Lundeberg J

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Family name Lundeberg
Given name Joakim
Initials J
ORCID

ORCID 0000-0003-4313-1601
Affiliations

72 publications

PubMed DOI Crossref
Spatial architecture of development and disease.
Lázár E, Lundeberg J
Nat. Rev. Genet. 27 (2) 118-136 [2026-02-00; online 2025-09-30]
PubMed DOI Crossref
Spatial single-cell atlas reveals regional variations in healthy and diseased human lung.
Firsova AB, Marco Salas S, Kuemmerle LB, ..., Nawijn MC, Samakovlis C
Nat Commun 16 (1) 9745 [2025-11-05; online 2025-11-05]
PubMed DOI Crossref
Spatiotemporal gene expression and cellular dynamics of the developing human heart.
Lázár E, Mauron R, Andrusivová Ž, ..., Adameyko I, Lundeberg J
Nat. Genet. 57 (11) 2756-2771 [2025-11-00; online 2025-10-29]
DOI Crossref
Epithelial dysfunction as a driver of symptoms in gastrointestinal disorders
Denadai-Souza A, Denadai-Souza A, Modave E, ..., Voet T, Boeckxstaens G
- - (-) - [2025-09-11; online 2025-09-11]
PubMed DOI Crossref
Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data.
Li T, Yang Q, Acs B, ..., Chen X, Hartman J
NPJ Precis Oncol 9 (1) 310 [2025-09-09; online 2025-09-09]
Camilla Engblom SciLifeLab Fellow
PubMed DOI Crossref
Putting cancer immunotherapy into spatial context in the clinic.
Engblom C, Lundeberg J
Nat. Biotechnol. 43 (4) 471-476 [2025-04-00; online 2025-04-15]
Camilla Engblom SciLifeLab Fellow
DOI Crossref
Rare gain-of-function regulatory mutations explain the missing heritability of bicuspid aortic valve
Zhigulev A, Petersson Sjögren M, Buyan A, ..., Björck HM, Sahlén P
- - (-) - [2025-02-23; online 2025-02-23]
PubMed DOI Crossref
High-parametric protein maps reveal the spatial organization in early-developing human lung.
Sariyar S, Sountoulidis A, Hansen JN, ..., Lundberg E, Ayoglu B
Nat Commun 15 (1) 9381 [2024-10-30; online 2024-10-30]
PubMed DOI Crossref
snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.
Wang T, Roach MJ, Harvey K, ..., Swarbrick A, Martelotto LG
Commun Biol 7 (1) 1340 [2024-10-16; online 2024-10-16]
DOI Crossref
A topographic lung cell atlas reveals regional variation in cell-type specific gene programs and identifies healthy and diseased cellular neighborhoods
Samakovlis C, Firsova A, Salas SM, ..., Nilsson M, Nawijn M
- - (-) - [2024-10-07; online 2024-10-07]
PubMed DOI Crossref
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract.
Monasterio G, Morales RA, Bejarano DA, ..., Das S, Villablanca EJ
Nat Protoc 19 (10) 3085-3137 [2024-10-00; online 2024-06-21]
PubMed DOI Crossref
Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution.
Hildebrandt F, Iturritza MU, Zwicker C, ..., Lundeberg J, Ankarklev J
Nat Commun 15 (1) 7105 [2024-08-19; online 2024-08-19]
PubMed DOI Crossref
Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis.
Franzén L, Olsson Lindvall M, Hühn M, ..., Ståhl PL, Hornberg JJ
Nat. Genet. 56 (8) 1725-1736 [2024-08-00; online 2024-07-01]
PubMed DOI Crossref
A community effort to track commercial single-cell and spatial 'omic technologies and business trends.
De Jonghe J, Opzoomer JW, Vilas-Zornoza A, ..., Cribbs AP, Taylor-King JP
Nat. Biotechnol. 42 (7) 1017-1023 [2024-07-00; online 2024-07-18]
PubMed DOI Crossref
Spatial multimodal analysis of transcriptomes and metabolomes in tissues.
Vicari M, Mirzazadeh R, Nilsson A, ..., Andrén PE, Lundeberg J
Nat. Biotechnol. 42 (7) 1046-1050 [2024-07-00; online 2023-09-04]
DOI Crossref
Spatial transcriptomics Visium data for mouse bleomycin model of lung fibrosis
Franzén L, Lindvall MO, Hühn M, ..., Ståhl PL, Hornberg JJ
- - (-) - [2024-05-02]
PubMed DOI Crossref
Spatial landmark detection and tissue registration with deep learning.
