma Andersson, Paulo Czarnewski, Johannes Olegård, Lukas Käll, Joakim Lundeberg
Spatial landmark detection and tissue registration with deep learning. Nature methods 21 (4) (2024)
Markus Ekvall, Ludvig Bergenstråhle, Alma Andersson, Paulo Czarnewski, Johannes Olegård, Lukas Käll, Joakim Lundeberg
Spatial landmark detection and tissue registration with deep learning. Nature methods 21 (4) (2024)
Markus Ekvall, Ludvig Bergenstråhle, Alma Andersson, Paulo Czarnewski, Johannes Olegård, Lukas Käll, Joakim Lundeberg
Spatial landmark detection and tissue registration with deep learning. Nature methods 21 (4) (2024)
Kévin LeBrigand, Joseph Bergenstråhle, Kim Thrane, Annelie Mollbrink, Konstantinos Meletis, Pascal Barbry, Rainer Waldmann, Joakim Lundeberg
The spatial landscape of gene expression isoforms in tissue sections. Nucleic acids research (2023)
Xiaofei Li, Zaneta Andrusivova, Paulo Czarnewski, Christoffer Mattsson Langseth, Alma Andersson, Yang Liu, Daniel Gyllborg, Emelie Braun, Ludvig Larsson, Lijuan Hu, Zhanna Alekseenko, Hower Lee, Christophe Avenel, Helena Kopp Kallner, Elisabet Åkesson, Igor Adameyko, Mats Nilsson, Sten Linnarsson, Joakim Lundeberg, Erik Sundström
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin. Nature neuroscience 26 (5) (2023)
Marco Vicari, Reza Mirzazadeh, Anna Nilsson, Reza Shariatgorji, Patrik Bjärterot, Ludvig Larsson, Hower Lee, Mats Nilsson, Julia Foyer, Markus Ekvall, Paulo Czarnewski, Xiaoqun Zhang, Per Svenningsson, Lukas Käll, Per E Andren, Joakim Lundeberg
Spatial multimodal analysis of transcriptomes and metabolomes in tissues. Nature biotechnology (2023)
Alexandros Sountoulidis, Sergio Marco Salas, Emelie Braun, Christophe Avenel, Joseph Bergenstråhle, Jonas Theelke, Marco Vicari, Paulo Czarnewski, Andreas Liontos, Xesús M Abalo, Žaneta Andrusivová, Reza Mirzazadeh, Michaela Asp, Xiaofei Li, Lijuan Hu, Sanem Sariyar, Anna Martinez Casals, Burcu Ayoglu, Alexandra B Firsova, Jakob Michaëlsson, Emma Lundberg, Carolina Wählby, Erik Sundström, Sten Linnarsson, Joakim Lundeberg, Mats Nilsson, Christos Samakovlis
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung. Nature cell biology 25 (2) (2023)
Reza Mirzazadeh, Zaneta Andrusivova, Ludvig Larsson, Phillip T Newton, Leire Alonso Galicia, Xesús M Abalo, Mahtab Avijgan, Linda Kvastad, Alexandre Denadai-Souza, Nathalie Stakenborg, Alexandra B Firsova, Alia Shamikh, Aleksandra Jurek, Niklas Schultz, Monica Nistér, Christos Samakovlis, Guy E Boeckxstaens, Joakim Lundeberg
Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples. Nature communications 14 (1) (2023)
Xiaofei Li, Zaneta Andrusivova, Paulo Czarnewski, Christoffer Mattsson Langseth, Alma Andersson, Yang Liu, Daniel Gyllborg, Emelie Braun, Ludvig Larsson, Lijuan Hu, Zhanna Alekseenko, Hower Lee, Christophe Avenel, Helena Kopp Kallner, Elisabet Åkesson, Igor Adameyko, Mats Nilsson, Sten Linnarsson, Joakim Lundeberg, Erik Sundström
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin. Nature neuroscience 26 (5) (2023)
