Publications

Preprints


The spatial transcriptomic landscape of the healing intestine following damage
Parigi S, Larsson L, Das S, Ramirez Flores RO, Frede A,Tripathi KP, Diaz OE, Selin K, Morales  RA, Luo X, Monasterio  G, Engblom C, Gagliani N, Saez-Rodriguez J, Lundeberg J, Villablanca EJ
Available at bioRxiv (2021)

Cell types and clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics
Ratz M, von Berlin L, Larsson L, Martin M, Orzechowski Westholm J, La Manno G, Lundeberg J, Frisén J
Available at bioRxiv (2021)

The spatial landscape of gene expression isoforms in tissue sections
Lebrigand K, Bergenstråhle J, Thrane K, Mollbrink A, Barbry P, Waldmann R, & Lundeberg J
Available at bioRxiv (2020)

Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the liver
Hildebrandt FFA, Andersson A, Saarenpaa S, Larsson L,Van Hul N, Kanatani S, Masek J, Ellis E, Barragan A, Mollbrink A, Andersson ER, Lundeberg J, Ankarklev J
Available at bioRxiv (2020)

Genome-wide Spatial Expression Profiling in FFPE Tissues
Gracia Villacampa E, Larsson L, Kvastad L, Andersson A, Carlson J, & Lundeberg J
Available at bioRxiv (2020)

Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships
Andersson A, Larsson L, Stenbeck L, Salmén F, Ehinger A, Wu S, Al-Eryani G, Roden D, Swarbrick A, Borg Å, Frisén J, Engblom C, & Lundeberg J
Available at bioRxiv (2020)

Super-resolved spatial transcriptomics by deep data fusion
Bergenstråhle L, He B, Bergenstråhle J, Andersson A, Zou J, Lundeberg J & Maaskola J
Available at bioRxiv (2020)

Charting Tissue Expression Anatomy by Spatial Transcriptome Deconvolution
Maaskola J, Bergenstråhle L, Jurek A, Fernández Navarro J, Lagergren J, & Lundeberg J
Available at bioRxiv (2018)

Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors
Salmén F, Vickovic S, Larsson L, Stenbeck L, Vallon-Christersson J, Ehinger A, Häkkinen J, Borg Å, Frisén J, Ståhl PL & Lundeberg J
Available at bioRxiv (2018)

2021


Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin
Bäckdahl J, Franzén L, Massier L, Li Q, Jalkanen J, Gao H, Andersson A, Bhalla N, Thorell A, Rydén M, Ståhl PL, Mejhert N
Cell Metabolism (10 Aug 2021)

Single cell and spatial transcriptomics in human tendon disease indicate dysregulated immune homeostasis
Akbar M, MacDonald L, Crowe LAN, Carlberg K, Kurowska-Stolarska M, Ståhl PL, Snelling SJB, McInnes IB, Millar NL
Ann Rheum Dis. (17 May 2021)

A new era for plant science: spatial single-cell transcriptomics
Giacomello S
Current Opinion in Plant Biology (Apr 2021)

A New Era for Space Life Science: International Standards for Space Omics Processing
Rutter L, Barker R, Bezdan D, Cope H, Costes SV, Degoricija L, Fisch KM, Gabitto MI, Gebre S, Giacomello S, Gilroy S, Green SJ, Mason CE, Reinsch SS, Szewczyk NJ, Taylor DM, Galazka JM, Herranz R, Muratani M
Patterns (11 Dec 2020)

sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling
Andersson A, Lundeberg J
Oxford Bioinformatics (11 March 2021)

The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
Kvastad L, Carlberg K, Larsson L, Villacampa EG, Stuckey A, Stenbeck L, Mollbrink A, Zamboni M, Magnusson JP, Basmaci E, Shamikh A, Prochazka G, Schaupp AL, Borg Å, Fugger L, Nistér M, Lundeberg J
Communications Biology (8 Jan 2021)

Spatially resolved transcriptomics adds a new dimension to genomics
Larsson L, Frisén J, Lundeberg J
Nature Methods (6 Jan 2021)

2020


Single-Stranded Oligonucleotide-Mediated Inhibition of Respiratory Syncytial Virus Infection
Pålsson SA, Dondalska A, Bergenstråhle J, Rolfes C, Björk A, Sedano L, Power UF, Rameix-Welti MA, Lundeberg J, Wahren-Herlenius M, Mastrangelo P, Eleouet JF, Le Goffic R, Galloux M, Spetz AL
Frontiers in Immunology (8 Dec 2020)

