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KTH Royal Institute of Technology: Stockholm, Stockholm, SE

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KTH Royal Institute of Technology

Works (25)

A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract

Nature Protocols
2024-10 | Journal article
DOI: 10.1038/s41596-024-01001-2
Contributors: Gustavo Monasterio; Rodrigo A. Morales; David A. Bejarano; Xesús M. Abalo; Jennifer Fransson; Ludvig Larsson; Andreas Schlitzer; Joakim Lundeberg; Srustidhar Das; Eduardo J. Villablanca
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Spatial landmark detection and tissue registration with deep learning

Nature Methods
2024-04 | Journal article
DOI: 10.1038/s41592-024-02199-5
Contributors: Markus Ekvall; Ludvig Bergenstråhle; Alma Andersson; Paulo Czarnewski; Johannes Olegård; Lukas Käll; Joakim Lundeberg
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Crossref

Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization

Bioinformatics
2023-10-03 | Journal article
DOI: 10.1093/bioinformatics/btad626
Contributors: Ludvig Larsson; Lovisa Franzén; Patrik L Ståhl; Joakim Lundeberg; Macha Nikolski
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Crossref

Expansion spatial transcriptomics

Nature Methods
2023-08 | Journal article
DOI: 10.1038/s41592-023-01911-1
Contributors: Yuhang Fan; Žaneta Andrusivová; Yunming Wu; Chew Chai; Ludvig Larsson; Mengxiao He; Liqun Luo; Joakim Lundeberg; Bo Wang
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Crossref

Spatial landmark detection and tissue registration with deep learning

2023-08-26 | Preprint
DOI: 10.1101/2023.08.24.554614
Contributors: Markus Ekvall; Ludvig Bergenstråhle; Alma Andersson; Paulo Czarnewski; Johannes Olegård; Lukas Käll; Joakim Lundeberg
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Crossref

The spatial landscape of gene expression isoforms in tissue sections

Nucleic Acids Research
2023-05-08 | Journal article
DOI: 10.1093/nar/gkad169
Contributors: Kevin Lebrigand; Joseph Bergenstråhle; Kim Thrane; Annelie Mollbrink; Konstantinos Meletis; Pascal Barbry; Rainer Waldmann; Joakim Lundeberg
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Crossref

Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics

Nature Neuroscience
2022-03 | Journal article
DOI: 10.1038/s41593-022-01011-x
Contributors: Michael Ratz; Leonie von Berlin; Ludvig Larsson; Marcel Martin; Jakub Orzechowski Westholm; Gioele La Manno; Joakim Lundeberg; Jonas Frisén
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Crossref

A Landmark-based Common Coordinate Framework for Spatial Transcriptomics Data

2021-11-13 | Other
DOI: 10.1101/2021.11.11.468178
Contributors: Alma Andersson; Žaneta Andrusivová; Paulo Czarnewski; Xiaofei Li; Erik Sundström; Joakim Lundeberg
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Crossref

Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer

Cancers
2021-09-28 | Journal article
DOI: 10.3390/cancers13194837
Contributors: Eduard Chelebian; Christophe Avenel; Kimmo Kartasalo; Maja Marklund; Anna Tanoglidi; Tuomas Mirtti; Richard Colling; Andrew Erickson; Alastair Lamb; Joakim Lundeberg et al.
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Crossref

Cell types and clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics

2021-09-01 | Other
DOI: 10.1101/2021.08.31.458418
Contributors: Michael Ratz; Leonie von Berlin; Ludvig Larsson; Marcel Martin; Jakub Orzechowski Westholm; Gioele La Manno; Joakim Lundeberg; Jonas Frisén
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Crossref

The spatial landscape of clonal somatic mutations in benign and malignant tissue

2021-07-30 | Preprint
DOI: 10.21203/rs.3.rs-745238/v1
Contributors: Joakim Lundeberg; Andrew Erickson; Emelie Berglund; Mengxiao He; Maja Marklund; Reza Mirzazadeh; Niklas Schultz; Linda Kvastad; Alma Andersson; Ludvig Bergenstråhle et al.
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Crossref

Spatially resolved transcriptomics adds a new dimension to genomics

Nature Methods
2021-01 | Journal article
DOI: 10.1038/s41592-020-01038-7
Contributors: Ludvig Larsson; Jonas Frisén; Joakim Lundeberg
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Crossref

Seamless integration of image and molecular analysis for spatial transcriptomics workflows