Alexandros Sountoulidis, Sergio Marco Salas, Emelie Braun, Christophe Avenel, Joseph Bergenstråhle, Jonas Theelke, Marco Vicari, Paulo Czarnewski, Andreas Liontos, Xesús M Abalo, Žaneta Andrusivová, Reza Mirzazadeh, Michaela Asp, Xiaofei Li, Lijuan Hu, Sanem Sariyar, Anna Martinez Casals, Burcu Ayoglu, Alexandra B Firsova, Jakob Michaëlsson, Emma Lundberg, Carolina Wählby, Erik Sundström, Sten Linnarsson, Joakim Lundeberg, Mats Nilsson, Christos Samakovlis
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung. Nature cell biology 25 (2) (2023)
Yuhang Fan, Žaneta Andrusivová, Yunming Wu, Chew Chai, Ludvig Larsson, Mengxiao He, Liqun Luo, Joakim Lundeberg, Bo Wang
Expansion spatial transcriptomics. Nature methods (2023)
Xiaofei Li, Zaneta Andrusivova, Paulo Czarnewski, Christoffer Mattsson Langseth, Alma Andersson, Yang Liu, Daniel Gyllborg, Emelie Braun, Ludvig Larsson, Lijuan Hu, Zhanna Alekseenko, Hower Lee, Christophe Avenel, Helena Kopp Kallner, Elisabet Åkesson, Igor Adameyko, Mats Nilsson, Sten Linnarsson, Joakim Lundeberg, Erik Sundström
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin. Nature neuroscience (2023)
Emelie Braun, Miri Danan Gotthold, Lars E Borm, Ka Wai Lee, Elin Vinsland, Peter Lönnerberg, Lijuan Hu, Xiaofei Li, Xiaoling He, Žaneta Andrusivová, Joakim Lundeberg, Roger A Barker, Ernest Arenas, Erik Sundström, Sten Linnarsson
Comprehensive cell atlas of the first-trimester developing human brain. Science (New York, N.Y.) 382 (6667) (2023)
Xiaofei Li, Zaneta Andrusivova, Paulo Czarnewski, Christoffer Mattsson Langseth, Alma Andersson, Yang Liu, Daniel Gyllborg, Emelie Braun, Ludvig Larsson, Lijuan Hu, Zhanna Alekseenko, Hower Lee, Christophe Avenel, Helena Kopp Kallner, Elisabet Åkesson, Igor Adameyko, Mats Nilsson, Sten Linnarsson, Joakim Lundeberg, Erik Sundström
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin. Nature neuroscience 26 (5) (2023)
Reza Mirzazadeh, Zaneta Andrusivova, Ludvig Larsson, Phillip T Newton, Leire Alonso Galicia, Xesús M Abalo, Mahtab Avijgan, Linda Kvastad, Alexandre Denadai-Souza, Nathalie Stakenborg, Alexandra B Firsova, Alia Shamikh, Aleksandra Jurek, Niklas Schultz, Monica Nistér, Christos Samakovlis, Guy E Boeckxstaens, Joakim Lundeberg
Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples. Nature communications 14 (1) (2023)
Xiaofei Li, Zaneta Andrusivova, Paulo Czarnewski, Christoffer Mattsson Langseth, Alma Andersson, Yang Liu, Daniel Gyllborg, Emelie Braun, Ludvig Larsson, Lijuan Hu, Zhanna Alekseenko, Hower Lee, Christophe Avenel, Helena Kopp Kallner, Elisabet Åkesson, Igor Adameyko, Mats Nilsson, Sten Linnarsson, Joakim Lundeberg, Erik Sundström
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin. Nature neuroscience (2023)
Alexandros Sountoulidis, Sergio Marco Salas, Emelie Braun, Christophe Avenel, Joseph Bergenstråhle, Jonas Theelke, Marco Vicari, Paulo Czarnewski, Andreas Liontos, Xesús M Abalo, Žaneta Andrusivová, Reza Mirzazadeh, Michaela Asp, Xiaofei Li, Lijuan Hu, Sanem Sariyar, Anna Martinez Casals, Burcu Ayoglu, Alexandra B Firsova, Jakob Michaëlsson, Emma Lundberg, Carolina Wählby, Erik Sundström, Sten Linnarsson, Joakim Lundeberg, Mats Nilsson, Christos Samakovlis
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung. Nature cell biology 25 (2) (2023)
