Lundeberg J

JSON
CSV
XLSX
TXT
Family name Lundeberg
Given name Joakim
Initials J
ORCID

ORCID 0000-0003-4313-1601
Affiliations

43 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]
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
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]
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
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]
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]
DOI Crossref
snPATHO-seq: unlocking the pathology archives
Wang T, Harvey K, Morlanes JE, ..., Swarbrick A, Martelotto L
- - (-) - [2023-12-08; online 2023-12-08]
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
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
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]
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]
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
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 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
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
- - (-) - [2020-08-24; online 2020-08-24]
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
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
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
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