Lundeberg J

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Family name Lundeberg
Given name Joakim
Initials J
ORCID

ORCID 0000-0003-4313-1601
Affiliations

97 publications

PubMed DOI Crossref
In-depth patient-specific analysis of tumor heterogeneity in melanoma brain metastasis: Insights from spatial transcriptomics and multi-region bulk sequencing.
Sharma N, Rájová J, Mermelekas G, ..., Pernemalm M, Eriksson H
Transl Oncol 59 (-) 102468 [2025-07-15; online 2025-07-15]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] Bioinformatics Support for Computational Resources [Service]
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]
In Situ Sequencing [Service]
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]
Bioinformatics Support for Computational Resources [Service]
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]
In Situ Sequencing [Collaborative]
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
- - (-) - [2024-01-25; online 2024-01-25]
Spatial Proteomics [Service]
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 382 (6675) eadf8486 [2023-12-08; online 2023-12-08]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Short read NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial multimodal analysis of transcriptomes and metabolomes in tissues.
Vicari M, Mirzazadeh R, Nilsson A, ..., Andrén PE, Lundeberg J
Nat. Biotechnol. - (-) - [2023-09-04; online 2023-09-04]
In Situ Sequencing [Collaborative] Spatial Mass Spectrometry [Collaborative]
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]
NGI Short read [Service] NGI Spatial omics NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service] In Situ Sequencing [Collaborative] NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] In Situ Sequencing [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
NGI Short read [Service] NGI Spatial omics NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
In Situ Sequencing [Service]
PubMed DOI Crossref
Genome-wide spatial expression profiling in formalin-fixed tissues.
Gracia Villacampa E, Larsson L, Mirzazadeh R, ..., Carlson J, Lundeberg J
Cell Genomics 1 (3) 100065 [2021-12-08; online 2021-12-08]
NGI Short read [Service] NGI Spatial omics [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Support for Computational Resources [Service]
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]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]
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]
In Situ Sequencing [Collaborative] Spatial Proteomics
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 370 (6512) eabb8795 [2020-10-02; online 2020-10-03]
Eukaryotic Single Cell Genomics (ESCG) [Service] Integrated Microscopy Technologies Stockholm [Service]
PubMed DOI Crossref
Genetic association of gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients using whole-exome sequencing.
Svedberg A, Björn N, Sigurgeirsson B, ..., Lundeberg J, Gréen H
Lung Cancer 147 (-) 106-114 [2020-09-00; online 2020-07-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.
Ji AL, Rubin AJ, Thrane K, ..., Lundeberg J, Khavari PA
Cell 182 (2) 497-514.e22 [2020-07-23; online 2020-06-23]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues.
Berglund E, Saarenpää S, Jemt A, ..., Lundeberg J, Giacomello S
BMC Genomics 21 (1) 298 [2020-04-15; online 2020-04-15]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genes and variants in hematopoiesis-related pathways are associated with gemcitabine/carboplatin-induced thrombocytopenia.
Björn N, Sigurgeirsson B, Svedberg A, ..., Lundeberg J, Gréen H
Pharmacogenomics J. 20 (2) 179-191 [2020-04-00; online 2019-10-15]
Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J
Cell 179 (7) 1647-1660.e19 [2019-12-12; online 2019-12-14]
Advanced FISH Technologies Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
High-definition spatial transcriptomics for in situ tissue profiling.
Vickovic S, Eraslan G, Salmén F, ..., Regev A, Ståhl PL
Nat. Methods 16 (10) 987-990 [2019-10-00; online 2019-09-09]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection.
Poux C, Dondalska A, Bergenstråhle J, ..., Tregoning JS, Spetz AL
Front Immunol 10 (-) 2161 [2019-09-12; online 2019-09-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.
Maniatis S, Äijö T, Vickovic S, ..., Bonneau R, Phatnani H
Science 364 (6435) 89-93 [2019-04-05; online 2019-04-06]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A radical switch in clonality reveals a stem cell niche in the epiphyseal growth plate.
Newton PT, Li L, Zhou B, ..., Sävendahl L, Chagin AS
Nature 567 (7747) 234-238 [2019-03-00; online 2019-02-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.