Ekvall M, Bergenstråhle L, Andersson A, ..., Käll L, Lundeberg J
Nat. Methods 21 (4) 673-679 [2024-04-00; online 2024-03-04]
DOI Crossref
Spatial Dynamics of the Developing Human Heart
Lázár E, Mauron R, Andrusivová Ž, ..., Adameyko I, Lundeberg J
- - (-) - [2024-03-14; online 2024-03-14]
DOI Crossref
High-parametric protein maps reveal the spatial organization in early-developing human lung
Sariyar S, Sountoulidis A, Hansen JN, ..., Lundberg E, Ayoglu B
- - (-) - [2024-01-25; online 2024-01-25]
DOI Crossref
Host-Pathogen Interactions in the Plasmodium -Infected Mouse Liver at Spatial and Single-Cell Resolution
Hildebrandt F, Urrutia-Iturritza M, Zwicker C, ..., Lundeberg J, Ankarklev J
- - (-) - [2023-12-22; online 2023-12-22]
PubMed DOI Crossref
Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics.
Engblom C, Thrane K, Lin Q, ..., Lundeberg J, Frisén J
Science (New York, N.Y.) 382 (6675) eadf8486 [2023-12-08; online 2023-12-08]
Camilla Engblom SciLifeLab Fellow
PubMed DOI Crossref
Comprehensive cell atlas of the first-trimester developing human brain.
Braun E, Danan-Gotthold M, Borm LE, ..., Sundström E, Linnarsson S
Science (New York, N.Y.) 382 (6667) eadf1226 [2023-10-13; online 2023-10-13]
PubMed DOI Crossref
Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization.
Larsson L, Franzén L, Ståhl PL, Lundeberg J
Bioinformatics 39 (10) - [2023-10-03; online 2023-10-17]
PubMed DOI Crossref
Expansion spatial transcriptomics.
Fan Y, Andrusivová Ž, Wu Y, ..., Lundeberg J, Wang B
Nat. Methods 20 (8) 1179-1182 [2023-08-00; online 2023-06-22]
PubMed DOI Crossref
The spatial landscape of gene expression isoforms in tissue sections.
Lebrigand K, Bergenstråhle J, Thrane K, ..., Waldmann R, Lundeberg J
Nucleic Acids Res. 51 (8) e47 [2023-05-08; online 2023-03-18]
PubMed DOI Crossref
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.
Li X, Andrusivova Z, Czarnewski P, ..., Lundeberg J, Sundström E
Nat. Neurosci. 26 (5) 891-901 [2023-05-00; online 2023-04-24]
PubMed DOI Crossref
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.
Sountoulidis A, Marco Salas S, Braun E, ..., Nilsson M, Samakovlis C
Nat. Cell Biol. 25 (2) 351-365 [2023-02-00; online 2023-01-16]
PubMed DOI Crossref
Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples.
Mirzazadeh R, Andrusivova Z, Larsson L, ..., Boeckxstaens G, Lundeberg J
Nat Commun 14 (1) 509 [2023-01-31; online 2023-01-31]
DOI Crossref
Spatial Multimodal Analysis of Transcriptomes and Metabolomes in Tissues
Vicari M, Mirzazadeh R, Nilsson A, ..., Andrén PE, Lundeberg J
- - (-) - [2023-01-27; online 2023-01-27]
DOI Crossref
Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue
Engblom C, Thrane K, Lin Q, ..., Lundeberg J, Frisén J
- - (-) - [2022-11-24; online 2022-11-24]
Camilla Engblom SciLifeLab Fellow
DOI Crossref
Comprehensive cell atlas of the first-trimester developing human brain
Braun E, Danan-Gotthold M, Borm LE, ..., Sundström E, Linnarsson S
- - (-) - [2022-10-25; online 2022-10-25]
PubMed DOI Crossref
Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones.
Marklund M, Schultz N, Friedrich S, ..., Sonnhammer E, Lundeberg J
Nat Commun 13 (1) 5475 [2022-09-17; online 2022-09-17]
PubMed DOI Crossref
Spatially resolved clonal copy number alterations in benign and malignant tissue.
Erickson A, He M, Berglund E, ..., Lamb AD, Lundeberg J
Nature 608 (7922) 360-367 [2022-08-00; online 2022-08-10]
PubMed DOI Crossref
Identification of early neurodegenerative pathways in progressive multiple sclerosis.
Kaufmann M, Schaupp AL, Sun R, ..., Mann M, Fugger L
Nat. Neurosci. 25 (7) 944-955 [2022-07-00; online 2022-06-20]
PubMed DOI Crossref
Super-resolved spatial transcriptomics by deep data fusion.
Bergenstråhle L, He B, Bergenstråhle J, ..., Lundeberg J, Maaskola J
Nat. Biotechnol. 40 (4) 476-479 [2022-04-00; online 2021-11-29]
PubMed DOI Crossref
Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.