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography
Andersson A, Bergenstråhle J, Asp M, Bergenstråhle L, Jurek A, Fernández Navarro J, & Lundeberg J
Communiations Biology (9 Oct 2020)

A latent lineage potential in resident neural stem cells enables spinal cord repair
Llorens-Bobadilla E, Chell JM, Le Merre P, Wu Y, Zamboni M, Bergenstråhle J, Stenudd M, Sopova E, Lundeberg J, Shupliakov O, Carlén M, Frisén J
Science (2 Oct 2020)

Spatial Transcriptomics Reveals Genes Associated with Dysregulated Mitochondrial Functions and Stress Signaling in Alzheimer Disease
Navarro JF, Croteau DL, Jurek A, Andrusivova Z, Yang B, Wang Y, Ogedegbe B, Riaz T, Støen M, Desler C, Rasmussen LJ, Tønjum T, Galas MC, Lundeberg J, Bohr VA
iScience (15 Sep 2020)

Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease
Chen WT, Lu A, Craessaerts K, Pavie B, Sala Frigerio C, Corthout N, Qian X, Laláková J, Kühnemund M, Voytyuk I, Wolfs L, Mancuso R, Salta E, Balusu S, Snellinx A, Munck S, Jurek A, Fernandez Navarro J, Saido TC, Huitinga I, Lundeberg J, Fiers M, De Strooper B
Cell (20 Aug 2020)

Seamless integration of image and molecular analysis for spatial transcriptomics workflows
Bergenstråhle J, Larsson L, & Lundeberg J
BMC Genomics (14 July 2020)

Molecular Atlas Of The Adult Mouse Brain
Ortiz C, Navarro JF, Jurek A, Märtin A, Lundeberg J, & Meletis K.
Science advances (26 June 2020)

Integrating Spatial Gene Expression and Breast Tumour Morphology via Deep Learning
He B, Bergenstråhle L, Stenbeck L, Abid A, Andersson A, Borg Å, Maaskola J, Lundeberg J, & Zou J
Nature biomedical engineering (22 June 2020)

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
Ji AL, Rubin AJ, Thrane K, Jiang S, Reynold DL, Meyers RM, Guo MG, George BM, Mollbrink A, Bergenstråhl J, Larsson L, Bai Y, Zhu B, Bhaduri A, Meyers JM, Rovira-Clavé X, Tyler Hollmig S, Aasi SZ, Nolan GP, Lundeberg J & Khavari PA
Cell (23 June 2020)

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration
Asp M, Bergenstråhle J & Lundeberg J
BioEssays (04 May 2020)

SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation
Bergenstråhle J, Bergenstråhle L & Lundeberg J
BMC Bioinformatics (29 April 2020)

Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues
Berglund E, Saarenpää S, Jemt A, Gruselius J, Larsson L, Bergenstråhle L, Lundeberg J & Giacomello S
BMC Genomics (15 April 2020)

Identification and Transfer of Spatial Transcriptomics Signatures for Cancer Diagnosis
Yoosuf N, Navarro JF, Salmén F, Ståhl PL, Daub CO
Breast Cancer Res. (13 January 2020)

2019


A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart
Asp M, Giacomello S, Larsson L, Wu C, Fürth D, Qian X, Wärdell E, Custodio J, Reimegård J, Salmén F, Österholm C, Ståhl PL, Sundström E, Åkesson E, Bergmann O, Bienko M, Månsson-Broberg A, Nilsson M, Sylvén C, Lundeberg J
Cell (12 December 2019)

Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics
Carlberg K, Korotkova M, Larsson L, Catrina AI, Ståhl PL, Malmström V
Scientific Reports (12 December 2019)

A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection
Poux C, Dondalska A, Bergenstråhle J, Pålsson S, Contreras V, Arasa C, Järver P, Albert J, Busse DC, LeGrand R, Lundeberg J, Tregoning JS, Spetz AL
Frontiers in Immunology (12 September 2019)