Salmén F, Ståhl PL, Mollbrink A, ..., Frisén J, Lundeberg J
Nat Protoc 13 (11) 2501-2534 [2018-11-00; online 2018-10-26]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Global Proteomics and Proteogenomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma
Thrane K, Eriksson H, Maaskola J, Hansson J, Lundeberg J
Cancer Res 78 (20) 5970-5979 [2018-10-15; online 2018-10-15]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
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]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.
Dias DO, Kim H, Holl D, ..., Göritz C, Frisén J
Cell 173 (1) 153-165.e22 [2018-03-22; online 2018-03-01]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.
Ameur A, Dahlberg J, Olason P, ..., Magnusson PK, Gyllensten U
Eur. J. Hum. Genet. 25 (11) 1253-1260 [2017-11-00; online 2017-08-23]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
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]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatially resolved transcriptome profiling in model plant species.
Giacomello S, Salmén F, Terebieniec BK, ..., Street NR, Lundeberg J
NPLANTS 3 (-) 17061 [2017-05-08; online 2017-05-08]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.
Zhu Y, Engström PG, Tellgren-Roth C, ..., Scheynius A, Lehtiö J
Nucleic Acids Res. 45 (5) 2629-2643 [2017-03-17; online 2017-01-20]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Proteomics Mass spectrometry [Technology development] Global Proteomics and Proteogenomics [Technology development] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Comparison of whole genome amplification techniques for human single cell exome sequencing.
Borgström E, Paterlini M, Mold JE, Frisen J, Lundeberg J
PLoS ONE 12 (2) e0171566 [2017-02-16; online 2017-02-16]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle.
Sigurgeirsson B, Åmark H, Jemt A, ..., Lundeberg J, Gidlöf S
Biol. Reprod. 96 (1) 24-33 [2017-01-01; online 2017-04-11]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.
Jemt A, Salmén F, Lundmark A, ..., Yucel-Lindberg T, Lundeberg J
Sci Rep 6 (-) 37137 [2016-11-16; online 2016-11-16]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Ståhl PL, Salmén F, Vickovic S, ..., Lundeberg J, Frisén J
Science 353 (6294) 78-82 [2016-07-01; online 2016-07-02]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Fluorescence Tissue Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]
PubMed DOI Crossref
Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities.
Gréen H, Hasmats J, Kupershmidt I, ..., Peterson C, Lundeberg J
Clin. Cancer Res. 22 (2) 366-373 [2016-01-15; online 2015-09-16]
Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis.
Bersani C, Huss M, Giacomello S, ..., Lui WO, Wiman KG
Oncotarget 7 (2) 1895-1911 [2016-01-12; online 2015-12-18]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Transcriptome analysis reveals mucin 4 to be highly associated with periodontitis and identifies pleckstrin as a link to systemic diseases.
Lundmark A, Davanian H, Båge T, ..., Lundeberg J, Yucel-Lindberg T
Sci Rep 5 (-) 18475 [2015-12-21; online 2015-12-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring.
Kvastad L, Werne Solnestam B, Johansson E, ..., Latta D, Lundeberg J
Sci Rep 5 (-) 16519 [2015-11-12; online 2015-11-12]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).
Delhomme N, Sundström G, Zamani N, ..., Grabherr MG, Street NR
PLoS ONE 10 (9) e0139080 [2015-09-28; online 2015-09-28]
Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures.
Stödberg T, McTague A, Ruiz AJ, ..., Wedell A, Kurian MA
Nat Commun 6 (-) 8038 [2015-09-03; online 2015-09-03]
Clinical Genomics Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution.
Sahlén P, Abdullayev I, Ramsköld D, ..., Lundeberg J, Sandberg R
Genome Biol. 16 (-) 156 [2015-08-03; online 2015-08-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Toward Rare Blood Cell Preservation for RNA Sequencing.
Vickovic S, Ahmadian A, Lewensohn R, Lundeberg J
J Mol Diagn 17 (4) 352-359 [2015-07-00; online 2015-05-16]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Endonuclease specificity and sequence dependence of type IIS restriction enzymes.
Lundin S, Jemt A, Terje-Hegge F, ..., Lexow P, Lundeberg J
PLoS ONE 10 (1) e0117059 [2015-01-28; online 2015-01-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing.