Ratz M, von Berlin L, Larsson L, ..., Lundeberg J, Frisén J
Nat. Neurosci. 25 (3) 285-294 [2022-03-00; online 2022-02-24]
DOI Crossref
Clonally heritable gene expression imparts a layer of diversity within cell types
Mold JE, Weissman MH, Ratz M, ..., Michaëlsson J, Frisén J
- - (-) - [2022-02-16; online 2022-02-16]
PubMed DOI Crossref
The spatial transcriptomic landscape of the healing mouse intestine following damage.
Parigi SM, Larsson L, Das S, ..., Lundeberg J, Villablanca EJ
Nat Commun 13 (1) 828 [2022-02-11; online 2022-02-11]
Camilla Engblom SciLifeLab Fellow
DOI Crossref
Developmental origins of cell heterogeneity in the human lung
Sountoulidis A, Salas SM, Braun E, ..., Nilsson M, Samakovlis C
- - (-) - [2022-01-12; online 2022-01-12]
PubMed DOI Crossref
Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver.
Hildebrandt F, Andersson A, Saarenpää S, ..., Lundeberg J, Ankarklev J
Nat Commun 12 (1) 7046 [2021-12-02; online 2021-12-02]
DOI Crossref
A Landmark-based Common Coordinate Framework for Spatial Transcriptomics Data
Andersson A, Andrusivová Ž, Czarnewski P, ..., Sundström E, Lundeberg J
- - (-) - [2021-11-13; online 2021-11-13]
PubMed DOI Crossref
Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions.
Andersson A, Larsson L, Stenbeck L, ..., Engblom C, Lundeberg J
Nat Commun 12 (1) 6012 [2021-10-14; online 2021-10-14]
SciLifeLab Fellow
PubMed DOI Crossref
Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer.
Chelebian E, Avenel C, Kartasalo K, ..., Lundeberg J, Wählby C
Cancers (Basel) 13 (19) - [2021-09-28; online 2021-09-28]
DDLS Fellow Kimmo Kartasalo
DOI Crossref
Cell types and clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics
Ratz M, von Berlin L, Larsson L, ..., Lundeberg J, Frisén J
- - (-) - [2021-09-01; online 2021-09-01]
PubMed DOI Crossref
A roadmap for the Human Developmental Cell Atlas.
Haniffa M, Taylor D, Linnarsson S, ..., Webb S, Human Cell Atlas Developmental Biological Network
Nature 597 (7875) 196-205 [2021-09-00; online 2021-09-08]
PubMed DOI Crossref
A single-cell and spatially resolved atlas of human breast cancers.
Wu SZ, Al-Eryani G, Roden DL, ..., Perou CM, Swarbrick A
Nat. Genet. 53 (9) 1334-1347 [2021-09-00; online 2021-09-06]
DOI Crossref
Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the liver
Hildebrandt F, Andersson A, Saarenpää S, ..., Lundeberg J, Ankarklev J
- - (-) - [2021-01-12; online 2021-01-12]
PubMed DOI Crossref
The spatial RNA integrity number assay for in situ evaluation of transcriptome quality.
Kvastad L, Carlberg K, Larsson L, ..., Nistér M, Lundeberg J
Commun Biol 4 (1) 57 [2021-01-08; online 2021-01-08]
PubMed DOI Crossref
Spatially resolved transcriptomics adds a new dimension to genomics.
Larsson L, Frisén J, Lundeberg J
Nat. Methods 18 (1) 15-18 [2021-01-00; online 2021-01-08]
DOI Crossref
Human Developmental Cell Atlas: milestones achieved and the roadmap ahead
Haniffa M, Taylor D, Linnarsson S, ..., Vento-Tormo R, Webb S
- - (-) - [2020-10-12; online 2020-10-12]
PubMed DOI Crossref
Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography.
Andersson A, Bergenstråhle J, Asp M, ..., Fernández Navarro J, Lundeberg J
Commun Biol 3 (1) 565 [2020-10-09; online 2020-10-09]
PubMed DOI Crossref
A latent lineage potential in resident neural stem cells enables spinal cord repair.
Llorens-Bobadilla E, Chell JM, Le Merre P, ..., Carlén M, Frisén J
Science (New York, N.Y.) 370 (6512) - [2020-10-02; online 2020-10-03]
PubMed DOI Crossref
Spatially Resolved Transcriptomes-Next Generation Tools for Tissue Exploration.
Asp M, Bergenstråhle J, Lundeberg J
Bioessays 42 (10) e1900221 [2020-10-00; online 2020-05-04]
DOI Crossref
The spatial landscape of gene expression isoforms in tissue sections
Lebrigand K, Bergenstråhle J, Thrane K, ..., Waldmann R, Lundeberg J
bioRxiv - (-) - [2020-08-24; online 2020-08-24]
PubMed DOI Crossref
Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients.