BMC Genomics
2020-12 | Journal article
DOI: 10.1186/s12864-020-06832-3
Contributors: Joseph Bergenstråhle; Ludvig Larsson; Joakim Lundeberg
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Crossref

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration

BioEssays
2020-10 | Journal article
DOI: 10.1002/bies.201900221
Contributors: Michaela Asp; Joseph Bergenstråhle; Joakim Lundeberg
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Crossref

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography

Communications Biology
2020-10-09 | Journal article
DOI: 10.1038/s42003-020-01247-y
Contributors: Alma Andersson; Joseph Bergenstråhle; Michaela Asp; Ludvig Bergenstråhle; Aleksandra Jurek; José Fernández Navarro; Joakim Lundeberg
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Crossref

A latent lineage potential in resident neural stem cells enables spinal cord repair

Science
2020-10-02 | Journal article
DOI: 10.1126/science.abb8795
Contributors: Enric Llorens-Bobadilla; James M. Chell; Pierre Le Merre; Yicheng Wu; Margherita Zamboni; Joseph Bergenstråhle; Moa Stenudd; Elena Sopova; Joakim Lundeberg; Oleg Shupliakov et al.
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Crossref

The spatial landscape of gene expression isoforms in tissue sections

2020-08-24 | Preprint
DOI: 10.1101/2020.08.24.252296
Contributors: Kevin Lebrigand; Joseph Bergenstråhle; Kim Thrane; Annelie Mollbrink; Konstantinos Meletis; Pascal Barbry; Rainer Waldmann; Joakim Lundeberg
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Crossref

Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients

npj Systems Biology and Applications
2020-08-24 | Journal article
DOI: 10.1038/s41540-020-00146-6
Contributors: Niclas Björn; Tejaswi Venkata Satya Badam; Rapolas Spalinskas; Eva Brandén; Hirsh Koyi; Rolf Lewensohn; Luigi De Petris; Zelmina Lubovac-Pilav; Pelin Sahlén; Joakim Lundeberg et al.
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Crossref

Genome-wide Spatial Expression Profiling in FFPE Tissues

2020-07-25 | Preprint
DOI: 10.1101/2020.07.24.219758
Contributors: Eva Gracia Villacampa; Ludvig Larsson; Linda Kvastad; Alma Andersson; Joseph Carlson; Joakim Lundeberg
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Crossref

Molecular atlas of the adult mouse brain

Science Advances
2020-06-26 | Journal article
DOI: 10.1126/sciadv.abb3446
Contributors: Cantin Ortiz; Jose Fernandez Navarro; Aleksandra Jurek; Antje Märtin; Joakim Lundeberg; Konstantinos Meletis
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Crossref

Integrating spatial gene expression and breast tumour morphology via deep learning

Nature Biomedical Engineering
2020-06-22 | Journal article
DOI: 10.1038/s41551-020-0578-x
Contributors: Bryan He; Ludvig Bergenstråhle; Linnea Stenbeck; Abubakar Abid; Alma Andersson; Åke Borg; Jonas Maaskola; Joakim Lundeberg; James Zou
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Crossref

Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction

Scientific Reports
2019-02-28 | Journal article
DOI: 10.1038/s41598-019-39445-2
Contributors: Sarbashis Das; Christoffer Frisk; Maria J. Eriksson; Anna Walentinsson; Matthias Corbascio; Camilla Hage; Chanchal Kumar; Michaela Asp; Joakim Lundeberg; Eva Maret et al.
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Crossref

Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays

Nature Protocols
2018-11 | Journal article
DOI: 10.1038/s41596-018-0046-1
Contributors: Stefania Giacomello; Joakim Lundeberg
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Crossref

Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems

Scientific Reports
2018-08-09 | Journal article
DOI: 10.1038/s41598-018-29920-7
Contributors: Yue O. O. Hu; Nelson Ndegwa; Johannes Alneberg; Sebastian Johansson; Jürg Brendan Logue; Mikael Huss; Max Käller; Joakim Lundeberg; Jens Fagerberg; Anders F. Andersson
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Crossref

Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics

Scientific Reports
2018-06-19 | Journal article
DOI: 10.1038/s41598-018-27627-3
Contributors: Anna Lundmark; Natalija Gerasimcik; Tove Båge; Anders Jemt; Annelie Mollbrink; Fredrik Salmén; Joakim Lundeberg; Tülay Yucel-Lindberg
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Crossref
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