Xiaofei Li, Zaneta Andrusivova, Paulo Czarnewski, Christoffer Mattsson Langseth, Alma Andersson, Yang Liu, Daniel Gyllborg, Emelie Braun, Ludvig Larsson, Lijuan Hu, Zhanna Alekseenko, Hower Lee, Christophe Avenel, Helena Kopp Kallner, Elisabet Åkesson, Igor Adameyko, Mats Nilsson, Sten Linnarsson, Joakim Lundeberg, Erik Sundström
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin. Nature neuroscience (2023)
Reza Mirzazadeh, Zaneta Andrusivova, Ludvig Larsson, Phillip T Newton, Leire Alonso Galicia, Xesús M Abalo, Mahtab Avijgan, Linda Kvastad, Alexandre Denadai-Souza, Nathalie Stakenborg, Alexandra B Firsova, Alia Shamikh, Aleksandra Jurek, Niklas Schultz, Monica Nistér, Christos Samakovlis, Guy E Boeckxstaens, Joakim Lundeberg
Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples. Nature communications 14 (1) (2023)
Alexandros Sountoulidis, Sergio Marco Salas, Emelie Braun, Christophe Avenel, Joseph Bergenstråhle, Jonas Theelke, Marco Vicari, Paulo Czarnewski, Andreas Liontos, Xesús M Abalo, Žaneta Andrusivová, Reza Mirzazadeh, Michaela Asp, Xiaofei Li, Lijuan Hu, Sanem Sariyar, Anna Martinez Casals, Burcu Ayoglu, Alexandra B Firsova, Jakob Michaëlsson, Emma Lundberg, Carolina Wählby, Erik Sundström, Sten Linnarsson, Joakim Lundeberg, Mats Nilsson, Christos Samakovlis
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung. Nature cell biology (2023)
Xiaofei Li, Zaneta Andrusivova, Paulo Czarnewski, Christoffer Mattsson Langseth, Alma Andersson, Yang Liu, Daniel Gyllborg, Emelie Braun, Ludvig Larsson, Lijuan Hu, Zhanna Alekseenko, Hower Lee, Christophe Avenel, Helena Kopp Kallner, Elisabet Åkesson, Igor Adameyko, Mats Nilsson, Sten Linnarsson, Joakim Lundeberg, Erik Sundström
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin. Nature neuroscience 26 (5) (2023)
Alexandros Sountoulidis, Sergio Marco Salas, Emelie Braun, Christophe Avenel, Joseph Bergenstråhle, Jonas Theelke, Marco Vicari, Paulo Czarnewski, Andreas Liontos, Xesús M Abalo, Žaneta Andrusivová, Reza Mirzazadeh, Michaela Asp, Xiaofei Li, Lijuan Hu, Sanem Sariyar, Anna Martinez Casals, Burcu Ayoglu, Alexandra B Firsova, Jakob Michaëlsson, Emma Lundberg, Carolina Wählby, Erik Sundström, Sten Linnarsson, Joakim Lundeberg, Mats Nilsson, Christos Samakovlis
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung. Nature cell biology 25 (2) (2023)
Camilla Engblom, Kim Thrane, Qirong Lin, Alma Andersson, Hosein Toosi, Xinsong Chen, Embla Steiner, Chang Lu, Giulia Mantovani, Michael Hagemann-Jensen, Sami Saarenpää, Mattias Jangard, Julio Saez-Rodriguez, Jakob Michaëlsson, Johan Hartman, Jens Lagergren, Jeff E Mold, Joakim Lundeberg, Jonas Frisén
Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics. Science (New York, N.Y.) 382 (6675) (2023)
Xiaofei Li, Zaneta Andrusivova, Paulo Czarnewski, Christoffer Mattsson Langseth, Alma Andersson, Yang Liu, Daniel Gyllborg, Emelie Braun, Ludvig Larsson, Lijuan Hu, Zhanna Alekseenko, Hower Lee, Christophe Avenel, Helena Kopp Kallner, Elisabet Åkesson, Igor Adameyko, Mats Nilsson, Sten Linnarsson, Joakim Lundeberg, Erik Sundström
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin. Nature neuroscience 26 (5) (2023)