Björn N, Badam TVS, Spalinskas R, ..., Gustafsson M, Gréen H
NPJ Syst Biol Appl 6 (1) 25 [2020-08-24; online 2020-08-24]
PubMed DOI Crossref
Integrating spatial gene expression and breast tumour morphology via deep learning.
He B, Bergenstråhle L, Stenbeck L, ..., Lundeberg J, Zou J
Nat Biomed Eng 4 (8) 827-834 [2020-08-00; online 2020-06-22]
DOI Crossref
Genome-wide Spatial Expression Profiling in FFPE Tissues
Villacampa EG, Larsson L, Kvastad L, ..., Carlson J, Lundeberg J
- - (-) - [2020-07-25; online 2020-07-25]
PubMed DOI Crossref
Seamless integration of image and molecular analysis for spatial transcriptomics workflows.
Bergenstråhle J, Larsson L, Lundeberg J
BMC Genomics 21 (1) 482 [2020-07-14; online 2020-07-14]
PubMed DOI Crossref
Molecular atlas of the adult mouse brain.
Ortiz C, Navarro JF, Jurek A, ..., Lundeberg J, Meletis K
Sci Adv 6 (26) eabb3446 [2020-06-00; online 2020-06-26]
PubMed DOI Crossref
Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.
Maniatis S, Äijö T, Vickovic S, ..., Bonneau R, Phatnani H
Science (New York, N.Y.) 364 (6435) 89-93 [2019-04-05; online 2019-04-06]
Sanja Vickovic SciLifeLab Fellow
PubMed DOI Crossref
Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction.
Das S, Frisk C, Eriksson MJ, ..., Linde C, Persson B
Sci Rep 9 (1) 3179 [2019-02-28; online 2019-02-28]
PubMed DOI Crossref
Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays.
Giacomello S, Lundeberg J
Nat Protoc 13 (11) 2425-2446 [2018-11-00; online 2018-10-26]
PubMed DOI Crossref
Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis.
Järver P, Dondalska A, Poux C, ..., LeGrand R, Spetz AL
Sci Rep 8 (1) 15841 [2018-10-26; online 2018-10-26]
PubMed DOI Crossref
Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.
Hu YOO, Ndegwa N, Alneberg J, ..., Fagerberg J, Andersson AF
Sci Rep 8 (1) 11907 [2018-08-09; online 2018-08-09]
DOI Crossref
Spatiotemporal Dynamics of Molecular Pathology in Amyotrophic Lateral Sclerosis
Maniatis S, Äijö T, Vickovic S, ..., Bonneau R, Phatnani H
bioRxiv - (-) - [2018-08-09; online 2018-08-09]
Sanja Vickovic SciLifeLab Fellow
DOI Crossref
Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors
Salmén F, Vickovic S, Larsson L, ..., Ståhl PL, Lundeberg J
- - (-) - [2018-06-29; online 2018-06-29]
Sanja Vickovic SciLifeLab Fellow
PubMed DOI Crossref
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.
Berglund E, Maaskola J, Schultz N, ..., Helleday T, Lundeberg J
Nat Commun 9 (1) 2419 [2018-06-20; online 2018-06-20]
Affiliated researcher Sanja Vickovic SciLifeLab Fellow
PubMed DOI Crossref
Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics.
Lundmark A, Gerasimcik N, Båge T, ..., Lundeberg J, Yucel-Lindberg T
Sci Rep 8 (1) 9370 [2018-06-19; online 2018-06-19]
PubMed DOI Crossref
Spatial detection of fetal marker genes expressed at low level in adult human heart tissue.
Asp M, Salmén F, Ståhl PL, ..., Linde C, Lundeberg J
Sci Rep 7 (1) 12941 [2017-10-11; online 2017-10-11]
Affiliated researcher Sanja Vickovic SciLifeLab Fellow
PubMed DOI Crossref
BESST--efficient scaffolding of large fragmented assemblies.
Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L
BMC Bioinformatics 15 (1) 281 [2014-08-15; online 2014-08-15]
PubMed DOI Crossref
The Norway spruce genome sequence and conifer genome evolution.
Nystedt B, Street NR, Wetterbom A, ..., Lundeberg J, Jansson S
Nature 497 (7451) 579-584 [2013-05-30; online 2013-05-22]
PubMed DOI Crossref
Improved gap size estimation for scaffolding algorithms.
Sahlin K, Street N, Lundeberg J, Arvestad L
Bioinformatics 28 (17) 2215-2222 [2012-09-01; online 2012-08-28]
SciLifeLab Data Centre
Publications 9.5.1