Lindholm ME, Huss M, Solnestam BW, ..., Lundeberg J, Sundberg CJ
FASEB J. 28 (10) 4571-4581 [2014-10-00; online 2014-07-11]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
The Chironomus tentans genome sequence and the organization of the Balbiani ring genes.
Kutsenko A, Svensson T, Nystedt B, ..., Visa N, Wieslander L
BMC Genomics 15 (-) 819 [2014-09-27; online 2014-09-27]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
BESST--efficient scaffolding of large fragmented assemblies.
Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L
BMC Bioinformatics 15 (-) 281 [2014-08-15; online 2014-08-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Nuclease-assisted suppression of human DNA background in sepsis.
Song Y, Giske CG, Gille-Johnson P, ..., Lundeberg J, Gyarmati P
PLoS ONE 9 (7) e103610 [2014-07-30; online 2014-07-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Analysis of stranded information using an automated procedure for strand specific RNA sequencing.
Sigurgeirsson B, Emanuelsson O, Lundeberg J
BMC Genomics 15 (-) 631 [2014-07-28; online 2014-07-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.
Alexeyenko A, Nystedt B, Vezzi F, ..., Wu CC, Lundeberg J
BMC Genomics 15 (-) 439 [2014-06-06; online 2014-06-06]
Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The age and genomic integrity of neurons after cortical stroke in humans.
Huttner HB, Bergmann O, Salehpour M, ..., Lundeberg J, Frisén J
Nat. Neurosci. 17 (6) 801-803 [2014-06-00; online 2014-04-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Sequencing degraded RNA addressed by 3' tag counting.
Sigurgeirsson B, Emanuelsson O, Lundeberg J
PLoS ONE 9 (3) e91851 [2014-03-14; online 2014-03-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Visual detection of DNA on paper chips.
Song Y, Gyarmati P, Araújo AC, ..., Brumer H, Ståhl PL
Anal. Chem. 86 (3) 1575-1582 [2014-02-04; online 2014-01-17]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Assessment of whole genome amplification for sequence capture and massively parallel sequencing.
Hasmats J, Gréen H, Orear C, ..., Käller M, Lundeberg J
PLoS ONE 9 (1) e84785 [2014-01-07; online 2014-01-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Integrated molecular portrait of non-small cell lung cancers.
Lazar V, Suo C, Orear C, ..., Hansson J, Pawitan Y
BMC Med Genomics 6 (-) 53 [2013-12-03; online 2013-12-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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High expression of glycolytic and pigment proteins is associated with worse clinical outcome in stage III melanoma.
Falkenius J, Lundeberg J, Johansson H, ..., Hansson J, Egyhazi Brage S
Melanoma Res. 23 (6) 452-460 [2013-12-00; online 2013-10-17]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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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]
Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support for Computational Resources Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Hereditary uveal melanoma: a report of a germline mutation in BAP1.
Höiom V, Edsgärd D, Helgadottir H, ..., Emanuelsson O, Hansson J
Genes Chromosomes Cancer 52 (4) 378-384 [2013-04-00; online 2013-01-23]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.
Lundin S, Gruselius J, Nystedt B, ..., Käller M, Lundeberg J
Sci Rep 3 (-) 1186 [2013-03-09; online 2013-03-09]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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TagGD: fast and accurate software for DNA Tag generation and demultiplexing.
Costea PI, Lundeberg J, Akan P
PLoS ONE 8 (3) e57521 [2013-03-04; online 2013-03-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis.
Gioti A, Nystedt B, Li W, ..., Heitman J, Scheynius A
MBio 4 (1) e00572-e00512 [2013-01-22; online 2013-01-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines.
Akan P, Alexeyenko A, Costea PI, ..., Uhlén M, Lundeberg J
Genome Med 4 (11) 86 [2012-11-18; online 2012-11-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics
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Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.
Solnestam BW, Stranneheim H, Hällman J, ..., Lundeberg J, Akan P
BMC Genomics 13 (-) 574 [2012-10-30; online 2012-10-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics
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Gene expression profiles in paired gingival biopsies from periodontitis-affected and healthy tissues revealed by massively parallel sequencing.
Davanian H, Stranneheim H, Båge T, ..., Lundeberg J, Yucel-Lindberg T
PLoS ONE 7 (9) e46440 [2012-09-28; online 2012-09-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Identification of candidate SNPs for drug induced toxicity from differentially expressed genes in associated tissues.