High-density spatial transcriptomics arrays for in situ tissue profiling
Vickovic S, Eraslan G, Salmén F, Klughammer J, Stenbeck L, Äijö T, Bonneau R, Bergenstråhle L, Fernandéz Navarro J, Gould J, Ronaghi M, Frisén J, Lundeberg J, Regev A, Ståhl PL
Nature Methods (9 September 2019)

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis
Maniatis S, Äijö T, Vickovic S, Braine C, Kang K, Mollbrink A, Fagegaltier D, Andrusivova Z, Saarenpää S, Saiz-Castro G, Cuevas M, Watters A, Lundeberg J, Bonneau R, Phatnani H
Science (5 April 2019)

ST Viewer: A tool for analysis and visualization of Spatial Transcriptomics datasets
Fernández Navarro J, Lundeberg J and Ståhl PL
Bioinformatics (15 March 2019)

2018


Barcoded solid phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections
Salmén F, Ståhl PL, Mollbrink A, Fernández Navarro J, Vickovic S, Frisén J & Lundeberg J
Nature Protocols (2018)

Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays
Giacomello S and Lundeberg J
Nature Protocols (2018)

Dissecting genetic heterogeneity in Stage III cutaneous malignant melanoma with spatially resolved transcriptomics
Thrane K, Eriksson H, Maaskola J, Hansson J, and Lundeberg J
Cancer Research (2018)

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
Berglund E, Maaskola J, Schultz N, Friedrich S, Marklund M, Bergenstråhle J, Tarish F, Tanoglidi A, Vickovic S, Larsson L, Salmeń F, Ogris C, Wallenborg K, Lagergren J, Ståhl P, Sonnhammer E, Helleday T, Lundeberg J
Nature Communications (2018)

Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics
Lundmark A, Gerasimcik N, Båge T, Jemt A, Mollbrink A, Salmén F, Lundeberg J, Yucel-Lindberg T
Scientific Reports (2018)

ST Spot Detector: a web-based application for automatic spot and tissue detection for Spatial Transcriptomics image data sets
Wong K, Navarro JF, Bergenstråhle L, Ståhl PL, Lundeberg J
Bioinformatics (2018)

2017


Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
Asp M, Salmén F, Ståhl PL, Vickovic S, Felldin U, Löfling M, Navarro JF, Maaskola J, Eriksson MJ, Persson B, Corbascio M, Persson H, Linde C, Lundeberg J
Scientific Reports (2017)

ST Pipeline: an automated pipeline for spatial mapping of unique transcripts
Navarro J F, Sjöstrand J, Salmén F, Lundeberg J, Ståhl PL
Bioinformatics (2017)

Spatially resolved transcriptome profiling in model plant species
Giacomello S, Salmén F, Terebieniec B K, Vickovic S, Navarro J F, Alexeyenko A, Reimegård J, McKee L S, Mannapperuma C, Bulone V, Ståhl P L, Sundström J F, Street N R, Lundeberg J
Nature Plants (2017)

2016


An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
Jemt A, Salmén F, Lundmark A, Mollbrink A, Fernández Navarro J, Ståhl PL, Tülay YL, Lundeberg J
Scientific Reports (2016)

Massive and parallel expression profiling using microarrayed single-cell sequencing
Vickovic S, Ståhl PL, Salmén F, Giatrelis S, Westholm JO, Mollbrink A, Fernández Navarro J, Custodio J, Bienko M, Sutton LA, Rosenquist R, Frisén J, Lundeberg J
Nature Communications (2016)

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
Ståhl PL, Salmén F, Vickovic S, Lundmark A, Fernández Navarro J, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, PI Costea, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J
Science (2016)

2015


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, Nygren AO, Laddach N, Sahlén P, Vickovic S, Bendigtsen SC, Aaserud M, Floer L, Borgen E, Schwind C, Himmelreich R, Latta D, Lundeberg J
Scientific Reports (2015)

Toward Rare Blood Cell Preservation for RNA Sequencing
Vickovic S, Ahmadian A, Lewensohn R, Lundeberg J
The Journal of Molecular Diagnostics (2015)

2014


Sequencing degraded RNA addressed by 3′ tag counting
Sigurgeirsson B, Emanuelsson O, Lundeberg J
PLoS One (2014)

2013


TagGD: fast and accurate software for DNA Tag generation and demultiplexing
Costea PI, Lundeberg J, Akan P
PLoS One (2013)