Alexandros Sountoulidis, Sergio Marco Salas, Emelie Braun, Christophe Avenel, Joseph Bergenstråhle, Jonas Theelke, Marco Vicari, Paulo Czarnewski, Andreas Liontos, Xesús M Abalo, Žaneta Andrusivová, Reza Mirzazadeh, Michaela Asp, Xiaofei Li, Lijuan Hu, Sanem Sariyar, Anna Martinez Casals, Burcu Ayoglu, Alexandra B Firsova, Jakob Michaëlsson, Emma Lundberg, Carolina Wählby, Erik Sundström, Sten Linnarsson, Joakim Lundeberg, Mats Nilsson, Christos Samakovlis
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung. Nature cell biology 25 (2) (2023)
Reza Mirzazadeh, Zaneta Andrusivova, Ludvig Larsson, Phillip T Newton, Leire Alonso Galicia, Xesús M Abalo, Mahtab Avijgan, Linda Kvastad, Alexandre Denadai-Souza, Nathalie Stakenborg, Alexandra B Firsova, Alia Shamikh, Aleksandra Jurek, Niklas Schultz, Monica Nistér, Christos Samakovlis, Guy E Boeckxstaens, Joakim Lundeberg
Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples. Nature communications 14 (1) (2023)
Michael Ratz, Leonie von Berlin, Ludvig Larsson, Marcel Martin, Jakub Orzechowski Westholm, Gioele La Manno, Joakim Lundeberg, Jonas Frisén
Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics. Nature neuroscience 25 (3) (2022)
Sara M Parigi, Ludvig Larsson, Srustidhar Das, Ricardo Omar Ramirez Flores, Annika Frede, Kumar P Tripathi, Oscar E Diaz, Katja A Selin, Rodrigo A Morales, Xinxin Luo, Gustavo Monasterio, Camilla Engblom, Nicola Gagliani, Julio Saez-Rodriguez, Joakim Lundeberg, Eduardo J Villablanca
The spatial transcriptomic landscape of the healing mouse intestine following damage. Nature communications 13 (1) (2022)
Max Kaufmann, Anna-Lena Schaupp, Rosa Sun, Fabian Coscia, Calliope A Dendrou, Adrian Cortes, Gurman Kaur, Hayley G Evans, Annelie Mollbrink, José Fernandéz Navarro, Jana K Sonner, Christina Mayer, Gabriele C DeLuca, Joakim Lundeberg, Paul M Matthews, Kathrine E Attfield, Nicolaus Kröger, Matthias Mann, Lars Fugger
Identification of early neurodegenerative pathways in progressive multiple sclerosis. Nature neuroscience 25 (7) (2022)
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 Geoffrey Mills, Alastair D Lamb, Joakim Lundeberg
Spatially resolved clonal copy number alterations in benign and malignant tissue. Nature 608 (7922) (2022)
Maja Marklund, Niklas Schultz, Stefanie Friedrich, Emelie Berglund, Firas Tarish, Anna Tanoglidi, Yao Liu, Ludvig Bergenstråhle, Andrew Erickson, Thomas Helleday, Alastair D Lamb, Erik L L Sonnhammer, Joakim Lundeberg
Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones. Nature communications 13 (1) (2022)
Ludvig Larsson, Jonas Frisén, Joakim Lundeberg
Spatially resolved transcriptomics adds a new dimension to genomics. Nature methods 18 (1) (2021)
Sunny Z Wu, Ghamdan Al-Eryani, Daniel Lee Roden, Simon R Junankar, Kate Harvey, Alma Andersson, Aatish Thennavan, Chenfei Wang, James R Torpy, Nenad Bartonicek, Taopeng Wang, Ludvig Larsson, Dominik C Kaczorowski, Neil I Weisenfeld, Cedric R Uytingco, Jennifer G Chew, Zachary W Bent, Chia-Ling Chan, Vikkitharan Gnanasambandapillai, Charles-Antoine Dutertre, Laurence Gluch, Mun N Hui, Jane Beith, Andrew Parker, Elizabeth Robbins, Davendra Segara, Caroline Cooper, Cindy Mak, Belinda Chan, Sanjay Warrier, Florent Ginhoux, Ewan Millar, Joseph E Powell, Stephen R Williams, X Shirley Liu, Sandra O'Toole, Elgene Lim, Joakim Lundeberg, Charles M Perou, Alexander Swarbrick