Hasmats J, Kupershmidt I, Rodríguez-Antona C, ..., Lundeberg J, Green H
Gene 506 (1) 62-68 [2012-09-10; online 2012-07-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Stepping stones in DNA sequencing.
Stranneheim H, Lundeberg J
Biotechnol J 7 (9) 1063-1073 [2012-09-00; online 2012-08-08]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Validation of whole genome amplification for analysis of the p53 tumor suppressor gene in limited amounts of tumor samples.
Hasmats J, Green H, Solnestam BW, ..., Bjursell M, Lundeberg J
Biochem. Biophys. Res. Commun. 425 (2) 379-383 [2012-08-24; online 2012-07-31]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Toward the single-hour high-quality genome.
Ståhl PL, Lundeberg J
Annu. Rev. Biochem. 81 (-) 359-378 [2012-03-20; online 2012-03-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Signaling pathways involved in the regulation of TNFα-induced toll-like receptor 2 expression in human gingival fibroblasts.
Davanian H, Båge T, Lindberg J, ..., Sällberg Chen M, Yucel-Lindberg T
Cytokine 57 (3) 406-416 [2012-03-00; online 2012-01-10]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Adenosine kinase deficiency disrupts the methionine cycle and causes hypermethioninemia, encephalopathy, and abnormal liver function.
Bjursell MK, Blom HJ, Cayuela JA, ..., Lundeberg J, Wedell A
Am. J. Hum. Genet. 89 (4) 507-515 [2011-10-07; online 2011-10-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Scalable transcriptome preparation for massive parallel sequencing.
Stranneheim H, Werne B, Sherwood E, Lundeberg J
PLoS ONE 6 (7) e21910 [2011-07-07; online 2011-07-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Translational database selection and multiplexed sequence capture for up front filtering of reliable breast cancer biomarker candidates.
Ståhl PL, Bjursell MK, Mahdessian H, ..., Jirström K, Lundeberg J
PLoS ONE 6 (6) e20794 [2011-06-15; online 2011-06-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Large scale library generation for high throughput sequencing.
Borgström E, Lundin S, Lundeberg J
PLoS ONE 6 (4) e19119 [2011-04-27; online 2011-04-27]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Sun-induced nonsynonymous p53 mutations are extensively accumulated and tolerated in normal appearing human skin.
Ståhl PL, Stranneheim H, Asplund A, ..., Pontén F, Lundeberg J
J. Invest. Dermatol. 131 (2) 504-508 [2011-02-00; online 2010-10-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Defining the transcriptome and proteome in three functionally different human cell lines.
Lundberg E, Fagerberg L, Klevebring D, ..., Mann M, Uhlen M
Mol. Syst. Biol. 6 (-) 450 [2010-12-21; online 2010-12-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics
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Analysis of transcript and protein overlap in a human osteosarcoma cell line.
Klevebring D, Fagerberg L, Lundberg E, ..., Uhlén M, Lundeberg J
BMC Genomics 11 (-) 684 [2010-12-02; online 2010-12-02]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure Spatial Proteomics
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Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.
Hedskog C, Mild M, Jernberg J, ..., Andersson B, Albert J
PLoS ONE 5 (7) e11345 [2010-07-07; online 2010-07-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Classification of DNA sequences using Bloom filters.
Stranneheim H, Käller M, Allander T, ..., Arvestad L, Lundeberg J
Bioinformatics 26 (13) 1595-1600 [2010-07-01; online 2010-05-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Increased throughput by parallelization of library preparation for massive sequencing.
Lundin S, Stranneheim H, Pettersson E, Klevebring D, Lundeberg J
PLoS ONE 5 (4) e10029 [2010-04-06; online 2010-04-06]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines.
Klevebring D, Bjursell M, Emanuelsson O, Lundeberg J
PLoS ONE 5 (3) e9762 [2010-03-25; online 2010-03-25]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Gene-specific FACS sorting method for target selection in high-throughput amplicon sequencing.
Sandberg J, Neiman M, Ahmadian A, Lundeberg J
BMC Genomics 11 (-) 140 [2010-02-26; online 2010-02-26]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
SciLifeLab Data Centre
Publications 9.5.1