A single-cell and spatially resolved atlas of human breast cancers. Nature genetics 53 (9) (2021)
Linda Kvastad, Konstantin Carlberg, Ludvig Larsson, Eva Gracia Villacampa, Alexander Stuckey, Linnea Stenbeck, Annelie Mollbrink, Margherita Zamboni, Jens Peter Magnusson, Elisa Basmaci, Alia Shamikh, Gabriela Prochazka, Anna-Lena Schaupp, Åke Borg, Lars Fugger, Monica Nistér, Joakim Lundeberg
The spatial RNA integrity number assay for in situ evaluation of transcriptome quality. Communications biology 4 (1) (2021)
Franziska Hildebrandt, Alma Andersson, Sami Saarenpää, Ludvig Larsson, Noémi K M van Hul, Sachie Kanatani, Jan Masek, Ewa C S Ellis, Antonio Barragan, Annelie Mollbrink, Emma Rachel Andersson, Joakim Lundeberg, Johan Ankarklev
Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver. Nature communications 12 (1) (2021)
Alma Andersson, Ludvig Larsson, Linnea Stenbeck, Fredrik Salmén, Anna Ehinger, Sunny Z Wu, Ghamdan Al-Eryani, Daniel Lee Roden, Alexander Swarbrick, Åke Borg, Jonas Frisén, Camilla Engblom, Joakim Lundeberg
Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions. Nature communications 12 (1) (2021)
Eduard Chelebian, Christophe Avenel, Kimmo Kartasalo, Maja Marklund, Anna Tanoglidi, Tuomas K Mirtti, Richard Colling, Andrew M Erickson, Alastair D Lamb, Joakim Lundeberg, Carolina Wählby
Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer. Cancers 13 (19) (2021)
Muzlifah A Haniffa, Deanne M Taylor, Sten Linnarsson, Bruce J Aronow, Gary D Baider, Roger A Barker, Pablo G Camara, J Gray Camp, Alain Chédotal, Andrew J Copp, Heather C Etchevers, Paolo Giacobini, Berthold Göttgens, Guoji Guo, Ania Hupalowska, Kylie R James, Emily Kirby, Arnold R Kriegstein, Joakim Lundeberg, John C Marioni, Kerstin B Meyer, Kathy K Niakan, Mats Nilsson, Bayanne Olabi, Dana Pe'er, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Rahul Satija, Sarah A Teichmann, Barbara Treutlein, Roser Vento-Tormo, Simone Webb, null null
A roadmap for the Human Developmental Cell Atlas. Nature 597 (7875) (2021)
Ludvig Bergenstråhle, Bryan He, Joseph Bergenstråhle, Xesús M Abalo, Reza Mirzazadeh, Kim Thrane, Andrew L Ji, Alma Andersson, Ludvig Larsson, Nathalie Stakenborg, Guy Boeckxstaens, Paul A Khavari, James Y Zou, Joakim Lundeberg, Jonas Maaskola
Super-resolved spatial transcriptomics by deep data fusion. Nature biotechnology (2021)
Niclas Björn, Tejaswi Venkata Satya Badam, Rapolas Spalinskas, Eva Brandén, Hirsch Koyi, Rolf Lewensohn, Luigi De Petris, Zelmina Lubovac-Pilav, Pelin Sahlén, Joakim Lundeberg, Mika Gustafsson, Henrik Gréen
Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients. NPJ systems biology and applications 6 (1) (2020)
Michaela Asp, Joseph Bergenstråhle, Joakim Lundeberg
Spatially Resolved Transcriptomes-Next Generation Tools for Tissue Exploration. BioEssays : news and reviews in molecular, cellular and developmental biology 42 (10) (2020)
Cantin Ortiz, José Fernandéz Navarro, Aleksandra Jurek, Antje Märtin, Joakim Lundeberg, Konstantinos Meletis
Molecular atlas of the adult mouse brain. Science advances 6 (26) (2020)
Alma Andersson, Joseph Bergenstråhle, Michaela Asp, Ludvig Bergenstråhle, Aleksandra Jurek, José Fernandéz Navarro, Joakim Lundeberg
Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography. Communications biology 3 (1) (2020)
Joseph Bergenstråhle, Ludvig Larsson, Joakim Lundeberg
Seamless integration of image and molecular analysis for spatial transcriptomics workflows. BMC genomics 21 (1) (2020)
Enric Llorens-Bobadilla, James M Chell, Pierre Le Merre, Yicheng Wu, Margherita Zamboni, Joseph Bergenstråhle, Moa Stenudd, Elena Sopova, Joakim Lundeberg, Oleg Shupliakov, Marie Carlén, Jonas Frisén
A latent lineage potential in resident neural stem cells enables spinal cord repair. Science (New York, N.Y.) 370 (6512) (2020)
Bryan He, Ludvig Bergenstråhle, Linnea Stenbeck, Abubakar Abid, Alma Andersson, Åke Borg, Jonas Maaskola, Joakim Lundeberg, James Y Zou
Integrating spatial gene expression and breast tumour morphology via deep learning. Nature biomedical engineering 4 (8) (2020)
Sarbashis Das, Christoffer Frisk, Maria J Eriksson, Anna Walentinsson, Matthias Corbascio, Camilla Hage, Chanchal Kumar, Michaela Asp, Joakim Lundeberg, Eva Maret, Hans Persson, Cecilia Linde, Bengt Persson
Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction. Scientific reports 9 (1) (2019)
Stefania Giacomello, Joakim Lundeberg
Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays. Nature protocols 13 (11) (2019)
Silas Maniatis, Tarmo Äijö, Sanja Vickovic, Catherine Braine, Kristy Kang, Annelie Mollbrink, Delphine Fagegaltier, Žaneta Andrusivová, Sami Saarenpää, Gonzalo Saiz-Castro, Miguel Cuevas, Aaron Watters, Joakim Lundeberg, Richard A Bonneau, Hemali Phatnani
Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis. Science (New York, N.Y.) 364 (6435) (2019)
Anna Lundmark, Natalija Gerasimcik, Tove Båge, Anders Jemt, Annelie Mollbrink, Fredrik Salmén, Joakim Lundeberg, Tülay Yucel-Lindberg
Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics. Scientific reports 8 (1) (2018)
Emelie Berglund, Jonas Maaskola, Niklas Schultz, Stefanie Friedrich, Maja Marklund, Joseph Bergenstråhle, Firas Tarish, Anna Tanoglidi, Sanja Vickovic, Ludvig Larsson, Fredrik Salmén, Christoph Ogris, Karolina Wallenborg, Jens Lagergren, Patrik Ståhl, Erik Sonnhammer, Thomas Helleday, Joakim Lundeberg
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. Nature communications 9 (1) (2018)
Peter Järver, Aleksandra Dondalska, Candice Poux, AnnSofi Sandberg, Joseph Bergenstråhle, Annette E Sköld, Nathalie Dereuddre-Bosquet, Fréderic Martinon, Sandra Pålsson, Eman Zaghloul, David Brodin, Birgitta Sander, Kim A Lennox, Mark A Behlke, Samir El-Andaloussi, Janne Lehtiö, Joakim Lundeberg, Roger LeGrand, Anna-Lena Spetz
Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis. Scientific reports 8 (1) (2018)
Yue O O Hu, Nelson Ndegwa, Johannes Alneberg, Sebastian Johansson, Jürg Brendan Logue, Mikael Huss, Max Käller, Joakim Lundeberg, Jens Fagerberg, Anders F Andersson
Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems. Scientific reports 8 (1) (2018)
Michaela Asp, Fredrik Salmén, Patrik L Ståhl, Sanja Vickovic, Ulrika Felldin, Marie Löfling, José Fernandez Navarro, Jonas Maaskola, Maria J Eriksson, Bengt Persson, Matthias Corbascio, Hans Persson, Cecilia Linde, Joakim Lundeberg
Spatial detection of fetal marker genes expressed at low level in adult human heart tissue. Scientific reports 7 (1) (2017)